Subject Index

Absidia,973 culture, 87,1156--1160 Adaptive response, 609 Abyssal zone, 575 chemolithotrophs, 1156--1158 Adaptor ligation peR, genes and genomes Acanthamoeba heterotrophs, 1158 mediating biodegradation, airborne, 933 liquid medium, 1156-1158 1083 clinical syndrome, 225 mixotrophs, 1158 Adenine incorporation into nucleic acids, culture, 86 solid media, 1158-1160 measurement of secondary produc­ sampling, 267 detaching cells from solid substrate, tion, 427 waterborne, 225,265 1160 Adenosine phosphosulfate reductase, 503, Acanthamoeba castellanii, 265 enumeration 901 Accuracy, 211 classical, 1160 Adenovirus, 94 Acenaphrhene, mycoremediation, 1100, molecular means, 1160-1161 airborne, 964, 1019, 1021 1102 extreme, 1155 clinical syndrome, 225 Acenaphthylene, mycoremediation, 1100, moderate, 1155 detection, 232 1102 phylogenetic relationships, 1156 marine recreational waters, 286 Acetate, culture medium, 72, 74 preservation, 1162-1163 shellfish, 319 Acetobccter, endophytic, 640-643, 646 sulfur-oxidizing, 1155 UV inactivation, 329 Acetogenesis, landfill, 819-820, 827-828 Acidovarax waterborne, 225, 230, 232 Acetonema, 23, 28 endophytic, 643 Adjunct, PeR-based methods, 682 Acetylene iron-oxidizing, 1152 Adsorbents, virus, 291-292 methanotroph inhibition, 823 Acid-producing bacteria Advanced oxidation processes, water treat­ nitrification inhibitor, 515 oil field, 901 ment, 330-331 Acetylene block method, denitrification, oil field water system, 902-903 Aeration tank, airborne microorganisms, 517,691~92, 864 Acinetobacter 931 Acetylene reduction assay, nitrogen fixa­ airborne, 991 Aerobacter, endophytic, 643 tion, 513, 688-689 endophytic, 643 Aerobe, 25 ~-N-Acetylhexosaminidase,airborne Acinetobacter calcoaceticus, 991 culture, 74 fungi,955 Acremonium lipid biomarkers, 116--117 Acetylmannan esterase, 1090 airborne, 975 Aerobic respiration, 23-24 Acerylxylan esterase, 1090 spore discharge, 974 subsurface, 862-864 Achromatium, 502-503 Acremonium obclavatum, 982 terminal electron-accepting reaction, Achromobacter, endophytic, 640, 642 Acridine orange, 47, 54, 57, 645, 878, 862-864 Acid mine drainage, 1161 1116 Aerobiology, 925, seealso Airborne Acidianus, 23 metabolic activity of soil- and plant­ microorganisms Acidibacillus caldus, 1157 associated microbes, 699-701 Aerococcus, airborne, 989 Acidic environment, 1155 Acridine orange direct count, 700 Aeromonas Acidimicrobium ferrooxidans, 1157 landfill microbes, 824, 827 clinical syndrome, 223, 225 Acidiphilium, 1157, 1159, 1240 monitoring freshwaters and drinking freshwarers and drinking waters, 252, Acidiphilium cryptum, 1159, 1244 waters, 258 257 Acidisphaera, 1159 Actinomyces, endophytic, 642-643 shellfish, 227, 311 Acidisphaera rubrifaciens, 1157 Actinomyces oLivaceus, 117 wastewater and sludge, 304 Acidithiobacillus ferrooxidans, 1157, Actinomvcetes, airborne, 928, 931, 933, waterborne, 223, 225, 228, 232-233 1159-1160, 1162,1244 990, 992 Aeromonas caviae, 252 Acidithiobacillus thiooxidans, 1157, 1162 Activated sludge processing Aeromonas hydrophila, 222-223, 233, 252, Acidobacterium, 76, 1159 airborne microorganisms, 931 304,568,1138,1141 Acidocella, 1157 foaming and bulking, 672 Aeromonas jandaei, 252 "Acidocella aromatica," 1158, 1159 Activation velocity, 888 Aeromonas schubertii, 252 Acidomonas methanolica, 1157 Acure gastrointestinal illness, waterborne Aeromonas veronii, 252 Acidophile, 25, 1155-1165 pathogens, 227-228 Aeroponic culture, arbuscular mycorrhizal activities, 1161-1162 Acylated homoserine lactone, 567 fungi, 630 ~ .: biology, 1155-1157 Acyl-ornithine lipids, 117 Aerosol, see Bioaerosol 1251 1252 • SUBJECT INDEX

Aerosol challenge study, viruses, catastrophe model, 967 Alpine tundra, fungal community, 615--616 A 1019-1021, 1024 dispersion model, 967 AlpP protein, 569 A Affinity capture method, genes and exponential decay model, 966 Alternaria A genomes mediating biodegradation, kinetic model, 966 airborne, 929-930, 933, 974-975, A 1083 viruses, 926, 930--933,963-964, 977-978 A Affinity chromatography, virus concentra­ 1016-1030 plant pathogens, 1032, 1036, 1038-1039 A tion, 291 Airborne mycotoxin, 926, 928, 931, 933, water activity for growth, 973 A Aflatoxin, 979-980 955,972,978-982 Alternaria alternaw, 933, 1038 A African swine fever virus, 1019 Air-conditioning system, see HVAC system Alternaria brassicae, 1038 A Agar, 73, 1159 Aircraft, airborne viruses, 1022, 1024 Alternaria porri, 1038 Agar contact procedure, surface sampling, Air-handling system Alternaria solani, 1038 946 airborne bacteria and endotoxin, 992 Alternative hypothesis, 210, 212 Agar plating, isolation of algae and proto­ airborne microorganisms, 926, 928 Altruism, 10, 12 A zoa, 81 Air-water interface, preparation for Aluminum, toxic metal resistance, A Agricultural pathogens, seealso Plant mictoscopy, 41 1166-1182 A pathogens Akamara(domain), 4 Amino acids, culture medium, 72 A airborne, 1031-1037 Akinete, 28 p-Amincbenzoic acid, culture medium, 71 A Agricultural practices/facilities Albugo occidenwlis, 1043 Ammonia airborne bacteria and endotoxin, Alcaligenes marine environment, 511-522 A 989-990, 994, 997 airborne, 990 oxidation under anaerobic conditions, airborne microorganisms, 926, 928, endophytic, 642--643, 646 29 932-933,979 subsurface transport, 874 Ammonia monooxygenase, 513, 670, airborne mycotoxins, 981 Alcian blue, 835 693-694, 722 Agricultural soil Alcohol, field sterilization of sampling Ammonia oxygenase, 514-515 long-term research sites, 183, 185-188 equipment, 294 Ammonia-oxidizing bacteria, 690 microbial community, 784-785 Alexa dyes, 57 Costa Rican soil, 614-615 Agrobacterium Alexandrium cateneUa, 380 long-term research in Monterey Bay, endophytic, 642--643 Alexandrium minutum,380 185--186 plant pathogens, 1034 Alexandrium Wmarense, 380 marine environment, 513-515 Air drying, soil samples, 604--606 Algae, 224, seealso Protist microarray analysis, 672 Airborne endotoxin, 926, 928-932, agar plating, 81 Ammonium, culture medium, 69-70, 72 954-955, 989-1004 airborne, 925-926, 933 Ammonium microprobe, 174 Al Airborne microorganisms, see also culture, 79-92 Amnesic shellfish poisoning, 380, 382 AI Bioaerosol definition, 454 amoA genes, 514, 694 AI adaptations, 14 enrichment culture, 80 Amoeba, 80, 265, see also Protist; Protozoa algae, 925-926, 933 geographical distribution, 14 agar culture, 86-87 AI analysis, 952-960 isolation, 80-82 airborne, 933 Ar bacteria, 926, 928-934, 953-954, 963, limitation to cultivation procedures, 89 aquatic environment 989-1004 long-term preservation, 89--90 benthic vs. pelagic, 463 biochemical assays,954--955 maintenance methods, 82--83 community structure, 454-468 culture media and incubation, 952-953 marine culture medium, 85-86 emerging technologies, 956-957 bacterial colonization of, 569 food organisms, 85-86 Ar enumeration, 953 biofilms on, 563-574 cysts, 87, 265 environmental hazards, 14 oxygen consumption, 340-341 freshwater, 85 fate, 961-965 subculturing, 83 identification, 455 flow cvtornetry, 954 toxic effects isolation, 81 An fungi, 925-926, 928--934, 939, 952-955, clogging/damaging gills, 378-379 liquid culture, 87 972-979 hypoxia, 378-379, 408,417 maintenance methods, 85-87 human exposure, 932-934 toxins, 378-390, 408 marine, 86 identification, 953 toxicity bioassays using, 347--349 naked, 455 immunoassays, 954 wastewater, 340-341 oligotrophic oceanic environment, 457 inactivation mechanisms, 965-966 waterborne pathogens, 234-237 soil,85 An legionellae, 928-929,932, 1005-1015 Algal bloom, 79, 235, 378, 408 subculturing, 86-87 An measurement, 933-934 harmful,379-383 testate, 87, 455 An microarray technology, 956--957 Algal growth test, wastewater treatment Amphilonche elongaw, 457-458 microscopy, 953-954 efficiency, 342-343 Amplified fragment length polymorphism An pathogens, 925, 932-934 Alg@line, 418 arthropod pathogens in soil, 774 An PCR-based methods, 955-957 Algorithms, genetic, seeGenetic algo­ arthropod-associated microorganisms, plant pathogens, 1031-1047 rithms 777 An protozoa, 926, 928, 933 Alicyclobacillus, 1157 legionellae, 1011 repair mechanisms and resuscitation, Alkaline phosphatase, 525 Amplified rDNA restriction analysis, 142 966 monitoring metabolic activity in acidophiles, 1161 sampling, 939-951 biofilms, 55 aquifer microbes, 853 i bioaerosol sampling, 939-946 Alkaliphile, 25, 87 Amplified ribosomal intergenic spacer Ap surface sampling, 946-947 Alkvlbenzene, degradation in aquifer, 848 analysis, see ARISA Ap, transport, 961, 968 Allergic bronchopulmonary aspergillosis, Amylase, landfill, 829 ApI viability 978 Anabaena, 224--225, 235, 384 Api humidity effect, 961-962 Allergy Anabaena circinalis, 386 Ap microbial factors, 962 airborne fungi, 976-978 Anabaenopsis, 384 Ap open-air factors, 962 fungal spores, 974 Anaerobe, 25 AP oxygen effect, 962 Allescheria, lignocellulolytic, 1107 culture, 71, 74 Ap sunlight effect, 962 Allvlthiourea, nitrification inhibitor, 515 lipid biomarkers, 116-11 7 AP temperature effect, 962 Almandine, nitrate-dependent microbi-' Anaerobic decomposition, landfill, Ap viability models, 966-967 oxidation, 1150-1151 818-842 Ap SUBJECT INDEX • 1253

Anaerobic flow cell, 1241-1242 Apple scab, 1036, 1038 transformation by-products and metabo­ Anaerobic glove box, 74 Aquabacterium, iron-oxidizing, 1152 lites, 848-849 Anaerobic respiration, 23-24 Aquaculture, 378 uranium, 854 Anaerobic technique, 1239-1240 Aquatic environment, seealso Waterborne Aquifex, 27 Anaeromyxobacter dehalogenans, 1244 disease; Marine entries o-Arabinofuranosidase, 1090 Anaeroplasma, 115 bacteria, organic carbon cycling, Arabinosidase, 1090 Analysis of variance (ANOYA), 212-213 479--487 ARB aligner, 609 Analytical imaging, 40--68 biofilms on living surfaces, 563-574 Arbitrarily primed PCR Anammox reaction, 29, 515-516, 688 C I metabolism, 488--496 DNA fingerprinting, 679 anammox organisms, 516 CLSM imaging, 58 legionellae, 1011 measurement, 693 community structure soil isolates, 656 soil, 693 archaea, 434--444 Arbuscular mycorrhizal fungi, 627--637 Anatoxin, 384, 386 bacteria, 434--444 community fingerprinting, 633 Andersen sampler, 1010, 1018 fungi, 469--478 culture, 629--630 Andes virus, 1021 genetic and genomic assessments, aeroponic and hydroponic cultures, Andrews LTER site, 186 394 630 Aniline blue-lactic acid stain, endophytic metabolic activity assessment, disinfection of propagules, 629--630 bacteria, 645 395-396 monoxenic culture, 630 Animal feed production, airborne bacteria protists, 454--468 pot culture, 630 and endotoxin, 990, 994 viruses, 445--453 soilless media, 620 Animal virus, seealso Yirus culture of microorganisms, 399--406 traditional methods, 629--630 airborne, 1022-1024 iron cycling, 540-562 fatty acids, 631--632 assay, 93-100, 620--623 legionellae, 1006-1008, 1011-1012 genome-wide methods, 633 cultivation, 93-100 long-term research sites, 183-187 identification, 628 pathogens, 1022-1024 manganese cycling, 540-542 immunoassays, 631 soil,618--626 metal cycling, 540-562 infectivity assay, 629 Annual limit of intake, radionuclides, methods in aquatic microbial ecology, interactions with arthropods, 776 1198-1199 393-398 isolation from soil, 627--628 Anode nitrogen cycling, 511-522 molecular methods, 632--633 bacterial electrode device, 1139 phosphorus cycling, 523-539 most-probable-number assay, 629 definition, 1138 primary production, 407--419, 429 PCR-based methods, 632--633 ANOYA,212-213 sampling, 400--401, 497 propagule assay, 628--629 Anthracene, mycoremediation, 1100-1102 secondary production, 421--433 protein and isozyme analyses, 631 Antibioticfs), medium for cell culture of sulfur cycling, 497-510 quantification viruses, 95-96 Aqueous environment, chemical speciation chitin content, 631--632 Antibiotic resistance, 758, 989 of metals, 1196-1198 ergosterol, 632 Antibiotic resistance analysis Aquifer, seealso Groundwater fatty acid analysis, 632 indication of fecal contamination, 286, biogeochemistry, 843-858 glomalin, 632 326 chemical measurements of reactive molecular methods, 633--634 microbial source tracking methods, 253, species, 847-849 soilborne hyphae, 629 307 comprehensive integrative studies, root colonization, 628 Antibiotic-resistant bacteria 851-854 clearing and staining of roots, 628 indicator organisms, 350 experimental approaches, 849-851 quantification, 628 pathogens, 350 carbon cycling, 845 screening and separation of variants, wastewater, 349-350 community structure, 843-858 633 Antibody-based approach, seealso denitrification, 849 spores, 627-628, 631 Fluorescent-antibody technique dissolved inorganic carbon, 847, 849 terminal RFLP, 633 monitoring bacteria in aquatic environ­ dissolved organic carbon, 843, 845 Arbuscule, 628 ment, 435 electron acceptors, 843, 845-850 Archaea, 26-27, seealso Bacteria monitoring marine recreational waters, electron donors, 845-848 aquatic environment, community struc­ 284 enumeration of groups of bacteria, 852 ture, 434--444 Antibody-based biosensor, 175 flow of water through, 844 lipid biomarkers, 435 Anticrop biological warfare, 1041-1042 geochemistry, 796 organic carbon cycling in oceans, 482 Antigen, preparation for antiserum devel­ granular, microbial transport, 881-882 Archiving, CLSM data, 59 opment,714 heterogeneity, 843, 845-846, 862-863 Arcobacter, oil field, 901 Antillatoxin, 384 hydrogen gas, 848-849 Arctic LTER site, 188 Antimony, toxic metal resistance, in situ microcosms, 850-851 ARISA (amplified ribosomal intergenic 1166-1182 iron cycling, 845, 847, 850 spacer analysis) Antiserum development isotopic signatures, 849 bacteria in aquatic environment, antigen preparation, 714 laboratory batch and column studies, 437--438 blood harvest and preparation of collect­ 849-850 biofilm community, 564-565 ed antiserum, 715 manganese, 845, 848 community structure analysis, 146, 148 immunization, 714-715 methanogenesis, 851 indicator molecules in soil extracts, Aphanatoxin, 385-386 nitrate, 843, 845, 850, 854 658--659 Aphanizomenon, 224-225, 235 organic contaminants, 845, 848 soil microbial community, 608 Aphanizomenon flos-aquae, 385-386 oxygen, 843, 845, 850 ARLEQUIN program, 1117 Aphanizomenon ovalisporum, 385 push-pull tests, 851, 853-854 Aromatic compounds, biodegradation, 11 Aphotic zone, 393 redox processes, 845-849 Arsenate Aphthovirus, 94 respiration, 845, 851 molybdenum blue detection, 1217 API RP-38 medium, 900 sampling, 846-847 reduction, 554 Apicomplexa, 265-266 subsurface microbial transport, 872-897 Arsenate reductase API-RST medium, 900 sulfate, 843, 845 detoxifying, 1215, 1218 Aplvsiatoxin, 383-384 sulfate reduction, 849-851, 854 respiratory, 1215, 1218 Apoplasmic nutrients, 639, 641 tracer tests, 851 assay, 1219 1254 • SUBJECT INDEX

Arsenate respiration, biochemical models, mesocosm studies, 769, 776 acidophiles, 1155-1157 1215 microcosm studies, 769, 776 Auxotroph, commensal relationships, 10 Arsenate-reducing bacteria, 1214-1215 molecular methods, 776-777 Avian influenza virus, airborne, 1016, Arsenate-respiring bacteria, 12I 4-1222 AFLP analysis, 777 1022 activity assays, 1220 microsatellites, 777 Avian vacuolar myelinopathv, 386 arsenate reduction mechanisms, 1220 molecular markers, 777 Azaspiracid, 380, 382-383 batch studies with sediments, 1220 specific primers, 777 Azaspiracid shellfish poisoning, 380, biochemistry, 1219 plant pathogens, 1033-1034 382-383 culture, 1215 spatial and temporal relationships, Azoarcus,endophytic, 642, 646 enrichment culture, 1218 769-770 Azobacter, endophytic, 642 future directions, 1220-1221 Artificial environment, 3-4 Azorhizobium, endophytic, 642 gene expression, 1219 Artificial seawater, 1231 Azospirasuillum, 1150 isolation, 1218 Aryl alcohol oxidase, 1089-1090 Azospirillum measuring abundance, 1218 Ascospore, 973-974, 1033 endophytic, 638, 640-642, 646 microbe-mineral interactions, 1220 Ascotricha, airborne, 974 motility, 28 molecular biology, 1219 Ascotricha chartarum, 975-976 rhizoplane, 719 PCR-based methods, 1219-1220 Ascorricha ermace«, 975-976 root colonization, 58 simulation of subsurface environments, Aspergillus Azotobacter, 23 1220 airborne, 929-931,933,972-977 Arsenic food spoilage, 973 aquatic environment, 541, 553-554 spore discharge, 973 Bacillus aqueous chemical speciation, 1196-1197 toxins, 979-981 airborne, 930, 989, 991-992 connection to iron and manganese volatile organic compounds, 982 arsenate respiration, 1216 cycles, 553 water activity for growth, 973 endophytic, 640, 642-645 c groundwater, 29 Aspergillus clavatus, 978, 980 endospore formation, 28 measurement Aspergillus j7avus, 713, 976, 979-981 immunofluorescence microscopy, 713 c HPLC and UV detection, 1217 Aspergillus fumigatus, 930-931, 933, 956, manganese oxidation, 1228 d rapid assays, 1216-1217 972,974-977, 979 metal cycling, 547 e sensitive techniques, 1218 toxin, 955 morphology, 23 il speciation methods, 1217 Aspergillus niger, 930, 974-976, 979, 1107 nutritional specialization, 26 n subsurface environment, 1214-1222 Aspergillus ochraceus, 980 signature lipids, 114 o toxic metal resistance, 1166-1182 Aspergillus parasiticus, 933, 979-981 size, 23 p Arsenic cycling, 1214-1215 Aspergillus versicolor, 927, 929, 979-982 species-level relationships, 159 s1 Arsenopyrite, nitrate-dependent microbial Assessment activities, 194 subsurface transport, 874-876 sl oxidation, 1150 Asthma, 927, 933, 993, 995-996, 1024 Bacillus anthracis, 150, 159,956 Sl Artesian well, sampling, 812--813 hygiene hypothesis, 996 airborne, 927 Arthrobacter Asthma-like syndrome, 994 spores, surface sampling, 947 \\ endophytic, 642-643 Asticcacautis , 23 Bacillus arsenicoselenatis, 1216 \\ morphology, 23 Astrovirus Bacillus atrophaeus, 947 signature lipids, 114, 117 clinical syndrome, 223 Bacillus brongniartii, 777 Bac subsurface transport, 874-876 shellfish, 313, 316, 319 Bacillus cereus, 159 Bac Arthrobacter crystallopoietes, 113 waterborne, 220, 223, 230, 366 Bacillus fastidiosus, 26 n Arthropodts) Atmospheric conditions, 961 Bacillus firmus, 115 plant pathogens associated with, Atomic force microscopy Bacillus macyae, 1216 s 1033-1034 metal-microbe interactions, 1203 Bacillus mojavensis, 639, 646 soil microbe-mineral interface, 1208-1209, Bacillus mycoides, 159 Bac epiedaphic (epigeic), 770 1241 Bacillus patchiness, 963 euedaphic, 770 ATP Bacillus prodigiosus, 963 Bac quantification, 771 dissolved organic phosphorus, 532 Bacillus selenitireducens, 1216, 1218 Bac sampling, 771 metabolic activity of soil- and plant­ Bacillus sphaericus, 772 Bac time spent in or on soil, 770 associated microbes, 699 Bacillus subtilis, 805, 963, 1178 Arthropod pathogens, soil, 769, 771-777 monitoring freshwaters and drinking Bacillus thuringiensis, 159,770,774-775 behavior of arthropods in response to, waters, 258 biocontrol agent, 1035 Bac 775 phosphorus cycling in marine environ­ selective media, 772 bioassays, 773 ment, 532 Bacillus violaceus, 963 diet incorporation, 774 Audit (quality assurance), 194 Bacteria extraction of pathogens followed by Auger electron-spectroscopy, microbe- airborne, 926, 928-934, 953-954, infectivity trials, 774 mineral interface, 1209 989-1004 soil baiting with arthropods, 773 Aujeszky's disease virus, 1021-1022 aerosol stability, 963, 965 dilution plating, 772-773 Aureobacterium, endophytic, 642 environments with high concentra­ extraction from soil and physical counts, Aureobasidium, airborne, 975, 977 tions of bacteria, 989-991 771-772 Aureobasidium pullulans, 472, 928, 931, 978 environments with low concentra­ microscopy, 774 Autoclave, 73 tions of bacteria, 990, 992 molecular methods, 774-775 Autocorrelation, 214 environments with moderate concen­ sampling, 772 Autofluorescence, quantification of micro­ trations of bacteria, 990-992 selective media, 772-773 bial diversity, 56 plant pathogens, 1034-1036 serology, 774 Automobile, airborne microorganisms, 931 viability, 962 Arthropod-microbe interactions in soil, Automobility, 13 aquatic environment 769-780 Autoradiography, seealso AR1SA,437-438 S behavior of arthropods in response to Microauroradiographv assemblage fingerprinting, 437-438 \ microbes, 775 bacterial carbon cycling in aquatic envi­ biofilms on living surfaces, 563-574 \ community studies, 777 ronment, 482-483 community metagenomics, 440-441 Ba( field studies, 769, 776 radionuclides, 1200 community structure, 434-444 B(l( impact of soil characteristics, 770-771 Autotroph, 9, 15-16,24, 26 culture, 434-435, 439 SUBJECT INDEX • 1255

denaturing gradient gel electrophore­ marine recreational waters, 285-286 Berlese funnel, extraction of arthropods sis, 438 signature lipids, 114-115, 117 from soil, 771 DNA fragment analysis, 437-438 wastewater and sludge, 307, 349 Bernoulli distribution, 204 DNA hybridization, 435 whole-genome probe, 143 Beta distribution, 204 DNA reassociation kinetics, 435-436 Bacteroides disrasonis, 285 Betaine, bioaerosol stabilizer, 966 FISH, 439-440 Bacteroides [ragilis phages BG 11 medium, 82 GC content, 436 freshwaters and drinking waters, 251, Bias, 211 immunological approaches, 435 253 sampling method, 200 lipid analysis, 435 marine recreational waters, 285-286 Bicarbonate buffer, culture medium, 74 low-molecular-weight RNA profiles, Bacteroides thetaiotaomiCTon, 285 Bifidobacterium 435 Baculovirus, soil, 772, 774 enterotoxins, 253 microdiversitv, 441 Baerrnann funnel, sampling soil nema­ marine recreational waters, 286 microscopy, 434 todes, 772 wastewater and sludge, 307 organic carbon cycling, 479-487, Bagassosis, 994 Bifidobacterium adolescentis, 286 see also Organic carbon cycling Bailer, groundwater sampling, 812 Bifidobacterium dentium, 286 PCR-based methods, 436-439 Bait insect, 773 Binomial distribution, 204-205 probe/micro autoradiography combina­ Balantidium coli, 224, 265 Bioaerosol, seealso Airborne microorgan­ tion,440 Balch technique, 74 isms quantitative probes, 439 Barley yellow dwarf virus, 1034 aerosol challenge studies, 1019-1021, RFLP analysis, 437-438 Barophile, 25, 575-590 1024 rRNA, 436-438 culture, 87, 583-584 analysis, 952-960 thermal gradient gel electrophoresis, Barotolerant microorganism, 575 definition, 925 438 Barrier, species, 7-8, 12-13 desiccation of droplets, 965-966 concentration from groundwater, biological barriers, 8 diurnal and annual variations, 962-963 878-879 chemical barriers, 8 exhaled, 1024 culture, 69-78 physical barriers, 8, 12 fate, 961-965 drinking water, 365-376 Basal medium gravitational settling and impaction, endophytic, see Endophytic bacteria carbon source, 71-72 925, 965 infectious dose, 222-226 electron acceptors, 72 inactivation mechanisms, 965-966 marine recreational waters, 281-283 energy source, 71-72 indoor environment, 926-932 ozone sensitivity, 331 mineral solutions, 69-70 inhalation, 925-926 preparing bacterial immunogens, 714 nitrogen source, 72, 75 land-applied biosolids, 351 shellfish, 311-312, 314-317, 320 preparation, 69-73 legionellae, 1006-1007, 1009-1010 sludge, 300-310 trace metal solution, 71 microbial aerosol stability, 963 subsurface transport studies, 882-883, vitamin solution, 70-71 microbial repair mechanisms and resus­ 888-889 Basidiospore, 973-974, 1033, 1041 citation, 966 wastewater, 300-310 BATS project, 183,429,528 origin waterborne pathogens, 223-224, Bayesian analysis generated from water sources, 925 229-230, 233-234 phylogenetic uncertainty, 613 release from soil or dry surface, 925 Bacteria (lineage), 26-27 topology of phylogenetic tree, 161-162, outdoor environment, man-made Bacterialartificial chromosome, 394 611,615 sources, 926 metagenomics of biodegradation organ­ BCECF-AM, 48 sampling, seeBioaerosol sampling isms, 1083 BD Oxygen Biosensor System, see BOOBS threat agents, 926-927, 954 soil metagenomics, library construction, technology transport, 925, 961, 968 1064 Bdellovibrio, 12,23 deposition and adhesion, 968 Bacterialbiomass production, 421-433, see BOOBS technology, 131-134, 136 particle release from surfaces, 968 also Secondary production Beach, see Marine recreational waters viability models, 966-967 Bacterialgrowth efficiency, 421, 429-430 Beaches Environmental Assessment and virus, 1016-1030 Bacterialrespiration, 421 Coastal Health (BEACH) Act, collection of naturally occurring Bacterialtracers, serendipitous, evaluating 280, 337 aerosols, 1024 contamination of subsurface sam­ Beauveria bassiana, 770, 772-773, 775-777 generation, 1016-1017, 1025 ples, 805 Beef extract, 73 retention and aging, 1017 Bacteriophage,seealso Coliphage Beggiatoa, 23, 28, 502-504 sampling, 1017-1018 aerosol stability, 964-965 Behavioral diversity, among prokaryotes, sources, 1018 cultivation-dependent analysis, 623--624 28 waterborne pathogens, 227,365-366 cultivation-independent analysis, 624 Beijerinck, M., 20 Bioaerosol sampling, 939-946, 952, freshwarers and drinking waters, 258 Beijerinckia, 14 1009-1010,1017-1018 genome characteristics, 759-760 Benthic lander, 580 collection methods horizontal gene transfer, 759-760, 763 Benthic zone electrostatic precipitation, 940 host range, 760 14C-Iabeledcarbon dioxide uptake test, filtration, 940-942, 953 indicators of fecal contamination, 326 411 gravitational settling, 940, 1010 life cycle, 760 protists, 455, 463 impaction, 939-940 lysogeniccycle, 760 Benzjcjanthracene, mycoremediation, liquid impingement, 940 lytic cycle, 760 1100-1102 collection time, 945 microscopy, 624 Benzene, degradation in subsurface, 850, impactor samplers, 940-944, 946, 953, plaque assay, 623--624 867 1010,1017 pseudolysogenic stages, 760 Benzo(b)fluoranthene, mycoremediation, liquid impinger sampler, 941-944, 953, soil, 623--624 1100-1102 1010, 1017 subsurface transport, 877 Benzo(k)fluoranthene, mycoremediation, lower quantitation limit of sampler, 945 wastewater, 913 1100,1102 number of samples, 946 water quality indicator, 239 Benzo(g,h,i)perylene, mycoremediation, sampler calibration, 946 Bacterioplankton, 421 1100 sampler performance, 942-945 Bacteroides Benzo[a]pyrene, mycorernediation, biological sampling efficiency, 944 electrode-reducing bacteria, 1141 1100-1102 collection efficiency, 943-944 1256 • SUBJECT INDEX

Bioaerosol sampling (continued) colonization of marine algae, 569-570 Bioreporter, 38, 169-173, see also Reporter upper quantitation limit of sampler, 945, microscopy, 569 gene system 953 Vilma on living surfaces, 570-571 BioSampler, 941-942, 944 Bioaerosol stabilizers, 966 internal dynamics, 569-570 Biosensor, 38, 169, 174-178, see also specific Bioaugmentation iron-reducing bacteria, 1240, 1243-1244 types mycoremediation, 1097-1106 legionellae, 1008 applications, 177 subsurface microbial transport, 872-897 on living surfaces, 563-574 attachment of biomolecule, 175 Biochelator, see Chelating agent microeukaryotes, 1112 biological component, 174-175 Biochemical methane potential test, land­ oil field water system, 902-904 computational component, 175 fill, 824-825, 830 plant-associated, 595 labeling strains for transport studies, Biochemical oxygen demand sampling, 1112 879-880

BOD5,335-341 sectioning for microscopy, 41 microfluidics, 175 kinetics of biological treatment studying microbial community, 563-566 transducer, 175-1 77 processes and, 341 gene libraries, 565-566 Biosolids, see Sludge measurement, 338-339 high-throughput fingerprinting tech­ Biostimulation, genetic algorithms, 1075, microbiological phenomena resulting in niques,564-565 1077 oxygen consumption, 340-341 metagenomic analysis, 566-567 Biosurfacrant-prcduclng organisms standard BOD curve and equation, molecular methods, 564-566 detection, 899 339-340 sampling design and analysis, 564 microbially enhanced oil recovery, 899, wastewater treatment efficiency, Biofilm coupon, 1240 907 335-341, 351 Biofilm reactor, groundwater sampling, Bioterrorism Biocide 812 airborne viruses, 1025 control of legionellae, 1011 Biofouling, oil field equipment, 898 anticrop biological warfare, 1041-1042 oil field water system, 903-904 Biogeochemical cycles, 3, 24 bioaerosol threat agents, 926-927, 954 Biocoenosis, 8 aquatic environment, 393 Biotin, culture medium, 71 Biocolumn, 580 bacteria in, 421 BioTox,346 Biocontrol agent, airborne bacteria, Biogeochemistry Biotransformation, 10, 1051 1034-1036 aquifer, 843-858 Bio-trap sampler, 902 Biodegradable organic matter, ozonated iron-reducing bacteria, 1239-1248 Bipolaris, 1036 waters, 331 Biogeography, microbial, 14-15 Bipolaris maydis, 1039 Biodegradation, 22, 1051, seealso Biolog technology, 127-129, 131-136,307 BiSKit, 947 Decomposition aquifer microbes, 852 Bismuth, toxic metal resistance, estimates of enzymatic potential in soil, average well color development, 1166-1182 678--679 133-134 Bismuth sulfite agar, 302 kinetics, 698 Ecoplate, 127 Bis-oxonol, 48 landfill,818-842 inoculum density, 127-128 Bivalves, seeShellfish Biodegradation microorganisms inspection of plates, 128 Bjerkandera, mycoremediation, 1101 5-bromo-2-deoxyuridine labeling, metabolic activity of soil- and plant­ Blastocystis hominis, 276 1081-1082 associated microbes, 699 Blastomyces dermatitidis, 977 commensal relationships, 10 microwell plates, 127-128 BlightBan A506, 1036 culturing techniques, 1080 phenotype microarray, 128 Blocking, experimental design, 202 denaturing gradient gel electrophoresis, Biological pump, 525 Bloom, 14 1080 Biological safety hood, 75 Blue mold, 1036-1038, 1043 enrichment strategies, 1080 Biologically available phosphorus, marine Blue-green algae, see Cyanobacteria FISH, 1080-1081 environment, 531-532 BMAA, 384, 386 genes and genomes mediating degrada­ Bioluminescence, bacterial, 29 Booster PCR, 678 tion Bioluminescent reporter, 170-171, 736 Bootstrap analysis, 162, 211, 213,611,613 affinity capture methods, 1083 advantages and disadvantages, 170-171 Bordetella, endophytic, 643 differential expression analysis, 1082 applications, 171 Bordetella pertussis, 117 PCR-based methods, 1082-1083 light measurement, 171 Botanical epidemiology, 1031 primer design, 1082 oxygen requirement, 170 Borrvns cinerea, 973, 978 suppressive subtraction hybridization, Biomass, microbial Boundary, species, 7-8, 12-13 1082 biomass-to-cell number conversions, Bovine herpesvirus, 1020-1021 identification, 1079-1088 112-113 Bovine rhinotracheitis virus, 964, 1019 metagenomics, 1079-1088 total viable, 112-113, 120 Bovine serum albumin, bioaerosol stabiliz­ community profiling, 1080-1081 Biomass production er,966 culture-dependent enrichment, 1080 deep-sea microorganisms, 578, 585 Box plot, 206-208 genes and genomes mediating degra­ microbially enhanced oil recovery, 899 BOX-PCR,307 dation, 1081-1083 Biomining, 1155, 1161 soil isolates, 656 library construction, 1084-1085 BIOoGEORGE probe, 902 Brachiola, 266 microarray analysis, 1083-1084 Bioreactor Bradyrhizobium, 11, 642 stable-isotope ptobing, 1081-1082 fungal solid-state fermentation, Bragg's law, 1184 Biodiversity, see Microbial diversity; 1110-1111 Brainerd diarrhea, 237 Prokaryotic diversity packed-bed, 1110-1111 Bran, substrate for fungal solid-state fer­ Biofilm, 3, 12, 21 rotating annular, 40-41, 105-106 mentation, 1109 analysis, Robbins device, 904 rotating drum, 1111 Brevetoxin, 380-381 aquatic environment, 563-574 tray reactor, 1110 Brevibacterium, endophytic, 640 chemical interactions between prokary­ Bioreactor landfill, 820 Brilliant green agar, 302 otes and eukaryotes, 563, 567-569 Bioremediation, 9-10, 17, 26 Bromide CLSM, 40--68 brown rot fungi in, 1122, 1126 conservative tracer in subsurface trans­ community culture, 101-111 endophytic bacteria in, 643, 646--647 port, 881-884 community structure, 563-567 fungus-based, seeMycoremediation drinking water, 331 diffusion within, 57 genetic algorithms, 1075, 1077 geochemical tracer, 806-808 formation, 13, 28, 567-569 subsurface microbial transport, 872-897 Bromodeoxyuridine uptake method SUBJECT INDEX • 1257

biodegradation microorganisms, Calcium carbonate, production in micro­ CARD-FISH {catalyzed reporter deposi­ 1081-1082 bially enhanced oil recovery, 899 tion-FISH),725-726 growth rates of individual cells, 428 Calcium hypochlorite, water treatment, anammox bacteria, 516 isolation of DNA of active bacteria, 329 bacteria in aquatic environment, 440 429 Calcofluor white, 48 biofilm community, 566 measurement of secondary production, Calcofluor white M2R, 645 nitrifying bacteria, 514 427--428 Calibration, measuring and test equipment, Cartridge filtration apparatus, waterborne Brown rot fungi 195-196 viruses, 292-293, 295-297 bioremediation, 1122, 1126 Calibration curve, 196 Casamino Acids, 72 culture, 1123 Calicivirus, 94 Casein soy peptone agar, 953 low-molecular-weight metabolites, airborne, 1018-1019 Catabolic diversity/evenness, 133 1122-1128 waterborne, 220, 232, 366, 369 Catabolic gene probe activity-based assays, 1125 Calorimetric biosensor, 177 biodegradation microorganisms, biochelators, 1122, 1124-1125 CALUX assays, 350-351 1083-1084 cyclic voltammetry, 1125 Campylobacter endophytic bacteria, 646 electron paramagnetic resonance and clinical syndrome, 223 soil microbial community, 660 spin trapping, 1125 drinking water, 369 Catabolic response profile, 130 hydrogen peroxide, 1122, 1124-1125 endophytic, 640 Catabolic versatility index, 133 hydroxyl radical, 1124-1125 oil field, 900-901 Catastrophe model, viability of aerosolized oxalate, 1122, 1124 wastewater and sludge, 300, 304 microbes, 967 purification and quantification, waterborne, 220, 223, 227, 229-230, Categorical response, 213 1123-1125 366 Categorical variables, associations among, potential applications, 1126 whole-genome probe, 143 208 soil block assays, 1123 Campylobacter coli, 300 Cathode substrate modification by metabolites, Campylobacter jejuni, 223, 672 bacterial electrode device, 1139-1140 1125-1126 Canada, drinking water and recreational definition, 1138 l3C_TMAH therrnochemolvsis, 1126 freshwater standards, 254 Caulobacter molecular beam MS, 1125-1126 Candida albicans, 956 endophytic, 643 near infrared spectroscopy, 1125-1126 Candle jar, 74 morphology, 23 Brucella, 927 Canola blackleg, 1043 stalk formation, 28 Brucella abortus, 117 Canonical correspondence analysis, 208 Cave, subsurface sampling, 810-811 Brucella melitensis, 117 CLPP data, 134 Caveat emptor principle, applied to risk BTEX compounds, degradation in aquifer, PLFA fingerprints, 783-786 assessment, 375-376 850 Capillary racetrack method, enrichment of Cell count, from seawater, 402 Buchnera, symbiosis, 29 magnetotactic bacteria, 1130-1132 Cell culture, virus assay, 94-95, 316, Buffer, culture medium, 74 CapLC-nanoelecrrospray ionization-MS­ 620-621 Buffered charcoal yeast extract agar, 1008­ MS, extracellular enzymes of P. antibiotics in media, 95-96 1009 chrysosporium, 1095 choice of cell cultures, 95 Building/building materials Carbamoyl toxin 2, 379 decontamination and detoxification of airborne bacteria and endotoxin, 992 Carbohydrate utilization profiling, micro­ samples, 95 airborne microorganisms, 926, 929-930, bial tracking methods, 253 isotonicity and pH, 94 974-978 Carbon cycling, see also Organic carbon materials, 95-96 airborne mycotoxins, 979-981 cycling quality control, 96 airborne viruses, 1024 aquifer, 845 Cell culture/PCR assay, viruses, 620-622 legionellae, 1011 bacteria in aquatic environment, 479­ Cell lysis, bacteria in soil, 684 Burkard spore trap, 953 487 Cell membrane, integrity as indicator of Burkholderia Carbon dioxide cell viability, 55 endophytic, 640, 642-643 culture medium, 72 Cell morphology species-level identification, 158-159 headspace analysis metabolic activity of soil- and plant­ subsurface transport, 874, 876 CLPP based on, 129-131, 133-136 associated microbes, 699-701 Burkholderia cepacia, 117, 158, 568, 1036 colorimetric detection, 131 prokaryotic diversity, 22-23 Burkholderia mallei, 159 radioactive test, 131 Cell number, biomass-to-cell number con­ Burkholderia pseudomallei, 159 subsurface, 861, 866 versions, 112-113 Burkholderia thailandensis, 159 terminal electron acceptor, 861 Cell size, prokaryotic diversity, 22-23 Butane torch, field sterilization of sampling Carbon dioxide evolution rate Cellobiase, 1107 equipment, 294 measurement of fungal growth, 1110 Cellobiohvdrolase, 1090, 1094, 1107,1122 tert- Butyl alcohol, degradation in subsur­ respirometry methods, 698--699 Cellobiose dehydrogenase, 1089-1090, face, 868 Carbon dioxide fixation, 407 1094 Byssinosis, 994 Carbon dioxide uptake by gas analysis Cell-to-cell communication, 28 14C-labeled carbon dioxide, 410--412 Cellulase, 1107 measurement of primary production, landfill, 829 Cable tool drilling, subsurface sampling, 409--410 Cellulomonas, endophytic, 643 796, 800-803 procedure, 409--412 Cellulose, see also Lignocellulosic biomass Cadmium Carbon disulfide, rnerhanotroph inhibi­ biodegradation, 1080, 1089-1097, 1122 aquatic environment, 541, 553 tion, 823 degradation in landfill, 820, 827-829, connection to iron and manganese Carbon mineralization, landfill, 830 831 cycles, 553 Carbon sequestration, soil, 707 measurement, 831 toxic metal resistance, 1166-1182 Carbon source, 15-16,25 refuse composition, 819 Caffeine, indicator of fecal contamination, culture medium, 71-72 wood degraded by brown rot fungi, 252 Carbon-13 TMAH thermochemolysis, 1125-1126 Calcium wood degraded by brown rot fungi, wood structure, 1089 aquatic environment, 541 1126 Central limit theorem, 210-211 culture medium, 70 Carboxvfluorescein diacetate, 48 Centrifugation method, cell extraction soil,707 Carboxylic acids, landfill, 831-832 from soil and roots, 717 1258 • SUBJECT INDEX

Cephalosporium toxins, 979 neutralization of disinfectants, 292 subsurface transport, 874 Cercospora, plant pathogens, 1033, 1036 water treatment, 330 sulfite-reducing, freshwaters and drink­ Cercospora arachidicola, 1043 Chlorite, in treated water, 330 ing waters, 251 Cereal leaf medium-Prescott agar, 85 "Chlorobium ferrooxidans," 1149 Clostridium aceticum, 70 Cc Cereal leaf-Prescott liquid medium, 85 Chlorochromatium aggregatum, 103 Clostridium acetobutylicum, 115 Cc Cereal leaf-75% seawater medium, 86 Chloromethane, 488 Clostridium botulinum, 927 Cereal rust, 1043 Chromatium, 23 Clostridium butyricum, 115, 1138, 1141 Ceriporia, mycoremediation, 1098, 1103 Chromite, nitrate-dependent microbial Clostridium perfringens, 251, 927 Cetiporiopsis subvermispora, 1107 oxidation, 1150 marine recreational waters, 281, CFDA/SE, 878 Chromium 284-285 Chaetomium aquatic environment, 541, 553 wastewater, 349 airborne, 974-976 connection to iron and manganese water quality indicator, 239 toxins, 979 cycles, 553 Clostridium welchii, 251 c Chaetomium cellulohticum, 1107 toxic metal resistance, 1166-1182 CLPP, seeCommunity-level physiological o Chain-of-custody procedures, 195 Chromobacterium violaceum, 568, 805 profiling c Chamorro people of Guam, 386 Chrysene, mvcorernediation, 1100, 1102 CLSM, seeConfocal laser scanning Character state, 612 Chryseobacterium, endophytic, 643 microscopy Chart, 204 Chrysiogenes arsenatis, 1216, 1218 CLUSTAL program, 161 c Chattonella antiqua, 379 Chrysochromulina ericina, 457-458 Clustal X aligner, 609 c Chelating agent Ciguatera fish poisoning, 380-382 Cluster analysis, 209-210 brown rot fungal metabolites, 1122, Ciliate, 80, 265, seealso Protist; Protozoa comparisons of microbial communities, 1124-1125 aquatic environment 613 c purification and quantification, 1124 benthic vs. pelagic, 463 functional gene array data, 1058 removing metals from water samples, community structure, 454-468 microarray data, 669-670 G 254 depth and seasonal distribution, CMEIAS image analysis, 712 subsurface, 867 463-464 FISH images, 727-728 Chemical(s) freshwater vs. marine, 462-463 geostatistics and, 721-722 G indicators of fecal contamination, culture, 83-85 with immunofluorescence microscopy, G 252-253,286 identification, 455 719-722 G wastewater, 350 oligotrophic oceanic environment, 457 Cl-metabolizing community G Chemical oxygen demand Citrate, culture medium, 74 aquatic environment, 488-496 G landfill, 831-832 Citrinin, 980 assessment, 492 wastewater treatment efficiency, 337, Citrobacter environmental detection of C, oxidizers, G 341 airborne, 990 489-492 Chemical speciation, metals in aqueous arsenate respiration, 1216, 1219 environmental genomics, 488-496 phase endophytic, 642 future directions, 493 analytical methods, 1197-1198 subsurface transport, 874 metagenomic analysis c definition, 1196 total coliforms, 249 large DNA insert libraries, 492 c preservation, 1196-1197 Citroviridin, 980 shotgun community sequencing, c Chemoautotroph, 16,407 Cladosporium 493 c Chernolithoautotroph, 407 airborne, 925, 927, 929-930, 933, methylotrophs, 488-496 C Chemolithotroph, 26, 72 974-975, 977 RNA detection, 492 acidophiles, 1156-1158 plant pathogens, 1032 stable-isotope probing, 492 aerobic, 408 spore discharge, 973 C. oxidizer, environmental detection Chemoorganotroph, 71 water activity for growth, 973 environmental arrays, 491-492 Chemostat, community culture, 104 Cladosporium carygenum, 1043 FlSH,490-491 Chemotaxis, 13, 28 Cladosporium cladosporioides, 975 FISH-based flow cytometric separation, ChemTax, 415-416 Cladosporium herbarum, 975, 982 490-491 c Chilomastix, landfill, 828 Cladosporium sphaerospermum, 975 PCR-based methods, 489-490 Chilomonas, 84-85 Clams, see Shellfish Coal tar waste, 854 Chi-square distribution, 204-205 Clark-style electrode, 414 Coastal area, see Marine recreational Chi-square statistic, 208 Classification, microbial, 4 waters Chitin Classification analysis, 209-210 Cobalt biodegradation, 1080 Clavibacter, endophytic, 642-643 aquatic environment, 541, 553 c quantification of arbuscular mycorrhizal Claviceps, toxins, 980 connection to iron and manganese fungi,631-632 Claviceps purpurea, 980 cycles, 553 Chitinase gene, 484 Clay particles, soil, organic carbon adsorp­ toxic metal resistance, 1168, 1176 Chlamydia, whole-genome probe, 143 tion, 707 Coccidioides immitis, 14-15,977 Chlamydia pneumoniae, 963 Clean Water Act, 325, 334 Coccus, 23 Chloramines,329 Climate, 14-15 Cockles, see Shellfish Chloride, conservative tracer in subsurface Climax community, 16 CODEGOP program, 1082 transport, 881-884 Clone library, 146 Codon bias, recently transferred DNA, Chlorinated ethvlenes, degradation in Clone-FlSH,723-724 764 aquifer, 849 Cloning Coenzyme F420, landfill, 830 Chlorinated solvents, degradation in DNA encoding enzymes hvdrolvzmg Coenzyme M, landfill, 830 aquifer, 848, 852-854 biopolvrners, 484-485 Coffee rust, 1036, 1039 Chlorine toxic metal resistance genes, 1174 Coherent anti-Stokes Raman scattering biocide in oil field water system, 903 Clonostachys rosea, 700 microscopy, 58-59 field sterilization of sampling equipment, Clostridium Coliform 294,619 arsenate respiration, 1216 airborne, 931 c neutralization of disinfectants, 292 endospore formation, 28 chlorine inactivation, 330 c water treatment, 329-330 morphology, 23 fecal, seeThermotolerant coltforms c Chlorine dioxide oil field, 901 marine recreational waters, 280 biocide in oil field water system, 903 signature lipids, 114 she llfish, 311 SUBJECT INDEX • 1259

thermotolerant, see Therrnotolerant bacteria, 434-444 Concentrated animal feeding operations, coliforms fungi,469-478 airborne bacteria and endotoxin, total, see Total coliforms genetic and genomic assessments, 394 989, 992, 994 Coltlert test kit, 282 metabolic activity assessment, Concurrent infection, 375 Coliphage, see also Bacteriophage 395-396 Coneiophora puteana, 1107 freshwaters and drinking waters, 251, protists, 454-468 Confirmatory factor analysis, 208 253 viruses, 445-453 Confocal laser scanning microscopy indicators of fecal contamination, 326 aquifer, 843-858 (CLSM), 40-68, 712-713 marine recreational waters, 285 biofilms on living surfaces, 563-567 applications, 54-58 subsurface transport, 877 bioreporters, biosensors, and micro­ archiving and storage of data, 59 wastewater, 349, 913 probes, 169-181 biofilm formation, 569 water quality indicator, 239 genomic DNA hybridization measures, calibration, 43 Colletotrichum gloeosporioides, 1043 143-145 color images, 52 Colletotrichum lagenarium, 1043 high-pressure marine environment, 578, computers and related equipment, 59 Collision-induced dissociation MS-MS 584-585 counting procedures, 42 spectra, extracellular enzymes of identification of microbes involved in 3-D image reconstruction, 45, 51-54, P. chrysosporium, 1093-1095 specific in situ functions, 748-757 713 Collozoumcaudatum, 457-458, 460 metagenomic analysis, see Metagenomics direct analysis of environmental sam­ Colonization, 15-16 nucleic acid fingerprints, 145-151 pies, 58 potential new habitats, 13 nucleic acid sequence measures, 139-143 fluorescent probes, 46-48 preemptive, 15-16 operational taxonomic unit, 609 imaging collection, 44-45 Colony hybridization, arthropod pathogens PCR-based methods, 679 metal-microbe interactions, 1201 in soil, 774 soil, 595, 652-662, 684, 777 motorized computer-controlled stage, Colony morphology alpine tundra, 615-616 42, 713 identification of soil bacteria, 653-654 ammonia-oxidizing bacteria, 614-615 objective lens, 44, 46 legionellae, 1009-1010 constructing phylogenies, 609-611 operation, 43-44 Colorless sulfur bacteria, 408, 497 direct extraction of indicator mole­ presentation and publication of images, ColorSeed, 269, 273 cules, 656-660 59 Colpidium, 84 DNA sequencing, 608-617 protozoa, 274 Columbia SK virus, 964 lipid fingerprinting, 781-792 pseudocoloring, 45 Column study, subsurface microbial trans­ methods based on laboratory cultiva­ rhizoplane microflora, 719 port, 872-877 tion, 653-654 specimen preparation and handling, Comamonas microarray analysis, 670-672 40-41 in biodegradation, 1083 phylogenetic analysis, 608-617 Confocal reflection contrast image, 45 endophytic, 643 sampling considerations, 652-653 Confounding factor, 202-203, 211, 214 subsurface transport, 874-876 strain identification, 654-656 Conidia, 471, 974 Cornetabolism, 26 Community theory, 103-104 Conjugation, 759-760 Commensalism, 4, 8, 10 Community-level physiological profiling integrative conjugative elements, CommOligo, 1054-1055 (CLPP), 38, 126-138 761-763 Communicable disease, 17 Biolog approach, 127-129, 134-136 transfer of metal resistance genes, Community, 6-19, 101 data analysis 1173 characteristics, 103 binary data (richness), 131-132 Conservative tracer, subsurface microbial climax, 16 continuous (quantitative) data, transport studies, 881-882 definition, 8 132-133 Consortium, 102 dominant species, 16-17 kinetic approaches, 134 cultivation, 101-111, see also involvement and homeostasis, 9-10 ordination analysis, 133-134 Community culture succession, 3, 16, 706-707 evaluating contamination of subsurface definition, 8 Community composition, lipid biomarkers, samples, 806 Constant-depth film fermenter, 106 115-117 headspace carbon dioxide detection, Constrained ordination analysis, PLFA fin­ lipopolysaccharide fatty acids, 115, 119 129-131, 133-136 gerprints, 784 plasmalogen lipids, 113, 115 historical context and evolution, 126 Contact irritants, cyanobacteria, 383-384 sphingolipide, 115 lipid biomarker analysis, 112-125 Contaminated environment, toxic-metal­ sterols, 115 oxygen consumption measurement, resistant bacteria, 1166-1182 Community culture, 38, 101-111 131-132, 134-136 Continuous-culture technique, landfill applications, 103 Comparative metagenomics, 1083 study, 824-826 chemostats, 104 Comparative statistics, 202-203 Continuous-flow laboratory simulation, constant-depth film fermenters, 106 Competition, 4, 7-10, 16 landfill cover, 833-834 continuous culture for studying surface climax communities, 16 Continuous-flow slide culture, 106-107 growth, 105 community theory, 103 Controlled experimental protocol, continuous-flow slide culture, 106-107 Competitive PCR 202-203 in situ cultivation, 108-109 airborne microorganisms, 956 Convergent tracer test, subsurface micro­ methods, 104-109 genes and genomes mediating biodegra­ bial transport, 884-886 rnicrostats, 107-108 dation, 1083 Cooking, 375 nutristats and gradostats, 104-105 Composite sample, 201-202 Cooliamonotis, 380-381 pure culture vs., 101-103 Composite sample unit, 211 Cooliatoxin, 380, 382 Robbins device, 106, 904 Composting Cooling tower rotating annular bioreactors, 40-41, airborne bacteria and endotoxin, 990, airborne bacteria and endotoxin, 992 105-106 992, 994 airborne microorganisms, 928, 933 storage and preservation, 109 airborne microorganisms, 928, 933, 979 legionellae, 1007-1008, 1012 Community fingerprint, 145-151 Compound-specific isotope analysis, Cooperation, community theory, 103 Community genomics, see Metagenomics aquifer, 849 Copepod, biofilm formation on, 570 Community structure Computer, see also Software Copiotroph, 25, 653 aquatic environment CLSM,59 Copper archaea, 434-444 quality assurance, 193 aquatic environment, 541, 553 1260 • SUBJECT INDEX

Copper (continued) PCR-based methods, 274-275 buffers, 74 Cvn connection to iron and manganese solid-phase cytometry, 274 cell culture for virus detection, 96 cycles, 553 drinking water, 265-279, 367-369, 375, electrode-reducing bacteria, 1143-1144 Cvn environmental waters, 254 918 endophytic bacteria, 641, 644 Cvn toxic metal resistance, 1166-1182 ecology, 266 gelling agents, 73, 1159-1160 Cvr Coprinus, airborne, 976 method 1623,267-274 ionic strength, 75 Coprostanol, 252 shellfish, 313-314, 316, 318 iron-oxidizing bacteria, 1151-1152 Cyt Core splitter, 809 source waters, 265-279 iron-reducing bacteria, 1240 Cy~ Coring, subsurface sampling, 796, 799-800, subsurface transport, 877 landfill microbes, 828-829 e 808-810 UV inactivation, 328-329 legionellae, 1009 n Com meal glucose agar, 85 viability markers, 275 magnetotactic bacteria, 1133 n Com smut, 1041 waterborne, 220, 224, 226-227, 231, manganese-oxidizing bacteria, Cyt Coronavirus, 94 238,240,366 1228-1232 Cyt airborne, 1020 Cryptosporidium hominis, 267 nitrogen source, 69-70 Cza waterborne, 220, 366 Cryptosporidium parvum, 58, 224, 267, 927 pH,73-75 Corrective action, 194 Cryptostroma corticale, 978 protozoa, 80 Correlation coefficient, 207-208 CTAB method, extraction/purification of quality control, 88-89 0(1( Correlation matrix, 208 soil DNA, 1063 redox potential, 74 0(1( Correlation study, long-term research site, CTC (5-cyano-2,3-tolyl-tetrazolium chlo­ salinity, 75 OA 184-185 ride), 48,54-55, 726 Salmonella, 302-303 I with process rates, 185-186 Cucurbit downy mildew, 1043 seawater-based, 400-401 OA in whole-system experiments, 186-188 Cultural evolution, 12 soil bacteria, 653 Correspondence analysis, 208 Culture, 37-38 sterilization, 73 Dai PLFA fingerprints, 783, 786 airborne microorganisms, 952-953 sulfate-reducing bacteria, 500--501,900 I Corrosion, microbially induced, oil field, algae, 79-92 sulfur-oxidizing bacteria, 504 Dal 898, 901-905 animal viruses, 93-100 troubleshooting, 88 Oa Corrosion coupon, 902-903 arbuscular mycorrhizal fungi, 629-630 undefined media, 72-73 Da Corynebacterium arsenate-respiring bacteria, 1215, 1218 Cupnavidus metallidurans, 1177 Oa endophytic, 640, 642 arthropod pathogens, 772-773 Curtobacterium, endophytic, 642-643 De signature lipids, 114 bacteria, 69-78 Curvularia Coscinodiscus concinnus, 457-458 from aquatic environment, 434-435, airborne, 933 De Cosmid/fosmid vector 439 plant pathogens, 1036 De metagenomics of biodegradation organ­ biodegradation microorganisms, 1080 Cy5,46 isms, 1083 brown rot fungi, 1123 Cyanobacteria, 232, 234-237, 240 soil metagenomics, 1064 community, seeCommunity culture avian vacuolar myelinopathy, 386 Oe "Cosmobacter millennium," 1152 dilute aquatic samples, 399-406 BMAA,386 De Cosmopolitan species, 9 extremophiles, 87-88 contact irritants, 383-384 Costa Rican soil, ammonia-oxidizing bac­ fungi,69-78 control, 235 teria, 614-615 high-throughput dilution to extinction culture, 72, 79-92 Cotton industry, airborne endotoxin, culture, 399-406 hepatotoxins, 384-385 994-995, 997 "in situ" incubation conditions, 76, 108­ lipopolysaccharide, 383-384 Coughing, 1018 109 maintenance methods, 82 Counting procedures, in microscopy, 42 landfill microbes, 828-829 neurotoxins Coxiella bumetii,927 larger-scale, 75 freshwater species, 384-386 Coxsackievirus, 94 legionellae, 1008-1009 marine species, 384 airborne, 964, 1019 magnetotactic bacteria, 1132-1134 nitrogen fixation, 511-513 clinical syndrome, 223 manganese oxide-reducing bacteria, pathogens, 224-225, 227 waterborne, 223, 232-233 1233-1234 sulfur-oxidizing, 505 Creosote compounds, degradation in manganese-oxidizing bacteria, 1228 toxins, 219, 227, 235, 383-386 aquifer, 850 methanotrophs, 836 Cyathus stercoreus, 1107 D Cresol, degradation in landfill, 820 microbes from high-pressure marine Cycad plant, 386 D Cruise ship, 237 environments, 583-584 Cyclic AMP assay, phosphorus cycling, Cryolander, 41 for microscopy studies, 40-41 525 D Cryopreservation oil field microbes, 898-901 Cyclic voltammetry, electrochemical D algae and protozoa, 90 oxygen requirement/tolerance, 72, behavior of fungal metabolites, isolates from high-throughput culture, 74-75 1125 404-405 P. chrysosporium, 1091 Cyclobacterium, 23 D Cryosectioning, 41 physicochemical factors, 73-75 Cyclospora cayetanensis Cryo-TEM, metal-microbe interactions, protozoa, 79-92, 266 detection, 235-236 o 1203-1204 quality control, 88-89 oocysts, 236 Cryptic growth, 340 soil bacteria, 653-654 waterborne, 228, 235-236, 265, 276 Cryptococcus, airborne, 976 sulfate-reducing bactetia, 499-502 Cvlindrospermopsin, 384-386 t Cryprococcus neoformans, 977 sulfur-oxidizing bacteria, 504 Cylindrospermopsis, 384-385 r CryPtosporidium temperature, 73, 83 Cylindrospermopsis raciborskii, 235,386 r biology, 266 toxic-metal-resistant bacteria, 1172­ Cypovirus, soil, 772 [ chlorine inactivation, 330 1173 Cyst [ clinical syndrome, 224 Culture medium amoebae, 87, 265 CLSM imaging, 58 acidophiles, 1156-1160 bacterial, 23 detection, 266-275 airborne microorganisms, 952-953 protozoa, 85, 89, 231 confocal microscopy, 274 algae, 79-80, 82-83 Cysteine-sulfide reducing agent, 74 ELlSA,274 anaerobic, 74 Cytochrome, iron-reducing bacteria, 1241, FACS, 274 barophiles, 583-584 1243-1244 FISH,274 basal medium, 69-73, see also Basal Cytochrome c oxidase gene, hyphornvcetes, microscopic particulate analysis, 275 medium 474 SUBJECT INDEX • 1261

Cytochrome oxidase, monitoring freshwa­ hyphomycetes, aquatic, 473-474 culture, 500, 900 ters and drinking waters, 257-258 indicator molecules in soil extracts, endospore formation, 28 Cytochrome PASO monooxygenase, 1100 658-659 Desulfovibrio, 670 Cytomegalovirus, 94 iron-reducing bacteria, 1242 culture, 500, 900 Cytometric analysis, FISH combined with, isolates from high-throughput culture, hydrogenase, 149 726 404 lipids, 114, 117 Cytopathic effect, virus, 97, 298,620-621 landfill microbes, 831 morphology, 23 Cytophaga magnetotactic bacteria, 1132 oil field, 901 endophytic, 640 metal-reducing and metal-oxidizing bac­ Desulfovibrio gigas, 117 motility, 28 teria, 552 Desulfovibrio magneticus, 1133 nutritional specialization, 26 methodology, 679 Desulfuromonas acetoxidans, 1138 Cytophaga allerginae, 963 microeukaryote assemblages, 1116 Detrended correspondence analysis, 208 Cytophaga-like bacteria, OOM uptake, 481 monitoring freshwaters and drinking PLFA fingerprints, 783 Czapek's agar, 75 waters, 259 Dextran, bioaerosol stabilizer, 966 protists in aquatic environment, 461 Dtacetoxvscnpenol, 980 soil microbial community, 608 Diapers, disposable, as subsurface pathogen Dactylella oviparasitica, 749 sulfur-oxidizing bacteria, 505 source, 912 Dactylomyces crusraeeus, 1107 viruses in aquatic environment, 450 Diaphanoeca grandis, 457-458 DAIME image analysis, 712 Denitrification, 688 Diarrheic shellfish poisoning, 380-381 FISH images, 726-728 abundance of denitrifying organisms, Diatom DAPI,46-47, 54, 402-403,445-446,480, 516 culture, 82, 89 699-700,878,954,1116 aquifer, 849 geographical distribution, 14 Data analysis, see also Statistical analysis diversity of denitrifying organisms signature lipids, 114

microarray experiment, 669--670 anammox organisms, 516 DiBAC 4,48 Data quality assessment, 194 conventional denitrifiers, 516 Dibenzo(a,h)anthracene, mycoremediation, Data reduction, 197 functional gene analysis, 693--694 1100 Data validation, 197 global and regional oceanographic Dichloran glycerol-If agar, 952 Data verification, 197 approaches, 517-518 Dichloroethene, degradation in subsurface, Death, from pathogens in drinking water, landfill, 820 868 367,369,375-376 marine environment, 515-517 Dichomitus squalens, 1099, 1101, 1107 Debrornoaplvslatoxin, 383 measurement, 864 Didinium, 84 Decanting density gradient centrifugation acetylene block method, 517, Didymella, plant pathogens, 1032, 1036 method, arbuscular mycorrhizal 691-692, 864 Die-off, microbial population. 357-363 fungi from soil, 627 denitrifier enzyme activity, 692 Diet incorporation bioassay, arthropod Dechloromonas, 1150 direct nitrogen flux, 516-517 pathogens in soil, 774 Decomposition, see also Biodegradation l5N tracer method, 517, 692---{)93, Difference imagery, 49, 51 enzyme-driven decomposition models 864--865 Differential expression analysis, genes and for soil, 708 microprobe, 174 genomes mediating biodegradation, extracellular enzymes in soil, 704-711 populations of denitrifying organisms, 1082 fungi in aquatic environment, 469-478 515-516 Diffusion landfill, 818-842 soil, 691--693 within biofilms, 57 leaves by aquatic hyphomycetes terminal electron-accepting reaction, enzymes in soil, 706, 708 dynamics of individual compounds, 860-862, 864-865 microenvironmental analysis, 57 470 Density centrifugation method, cell extrac­ Diffusion growth chamber, soil bacteria, enzymatic activities, 470-471 tion from soil, 717 654 sample collection, preparation, and Density gradient centrifugation, isolation Digital imaging, see Image processing exposure,469-470 of protists, 81 Diglycerides, community metabolic status, statistical analysis of mass loss, 470 Density histogram, 206-207 116 soil, microbial succession and, 707 Dental clinic, airborne bacteria and endo­ Dilution culture, 399-406, see also High­ Deconvolution, 52-54 toxin, 992 throughput dilution to extinction Deep sea, 575, seealso High-pressure Deoxynivalenol, 980-982 culture marine environment Department of Transportation, U.S., ship­ Dilution method, isolation of algae and Deep-sea hydrothermal vent, 575 ping infectious material, 270 protozoa, 80 Defined substrate method, monitoring Descriptive statistics, 199-207 2,5-Dirnerhoxv-I ,4-benzoquinone, 1122 marine recreational waters, Desert ecosystem, long-term research sites, 4,5- Dimethoxy-I ,2-benzoquinone, 1122 282-283 183 4,5-Dimethoxycatechol, 1124 Degenerate PCR, viruses in aquatic envi­ Desulfitobacterium, 1216 2,s-Dimethoxyhydroquinone, 1124 ronment, 449-450 Desulfitobacterium frappieri, 1216 Dimethvlarsonlc acid, 1197 Degenerate primed random amplification Desulfitobacterium hafniense, 1216 Dimethvlsulfide, 479, 481, 505 of polymorphic DNA, viruses in Desulfobacter Dlmethvlsulfoniopropionate, 479, 481 aquatic environment, 449 oil field, 901 Dinitrovibrio acetiphilus, 900 Degradation, seeBiodegradation signature lipids, 114 Dinoflagellate, neurotoxins, 386-387 Dehalococcoides, signature lipids, 114 Desulfobolus, metal cycling, 544 Dinophysis acumuinata, 381 Deleya, endophytic, 643 Desulfobolus propionicus, 1138 Dinophysis acuta, 381 Deltatox, 346 Desulfobulbus Dinophysis fortii, 381 Denaturing gradient gel electrophoresis, oil field, 901 Dinophysis norvegica, 381 184 signature lipids, 114 Dinophysistoxin, 380-381

acidophiles, 1161 Desulfobulbus propionicus, 1141 DiOC 6,48 aquifer microbes, 852-853 Desulfomicrobium, 1216 Diplomonad, 27 arbuscular mycorrhizal fungi, 633 Desulfomonile, lipids, 114 Direct assay method, bacteriophage in soil, bacteria in aquatic environment, 438 Desulfomonile tiedjei, 69 623---{)24 biodegradation microorganisms, 1080 Desulfosporosinus, 1159, 1216 Direct count procedure, 54 biofilm community, 564--565 Desulfosporosinus auripigmentum, 1216 Direct total microbial count, freshwaters community structure analysis, 146, 149 Desulfotomaculum and drinking waters, 258 1262 • SUBJECT INDEX

Direct tracer approach, community meta­ from soil, 684, 1063-1066 indicator organisms, 249-252 E( bolic activity, 395 from soil or microbes, 667 public health significance, 254 E< Directed adsorption, virus concentration, labeling for microarrav experiment, 668 infectious disease risk, 365-376 E< 291-292 metabolic activity of soil- and plane­ calculating risk estimation, 367-371 elution and reconcentration of virus, associated microbes, 699 caveat emptor principle, 375-376 291-292, 296-297 "nonliving" nucleic acids in marine exposure level, 365 El Discriminant function analysis environment, 532-533 meaning of risk estimation, 371-375 CLPP data, 134 sample preparation for PCR, 305-306 probability of death, 367, 369, El functional gene array data, 1058 DNA base ratio, 157 375-376 El Discriminate analysis, 210, 213 DNA chip, see Microarray probability of illness, 367-368,376 Disinfectant, inactivation with sodium DNA fingerprinting probability of infection, 365-367 EI thiosulfate, 254, 292, 294 community structure analysis, 145-151 variables, 365-367 Disinfection legionellae, 1011 monitoring drinking water, 325 PCR-based methods, 679 bacteriophages, 258 El UV light, 328-329 soil isolates, 655--656 enzyme-specific tests, 257-258 Disinfection by-products, 330-331 viruses in aquatic environment, 449 membrane filtration method, 255-257 EI Dispersal, see Microbial dispersal DNA footprinting, toxic metal resistance molecular methods, 259 E Dispersion model, viability of aerosolized genes, 1177 most-probable-number method, microbes, 967 DNA fragment analysis 254-255 E Displacement, 16 Cj-metabolizing populations, 492--493 presence-absence method, 257 Dissimilatory copper nitrite reductase, 722 hvphomvcetes, aquatic, 474 rapid tests, 258-259 Dissimilarory metal-reducing bacteria, 543 DNA hybridization multibarrier approach, 325 culture-based methods, 551 bacteria in aquatic environment, 435 parasites, 224 molecular methods, 553-554 community structure analysis, 143-145 pollution source, 252-254 Dissimilatory nitrate reduction, 693 deep-sea microorganisms, 585 protection, 914-921 terminal electron-accepting reaction, DNA reassociation kinetics, 144-145 protozoa, 231, 265-279, 365-376 864-865 mobile gene elements, 763 recovery of injured bacteria, 259 Dissimilatory sulfite reductase, 503 phylogenetic studies, 157 sample col1ection, transport, and stor­ oil field bacteria, 901 sulfate-reducing bacteria, 502 age, 254 Dissolved inorganic carbon, aquifer, 847, toxic metal resistance genes, 1174-1175 sources of microbial contamination, 849 viruses in aquatic environment, 450--451 325-326 E Dissolved organic carbon DNA library, 21 standards/guidelines, 254 E aquifer, 843, 845 toxic metal resistance genes, 1174 surface water sources, 328 carbon cycling in ocean, 479--487 DNA microarrav, see Microarray viruses, 223, 230-231, 295,365-376 consumption by deep-sea microorgan­ DNA probe Drinking water well, 327-328, 912-922 isms, 578 community structure analysis, 140-142 Groundwater Rule, 914, 920--921 Dissolved organic matter (DOM), 479--487 functional, 140 protection, 797, see also Wellhead pro­ consumption of alga-derived component group-specific (phylogenetic or taxo­ tection area ofDOM,481 nomic), 140-141 setback distances, state requirements, effect on subsurface microbial transpott, total genomic, 140 916-917 873 DNA reassociation kinetics Source Water Assessment and environmental DNA for enzymes bacteria in aquatic environment, Protection Programs, 914-921 E hydrolyzing biopolymers, 483--485 435--436 delineation of source water protection high-molecular-weight compounds, community structure analysis, 144-145 areas, 914-918 479--480 DNA sequence determination of public water supply E low-molecular-weight compounds, aligning sequences, 609 susceptibility, 919-921 479--480 phylogenetic studies, 160 source inventories in water protection phylogenetic groups and DOM uptake, soil microbial community, 608-617 areas, 918 481 toxic metal resistance genes, 1175-1177 sources of contamination, 912-914 single-cell analysis of DOM consump­ DNA stain, 54 zone of influence of pumping well, tion, 480--483 DNADIST program, 1117 914-915 Dissolved organic phosphorus, marine DO sag equation, 338 Drop col1apse method, biosurfactant pro­ environment, 523-526, 530--531, Document control, quality assurance pro­ duction, 899 533 gram, 193 Droplet freezing assay, ice nucleation activ­ global patterns, 526-530 DOM, see Dissolved organic matter ity, 740-742 Distance matrix, phylogeny construction, Domoic acid, 380, 382 Droplet nuclei, 1016 609--610 Dormancy, 26 Dry rot fungi, 976 Distance method Doublet cell, subsurface microbial trans­ Drying, preservation of algae and protozoa, assessing whether two communities dif­ port, 884 89 fer, 611 Downstream processing, fungal solid-state Dry-labbing, 197 topology of phylogenetic tree, 161 fermentation system, 1111 dsrAB genes, sulfate-reducing bacteria, 503 Ditylum /nightwe!!ii, 457--458 Dracunculus medinensis, waterborne, 220, Dust, airborne microorganisms, 930, 933 Divergent tracer test, subsurface microbial 224, 226, 366 transport, 884-886 Drech5lera, plant pathogens, 1032, 1036 DMSO Drilling, subsurface sampling, 796, 799 Early blight, 1036 metabolism, 505 Drilling fluid, 803-804, 806-807, 809 Eastern equine encephalomyelitis virus, preservation of acidophiles, 1162 Drinking water, 219, 222-264, seealso 927 DNA Source waterfs); Water treatment Ebola virus, 927 extraction algae, 224 Echinamoeba, 265 from bacterial cells, 1173 arsenic, 1214-1222 Echovirus, 94 from environmental samples, bacteria, 223-224, 229-230, 365-376 clinical syndrome, 223 139-140, 1112-1113, 1172, control of microorganisms, 325-333 minimum infectious dose, 366 1219-1220 finished, 259, 265-279 waterborne, 223, 232-233 from landfill sample, 831 groundwater sources, 328 Ecological proteomics, 709 SUBJECT INDEX • 1263

Ecologist, 17 protozoa, 276 varlability of responsiveness of airway Ecoplate, 127 waterborne disease, 231-237 and lung, 993 Ecosystem Emericella assay, 954-955 interactions between members, 4 airborne, 933, 974 cyanobacteria, 235 long-term research site, 182-189 water activity for growth, 973 measurement EDTA, removing metals from water sam­ Emiliania huxleyi virus, 450 chemical methods and immunoassays, ples, 254 Emodin, 980 997 Efflux pump, toxic metals, 1168 Emulsifying organisms, microbially Limulus amebocyte lysate assay, Electric paramagnetic resonance, fungal enhanced oil recovery, 899 954-955,996-997 metabolites, 1125 Encephafitozoon, waterborne, 236, 266, 276 potency, 997 Electrochemical RNA hybridization, moni­ En<:ephafitozoon cuniculi, 276 recognition, 993 toring marine recreational waters, Encephalitozoon hellem, 276 settled, 997 284 Encephafitozoon intestinalis, 236, 276 structure, 992-993 Electrochemical techniques, measurement Encephalomyocarditis virus, 964 Endotoxin unit, 954-955 of primary production, 414-415 Endemic disease, waterborne, 228-229 Endoxylanase, 1090, 1094 Electrochemical transducer, 175 Endocrine disrupters Energy dispersive spectroscopy, metal­ Electrocoagulation, generation of viral vitellogenin gene expression assay, 351 microbe interactions, 1201-1202 aerosols, 1021 wastewater, 350 Energy source, 15, 24 Electrode-reducing bacteria, 1137-1146 Endoglucanase, 1090, 1094, 1107, 1122 culture medium, 71-72 components of bacterial electrode Endohydrolase, 704 Enrichment culture, 21-22,38,71,102 devices, 1139-1140 Endomannanase, 1090 algae, 80 culture medium, 1143-1144 Endophytic bacteria, 638-651 arsenate-respiring bacteria, 1218 direct interactions with electrodes, in bioremediation, 643, 646-647 biodegradation microorganisms, 1080 1137-1138 colonization of plants, 644-645 iron-oxidizing bacteria, 1151 laboratory fuel cells, 1140-1141 culture media, 641, 644 iron-reducing bacteria, 1240 sample experiment, 1142-1143 definition, 638 manganese oxide-reducing bacteria, physiology, 1141-1142 immunological localization, 645 1233-1234 potentiostats, 1140-1141, 1143 in planta visualization, 645-647 manganese-oxidizing bacteria, 1228 sediment fuel cells, 1140-1141 inoculations ami plant culture, 644-645 protozoa, 80 terminology, 1138-1139 isolation, 640-645 Enrichment technique, bacteriophage in Electromigration, protozoa, 81 physical techniques, 641 soil, 623-624 Electron acceptor, 24 plant tissue direct technique, 641 Entamoeba, waterborne, 220 aquifer, 843, 845-850 prewash of plant material, 640 Entamoebacoli, 265 culture medium, 72 surface sterilization of plant material, Entamoeba hiswlytica electrode-reducing bacteria, 1137-1146 638, 640-641 clinical syndrome, 224 iron(Ill), 1239 localization in roots, 722-723 waterborne, 224, 231, 265,366 iron-oxidizing bacteria, 1150 metabolic activity, measurement, Enteric bacteria, shellfish, 312 manganese OXides, 1223 645-646 Enteric organisms, waterborne disease, subsurface, 860-871 microscopy, 639, 645 222-248 terminal, see Terminal electron-accept­ nonculturable, 646 Enteric viruses ing reaction nucleic acid hybridization localization, airborne, 964 Electron donor, 24 645 shellfish, 313, 317-319 aquifer, 845-848 plant growth responses, 646-647 soil, 618-626 subsurface, 860-861 reporter gene systems, 645-646 Eruerobacter Electron microscopy from roots and leaves, 641 airborne, 989, 991 landfill, 830 from seeds and stems, 640-641 endophytic, 640, 642-643, 646 magnetoractic bacteria, 1130 species, 639, 642-643 subsurface transport, 874, 876 manganese oxides, 1226 staining, 645 total coliforms, 249 metal-microbe interactions, 1201-1203, surrogate transformations in plants, Enterobacter agglomerans, 989, 991 1205 647 Enterobacter clOacae, 963, 991 radionuclides, 1200 use in plant protection, 639, 642-643, Enterobacterial repetitive intergenic con­ viruses, 93, 97 646-647 sensus sequence peR, 679 in aquatic environment, 445-447 Endophytic fungi, 638 Enterococci Electron probe microanalysis, microbe­ Endopolygalacturonase, 1094 airborne, 989 mineral interface, 1205 Endospore, 23, 28 freshwaters and drinking waters, 250, Electron spin resonance, fungal metabo­ Endosymbiosis, 11 255-256 lites, 1125 Endotoxin, 992-996 marine recreational waters, 280-283, Electron transport system, indicators of cell airborne, 926,928-932,954-955, 286 viability, 55 989-1004 membrane filtration method, 256 Electronic data, quality assurance, 193-194 asthma and, 993, 995-996 most-probable-number method, 255-256 Electrostatic precipitation, bioaerosol sam­ asthma-like syndrome and, 994 wastewater, 337 pling, 940 environments with high concentra­ water quality indicator, 239 ELISA (enzyme-linked immunosorbent tions of toxin, 989-991 Enterococcus avium, 250 assay) environments with low concentra­ Enterococcus cecorum, 250 acidophiles, 1160 tions of toxin, 990, 992 Enterococcus durans, 250 airborne microorganisms, 954 environments with moderate concen­ Enterococcus faecalis, 250, 763 bacteria in wastewater and sludge, trations of toxin, 990-992 Enterococcus faecium, 250 306-307 hypersensitivity pneumonitis, Enterococcus gallinarum, 250 hvphomvcetes, aquatic, 472 994-996 Enterococcus hirae, 250 protozoa, 274 inhalation and lung inflammation, Enterocytozoon, waterborne, 232, 236, 266, Elitism, 1074 993 276 Embedding methods, 41 occupational environments, 994 Enterocytozoon bieneusi, 236, 265, 276 Emergence trap, 771 organic dust toxic syndrome, 994 Enterolert test kit, 282 Emerging infections sampling, 996-997 Enterovirus, 94 1264 • SUBJECT INDEX

Enterovirus (continued) metabolic activity of soil- and plant­ Ethical issues ass~ clinical syndrome, 223 associated microbes, 699-701 digital imaging, 42-43 detection, 233 metal-microbe interactions, 1201 in research, 197-198 r drinking water, 367-369 Single-cell analysis of DOM consump­ Ethidium bromide, 878 carl marine recreational waters, 286 tion, 480 Ethmodiscus rex, 457-458 car: shellfish, 319 sulfur-oxidizing bacteria, 505 Ethylene, methanotroph inhibition, 823 cla! subsurface transport, 877 viruses in aquatic environment, 445-446 Eubacterium, oil field, 901 cliff UV inactivation, 329 Epiphyte, removal from filamentous algae, Euearya, 26-27 fur waterborne, 220, 223, 230, 232-233, 81 Euglena kin 366 Epstein-Barr virus, 94 culture, 84-85 mil Entomopathogens, see Arthropod patho­ Epulopiscium, 23, 28 waterborne, 265 me gens Equid herpesvirus 1, 1020 Euglena medium, 84-85 Entomophaga maimaiga, 770, 772-773, 777 Equilibrium relative humidity, 973 Eukaryota (Eucarya), 4 Enumeration of microorganisms, 54 ER-CALUX bioassay, 350 Eukaryote, see Microeukaryote assemblage acidophiles, 1160-1161 Ergosterol, 115 Euphotic zone, 393 mj aquifer ecosystem, 852 airborne fungi, 955 Euplotes woodru[fi, 457-458, 460 pn iron-oxidizing bacteria, 1151-1152 arbuscular mycorrhizal fungi, 632 European Economic Community, drinking iron-reducing bacteria, 1242 soil fungi, 782 water and recreational freshwater landfill, 824, 827-828 Ergot, 980 standards, 254 magnerotactic bacteria, 1130-1132 Error, 197 Eurotium manganese-oxidizing bacteria, 1228 honest, 197 airborne, 974 pathogens in wastewater, 349 from negligence, 197 water activity for growth, 973 sulfate-reducing bacteria, 499-502 type 1,211-212 Eutrophication, 378, 387, 408, 417 Environmental freshwater, 249-264 type II, 211-212 Evanescent-wave excitation biosensor, indicator organisms, 249-252 Erwinia 176-177 Extr: public health significance, 254 endophytic, 640, 642-643 Evaporative condenser, legionellae, 1007, monitoring plant pathogens, 1034 1012 Extr bacteriophages, 258 Erwinia carotovora, 1034 Evolution, 7, 12, 15 enzyme-specific tests, 257-258 Erwinia herbicola, 963 cultural, 12 o membrane filtration method, 255-257 Erysiphe, plant pathogens, 1032 genetic algorithms, 1072-1078 molecular methods, 259 Escape in space, 13 horizontal gene transfer, 26-27 most-probable-number method, Escape in time, 13 microbes and macrobes, 6 Fdi 254-255 Escherichia parallel, 7 F st presence-absence method, 257 endophytic,643 Evolution strategies, 1077 Fab rapid tests, 258-259 size, 23 Evolutionary distance, 162-163 FA< pollution source, 252-254 wastewater and sludge, 300 Evolutionary models, 162,611 Fac recovery of injured bacteria, 259 Escherichia coli Evolutionary programming, 1077 FAl sample collection, transport, and stor­ airborne, 931-932, 963, 965, 989, 991 Evolutionary tree, seePhylogenetic tree age, 254 clinical syndrome, 223 EXAFS (extended X-ray absorption fine- Fac Environmental gene tags, 394, 1084 drinking water, 369 structure) spectroscopy, 1185-1191, "Fa Environmental genomics, see enterohernorrhagic, 223, 233 1197,1206 FlU: Metagenomics enteroinvasive, 223 Exohydrolase, 704 Fag Environmental microbiology enteropathogenic, 223 Exophiala, airborne, 975 Fal scope, 3-5 enterotoxigenic, 223, 229 Exopolymer stains, 47 Far terminology, 7-8 freshwaters and drinking waters, 250, 255 Exopolysaccharide,57 Fa! Environmental waters marine recreational waters, 280-283, Exospore, 23, 28 Fal modeling fate of microorganisms in, 286 Experimental design, identification of 355-364 metagenomic cloning, 1083 microbes involved in specific in viruses, 290-299 most-probable-number method, 255 situ functions, 748-757 Enzymes response to toxic metals, 1178 Exponential decay equation, 470 cell-associated, in situ immunolabeling, serotyping, microbial tracking methods, Exponential decay model 722-723 253 microbial die-offs, 357-363 Fa environmental DNA for enzymes shellfish, 227 viability of aerosolized microbes, hydrolyzing biopolymers, 483-485 subsurface transport, 874--876, 880 966 extracellular, seeExtracellular enzymes thermotolerant coliforms, 250 Expression vector, monitoring gene expres­ isoenzymes of arbuscular mycorrhizal total coliforms, 249 sion in situ, 55-56 fungi,631 wastewater, 337 Extended gene content, 164 FI landfill, 824, 827, 829 water quality indicator, 239 Extinction, 13 leaf decomposition by aquatic waterborne, 222-223, 229-230, 233, Extinction culture, 399-406, see also High­ FI hyphomycetes, 470-471 240 throughput dilution to extinction soil, 678-679, 704-711 Escherichia coli 0157:H7, 222-223, 226, culture EPA method 1601,326 233,673,927 Extracellular enzymes Epicoccum E-Screen, 350 glycosylation, 1095 airborne, 933, 974 Esterase, landfill, 829 mycoremediation, 1097-1106 F plant pathogens, 1032, 1036 Estrogens P. chrysosporium spore discharge, 973 CALUX assays, 350-351 isolation, 1091 Epidemic disease, waterborne, 227-228 E-Screen, 350 proteomic analysis, 1089-1096 Epifluorescence microscopy, 43 recombinant yeast estrogen screen assay, removal of lignin, 1091 bacteria in aquatic environment, 350 two-dimensional gels, 1091-1093 402-403, 434 wastewater, 350-351 wood-degrading fungi, 1089-1096 biofilm formation, 569 Estuary, 393 Extracellular enzymes, soil, 704-711 deep-sea microorganisms, 578, 584 long-term research site, 185 activity endophytic bacteria, 645 possible estuary-associated syndrome, abiotic controls, 706-707 enumeration of microorganisms, 54 386-387 plant controls, 706 SUBJECT INDEX • 1265

assay, 704-705 FC/FS ratio, 253-254 Flotation method, sampling soil nerna­ measurement principles, 707-708 freshwaters and drinking waters, 250 todes,772 microplate assays, 708 membrane filtration method, 256-257 Flow cell, 40-41, 47,106-107 carbon cycling and, 707 Feeding guild, 126, 456 anaerobic, 1241-1242 carbon sequestration and, 707 Feedlot waste, substrate for fungal solid­ Flow cyrometry classification, 704-705 state fermentation, 1109 airborne microorganisms, 954, 957

diffusion, 706, 708 Feeley-Gorman agar, 1009 FISH-based, C j oxidizers, 490-491 future directions, 708-709 Fenton reaction, wood degradation by isolation of protists, 81 kinetics, 706-707 brown rot fungi, 1122-1128 quantification of green fluorescent pro­ mineral-carbon interactions, 707 Fermentation, 23-24, see also Fungal solid­ tein, 737 models state fermentation system Flowthrough column enzyme-driven decomposirion models, aquifer, 845 aquifer biogeochemistry, 850 708 industrial, genetic algorithms, 1075, downtlow mode, 886-887 soil structure models, 708 1077 packing procedures, 886 mycoremediarion, 1097-1106 landfill, 819-820 precluding air bubbles, 886 production Ferrihvdrite, end product of iron oxidation, subsurface microbial transport, 886-887 economic framework, 705 1150-1151 upflow mode, 886-887 effects of plant inputs, 706 "Ferrimicrobium acidiphilum," 1157, 1159 Fluoranthene, mycoremediation, invasive plant species, 706 Ferroglobus placidus, 1152 1100-1102 microbial communiry controls, Ferroplasma acidarmanus, 1157 Fluorene, mvcorernediation, 1100, 1102 705-706 Ferroplasma acidophilum, 1157 Fluorescein, 954 mycorrhizal fungi, 706 Ferrozine colorimetric assay, iron(lI) in geochemical tracer, 806 by roots, 706 subsurface, 865 Fluorescein diacetate, 48, 54-55 taxonomic distribution, 705 Ferry boats, carrying monitoring equip­ Fluorescein Isothiocvanare, see FITC Extracellular polysaccharide, iron-reducing ment, 418 Fluorescence exclusion, 56-57 bacteria, 1243-1244 FerryMon, 418 Fluorescence immunoassay, airborne Extremophile, 1155, seealso High-pressure Fertilizer microorganisms, 954 marine environment nitrogen, 692 Fluorescence in situ hybridization (FISH), culture, 87-88 whole-lake fertilization experiment, 395,712,723-728 186-187 acidophiles, 1161-1162 Fervidobacterium, 27 anammox bacteria, 516 F distribution, 204-205 Field sterilization, sampling equipment, aquifer microorganisms, 854 F statistic, 212 294 bacteria in aquatic environment, Fabrication of results, 197 Field study, arthropod-microbe interactions 439-440 FACE program, 183 in soil, 769, 776 bacterial carbon cycling in aquatic envi­ Facilitation, 8 Filter sterilization, 73 ronment, 482-483 FACS, see Fluorescence-activated cell Filtration method biodegradation microorganisms, sorter bioaerosol sampling, 940-942, 953 1080-1081 Factor analysis, 208 groundwater concentration, 813 biofilm community, 566 "Facultative," 24 isolation of picoplankton, 81 C, oxidizers, 490-491 Faenia rectivirgula, 978 wastewater concentration, 301 Clone-FISH,723-724 Fagirhiza pallida, 727 Fire blight, 1036 computer-assisted image analysis Falsification of results, 197 FISH, see Fluorescence in situ hybridiza­ CMEIAS, 727-728 Farmer's lung, 989 tion DAIME, 726-728 FastDNA SPIN kit for soil, 1064-1065 FlTC (fluorescein isorhiocvanate), 46, 54, cytometric analysis combined with, 726 Fatty acidls), seealso Phospholipid fatty 57, 713, 715, 774, 954 deep-sea microorganisms, 584 acids Fitness landscape analysis, 1076 denitrifying bacteria, 516 degradation in landfill, 819-820 Fitness trairs, for successful colonization, 15 dual-color, 1081 indicator molecules in soil extracts, Flabellula citata, 457-458 FlSH-MAR,725-726 656 Flagella, 28 bacteria in aquatic environment, 440 oxirane, 117 Flagellate, 80, 265, see also Protist; biodegradation microorganisms, Fatty acid methyl esters Protozoa 1080-1081 arbuscular mycorrhizal fungi, 631 aquatic environment contribution of major bacterial groups comparison to PLFA, 782 benthic vs. pelagic, 463 to secondary productivity, 427-428 extraction, 781 community structure, 454-468 metabolic activity of soil- and plant- soil microbial community, 655, 781-782 depth and seasonal distribution, associated microbes, 699 FDC method, measurement of secondary 463-464 hyphomycetes, aquatic, 472 production, 427 freshwater vs. marine, 462-463 landfill microbes, 831 Fecal coliforms, 238-239, see also culture, 83-85 magnetotactic bacteria, 1132 Thermotolerant coliforms identification, 455 metal-reducing and metal-OXidizing bac­ airborne, 932, 989 maintenance conditions, 85 teria, 552 FC/FS ratio, 253-254 oligotrophic oceanic environment, 457 rnerhanorrophs, 836 wastewater, 337, 349 Flavivirus, 94 methodology Fecal contamination Flavobacterium accessibility of probe target site, 723 marine recreational waters, 280-281, endophytic, 640, 642-643 community "environmental" samples, 286-287 lipids, 117 723-724 shellfish, 311-312 Flexibacter, 28 fixation step, 724 source waters, 326 Floating-filter method, culture of aci­ general protocol, 724 sterols as indicators, 252 dophiles, 1160 hybridization step, 724 wastewater and sludge, 307 Floc, CLSM imaging, 58 obstacles and limitations, 724 waterborne disease, 222-248 Flocculation method oligonucleotide probe development, Fecal streptococci cell extraction and recovery from soil 723 airborne, 931-932 and roots, 716-717 optimizing hybridization conditions, definition, 250 virus concentration, 291 724 1266 • SUBJECT INDEX

Fluorescence in situ hybridization (FISH) in situ immunolabeling of cell-associated measurement of microbial activity, my (continued) enzymes, 722-723 1059-1060 my probes for culturable microbes in pure legionellae, 1010 hybridization procedure, 1056-1057 pre culture, 723 monitoring freshwaters and drinking image analysis sig removal of unspecific bound probes, waters, 259 data normalization, 1057-1058 soi 724 staining of extracted microbes preprocessing, 1057 spc microeukaryote assemblages, 1116 filter preparation, 717 removal of outliers, 1057 nitrifying bacteria, 514 staining microbes on filters, 717 signal-to-noise ratio, 1057 oil field microbes, 901 Focal Check beads, 43 measurement of mRNA, 1059-1060 protozoa, 274 Folic acid, culture medium, 71 probe design recent developments Fomitopsis pinicola, 1107 acquisition of gene sequence informa­ amplification of signal intensity, 725 Food industry, seealso Shellfish tion, 1052-1053 suI improved signal-to-noise ratio, airborne mycotoxins, 981 oligonucleotide probe design, vo 724-725 FoodNet, 312 1053-1055 wa polynucleotide probes, 725 Foot-and-mouth disease virus, 94, 964, oligonucleotide probes, 1053, 1059 wa targets other than rRNA, 725 1020, 1022 PCR-amplicon probes, 1053, 1059 wc single-cell analysis of DOM consump­ Forced-gradient tracer method, subsurface selection of target genes, 1052-1053 Fungi tion, 480--481 microbial transport, 884-886 quantitative, 1059 Furar sulfate-reducing bacteria, 502-503 Forest ecosystem, long-term research sites, sensitivity, 1059 Fusar Fluorescence lifetime imaging, 58 183, 186 soil, 670-672 air intracellular pH measurement, 58 Forest products industry, airborne bacteria specificity, 1059 ph Fluorescence microscopy, seealso and endotoxin, 991 standardization, 1059 spr to: Immunofluorescence microscopy Formaldehyde, C 1 metabolism, 489 Functional gradient essentials and advancements, 712-713 Formaldoxime method, measurement of creating gradients, 749 wa Fluorescence spectrometry, 173 manganesetll ), 1224-1225 identification of natural gradients, Fusar Fluorescence spectroscopy, laser-induced, Fouling organisms, 569 749-750 Fusar aqueous chemical speciation, 1197 Fountain, legionellae, 1007-1008 multiple, 749 Fusal Fluorescence-activated cell sorter (FACS) Fourier transform, 1189-1190 Functional metagenomics, 493 Fusal protozoa, 274 Fowlpox virus, 1020 Functional richness, 131-132 Fusid recombination from horizontal gene Feyns Erdschreiber medium, 86 dilution-extinction, 132 Fusol transfer, 764 Francisella, 220 Fungal solid-state fermentation system, Fluorescent microspheres Francisella rularensis, 927, 963 bioconversion of lignocellulosic conservative tracer in subsurface trans­ signature lipids, 114 biomass, 1107-1111 port, 884 waterborne, 366 aeration and agitation, 1109 a-Go geochemical tracer, 805-808 Frankia, signature lipids, 114 bioreactor design, 1110-1111 J3-G~ Fluorescent probe FRAP methods, 57 downstream processing, 1111 rru CLSM,46--48 Freezing, preservation of algae and proto­ fungal growth on substrates, 1109-1110 immunological, 56 zoa,90 inoculum type and preparation, 1108 Galle Fluorescent protein, commercially avail­ Frequency histogram, 206-207 lignocellulosic substrates, 1109 Galli, able, 172 Freshwater environment, 393, seealso moisture and water activity, 1108 Galli, Fluorescent reporter, 170, 172-173, Drinking water; Environmental monitoring fungal growth, 1110 Gam 736-738 freshwater; Recreational waters pH requirement, 1108-1109 Gam advantages and disadvantages, 172-173 Freshwater medium, 1233 temperature variation and control, 1109 Gam applications, 173 Freund's complete adjuvant, 715 Fungal spore source strength tester, 947 Gam fluorescence measurement, 173, 737-738 Freund's incomplete adjuvant, 715 Fungi, see also Microeukaryote assemblage Gam Fluorescent stains FRNA phage airborne, 925-926, 928-934, 939, Gare labeling strains for transport studies, freshwaters and drinking waters, 251 952-955, 972-979 Gas, 878-879 indicators of fecal contamination, 326 culture, 952-953 metabolic activity of soil- and plant­ marine recreational waters, 285 hypersensitivity pneumonitis, Gas associated microbes, 699-701 F-test, assessing whether two communities 978-979 Gas Viability stains, 48 differ, 611, 614-615 indoor populations, 972, 974-976 GasI Fluorescent-antibody technique, seealso Fuel cell organic dust toxic syndrome, 979 Gast Immunofluorescence microscopy electrode-reducing bacteria, pathogens, 976-979 Gaul antiserum development 1137-1146 plant pathogens, 1036-1041 GC antigen preparation, 714 terminology, 1138-1139 types of airborne populations, bs blood harvest and preparation of col­ Fuligo septica, 974 974-975 re lected antiserum, 715 Fumarate, culture medium, 72 alpine tundra community, 615-616 Gel immunization, 714-715 Functional diversity index, 133 aquatic environment, seealso Gel arthropod pathogens, 774 Functional gene analysis H yphomycetes, aquatic hi bacteria in wastewater and sludge, 306 methanotrophs, 836 community structure, 469--478 sc direct staining of microbes in processed nitrogen cycling, 693-694 arbuscular mycorrhizal, seeArbuscular Gel soil,717-718 Functional gene array, 150,670-672, mycorrhizal fungi fluorescent-antibody preparation, 1052-1062 arthropod pathogens, 772-773 713-714 biodegradation microorganisms, culture, 69-78 Gel< antibody purification, 715 1083-1084 decomposition in aquatic environment, Gell conjugation of antibody to fluo­ construction 469--478 Cl rochrome, 715 design and fabrication, 1055 endophytic, 638 t( immunofluorescence titer and speci­ nucleic acid preparation and labeling, ergosterol, 632, 782, 955 GelJ ficity of antimicrobial antibody, 1055-1056, 1059 identification, 953 GelJ 715-716 data acquisition, 1057-1058 landfill, 828 Gel prevention of cross-reacting antibody, data analysis, 1058 leaf-cutting ants and, 776 Gen 716 environmental studies, 1058-1060 Iignocellulolytic, 1107 Ger gclatin-Rl'TC conjugate counterstain, interference from contaminants, mycoremediation, 1097-1106, seealso 716 1058-1059 Mycoremediation ir SUBJECT INDEX • 1267

bacterial colonization of roots, 721-722 mycosis, 976-977 soil- and plant-associated bacteria, mycotoxin, seeMycotoxin 734-747 PLFA distribution in soils, 783, 785-786 preparing fungal immunogens, 714 Gene library, biofilm community, 565-566 Geothermal fluid, superheated, sampling, signature lipids, 114 Gene mining, 1083 580 soil,787 Gene probe, indicator molecules in soil Geothrix spores, 925, 947,953-954,972,974, extracts, 656-657 electrode-reducing bacteria, 1141, 1143 977, 1032-1033, 1036-1041 General aerobic bacteria iron reduction, 1242, 1244 discharge mechanisms, 973-974 culture medium, 901 Geothrix fermentans, 1138, 1141 extraction from soil, 772 oil field, 900-901 "Germ," 10 inoculum for solid-state fermentation, oil field water system, 902, 904-905 Giardia 1108 General linear model, 213 biology, 266 substrate characteristics, 972-973 Genetic algorithms, 1072-1078 clinical syndrome, 224 volatile organic compounds, 972, 982 algorithm source, 1074 detection, 266-275 water activity for growth, 972-973 alternative types of evolutionary compu­ confocal microscopy, 274 waterborne pathogens, 234-237 tation, 1077 ELISA,274 wood-degrading, 1089-1096 applications, 1075-1076 FACS, 274 Fungi-Fluor, 645 crossover step, 1072-1074 FISH,274 Furanones, 568 ecosystem manipulation, 1072 microscopic particulate analysis, 275 Fusarium combining organisms, 1074 PCR-based methods, 274-275 airborne, 933, 975, 977 manipulating environmental condi­ drinking water, 265-279, 367-368 plant pathogens, 1033, 1036 tions, 1074 ecology, 266 spore discharge, 974 fitness evaluation step, 1072-1073, Method 1623, 267-274 toxins, 979-981 1076-1077 minimum infectious dose, 366 water activity for growth, 973 initialization, 1073, 1076 shellfish, 313-314,316 Fusarium graminearum, 933, 981, 1043 microbial applications source water, 265-279 Fusarium head blight, 1043 algorithm design, 1076-1077 viability markers, 275 Fusarium oxysporum, 749, 1107 costly fitness evaluations, 1076 waterborne, 220, 224, 226-227, 229, Fusarium sporotrichioides, 933, 981 financial costs, 1077 231,238,240,366 Fusidane, 980 noisy experimental measurements, Gigaspora, 474, 631 Fusobacterium, microbial tracking methods, 1076 Gill breathing, algal interference, 379-380 253 mutation step, 1072-1074 Gliding motility, 28 representations, 1073-1075 Gliotoxin, 980 schematic outline, 1073 Globigerina bulloides, 457--458, 460 a-Galactosidase, 1090, 1094 selection step, 1072-1074 Globigerinoides sacculifer, 457, 460 13-Galactosidase, 735 variations, 1074 Gloeophyllum striatum, 1126 monitoring freshwaters and drinking Genetic programming, 1077 Gloeophyllum rrabeum, 1107, 1122, 1124 waters, 257 Genetically engineered microorganisms Gloeotrichia, 235 Galleria bait method, 773 airborne, 926, 1034-1036 Glornalm, arbuscular mycorrhizal fungi, Gallionella, metal cycling, 544, 549-550 environmental introduction, 9-10 632 Gallionella ferruginea, 1148 field application, 1035 Glomus, 474 Gambierdiscus, toxins, 219 GENIE,613 Glomus clarum, 627 Gambierdiscus toxicus, 381-382 Genome blast distance phylogeny, 164 Glomus inrraradices, 627, 631 Gambiertoxin, 380, 382 Genome conservation, 164 13-D-Glucan, airborne, 982 Gamma distribution, 204 Genome sequence, phylogenetic relation­ 13-1,3-Glucan assay, airborne fungi, 955 Gamma radiation, soil sterilization, 771 ships from, 26, 163-164 Glucan 1,3-13-glucosidase, 1094 Garciella nirratireducens, 900 Genome tree, 163-164 13-Gluconidase, see GUS assay Gas chromatography-MS, endotoxin mea­ Genomic analysis, see also Microarray 13-Glucosidase, 1090, 1094, 1122 surement, 997 C[ metabolism, 488--496 a-Glucuronidase, 1090 Gas delivery station, 1239-1240 community structure analysis, 143-145 13-Glucuronidase, 735 Gas hydrate capacitor, 29 comparative microbial genomics, 164 monitoring freshwaters and drinking GasPak system, 74 phylogenetic studies, 163-164 waters, 257 Gastroenteritis virus, 94, 1018 Genomic island, seeIntegrative conjuga­ Glutamate, bioaerosol stabilizer, 966 Gaussian distribution, 204-205, 211 tive element Glutathione, MnP-glutathione system, GC content, 157 Genotoxicity test, wastewater treatment 1101 bacteria in aquatic environment, 436 efficiency, 346 Glycerol, bioaerosol stabilizer, 966 recently transferred DNA, 764 Genotypic analysis, 157 Glycine betaine, preservation of aci­ Gel coring, 804 Geobacter, 670 dophiles, 1162 Gel microdroplet culture iron reduction, 1243 Glycolate, aquatic environment, 479 biodegradation microorganisms, 1080 metal cycling, 543 Glycosylation, extracellular enzymes, 1095 soil bacteria, 654 signature lipids, 114 Glyoxal oxidase, 1089-1090, 1108 Gel permeation chromatography, wood Geobacter elecrrodophilus, 1138 Goethite degraded by brown rot fungi, Geobacter metallireducens, 117,551,1138, biogenic, 1149 1125-1126 1243 end product of iron oxidation, Gelatin-RITC conjugate counterstain, 716 Geobacter sulfurreducens, 543, 671, 1138, 1150-1151 Gelling agent 1141,1243-1244 Gonyaulax, toxins, 219 culture medium, 73 Geochemical tracer, evaluating contamina­ Gonvautoxin, 379 toxicity, 1159-1160 tion of subsurface samples, 806 GOOD data set, 526 Gelman Envirochek filter, 270 Geochemistry, aquifer, 843-858 Good's buffer, 74 Gelrite,73 Geometric distribution, 204-205 Gordonia amaeae, 672 Gel-stabilized gradient plates, 41 Geomicrobiology, 1195-1210 Grab sampler, 580, 812, 863 Gemmata, 27 Geomyces, 973 Gracilaria coronopifolia, 383 Gene expression, seealso Microarray; Geosiphon,632 Gradostat, community culture, 104-105 Reporter gene system Geosrnin, 982 Grain elevator, airborne bacteria and endo­ in situ monitoring, 55-56 Geostatisrical analysis, 42 toxin, 990, 994 12G8 • SUBJECT INDEX

Gram stain H. J. Andrews LTER site, 186 Heterocyst, 28 for fluorescence microscopy, 56 Habitat, 7-8, 12 Heterodera schachtii, 748-749 quantification of microbial diversity, diversity of habitats, 28-30 Heteromita, landfill, 828 56 operational, 8 Heterosigma akashiwo, 448 Graph,204 potential, 8, 13 Heterotroph, 9, 15-16, 24, 340 Graphite furnace atomic adsorption spec­ Hadal zone, 575 acidophiles, 1155-1159 troscopy, aqueous chemical specia­ Haloacetic acids, biodegradation, 1080 primary, 340 tion, 1197 Halogenated rnethanes, 488---489 secondary, 340 Graphium, lignocellulolvtic, 1107 Halophile, 25, 27 Heterotrophic plate count, freshwaters and Grassland ecosystem, long-term research culture, 75, 88 drinking waters, 252 site, 186 high-pressure marine environment, 577 Hexidium iodide, 56 Gravitational settling method, bioaerosol Hand-held assay, airborne microorganisms, Hierarchical clustering, microarray data, sampling, 940, 1010 954 669 Green fluorescent protein, 47,712 Hantaan virus, 1020 High-performance liquid chromatography avGFP,l72 Hantavirus, 94, 927, 933 arsenic estimation, 1217 H bacterial intolerance of, 737 Hapalosiphon, 384 oxalate estimation, 1124 chromophore, 172-173 Hapatovirus, waterborne, 366 photopigrnent assessment, 415---417 commercial products, 172 Harenia papillomacea, 381 High-pressure marine environment, Hi enumeration of cells, 54 Harmful algal bloom, 378, 417 575-590 Hi geochemical tracer, 805, 808 marine poisonings, 379-383 community measurements, 578, Hi half-life, 737, 743 Hartmannella, 265, 267 584-585 labeling strains for transport studies, Hastigerina pelagica, 458 environments considered, 575 HI 878-879 Hawaii virus, 232 isolation and culturing of microorgan­ monitoring cell activity, 55 Hay infusion agar, 85 isms, 583-584 HI red-shifted, 173, 736 Hazardous waste disposal, 818 laboratory simulation HI reporter systems, 172-173,736--738, Hazardous waste site, mycoremediation, cold temperatures and elevated pres­ HI 742-743 1097-1106 sures, 580-582 advantages and disadvantages, Health care facility high temperatures and pressures, 172-173 airborne bacteria and endotoxin, 992 582-583 applications, 173 airborne microorganisms, 926, 930, 932 limitations yet to be overcome, 584-585 HI endophytic bacteria, 645-646 airborne viruses, 1024 physical disassociation of organisms, H~ fluorescence measurement, 173, legionellae, 1007-1008, 1012 577-579 737-738 Hektoen enteric agar, 302 pressure considerations, 576-577 in soil, 700-701 Helicobacter pylori sampling Hy transposon carrying gene for, 738 wastewater and sludge, 304 background rationale, 576-579 variants, 173, 726-738 waterborne, 228, 232, 234 cold deep environments, 579-580 Hy Green nonsulfur bacteria, 27 Helmmrhfs), waterborne, 224 contamination problems, 578 Hy Green rust, 1147, 1151 Helminthosporium, plant pathogens, 1036 effects of decompression, 576 Hy Green sulfur bacteria, 29, 505 Helminthosporium maydis, 14 equipment, 579-580, 585 Greigite, 1129 Hematite, end product of iron oxidation, hot deep environments, 580 Greigite-producing bacteria, 1132 1150-1151 substrate and redox considerations, 577 Griseofulvin, 980 Hemicellulose, see also Lignocellulosic bio­ temperature considerations, 576 Groundwater, see also Aquifer; Subsurface; mass water activity, 577 Well water biodegradation, 1089-1097, 1122 High-throughput dilution to extinction Hy arsenic, 1214-1222 degradation in landfill, 820, 827-828, culture, 435 I bacteria, 813 831 aquatic microbes, 399---406 contamination, 797 measurement, 831 cryopreservation, 404---405 leachate from landfill, 818, 845, 862, refuse composition, 819 estimating culturabilitv, 405 Hy 912 wood structure, 1089 screening enrichments and isolates drinking water sources, 328 Hemileia, 14 epifluorescence microscopy, 402--403 H) drinking water wells, 912-922 Hemileia vastatrix, 1036, 1039 PCR-based methods, 403---404 H) fecal contamination, 914 Hemin, culture medium, 70 seawater-based medium, 400-401 Hy modeling fate of microorganisms in, Hemolytic-uremic syndrome, 222 setup, 401--402 Hy 355-364 Hemorrhagic fever viruses, 1022 soil bacteria, 654 Hy protection strategies, 327,914-920 Henderson apparatus, 1018 subculturing, 404--405 sampling, 796, 799-800, 811-813, 846, Hepadnavirus, 94 Histogram, 205-207 3-1 863 Heparnavirus, 94 Histoplasma capsulatum, 671, 977 Hy subsurface microbial transport, 796, Hepatitis A virus, 94 Hoechst 2495, 57 872-897 clinical syndrome, 223 Hoechst 33258, 878 terminal electron-accepting reaction, shellfish, 227, 313, 316, 319-320 Hoffman modulation-contrast microscopy, Hy 860-871 UV inactivation, 328-329 43 Hy viruses, 295, 328, 812-813, 912 waterborne, 223, 229-230, 912 Hollow-fiber filtration, concentration of Hy waterborne disease, 229-231, 912-913 Hepatitis B virus, 94 groundwater, 813 Groundwater Rule, 327, 914 Hepatitis C virus, 94 Hollow-stem auger, subsurface sampling, Hy relationship to SWAPp, 920-921 Hepatitis E virus 800-802, 806-807 Growth, see Microbial growth clinical syndrome, 223 Homeostasis, 9-10 Growth rate, 17 detection, 237 Homologous sequences, phylogenetic H) Growth substrates, soil isolates, 654 shellfish, 227, 313 analysis, 160-161 Guillard's f/2 medium, 83 waterborne, 223, 230, 237, 369 Honest error, 197 H) GUS assay, endophytic bacteria, 645-646 Hepatotoxin, cyanobacterial, 235, 384-385 Horizontal gene transfer, 15, 26-27, gusA gene, reporter gene system, 735 Hepatovirus, waterborne, 220, 369 758-768 H) Gymnodinium, 457---458 Herbaspirillum, endophytic, 642-643, 646 bacteriophages, 759-760,763 H) Gymnodinium catenatum, 380 Heterohasidium annosum, 1107 evolutionary significance, 758, 764 Hj SUBJECT INDEX • 1269

future directions, 765 characterization of fungi on leaves, equipment, 48 insertion sequence, 761 471--472 ethical issues, 42--43 integrative conjugative elements, community structure, 471--475 functional gene array, 1057-1058 761-763 counting and identifying conidia, 471 image analysis software, 48--49 integrons, 761-763 cytochrome c oxidase gene, 474 Image restoration, 52-54 marine environment, 533 decomposition of leaves, 469--471 Immune response, 374 mechanisms, 758-759 dynamics of individual compounds, Immunity metagenomic analysis, 764 470 to illness, 374 microarray studies, 763-764 enzymatic activities, 470--471 to initial infection, 374 plasmids, 760-761, 763-764 sample collection, preparation, and to reinfection, 374 rates in environment, 765 exposure, 469--470 Immunization, exposure to aerosolized soil, 763-765 statistical analysis of mass loss, 470 virus, 1024-1025 retrospective approaches, 763-765 denaturing gradient gel electrophoresis, Immunoassay transposons, 761, 763 473--474 acidophiles, 1160 Hot water system DNA fragment analysis, 474 airborne microorganisms, 954 airborne microorganisms, 929 ELISA,472 arbuscular mycorrhizal fungi, 631 legionellae, 1008, 1012 fingerprinting approaches, 474 endotoxin, 997 HOTS program, 183,429,526,528,533 FISH,472 viruses, 93, 97-98 Hot-start PCR, 677--678 internal transcribed spacer analysis, Immunocompetence, 374 House dust, 930 472--473 Immunofluorescence method endotoxin, 995-996 microarrays, 475 denitrifying bacteria, 516 Human immunodeficiency virus, airborne, molecular methods, 472 nitrifying bacteria, 514 1021 nucleic acid analysis, 472--475 viruses, 97-98 Humate-respiring microorganisms, 868 PCR-based methods, 473--475 Immunofluorescence microscopy, 712, Humic acid, 845, 867-868, 1063, 1228 RFLP, 474 see also Fluorescent-antibody Humidifier rRNA,472--474 technique airborne bacteria and endotoxin, 992 single-stranded conformational polymor­ CMEIAS image analysis with, 719-722 airborne microorganisms, 928, 932-933, phism, 474 direct counting of bacteria in soil, 975 temperature gradient gel electrophoresis, 718-719 Hungate-type tube, 74 474 direct staining, 713, 717 HVAC system terminal RFLp, 473--474 microbes in processed soil, 717-718 airborne microorganisms, 92~928, 975 whole-genome amplification, 474 fluorochromes,713 legionellae, 1008 Hypochlorite indirect staining, 713-714, 717 Hvbrid single-particle Lagrangian inte­ field sterilization of sampling equipment, soil and root microbes, 712-723 grated trajectory model, 1032, 1038 294 cell extraction and recovery, 71~717 Hvdroethidine, 878 water treatment, 329-330 Immunofluorescence reaction score, Hydrogen fuel cell, 1137 Hypochlorous acid 717-718 Hydrogen gas biocide in oil field water system, 903 Immunological fluorescent probe, 56 aquifer, 848-849 water treatment, 329 Immunological method measurement, 86~867 Hypothesis endophvtes in plants, 645 subsurface, 866-867 alternative, 210,212 microeukaryote assemblages, 1116 terminal electron-accepting reaction, null, 210, 212 protists in aquatic environment, 462 86~867 Hypothesis testing, 210-213 Immunoperoxidase assay,viruses, 97-98 Hydrogen peroxide Hypothetical taxonomic unit, 159 Immunoresponsiveness, 374-375 brown rot fungal metabolite, 1122, Hypoxia Immunosensor, 177 1124-1125 harmful effects of algae, 378-379, 408, Immunosuppression, 375 detection and quantification, 1124-1125 417 Impact evaluation, 194 Hydrogen sulfide producers, freshwaters productivity responses, 417 Impaction method, bioaerosol sampling, and drinking waters, 252 Hypoxylon, 1107 939-940 Hydrogenobaculum acidophilum, 1157 Impactor sampler, 940-944, 946, 953, Hydrogenophaga, endophytic, 642--643 1010,1017 Hvdrogenotroph, 1137 Ice nucleation activity, 738-742 In situ cultivation, 76 Hydrolase, extracellular, 704 background level, 738 community culture, 108-109 Hydroponic culture, arbuscular mycorrhizal detection in environmental samples, 738 In situ landfill simulator, 826 fungi,630 evaluation in culture, 740 In situ microcosm, aquifer biogeochemistry, 3-Hydroxy fatty acid, 997 factors influencing 850-851 Hydroxyl radical membrane fluidity, 740 In situ reverse transcriptase PCR, iron­ brown rot fungal metabolite, 1124-1125 temperature, 740 reducing bacteria, 1243 detection and quantification, 1124-1125 labeling strains for transport studies, 880 inaZgene, see also Ice nucleation activity Hygiene, 226 quantification, 738-749 reporter gene systems, 738-742 Hygiene hypothesis, asthma, 996 droplet freezing assay, 740-742 construction of transcriptional Hypersensitivity pneumonitis, 978-979, response to changes in transcriptional fusions, 740 989, 994-996 activity, 739 InaZ protein, 739 Hyperspectral system, aircraft-based, mea­ sensitivity and range of detection, Indicator organism surement of primary production, 739-740 antibiotic-resistant, 350 418 lCR method, protozoa, 267 drinking water, 249-252 Hvpertherrnophile, 25, 27, 577, 580, 582 Ideonella, endophytic, 642, 646 public health significance, 254 culture, 583-584 Illness, from pathogens in drinking water, environmental freshwater, 249-252 Hyphae, arbuscular mycorrhizal fungi, 367-368,376 public health significance, 254 628--629 Image processing, 47-51 marine recreational waters, 280, Hypholoma fasciculare, 1102 analysis and data output, 49-51 284-286 Hyphomicrobium vulgare, 117 basic steps, 49 pathogenicity, 375 Hyphomycetes, aquatic, 469--478 deconvolution, 52-54 source waters, 325-326 1270 • SUBJECT INDEX

Indicator organism (continued) Iodide, conservative tracer in subsurface biogeochemical studies L wastewater, 335, 337, 349 transport, 881-884 open experimental systems, wastewater and sludge, 300 lodometric titration method, manganese 1241-1242 L water quality, 238-239 oxidation state, 1225 surface analysis techniques, L waterborne disease, 238-239 Ion chamber, 1184 1241-1242 Indino( 1,2,3,c,d)pyrene, mycoremediation, Ionic strength wet chemistry, 1241 L 1100 culture medium, 75 culture, 1239-1240 L Inductively coupled plasma MS effect on subsurface microbial transport, anaerobic technique, 1239-1240 aqueous chemical speciation, 1197 873 culture medium, 1240 measurement of manganese species, Iridescent virus, 774 cyrochromes, 1241, 1243-1244 1226 Iron enrichment culture, 1240 L Inductively coupled plasma optimal emis­ aqueous chemical speciation, 1197 evidence for Fe(Ill) reduction, 1242 /a sion spectroscopy, aqueous chemi­ effect on arsenic cycling, 1220 extracellular electron shuttle, 1244 L cal speciation, 1197 siderophores, 543 genome sequences, 1244 L: Industrial facility, airborne microorganisms, Iron cycling in situ reverse transcriptase PCR, L: 930-931 acidic environment, 1155 1243 L: Infection analysis microbe-mineral interface, 1241-1242 airborne fungi, 976-977 chemical profiling, 547-548 molecular ecology, 1242 definition, 374 cultivation-based methods, 551 nanowires, 1243-1244 Infection focus, plant disease, 1031 FeW) and Fetlll) extraction, 549 redox potential, 1244 Infectious bronchitis virus, 1020 molecular methods, 551-554 Irrigation, reuse-water, airborne micro­ Infectious dose, bacterial pathogens, process measurements, 549-551 organisms, 926, 932 222-226 aquatic environment, 540-562 Isiduli, 776 Infectivity assay, arbuscular mycorrhizal aquifer, 845, 847 Isosphaera, 27 fungi, 629 chelators In subsurface, 867-868 Isospora, waterborne, 265, 276 Influenza virus, 94 at circumneutral pH, 1147-1154 Isospora belli, 265, 276 airborne, 964, 1019-1021 connection to other metal cycles, Isospora hominis, 265, 276 Infrared spectroscopy, microbe-mineral 553-554 Isospora natalensis, 276 interface, 1207-1208 coupled Fe-Mn oxidation and reduction, Isotope dilution method Injured bacteria, recovery from freshwaters 547 community metabolic activity, 395 and drinking waters, 259 input to aquatic systems, 540 respirometry, 698 Inorganic salt solution, medium for proto­ iron oxides, 540-543 Isotope fraction analysis, methane oxida­ zoa, 84 magnetotactic bacteria, 1129 tion in landfill, 832-833 Inositol, bioacrosol stabilizer, 966 Mossbauer spectroscopy, 1206-1207, Iteron, 760 Insect, seeArthropod entries 1241 Insect vector, 14 lron(ll) oxidation, 543-547 water-related, 219, 227 abiotic, 1147 J agar, 644 Insecticidal protein, 1035-1036 acidophiles, 1156-1162 J medium, 1229 Insertion sequence, horizontal gene trans­ aerobic, 544-546 vitamin mix, 1231 fer, 761 anaerobic, 544-546 Japanese B encephalitis virus, 1019 INT,55 at circumneutral pH, 1147-1154 Jar technique, sulfate reduction in aquatic Integrative conjugative element, horizontal measurement, 549-551 environment, 498 gene transfer, 761-763 lron(ll)-oxidizing bacteria, 408, 1148--1149 Jarenia seliformis, 381 Integron electron acceptors, 1150 Jaworski's medium, 82-83 chromosomal, 762 end products of oxidarion, 1150-1151 Jukes-Cantor evolutionary model, 611 horizontal gene transfer, 761-763 enumeration, 1151-1152 [unin virus, 927,1020,1022 mobile (multiresistant), 761-762 identification, 1151-1152 Interference-reflectance microscopy, 43 isolation, 1151-1152 Internal positive control, PCR-based meth­ light-independent anaerobic, 1149-1152 ods, 956 nitrate-dependent, 1149-1152 k growth strategy, 15-17 Internal transcribed spacer analysis oxidation of insoluble FeW), 1150-1151 K medium, 1230 FISH targets, 725 photoautotrophic, 1148-1149 Kalkitoxin, 384 hyphomycetes, aquatic, 472-473 phylogenetic diversity, 1150 Kappa techniques, 197 microeukaryote assemblages, 1116 lron(lIl) oxide reduction, 543-545 Karenia bidigitata, 381 rRNA genes, 751 coupled to oxidation of inorganic com­ Karenia brevis, 381 Interquartile range, 206-208 pounds, 543-545 Kinetic approach, analysis of CLPP data, lnterspecies electron transfer, 11 coupled to oxidation of organics and 134 lnterspecies hydrogen transfer, 26 hydrogen, 543-544 Kinetic model subsurface, 866-867 measurement, 549 biological wastewater treatment, 338, Interval scanning microscopy, 43 lron(lIl) reduction, 547,1147 341 Intervention study, endemic waterborne acidophiles, 1157 viability of aerosolized microbes, 966 disease, 228-229 aquifer, 847, 850 Kingella, endophytic, 643 INT-formazan method, respirometry, 698­ measurement, 551, 865 King's B medium, 644 699 subsurface, 861-863, 865,867-868 Klebsiella Intoxication, waterborne, 219 lron(lll)-reducing bacteria, 1138, airborne, 989-990 Intraclass correlation, 197 1141-1142,1148,1151, endophytic, 640-643, 722-723 Intragenic spacer profile, soil microbial 1239-1248 subsurface transport, 874-876 community, 608 activity, abundance, and distribution, thermotolerant coliforms, 250 Introduced microorganisms, 9-10, see also 1242 total coliforms, 249 Released microorganisms attachment on solid-phase substrates, Klebsiella planticola, 963 fate in water, wastewater, and soil, 1243 Klebsiella pneumoniae, 700 355-364 biofilms, 1240, 1243-1244 K-means clustering, functional gene array Invasive plant species, extracellular enzyme in situ extracellular polysaccharide data, 1058 production, 706 labeling, 1243-1244 Kriging map, 721 L: SUBJECT INDEX • 1271

Laboratory batch reactor, landfill study, composition, 818, 822 acid or heat pretreatment, 1008-1009 826 methane oxidation, 798, 818, 820-822, air sampling, 1009-1010 Laboratory landfill simulator, 826 832-836 culture of water samples, 1008 Laboratory-acquired infection, airborne aerobic, 822 heat enrichment, 1009 viruses, 1018 anaerobic, 822 nonculture methods, 1010 Laccase, 1089-1090,1101-1102 factors affecting, 822-823 sample concentration, 1008 Lactobacillus laboratory systems, 833-834 water samples, 1007-1008 airborne, 989 methane oxidizer enumeration and ecology, 1005-1006 morphology, 23 identification, 836 identification, 1009-1010 subsurface transport, 874 molecular methods, 836 within protozoa, 265, 1006-1007 Lacrococcus, 23 physical and chemical evidence, signature lipids, 114 lacZ gene, reporter gene system, 735 835-836 subtyping, 1010-1011 Laenporus sulphureus, 1107 whole-landfill methane oxidation and waterborne, 220, 222, 225-226 Laminarinase, 1094 emissions, 832-833 Legionella-Iike amoebaI pathogen, 1006 Land management practices, 185 sample collection and processing, Legionellosis, 1005-1006 Landfill 834-835 Legionnaires' disease, 1005-1006 airborne microorganisms, 926, 931,933 Langat virus, 964 Length heterogeneity peR, bacteria in anaerobic decomposition, 818-842 Large-scale culture, 75 aquatic environment, 437-438 biochemical methane potential, Laser scanning microscopy, 43-46 Lentinus lepidius, 1107 824-825, 830 applications, 54-58 Lentivirus, 94 biological decomposition, 819--823 confocal, see Confocal laser scanning Lenzites trabeum, 1107 aerobic phase, 820 microscopy Lepidocrocite anaerobic phase, 820 3-D image reconstruction, 51-54 biogenic, 1149 factors limiting, 820 data presentation, 51-54 end product of iron oxidation, 1150-1151 phases of refuse decomposition, image collection, 44-45 LeptosPhaeria, plant pathogens, 1036 819-820 image processing, 47-51 Leptosphaeria maculans, 1043 trace organic compounds, 820 two-photon, 43, 45-46 Leptospira bioreactor landfill, 820 Laser therapy, generation of viral aerosols, clinical syndrome, 225 carbon-Ls turnover, 825, 829-830 1021 waterborne, 220, 225, 227 chemical measurements, 825,831-832 Lassa fever virus, 927,1020, 1022 Leptospira interrogans, 366 chemical oxygen demand, 831-832 Late blight of potato, 1031, 1036-1037, LeptospiriHum, 1159-1160 coenzyme F420, 830 1042-1043 Leptospirillumferriphilum, 1157,1162 coenzyme M, 830 Latent factor, 208 Leptospirillum ferrooxidans, 1157, description of sanitary landfill, 818-819 Lateral-flow assay, airborne microorgan­ 1159-1160 direct measures of microbial activity, isms, 954 Leptospirillum thennoferrooxidans, 1157 829-830 LBB method, see Leucoberbelin blue Leptothrix, manganese oxidation, 1228 electron microscopy, 830 method Leptothrix medium, 1229 enumeration of microorganisms, 824, Lead trace elements solution, 1232 827-828 aquatic environment, 541, 553 Leucine incorporation into protein enzymes, 824,827,829 connection to iron and manganese deep-sea microorganisms, 578 ether-linked lipids, 830 cycles, 553 empirical conversion factor, 426-427 fungi, 828 toxic metal resistance, 1166-1182 measurement of secondary production, habitat simulation and incubation con­ Leaf 422-423,425-426 ditions, 828-829 decomposition by hyphomycetes in rationale, advantages, and disadvan­ leachate collection system, 818 streams, 469-471 tages, 425-426 leachate contamination of groundwater, endophytic bacteria, 641 Leucoberbelin blue method, measurement 818, 845, 862, 912 Leaf spot, 1036 of manganese oxides, 1225 methane production, 797-798,818-820, Leaf-cutting ants, fungi associated with, Leuconostoc, endophytic, 640,643 825,827,829-833 776 Lewis acid, 1166 microbial processes, 797 Lectin, fluor-conjugated, study of Lewis base, 1166 microbiological measurements, 824--825, exopolvsaccharides, 57 J-L1BSHUFF, 611, 614-615,1117 827-831 Left-skewed distribution, 204 Lichen, 11 microbiological studies, 823-832 Legionella bozemanae, 1009 Light molecular methods for studying Legionella micdadei, 1009 aquatic environment, 393 microbes, 824, 830-831 Legionella pneumophila, 227, 230, 366, 963, measurement of bioluminescence, 171 protozoa, 820, 828 1006, 1010-1011 Light microscopy, 40 refuse composition, 819 Legionellae, 1005-1015 conventional,43 refuse metabolic capability, 824, 827­ aerosol transmission, 227 depth of field, 41 828 from aquatic environments, limits, 41-42 sample processing, 826-827 1006-1007 metal-microbe interactions, 1201 for chemical analysis, 827 airborne, 928-929, 932, 992, 1005-1015 novel,43 for microbiological analysis, 826-827 aquatic environment, 1006-1008, resolution, 41 sampling, 797, 823, 826-827 1011-1012 working distance, 41 systems for study, 823-826 clinical syndrome, 225 Light organ, 58 addition of inoculum, 823, 825 colony morphology, 1009-1010 Light regimen field-scale landfill, 823-824 control culture of algae, 83, 88 in situ landfill simulator, 826 aerosol transmission, 1012 culture of amoebae, 86 laboratory batch reactor, 826 amplifying reservoirs, 1012 culture of microorganisms, 72 laboratory landfill simulator, 826 biocides, 1011 Lignin, see also Lignocellulosic biomass laboratory-scale simulations, 823-824 environmental reservoirs and water biodegradation, 1089-1096 multistage continuous-culture tech­ supplies, 1011-1012 in landfill, 827-828, 831 nique, 824-826 culture, 71, 1008-1009 measurement, 831 viruses, 912 culture media, 1009 refuse composition, 819 Landfill cover detection, 1006-1011 wood structure, 1089 1272 • SUBJECT INDEX

Lignin peroxidase, 1094, 1100, 1107-1108 Loboea strobila, 457-458 future directions, 1134 Lignin-degrading enzymes, 1098 Log normal distribution, 204-205 isolation, 1132-1133 r white rot fungi, 1100-1101 Long Term Ecological Research (LTER) nonmagnetotactic mutants, 1134 Ma Lignocellulolytic fungi, 1107 site, 182-189 uncultivated, 1129-1132 Lignocellulosic biomass aquatic sites and experiments, 183 electron microscopy, 1130 ~ chemical components, 1107 terrestrial sites and experiments, 183 establishment and development of Ma degradation by brown rot fungi, Long-term research site, 38--39, 182-189 microcosms, 1129-1130 1122-1128 correlation studies, 184-185 habitats and occurrence, 1129-1130 fungal solid-state fermentation, with process rates, 185-186 identification and enumeration, 1107-1111, see alsoFungal solid­ in whole-system experiments, 1130-1132 state fermentation system 186-188 magnetic collection of cells, hydrolysis, 1107-1108 ecological questions, 182 1130-1131 r pretreatment, 1108 future studies, 188-189 molecular methods, 1131-1132 13-~ Limiting nutrient/resource, 13, 15-17 integrating microbial and ecosystem phylogenetic diversity, 1131-1132 Ma Limulus amebocyte lysate assay, endotoxin, studies, 183-184 Magnetotaxis, 1129 954-955, 996-997 LTER program, 182-189 Maillard reaction, 965-966 Ma Lineage-per-time plot, 613-615 Lordsdale virus, 232 Maitotoxin, 380, 382 Ma Linear model analysis, 213 Lower quartile. 206-208 Maize seedling assay, endophytic coloniza­ Ma Linear regression analysis, microbial sur­ Low-molecular-weight RNA profile, bacte­ tion, 644-645 Ma vival calculations, 358-363 ria in aquatic environment, 435 Malt and yeast extract-75% seawater agar, Ma Linker-amplified shotgun library method, LTER site, see Long Term Ecological 86 "M 447-448 Research site Malt extract agar, 75, 952 Ma Lipase, landfill, 829 Luciferase, 170-172, 736,879 Malt extract broth, 73 I Lipid(s) LUMIStox, 346 Manganese llC-labeled, substrates to trace in situ Lupin anthracnose, 1043 aquifer, 845, 848 metabolism, 117-118 lux genes biotransformations, 1223-1238 extraction, 118 labeling strains for transport studies, chemistry, 1223-1224 Lipid A, 992-993 879-880 measurement of manganese species, Lipid biomarker analysis, 112-125 reporter gene system, 170-171, 736 1224-1226 analytical sensitivity, 119-120 Lycogala epidendrum, 974 formaldoxime method for Mn(Il), arbuscular mycorrhizal fungi, 631-632 Lymphocryptovirus, 94 1224-1225 archaea, 435 Lyngbya, 235, 383 LBB method for manganese oxides, Ma bacteria in aquatic environment, 435 Lyngbya majuscula, 383-384 1225 community composition, 113-115 Lyngbya wollei, 386 spectroscopy and other methods, community metabolic status, 115-117 Lyngbyatoxin A, 383-384 1225-1226 Ma deep-sea microorganisms, 585 Lyophilization, algae and protozoa, 89-90 oxidation states, 1223 ( evaluating contamination of subsurface Lysergic acid, 980 soil, 707 I samples, 806 Manganese cycling, 1223-1238 Ma indicator molecules in soil extracts, 656 analysis I isotopically labeled lipids to trace in situ M medium, 1229 chemical profiling, 547-548 j metabolism, 117-119 MA plot, 669 cultivation-based methods, 551 landfill, 830 MAC complex molecular methods, 551-554 limitations, 119-120 aerosol transmission, 227 process measurements, 549-551 metabolic activity of soil- and plant­ freshwaters and drinking waters, aquatic environment, 540-562 associated microbes, 699 251-252 connection to other metal cycles, sample handling, 118 waterborne, 225, 232-234 553-554 signature lipids, procedure for lipid MacConkey agar, 644 coupled Fe-Mn oxidation and reduction, analysis, 118-120 Macroplankton, 458-460 547 soil isolates, 654-655 Maghemite, end product of iron oxidation, Manganese(Il) oxidation, 543-547 soil microbial community, 781-792 1150-1151 biotic and abiotic components, 1223 total viable microbial biomass, 112-113, Magnesium measurement, 550-551 120 aquatic environment, 541 Mn(lIl) intermediates and stepwise Mn validation, 119 culture medium, 70 oxidation, 1227-1228 Lipid phosphate, 112-113 Magnetic nanoparticle, 178 54Mn(Il) removal and particulate 54Mn Lipooligosaccharide, 993 Magnetite, 1129, 1147 formation, 1226-1227 Lipopolysaccharide, 993 end product of iron oxidation, oxidation and removal at high Mn(Il) cyanobacteria, 383-384 1150-1151 concentrations, 1226-1227 Ma Lipopolysaccharide fatty acids, community nitrate-dependent microbial oxidation, Manganese oxidets), 1223 Mu composition, 115, 119 1150 as electron acceptors, 1223 M~ Liquid impingement method, bioaerosol Magnetite-producing bacteria, 1132-1133 leucoberbelin blue method, 1225 sampling, 940 "Magnetobacterium bavaricum," 1132 o-MnOz' 1230 M2 Liquid impinger sampler, 941-944, 953, Magnetosome, 1129-1130, 1133-1134 speciation, 542-543 M~ 1010, 1017 Magnetosome genes, 1132, 1134 Manganese oxide reduction, 543-545, Mu Listeria, airborne, 989 Magnetospirillum, 1132 1223-1224 Ma Lirhorroph, 25 Magnetospirillum gryphiswaldense, 1132, assay, 1232 Litter bag, leaf decomposition in streams, 1134 coupled to oxidation of inorganic com­ Ma 470 Magnetospirillum magnetotaeticum, 1134 pounds, 543-545 Litter-degrading fungi, 1097 Magnetotactic bacteria, 1129-1136 coupled to oxidation of organics and Me LIVE/DEAD BacLight viability kit, 48, 55, cultivated hydrogen, 543-544 Me 700 genetic analysis, 1134 measurement, 549, 551, 1228-1232 Me Livestock facility maintenance and mass cultivation, o-MnOz synthesis, 1232 Me airborne bacteria and endotoxin, 989, 1133-1134 Manganese oxide-reducing bacteria I 994-995 physiology, 1134 culture, 1233-1234 I airborne viruses, 1022-1024 culture, 1132-1134 enrichment culture, 1233-1234 Me SUBJECT INDEX • 1273

isolation, 1233-1234 Medium, see Culture medium large DNA insert libraries, 492 phylogeny, 1232-1233 Megasphaera, 23 shotgun community sequencing, 493 Manganese-dependent peroxidase, Megasphaera elsdenii, 115 comparative, 1084 1100-1101, 1108 Melting domain, 658 definition, 1063 Mnf'-glutathione system, 1101 Membrane filtration method functional, 493 Manganese(ll}-oxidizing bacteria, 408 culture of acidophiles, 1159-1160 horizontal gene transfer, 764 culture, 1228 monitoring freshwaters and drinking large insert library approach, 440 culture medium, 1228-1232 waters, 255-257 library construction, 1063-1071 detection and enumeration, 1228 monitoring marine recreational waters, magnetotactic bacteria, 1132 enrichment culture, 1228 281-283 screening strategies, 566 isolation, 1228 Membrane transport, silver nanoparticles, sequencing strategy, 566 phylogeny, 1228 178 shotgun approach, 394, 440, 447--448 f3-Mannosidase, 1090 Memnoniella echinata, 975 soil, 660, 1063-1071, see also Soil Manufacturing plant, airborne microorgan­ Menaquinone, 116 metagenomics isms, 930 Mercaptoethanesulfonic acid, culture toxic-metal-resistant bacteria, Manure spreading, 989 medium, 70-71 1177-1178 Mapping task, 213-214 7-Mercaptoheptanoylthreonine phosphate, viruses in aquatic environment, 447--448 Marburg virus, 927 71 Merails) Marek's disease virus, 1019 Mercury aquatic environment, 540-562 Marine broth, 583 aquatic environment, 541, 553 aqueous chemical speciation, 1196-1198 "Marine desert," 533 connection to iron and manganese analytical methods, 1197-1198 Marine environment, 393 cycles, 553 defining speciation, 1196 bacterial organic carbon cycling, toxic metal resistance, 1166--1182 preservation, 1196-1197 479--487 Mernliporia incrassata, 974, 976 bioavailability, 1167 high-pressure, see High-pressure marine MES buffer, 74 metal-microbe interactions environment Mesocosm study atomic force microscopy, 1208-1209, long-term research sites, 183 aquifer biogeochemistry, 851 1241 nitrogen cycling, 511-522, 533-535 arthropod-microbe interactions in soil, auger electron spectroscopy, 1209 phosphorus cycling, 523-539 769,776 CSLM,1201 protists, 455, 457, 462--463 Mesodinium rubrnm, 79 electron microscopy, 1201-1202, viruses, 295, 450 Mesophile, acidophiles, 1157 1205 Marine medium, 75, 1233 Mesoplankton, 458--460 electron probe microanalysis, 1205 mineral stock, 1233 Mesorhizobium, lipids, 117 experimental design, 1195-1196 salt stock, 1233 Messenger RNA, functional gene arrays to infrared spectroscopy, 1207-1208 Marine poisonings measure, 1059-1060 iron-reducing bacteria, 1241-1242 cyanobacterial toxins, 383-386 Metabolic activity light microscopy, 1201 harmful algal blooms, 379-383 endogenous, oxygen consumption, 340 microbe-mineral interface, Marine recreational waters, 280-289 identification of microbes involved in 1203-1210 bacteria, 281-283 specific in situ functions, 748-757 Mossbauer spectroscopy, 1206--1207, fecal contamination, 280-281, 286--287 in planta activity of endophvtes, 646 1241 indicator organisms, 280, 284-286 in situ immunolabeling of cell-associated nuclear magnetic resonance, 1207 monitoring enzymes, 722-723 optical microscopy, 1205 antibody-based approach, 284 isotopically labeled lipids to trace in situ particle-induced X-ray emission, 1205 defined substrate method, 282-283 metabolism, 117-119 Raman spectroscopy, 1207-1208, electrochemical RNA hybridization, metabolic diversity, 21 1241 283-284 metabolic flexibility, 21 scanning tunneling microscopy, membrane filtration test, 281-283 microbial, usefulness for humans, 4 1208---1209 microarray, 283-284 plant-associated microbes, 697-703 secondary ion MS, 1209-1210 multiple-tube fermentation method, quantification X-ray absorption spectroscopy, 1206 281-283 analytical microscopy, 54-56 X-ray diffraction, 1205-1206 NASBA, 283-284 lipid analysis, 699 X-ray photoelectron spectroscopy, PCR-based methods, 283 microscopy, 699-701 1209, 1241 rapid methods, 283-284 nucleic acid pools and synthesis rates, microbial community in metal-impacted transcription-mediated amplification, 699 soils, 785 283-284 respirometry methods, 698-699 toxic-metal-resistant bacteria, viruses, 285-286 soil, 748-757 1166--1182 Marine snow, 463 soil-associated microbes, 697-703 transformations Marinomonas, 23 subsurface, 795 synchrotron-based techniques, Mass loss method, chemical analysis of Metabolomics, toxic-metal-resistant bacte­ 1183-1194 aquifers, 847 ria, 1178 techniques for studying, 1195-1213 Mass spectrometer, sensitivity, 120 Metagenorne, 21 wastewater, 346--347 Mastadenovirus, 94, 366 Metagenornics, 1051 Metal machining, airborne bacteria and Mastigamoeba, landfill, 828 aquatic environment, 394-396 endotoxin, 991 Maximum likelihood method, topology of bacteria in aquatic environment, Metalloenzymes, 1166--1167 phylogenetic tree, 161-162,610 440--441 Metallogenium, 1228 Maximum parsimony method, topology of biodegradation microorganisms, Metalloids, toxic-metal-resistant bacteria, phylogenetic tree, 161,610,615 1079-1088 1166--1182 Mean, 204 community profiling, 1080-1081 Metallomics, 1178 Measles virus, 94 culture-dependent enrichment, 1080 Metalloproteomics, 1178 Measurement method, study design, 195 genes and genomes mediating degra­ Metalworking fluids, airborne bacteria and Measuring and test equipment dation, 1081-1083 endotoxin,991,994 preventive maintenance, 196 library construction, 1084-1085 Metaproteomics, 395-396, 1178 use and calibration, 195-196 biofilm community, 566--567 Metarhizium anisopliae, 772, 775-777 Median, 206--208 C,-metabolizing populations, 488--496 Metatranscriptomics, 1178 1274 • SUBJECT INDEX

~ethane, 488-489 Methylobactenum, 488 functional genes in soil, 670-672 emission from landfill, 820, 832-833 endophytic, 642-643 pathogen detection, 671-672 measurement, 832, 866 Methylobactenum extorquens, 489 whole-genome array, 164 oxidation in landfill cover, 798, 818, ~ethylocaldum, 836 whole-genome open reading frame r 820-822, 832-836 Meth'llococcus, 488 arrays, 150 ~i, aerobic, 822 Methylococcus capsulatus, 489 Microarray experiment, 663-664 ~i( ~ethylocystis, anaerobic, 822 488, 836 Microarray laser scanner, 666, 668-669 Mi, factors affecting, 822-823 Methylomicrobium, 488 Microarray printer, 666-667, 671 ~i( laboratory systems, 833-834 Methylomonas, 488 Microauroradiographv, 56 molecular methods, 836 Methylophaga, 488 bacteria in aquatic environment, 440 ( FlSH-~AR, physical and chemical evidence, Methylophilus, 488 725-726 I ~ethylopila, 835-836 488 bacteria in aquatic environment, 440 ~i( whole-landfill methane oxidation and Methylosinus, 488, 878 biodegradation microorganisms, Mi' emissions, 832-833 Methylotroph, 26, 488--496 1080-1081 production, see also Methanogenesis Metopus , 85 contribution of major bacterial groups landfill, 797-798 ~etPAD, 346-347 to secondary productivity, 427--428 Methane monooxvgenase, 488, 670, 822, ~etPLATE, 346-347 metabolic activity of soil- and plant­ 836 Mexico virus, 232 associated microbes, 699 t Methane-oxidizing bacteria, 787 Microactinium, culture, 89 measurement of primary production, 417 [ enumeration and identification, 836 Microaerophile, 25, 74 metabolic activity of soil- and plant­ Mi' Merhanesulfontc acid, 488--489 Microalgae, aquatic biofilms, 564 associated microbes, 698 Mi' single-cell analysis of DOM consump­ Merhanethiol, 479, 505 Microarray,663-675 ~i( merhanotroph inhibition, 823 advantages, 1052 tion, 480 ~i( Methanobacterium formicicum, 827 airborne microorganisms, 956--957 ~icrobacterium,endophytic, 642 ~ethanobacterium Mi' omelianskii, 102 biodegradation microorganisms, Microbial biotechnology, 4 c ~ethanobacterium thermoautotrophicu11l, 70, 1083-1084 Microbial community, seeCommunity Mi, 75 c, oxidizers, 491-492 entries Methanobrevibacter rU11linantium, culture, 70 Microbial dispersal, 13 Mi' cDNA-based, 663 Mi' Methanogen, 26, 29 commercial resources, 670-671 active, 13 l coenzyme M, 830 community genome array, 150, 1052, by air, sea, and land, 13-14 enumeration in landfil1, 827-828 1084 passive, 14 evolution, 27 community structure analysis, 146, Microbial diversity, see also Prokaryotic molecular methods, 831 149-150,395 diversity Methanogenesis data analysis acidophiles, 1161 aquifer, 851 clustering, 669-670 functional richness and, 131-132 landfill, 818-820, 825, 827, 829-833 data extraction from microarray, 669 iron-oxidizing bacteria, 1150 subsurrace, 861-862, 866 normalization of data, 669 magnetotactic bacteria, 1131-1132 terminal electron-accepting reaction, design, 665-667 microdiversity, 441 861-862, 866 detection limit, 672-673 microeukaryotes in natural environ­ Methanol, 488--489 detection specificity, 150 ments, 1116-1117 biodegradation, 1081 environmental microbiology PCR-based methods, 679 Methanol dehydrogenase, 488, 1081 benefits, 672 productivity and, 427-429 ~ethano11licrobiu11l11lobile, 69-70 disadvantages and limitations, protists in aquatic environment, Methanopyrus, 23 672-673 454--456 Methanospirillum, 23 experimental procedure, 667-669 quantification, 56 Methanotroph, 25, 488 data analysis, 669-670 subsurface, 795 cometabolic activity, 822 hybridization process, 668 Microbial fuel cel1, 1137-1146 I culture, 836 labeling RNA or DNA, 667-668 Microbial growth Mi< enumeration and identification, 836 nucleic acid extraction from soil or analytical microscopy, 54-56 Mi high-affinity, 822 microbes, 667 microscopy studies, 40-41 Mi, landfill, 822, 832-836 scanning array with laser, 668-669 Microbial indicator, seeIndicator organism Mi lipid biomarkers, 114, 117 facility equipment, 666-667 Microbial loop, 79, 393, 459, 479 Mi low-affinity, 822 functional gene array, see Functional Microbial mat, microscopy, 434 Mi molecular methods, 836 gene array Microbial source tracking, bacteria in Mi soil, 670 gene expression arrays, 150 wastewater and sludge, 307 type I, 822-823, 836 genomic analysis, 164 Microbial survival study Mi type II, 822-823, 836 horizontal gene transfer, 763-764 under constrained natural exposure, 356 Mi Method 1623 for protozoa in water, hvphornvcetes, aquatic, 475 designing modeling analyses, 357 Mi 267-274 monitoring marine recreational waters, experimental design, 356-357 Mi holding times, 270 283-284 physical considerations, 356 Mi limitations, 273-274 nucleic acid amplification for, 673 statistical considerations, 356-357 microscopic examination, 272-273 nucleic acid biosensor, 177 performed in laboratory, 356 quality control, 267-270 oil field microbes, 901 survival calculations, 357-363 Mi sample filtration and elution, 270 oligonucleotide-based, 663-665 comparing accuracies of equation for­ sampling, 270 design and synthesis of probes, 665 mats, 361-363 Mi Methvl rert-butvl ether, degradation in sub­ probe spotting or printing, 665-666 linear regression, 358-363 surface, 868 size of probe, 665 Microbial tracking methods, 253 Mi Merhvlamine, 489 phylogenetic oligonucleotide array, 150, Microbial transport, see also Airborne Methvlated amines, 488 1052, 1084 microorganisms; Subsurface micro­ Mi ~ethylcystis, 23 protists in aquatic environment, 462 bial transport; Waterborne disease Merhvlfluoridc, nitrification inhibitor, 515 quantitation by using, 150 water, wastewater, and soil, 355-364 ~ethy!ibium petroleophilum, 489 reproducibility of results, 673 Microbially enhanced oil recovery, 872, ~ethylobacillus flagellatus, 489 schematic representation, 663-664 905-907 ~ethylobaeter, 488 soil microbiology, 670-672 assessing performance, 906 SUBJECT INDEX • 1275

injection protocol, 905-906 bacteria in aquatic environment, 434 Mossbauer spectroscopy, microbe-mineral microbial processes applied to field situa­ bacteriophages, 624 interface, 1206-1207 tions,906 continuous-flow slide culture, 106-107 Most-probable-number method microorganisms useful for, 899 emerging methods, 58--59 acidophiles. 1160 nutrient formulation, 905 endophytic bacteria, 639, 645 aquifer microbes, 852-853 Microcalorimeter, 177 experimental reproducibility, 42 arbuscular mycorrhizal fungi, 629 Microcantilever, 177 landfill, 830 arsenate-respiring bacteria, 1218 Microchemical analysis, 56-57 metabolic activity of soil- and plant- denitrifying bacteria, SIS Micrococcus associated microbes, 699-701 dissimilatory metal-reducing bacteria, airborne, 991 protozoa, 266, 272-273 551 endophytic, 640, 641 representative samplings for, 42 iron-oxidizing bacteria, 1151 lipids, 117 sectioning methods, 41 landfill microbes, 824, 827 Microcolony, within biofilm, 569-570 specimen preparation and handling, monitoring freshwaters and drinking Microcosm study 40-41 waters, 254 aquifer biogeochemistry, 849-851, 854 systems for cultivation and analysis, 40 monitoring wastewater and sludge, 301 arthropod-microbe interactions in soil, Microspheres, conservative tracer in sub­ MPN-RT-PCR,320 769,776 surface transport, 884 nitrogen-fixing organisms, 51Z biodegradation microorganisms, 1080 Microsporidia, 27 sulfate-reducing bacteria, 501-502 magnetotactic bacteria, 1129-1110 detection, 236 sulfur-oxidizing bacteria, 505 metal-microbe interactions, 1195-1196 drinking water, 265-266 viruses in aquatic environment, 448-449 Microcyst, 28 waterborne, 228, 232, 236-217,276 Motility, 13-14, 28 Microcvstin, 235, 384-385, 387 Microstat, community culture, 107-108 Motuporin, 387 Microcystis, 79, 224-225, 235, 384 Microtox, 346-347 12-MPA method, soluble reactive phos­ Microcystis aeruginosa, 235, 425 Migration, 12-14 phorus, 523-524, 526 Microecosystem, 102 cyclical, 12-13 mpniu estimation, 97 community culture, 101-111 Mine MTBE, degradation in aquifer, 849 Microelectrode study, 57 groundwater sampling, 811-812 Mucor Microenvironmenral analysis, 57-58 sampling subsurface, 800, 810-811 airborne, 974 Microeukaryote assemblage Mineral solution, culture medium, 69-70 water activity for growth, 973 biofilms, 1112 Mineral-carbon interactions, soil, 707 Mucor stolonifer, 978 community comparisons, 1116-1117 Minimal infectious dose, 365-367 Multichannel imaging, CLSM systems, 45 denaturing gradient gel electrophoresis, Minimal mineral salts medium, 1230 Multilocus sequence analysis 1116 Minurocellus polymorphus, 457-458 legionellae, 1011 diversity indices, 1116-1117 Mixed culture, 102 phylogenetic studies, 158--159, 163 DNA extraction, 1112-1113 Mixotroph, 25 Multiple linear regression analysis, micro­ FISH, 1116 acidophiles, 1155, 1157-1158 bial survival calculations, 360-361 future directions, 1117 Mobile gene elements, seealso Horizontal Multiple logistic regression, 208, 213 immunological methods, 1116 gene transfer Multiple regression model, 208 internal transcribed spacer analysis, soil,758-768 Multiple-barrier approach, waterborne- 1116 MODELTEST,611 disease prevention and control, na tural env ironments, 1112-1121 Modified semisoft Rappaport-Vassiliadis 239 nonviable cells, 1116 medium, 302-303 Multiple-tube fermentation method, moni­ PCR-based methods, 1113-1116 Molecular beam MS, wood degraded by toring marine recreational waters, PLFA,1116 brown rot fungi, 1125-1126 281-283 RFLP analysis, 1113-1116 Molecular fingerprints, 145~151 Multiplex PCR, 678 rRNA genes, 1113-1116 Molecular methods Multivariate analysis of variance, 133 sampling, 1112 arthropod pathogens in soil, 774-775 Multivariate techniques, 208-209 terminal RFLP, 1116 arthropod-microbe interactions in soil, PLFA fingerprints, 782-784 Microhabitat, 8, 29, 652 776-777 Mumps virus, 94 Micromanipulator, isolation of protists, 81 biases and errors, 438-439 Municipal solid waste, 818-819, seealso Micromonas pusilla virus, 448, 450 magnetotactic bacteria, 1131-1132 Landfill Microperfusion chamber, 40 measures of community structure, Murine leukemia virus, 1019 Micropipetting, isolation of protists, 81 139-156 Mussels, see Shellfish Microplankton, 458-460 methane oxidation in landfill cover, 836 Mutatox, 346 Microplate assay, extracellular enzymes in Molluscs, seeShellfish Mutualism, 4, 10,29, 103 soil,708 Moloney murine sarcoma and leukemia Mycobacterium Microplate reader, 708 virus complex, 1019 airborne, 932,991-992 Micropolyspora faeni, 928 Molybdate, inhibition of sulfate reduction, atypical, 251 Microprobe, 38, 173-174 505 clinical syndrome, 225 MicroResp system, 130-131, 134, B6 Molybdenum, aquatic environment, 541 freshwaters and drinking waters, Mlcrorespirometrv method, substrate- Molybdenum blue test, arsenate, 1217 251-252 induced respiration in soils, Monochloramine lipids, 114, 117 130-131 control of legionellae, 1011 morphology, 23 Microsatellite, arthropod-associated neutralization of disinfectants, 292 species-level identification, 158 microorganisms, 777 Monochromator, 1184-1185 subsurface transport, 874-875 Microscope stage, motorized, computer­ Monodicrys, lignocellulolytic, 1107 waterborne, 225-226, 228, 234 controlled, 42, 713 Monomerhvlarsinic acid, 1197 whole-genome probe, 143 Microscopic particulate analysis, protozoa, Monoxenic culture, arbuscular mycorrhizal Mycobacterium avium, see MAC complex 275 fungi,630 Mycobacterium immunogenum, 991, 994 Microscopy, 37, 40-68, seealsospecific types Monterey Bay (California), long-term Mycobacterium intracellulare, seeMAC of microscopy research site, 185-186 complex airborne microorganisms, 953-954 Moraxella, endophytic, 642-643 Mycobacterium kansasii, 234 aquifer microbes, 852 Morbillivirus, 94 Mycobacterium marinum, 234 arthropod pathogens in soil, 774 Mosaic plot, 208 Mycobacterium tuberculosis, 927, 932 1276 • SUBJECT INDEX

Mycoplasma Nested sampling, 203 Nitrite-oxidizing bacteria No( airborne, 963 Net relatedness index, 614-616 marine environment, 513-515 morphology, 23 Neural network, 209 soil,690 whole-genome probe, 143 PLFA fingerprint analysis, 783-784 Nitrite-reducing bacteria, oil field, unsupervised, 210 899-900, 904-905 Mycoplasma pneumoniae, 963 S Mycoremediation Neurotoxic shellfish poisoning, 380-381 Nurobactet, 26 No( PAH, 1097, 1100-1102 Neurotoxin, cyanobacterial, 235, 384-386 Nitrooacter hamburgensis, 514 No( PCDD/PCDF, 1097-1099 Neutral red, 96-97 Nitrogen NO( PCp, 1097 Neutral relationship, 4, 10 fertilizer, 692 NO! polychlorinated biphenyls, 1097 Neutrality, 10 wastewater, 335, 342 NO! soil cleanup, 1097-1106 Neutron radiography, arthropod behavior Nitrogen cycling NO! tracking fungi in treated soils, 1102-1103 studies, 775 aquatic environment, 511-522 Mycorrhizal fungi, 11, seealso Arbuscular Newcastle disease virus, 964, 1019, functional gene analysis, 693-694 NO! mycorrhizal fungi 1023-1024 future directions, 518 NO! enzyme production, 706 NEXAFS (near-edge X-ray absorption fine global and regional oceanographic Not Mycosis, 97&-977 structure) spectroscopy, 1190 approaches, 517-518 Mycoroxin Niche, 7 long-term research site, 18&-188 Not airborne, 926, 928, 931, 933, 955, 972, operational, 7-8 marine environment, 511-522, 533-535 Nor 978-982 potential, 7-8 quantification of nitrogen transforma- Nor assay, 954-955 Nickel tions, 687-696 Nor Myovirus, aquatic environment, 450 aquatic environment, 541, 553 soil, 670, 687-696 c Myxococcus, 23, 28 connection to iron and manganese Nitrogen-IS direct tracer assay fr Myxospore, 23, 28 cycles, 553 denitrification, 517, 692-693, 864-865 It Nicotinic acid, culture medium, 71 nitrification, 514-515 sl nif genes, 722 nitrogen fixation, 513,687-688 w N* values, 517-518 nifH gene, 511, 513, 693-694 Nitrogen fixation, 11 Naegleria Night soil, 618 abundance of nitrogen-fixing popula­ Nor culture, 86 Nigrospora tions, 512-513 waterborne, 220, 226, 366 airborne, 925 associative, 687 Nor Naegleria fowleri, 225, 265, 933 plant pathogens, 1036 diversity of nitrogen-fixing populations, Nor Nannochloris atomus, 457--458 spore discharge, 973 512 NOSI Nanoarchaeum, 22-23 Nile Red, 57 endophytic bacteria, 646-647 Nos: Nanoplankton, 458--460 Nipah virus, 927 functional gene analysis, 693-694 Nos: Nanowires, 28 niT genes, 516, 694 global and regional oceanographic nosZ iron-reducing bacteria, 1243-1244 Niskin bottle/bag, 497, 580 approaches, 517-518 Noti Naphthalenes Nitrapyrin, 690 marine environment, 511-513, 533-535 NP[ biodegradation, 1081, 1083 Nitrate measurement degradation in aquifer, 850, 854 aquifer, 843, 845, 850, 854 acetylene reduction assay, 513, mycoremediation, 1l00, 1102 culture medium, 72 688-689 Nvp NASBA, seeNucleic acid sequence-based marine environment, 511-522 lSNz direct tracer method, 513, N-S, amplification measurement, 506 687-688 Nue NAST aligner, 609 souring control in oil field, 904-905 ISN isotope dilution method, 688 National Oceanographic Data Center subsurface, 860-861, 864-865 nonsymbiotic,687 Nue (NOAA-NESDlS),525-526 Nitrate immobilization, 693 sediment, 512 Nue National Shellfish Sanitation Program, 311 Nitrate microprobe, 174 soil, 687-689 e> Natural selection, 9, 15 Nitrate reductase, 693-694 symbiotic, 687 e> under artificial conditions, 15 Nitrate reduction Nitrogen flux measurement, denitrifica­ Natural transformation, 533 coupled to iron oxidation, 546, tion, 516-517 h' Natural-gradient tracer method, subsurface 1149-1152 Nitrogen-IS isotope dilution method, m microbial transport, 884-886 terminal electron-accepting reaction, nitrogen fixation, 688 Near infrared spectroscopy, wood degraded 860-861,864-865 Nitrogen mineralization "r by brown rot fungi, 1125-1126 Nitrate-reducing bacteria measurement 61~16 Nearest taxon index, heterotrophic, 899-900 gross mineralization, 690 Nuc Near-field scanning optical microscopy, oil field, 899-900, 904-905 net mineralization, 689-690 Nue 58-59 Nitric oxide reductase, 693-694 soil,689-690 Nebulizer, bioaerosol generation, 1016 Nitrification, 688 Nitrogen source, culture medium, 69-70, Nue Neighborhood, &-19 aquatic environment, 408 72,75 Neighbor-joining method, 161,609 diversity of nitrifying organisms, 514 Nitrogen supplement, landfill cover, 823 in Nematode functional gene analysis, 693-694 Nitrogen-argon assay, denitrification, 517 soil long-term research in Monterey Bay, Nitrogenase, 687, 693 lo arthropod pathogens, 775 185-186 in situ immunolabeling, 722 Nue bioassay, 773-774 marine environment, 513-515 quantification, 513 extraction from soil, 772 measurement, 690-691 Nitrogenase reductase, 512, 722-723 cc suppressive soil, 748 inhibitor-based assays, 515 Nitrogenous oxygen demand, 339-340 pl Neosaxitoxin, 379 laboratory and field rates, 691 Nitrosococcus, 514 pi Neptunium ISN tracer methods, 514-515 Nitrosolobus, 185 pi environmental chemistry and biogeo­ oxygen demand, 340 Nitrosomonas, 26, 514 rF chemistry, 1199-1200 populations of nitrifying organisms, Nitrosomonas europa, 185 rF measurement, 1199-1200 513-514 Nitrosomonas marina, 185 Nuc oxidation states, 1199-1200 potential nitrification activity, 690-691 Nitrospina, 185 radiochemical techniques, 1198-1200 soil, 690-691 Nitrospira, 185, 1132 Nue Nested PCR, 677, 682-683 Nitrite, marine environment, 511-522 Nitrous oxide reductase, 693-694 Nested proliferation, community theory, Nitrite oxidoreductase, 514-515 Nivalenol, 980 103-104 Nitrite reductase, 516, 670, 693-694 Noble gas, geochemical tracers, 807 Nuc SUBJECT INDEX • 1277

Nocardia isolates hom high-throughput culture, comparisons of microbial communities, airborne, 989 402---403 613 endophytic, 642 single-cell analysis of DaM consump­ PLFA fingerprint analysis, 783 morphology, 23 tion, 480 Organic biocide, oil field water system, 903 signature lipids, 114 viruses in aquatic environment, 445---446 Organic carbon cycling Nodularia, 425 Nucleopolvhedrovirus, 771,773-774 bacteria in aquatic environment, Nodulariaspum~ena,384 Null hypothesis, 210, 212 479---487 Nodularin, 384-385, 387 Nutrient agar, 953 archaea, 482 Nominal data, 200, 208 Nutrient broth, 73 autoradiography, 482---483 Nonconformance, 194 Nutrient peptone agar, 644 cloning of environmental DNA, 479 Nonmctric multidimensional scaling, Nutristat, community culture, 104--105 consumption of alga-derived compo­ PLFA fingerprints, 783 Nutritional diversity, 25-26 nent of OOM, 481 Nonnutrient amoeba saline agar, 85 environmental DNA for enzymes Nonparametric statistical test, 213 hydrolyzing biopolymers, 483---485 Nontronite, nitrate-dependent microbial Objective lens, CLSM, 44, 46 FISH, 482---483 oxidation, 1151 Occlusion body, viruses in soil, 772, 774 phylogenetic groups and biomass pro­ Nonylphenol, 350 Ochratoxin, 980 duction, 482 Normal distribution, 204--205, 211 Ochrobacterium, endophytic, 643 phylogenetic groups and DaM Normalization, microarray data, 669 OchromoMs,457---458 uptake, 481 Norovirus 1-0cten-3-01, 982 SARlI bacteria, 481---482 clinical syndrome, 223 2-0cten-l-01, 982 single-cell analysis, 479 freshwaters and drinking waters, 251 OFRG (oligonucleotide fingerprinting of single-cell analysis of DOM consump­ marine recreational waters, 286 rRNA genes) method, 748, 750 rion, 480---482 shellfish, 227,313,316,319-320 Oil field, 797 deep-sea microorganisms, 578 waterborne, 220, 223, 226, 230--231, acid-producing bacteria, 901 soil, 707 240, 366 detrimental bacteria, 900--901 Organic carbon demand, 429 North American Plant Disease Forecast general aerohic bacteria, 900-901 Organic compounds Center, 1042-1043 microbial composition degradation in aquifer, 845, 849-850, North Temperate Lakes LTER, 184 cultivation-dependent methods, 854 Norwalk virus, 94, 223, 232, 313, 912 898-901 subsurtace,867-868 Nosema, 236, 266 cultivation-independent methods, terminal electron-accepting reaction, Nostoc, 235, 384,386 901 867-868 Nosioc commune, 114 microbially induced corrosion, 898, volatile, 955, 972, 982 nosZgene, 516, 694 901-905 Organic contaminants, seealsospecific com­ Notifiable disease, 240 microbiology, 898-911 pounds NPDES (National Pollutant Discharge nitrate- or nitrite-reducing bacteria, aquifer, 845, 848, 854 Elimination System) permit, 334­ 899-900, 904-905 degradation in landfill, 820 335,337,343-344,346 sampling, 898 wastewater, 350 Nvpoor medium, 644 slime-forming bacteria, 900--901 Organic dust toxic syndrome, 979, N-Serve, 515 souring, 898, 901-905 990--991,994 Nuclear magnetic resonance, microbe­ nitrate to control, 904-905 Organic matter mineral intertace, 1207 sulfate-reducing bacteria, 898-901 carbon cycling in aquatic environment, Nuclear waste, 1198 Oil field water system 479---487 Nucleic acidts}, seealso specific types biofilms, 902-904 dissolved, see Dissolved organic matter extracellular, 522-523 microbial activity metal binding, 1167 extraction from environmental samples, control,903-904 ozonated waters, 331 667,673 monitoring, 902-903 soil, 707, 770 hyphomycetes, aquatic, 472---475 recognition, 901-902 Organic sulfur oxidation, 505 metabolic activity of soil- and plant­ Oil recovery, microbially enhanced, 797, Organismal phylogeny, 160 associated microbes, 699 872, 905-907 Organotroph, 24-26 "nonliving," marine environment, assessing performance, 906 ori region, plasmids, 760 532-533 injection protocol, 905-906 Ornithine-linked lipids, 117 Nucleic acid biosensor, 177 microbial processes applied to field situa­ Omithocercus magnificus, 457---458 Nucleic acid fingerprinting, community tions,906 Orthologs, 160, 163-164 structure analysis, 145-151 microorganisms useful for, 899 Orthopoxvirus, 94 Nucleic acid hybridization, see also nutrient formulation, 905 Oscillatoria, 235, 384 Microarray Okadaic acid, 380-382, 385, 387 Oscillatoria nigroviridis, 383 indicator molecules in soil extracts, Oligotroph, 25 Osmotroph,454 656-660 soil, 653 Ostreococcus fauTi, 457---458 localization of endophyres in plants, 645 Oocyst, Cyclospora, 236 Osrreopsis siamensis, 380-381 Nucleic acid probe, 21, 38, 94, seealso Operational taxonomic unit, 159-160, OTFans,764 PCR-based methods 609 Outhouse, 618 community structure analysis, 140--142 Optical biosensor, 176-177 Overlay method, culture of acidophiles, phylogenetic nesting of probes, 140-142 Optical emission spectroscopy, mea­ 1159 phylogenetic probe design, 140 surement of manganese species, Overpotential, 1139 probe validation, 141 1226 Ovine herpesvirus, 1021 rRNA-based scissor probes, 143 Optical microscopy, microbe-mineral inter­ Oxalate rRNA-targeted, 140 face, 1205 brown rot fungal metabolite, 1122, 1124 Nucleic acid sequence, measures of com­ Optimization techniques, genetic algo­ purification and quantification, 1124 munity structure, 139 rithms, 1072-1078 Oxalate reduction method, manganese oxi­ Nucleic acid sequence-based amplification Orbivirus, 94 dation state, 1225 (NASBA), monitoring marine Ordinal scale, 200 Oxidation-reduction reactions, 23-24 recreational waters, 283 Ordination analysis Oxidative enzymes, extracellular, 705 Nucleic acid staining, 47, 54 CLPP data, 133 Oxirane fatty acids, 117 1278 • SUBJECT INDEX

Oxygen Partial least-squares analysis, PLFA finger­ indicator molecules in soil extracts, Peu aquifer, 843, 845, 850 prints, 783-784 658--659 Pen consumption Partial ordination method, PLFA finger­ inhibitors in environmental samples, CLPP based on, 131-132, 134-136 print analysis, 783 684, 955-956 microbial processes resulting in, Particle-induced X-ray emission, microbe­ isolates from high-throughput culture, 340-341 mineral interrace, 1205 403-404 respirometry methods, 698--699 Particular organic carbon, consumption by landfill microbes, 830--831 culture conditions, 72, 74-75, 85, 87 deep-sea microorganisms, 578 legionellae, 1010 effect on viability of airborne microor­ Particulate phosphorus limitations, 683, 955 \ ganisms, 962 marine environment, 523-526, 533 magnetotactic bacteria, 1132 Pen high-pressure marine environment, global patterns, 526-530 metal-reducing and metal-oxidizing bac­ Pe~ 577 production, 530-531 teria, 552 Pe~ subsurrace, 860, 863-864 particulate inorganic phosphorus, 525 methanotrophs, 836 Pe~ terminal electron-accepting reaction, particulate organic phosphorus, 525 methodology Pe~ 860 preconcentration, 525 basic protocol, 677 Per uptake rate as measurement of fungal Parvovirus, 94 confirmation of product ONA growth, 1110 Parvovirus B19, 94 sequences, 682--683 Oxygen biosensor, 131-132 Passive adsorption, virus concentration, internal positive controls, 956 Per Oxygen demand, wastewater, 336 291 isotopic vs. nonisotopic, 305 Oxygen electrode, 414 .Pasteurella, endophytic, 643 molecular probes and detection tech­ Pep oxygen in groundwater, 863 Pathogen(s),4 niques, 304-305 Per Oxygen mask, airborne viruses, 1022 airborne, 925, 932-934 PeR optimization, 682 Per Oxygen microprobe, 174 airborne fungi, 976-979 preventing contamination, 683 Pel Oxygen-based methods, measurement of airborne viruses, 1018-1022 primer design, 680--681, 955 primary production, 412-415 plant, seePlant pathogens primer selection, 304 electrochemical techniques, 414-415 Pathogenicity island, 762 primer specificity, 681 Pel Winkler method, 413-414 Patulin, 980 product sequencing, 683 Pel Oyster, seeShellfish PCDO sample preparation, 305-306 Pel Ozonation mycorernediation, 1097-1099 sample processing, 955 Per inactivation of airborne viruses, 1025 sources, 1098 sensitivity of detection, 681--682 water treatment, 330-331 PCOF standard reaction mixture (master Pel mycoremediation, 1097-1099 mix),677 sources, 1098 temperature cycling, 676--677 Pel P value, 212-213 PCP, mvcoremediation, 1097 universal primers, 681 Per Packed-bed bioreactor, 1110-1111 PCR-amplicon length heterogeneity, com­ microbial diversity, 679 Pel Packer and manifold system, groundwater munity structure analysis, 146, 148 microbial source tracking, 307 sampling, 811--812 PCR-based methods, 676--686, seealsospe­ microeukaryote assemblages, 1113-1116 PeT Paecilomyces cifictypes of PCR mobile gene elements, 763 Pel airborne, 933, 974-975, 977, 979 acidophiles, 1161 monitoring freshwaters and drinking Per lignocellulolytic, 1107 advantages, 955 waters, 259 Pel toxins, 981 airborne microorganisms, 955-957 monitoring marine recreational waters, Pe, water activity for growth, 973 aquifer microbes, 852-853 283 Pfi Paenibacillus, endophytic, 642--643 arbuscular mycorrhizal fungi, 632--633 MPN-RT-PCR,320 Pfi, Paenibacillus popilliae, 772 arsenate-respiring bacteria, 1219-1220 nitrifying bacteria, 514 pH PAH, see Polycyclic aromatic hydrocarbons arthropod pathogens in soil, 774-775 nitrogen-fixing organisms, 512-513 Palvtoxin, 380, 382 arthropod-associated microorganisms, oil field microbes, 901 Panellus stypticus, 1098 777 overview, 676 Pantoea bacteria in aquatic environment, pathogen detection, 678--680 endophytic, 642-643 436-439 protists in aquatic environment, subsurface transport, 876 bacteria in shellfish, 317, 320 461-462 Pantothenate, culture medium, 71 bacteria in wastewater and sludge, protozoa, 274-275 Ph Paper production facility, airborne bacteria 304-306 protozoa in shellfish, 318 Ph and endotoxin, 991 biases and errors, 438-439, 474 quality control, 305 Ph Papillomavirus, 94 biofilrn community, 566 quantification, 305 Ph airborne, 1018, 1021 C 1 oxidizers, 489-490 soil microorganisms, 684 Papulaspora, Ilgnocellulolvtic, 1107 ce 11 culture/PCR assay of viruses, toxic metal resistance genes, 1175-1177 Paracoccus denitrificans, 117, 489 620-622 viruses in aquatic environment, 449-450 Paraffin deposition, reduction by micro­ community structure, 679 viruses in shellfish, 317-319 bially enhanced oil recovery, 906 conditions, 304 viruses in soil, 620--622 Parainfluenza virus, 94 contamination, 683, 1113, 1172, 1175 white rot fungi, 1103 airborne, 1019-1021 denitrifying bacteria, 516 Peanut leafspot, 1043 Para logs, 160 detection of nonviable organisms, 683 Pearson product moment correlation, Paralytic shellfish poisoning, 379-380 detection of strains in transport studies, 207-208 Paramecium, 265 880 Pearson's correlation coefficients, 361 culture, 84-85 direct probing, 305 Pecan scab, 1043 waterborne, 265 ONA fingerprinting, 679 Pecrenotoxin, 380-381 Parameter-rich general reversible evolu­ estimates of enzymatic potential, Pediococcus, 23 tionary model, 611 678-679 Pedomicrobium standard medium, 1231 Paramyxovirus, 94 "eukaryote-specific" primers, 1113 mineral salt base, 1232 Paranosema locustae, 774 iron-reducing bacteria, 1242-1243 vitamin mix, 1231 Paraphysomonas imperforata, 457-458 genes and genomes mediating biodegra­ Peeper (sampler), 498 Parasite, waterborne, 224-225 dation, 1082-1083 Pelagibacter ubique (SARlI), 394-395, 400, a Parasitism, 4, 10, 16 history, 676 481-482 Pi Part 503 Rule (EPA), 336, 351 hvphomycetes, aquatic, 473-475 Pelagic environment, protists, 463 SUBJECT INDEX • 1279

Pelochromatium roseum, 117 Phellinus pini, 1107 phosphorus pool inventories and PeniciUium Phenanthrene, mycoremediation, fluxes, 525-532 airborne, 927-930, 933, 974-975, 978­ 1100--1102 soluble reactive phosphorus, 523-527, 979 Phenol, biodegradation, 820, 1081 532-534 food spoilage, 973 Phenol hydroxylase, 1082 global patterns, 526-530 spore discharge, 973 Phenotype microarray, 128 study methods toxins, 979-981 Phlebia, mvcoremediation, 1098 bioreporter molecules and macromol­ volatile organic compounds, 982 Phlebia lindmeri, 1098 ecules, 525 water activity for growth, 973 Phlebia radiata, 1107 isotopic tracers, 525 Penicillium camemberti, 973 Phoma toral dissolved phosphorus, 523-526, Penicillium casei, 978 airborne, 975, 977 528,532 Penicillium chrysogenum, 975 spore discharge, 974 Photoautotroph, 16, 72, 407 Penicillium jenthiUenum, 1107 water activity for growth, 973 Photobacterium, endophvtic, 643 Penicillium roqueforti, 973 Phosphate Photodiode array spectrophotometry, pho­ Peptide mass value, MALDI-TOF analysis, culture medium, 70 topigrnent assessment, 415-417 extracellular enzymes of P. lipid phosphate, 112-113 Phorohetcrotroph, 72 chrysosporium, 1093-1095 Phospholipid(s) Photo-oxidation method, total dissolved Peptide nucleic acid probe, fluorescence­ intact, analysis, 113 phosphorus, 524 labeled,724-725 structure, 113 Phoropigrnenrs Peptococcus, 253 Phospholipid fatty acids (PLFA), 38 measurement of primary production, Peptone, 73 anteiso-branched saturated, 117 415-418 Peranema, culture, 84-85 aquifer microbes, 851-852, 854 sulfur-oxidizing bacteria, 505 Percent minimum significant difference arthropod-associated microorganisms, Photorhnbdus, biocontrol agents, 1035-1036 level, whole-effluent toxicity tests, 776 Photorhabdus luminescens, 1035-1036 344 community composition, 113-115 Photosynthesis Percent probability, 374 comparison to FAME, 782 anoxygenic, 407-408 Percent viability, 405 cyclopropane, 115-116 coupled to iron oxidation, 545-546 Perchlorate, geochemical tracer, 806-807 extraction, 781 oxygenic, 407-408 Perchloroethene, degradation in landfill, future directions, 787 Phototaxis, 28 820 indicator molecules in soil extracts, 656 Phototroph, 23-25,407 Perfluorocarbon compound, geochemical iso-branched sarurared, 117 anoxygenic, 408. 505 tracer, 80(r808 metabolic activity of soil- and plant- culture, 72 Performance evaluation, 194 associated microbes, 699 iron-oxidizing bacteria, 1148-1149 Peridinium, 184 methanotrophs, 836 oxygenic, 408 Permeability profile modification, micro­ microeukaryote assemblages, 1116 Phreatamoeba, landfill, 828 bially enhanced oil recovery, 906 monoenoic, 115-116 Phthalic acid esters, degradation in landfill, Peronospora tabacina, 1036-1038, 1043 multivariate methods for analysis, 820 Peroxidase, white rot fungi, 1089-1090 782-784 PhyUobacterium, endophytic, 643 Persephonella marina, 117 pitfalls and limitations, 787 Phvllosphere Pervlene, mvcoremediation, 1102 procedure for lipid analysis, 118-120 definition, 697 Peziza, airborne, 974, 976 ratios ofPLFA, 115-116 metabolic activity of microbial commu­ Pfiesteria piscicida, 386, 1116 soil isolates, 655 nity.697 Pfiesteria shumwayae, 386 soil microbial community, 699, 781-787 PHYLOCOM,614 pH coupling PLFA fingerprinting and iso­ Phylogenetic fingerprint, 145-151 culture of flagellates and ciliates, 85 tope probing, 786-787 Phylogenetic niche conservation, 609 culture of microorganisms, 73-75 geostatistical analysis of fingerprints, Phylogenetic oligonucleotide array, 150 effect on subsurface microbial transport, 783, 785-786 Phylogenetic probe, 723 873 linking communiry composition to Phylogenetic studies, 38 intracellular, measurement, 58 environmental drivers, 784-785 acidophiles, 1156 microenvironmental analysis, 57-58 response of microbes to disturbances assessing whether two communities Phagotroph,454 and remediation, 785 differ, 612 Phakopsora meibomiae, 1040 spatial distribution, 783, 785-786 bootstrap analysis, 162,611 Phakopsora pachyrhizi, 1036, 1040--1041, statistical analysis and interpretation, general guidelines, 162-163 1043 782-784 genome tree, 163-164 Phanerochaete chrysosporium, see also White sulfate-reducing bacteria, 901 molecular markers, 157-158 rot fungi viable biomass measurement, 112, 120 multilocus sequence analysis, 158-159, culture, 1091 white rot fungi, 1102-1103 163 isolation of extracellular enzymes, 1091 Phosphorimager, 657 multiple gene analysis, 163 removal of lignin, 1091 Phosphorus, wastewater, 335, 342 random error, 162-163 lignocellulolvtic, 1107 Phosphorus cycling recA genes, 158 mycoremediation, 1098-1099, 1101-1102 biologically available phosphorus, rRNA genes, 157-159 oxidative enzymes, 1089-1090 531-532 rRNA studies, 157 proteomic analysis of extracellular dissolved organic phosphorus, 523-526, soil isolates, 655 enzymes, 1089-1096 530--531,533 soil microbial community, 608-617 confirmation with reverse transcrip­ ATp, 532 systematic error, 163 tase PCR, 1096 global patterns, 526-530 Phylogenetic test (Petesr, Phvlo-test), 612, in-gel digestion, 1093 ecological studies, 532-535 614-615 protein identification by MS, future directions, 535-536 Phylogenetic time lags, 609 1093-1095 inorganic phosphorus uptake, 530--531 Phylogenetic tree, 26-27, 159-160 two-dimensional gels, 1091-1093 marine environment, 523-539 construction, 159-163,609--611 spore preparation, 1090--1091 particulate phosphorus, 524-526, 533 collecting homologous sequences, Pharmaceuticals, wastewater, 350 global patterns, 526-530 160 Phase-contrast microscopy, 43 production, 530-531 creating good sequence alignment, metal-microbe interactions, 1201 phosphorus export, 530--531 160-161 1280 • SUBJECT INDEX

Phylogenetic ttee (continued) disease spread, 1031 Polycyclic aromatic hydrocarbons (PAH) Pri progressive sequence alignment, 161, escape from canopy, 1032 mycoremediation, 1097, 1100--1102 609 fungi, 1036--1041 sources, 1100 DNA-based, 160 long-distance transport, 1031-1032 Polv-Bvhvdroxv-alkanoares, community extracting information about biological rnacroscale spread, 1031 metabolic status, 116 Pri processes, 613-614 microscale spread, 1031 Polymer-producing organisms, microbially Pn genome tree approach, 163-164 movement in atmosphere, 1032 enhanced oil recovery, 899 Pte inferring tree topology passive dispersal, 1032-1033 Polvphasic taxonomy, 157 character-based methods, 161-162 survival in atmosphere, 1033 Polysaccharide, fermentation, 11 Pn distance-based methods, 161 viruses, 1033-1034 Polysporus arn:eps, 1107 evolutionary models, 162 soil, viruses, 624-625 Polvsulfide, 503 Pn integration of structural information, Plant-associated biofilm, 595 Polyrorny, 609 161 Plaque assay Pontiac fever, 1005-1006 Pn protein-based, 160 bacteriophages in freshwaters and drink­ POPO-3,47 Pn rooted, 160 ing waters, 258 Population, definition, 8 Pn unrooted, 160 viruses, 96--97, 298 Population study, rRNA gene-based, Phylogrid, 140 aquatic environment, 448-449 748-757 Phylo-test, seePhylogenetic test soil, 620, 622-624 Porcine reproductive and respiratory dis­ Physiological diversity, prokarvotes, 21-26 Plasmalogen lipids, 113, 115 ease virus, 1021 Phytophthora infesrans, 1031, 1036-1037, Plasmid Porcinosis, 994 Pn 1042-1043 construction of inaZ reporter gene sys­ Poria, airborne, 976 Pn 4Pi microscopy, 40-41, 53, 59 tern, 740 Poria placenta, 1107 PicoGreen, 47, 54 copy number, 760 Possible estuary-associated syndrome, Picophagus fJagellatus, 457-458 horizontal gene transfer, 760--761, 386-387 Picoplankron, 23, 81, 458-460 763-764 Postgate's media, 500 Picornavirus, 964, 1021 host range, 760-761 Potassium Picrophilus, 1157 incompatibility groups, 760 aquatic environment, 541 Piezoelectric biosensor, 176-177 rhizosphere, 763 culture medium, 69 Piezophtle, 25, 575 sludge, 763 geochemical tracer, 806-807 Pigeonpox virus, 964 toxic metal resistance genes, 1173-1174 Potato blight, 1031, 1036--1037, Pigging, oil field water system, 903 vector, soil metagenomics, 1064, 1067 1042-1043 Pigment analysis, seealso Photopigments Plasmodium, 14 Potato dextrose agar, 75 Ptl bacteria in aquatic environment, 434 Plate count broth, 73 Potato dextrose broth, 73 measurement of primary production, Plate wash PCR, soil bacteria, 654 Potato infusion broth, 73 Pn Pr, 415-418 Plat"Yarrweba weinsteini, 457-458 Potato starch industry, airborne bacteria Pili, type IV, 28 Plei;tophora, 236, 266 and endotoxin, 991 Pr, PIPES buffer, 74 Plesiomonas, shellfish, 227 Potentiostat, electrode-reducing bacteria, Pirellula, 27 Plesiomonas shigelloides, 223 1140-1141, 1143 Pitfall trap, 771 Pleurotus Poxvirus, 772 Pr Pithomyces, plant pathogens, 1036 airborne, 976 Precision, 211 Pr, Plagiarism, 197 mycoremediation, 1098-1099, 1101 Predation, 4, 8, 10-12 PI' Plagiopyla, 85 Pleurotus ostreatus, 1099, 1101-1102, 1107 Prescott's and Carrier's solution, 85 Pr Plan-apochrornat lens, 46 PLFA, seePhospholipid fatty acids Prescott's and James's medium, 84 Pr Planctomyces, 27 Plot, 204 Presence-absence method, monitoring Pr lipids, 114 Plotting positions, 205 freshwaters and drinking waters, Plankton, biofilm formation on, 570 Plumbing system, legionellae, 1007-1008 257 Plankton net, 455 Plutonium Pressure-retaining water sampler, 579-580 Planktonic sample environmental chemistry and biogeo­ Prevotella Pr HC-Iabeled carbon dioxide uptake test, chemistry, 1199-1200 marine recreational waters, 286 410-412 measurement, 1199-1200 wastewater and sludge, 307 PI concentration, 412 oxidation states, 1199-1200 Prey, 11-12 PI Planktothrix, 79, 81 radiochemical techniques, 1198-1200 Primary production, 6 PI Planktothrix agardhii, 235 Pneumocvsns carinii, airborne, 930 aquatic environment, 407-419, 429 PI Planktothrix rubescens, 235 Pneurnovirus, 94 biogeochemical significance, 407-408 Planus), seealso Rhizosphere Podospora anserina, 474 definition, 407 endophytic bacteria, 638-651 Podovirus, 450 diel and seasonal changes, 408, 412 used in plant protection, 642-643, Point intercept counting method, 42 ecological significance, 407-408 646-647 Poisson distribution, 204-205 measurement, 408-418 metabolic activity of plant-associated Polarizing microscopy, 43 biomass estimation, 409 microbes, 697-703 Polaromonas vacuolata, 1081 carbon dioxide uptake by gas analysis, reporter gene systems for plant­ Poliovirus, 94 409-410 associated bacteria, 734-747 airborne, 964 electrochemical techniques, 414-415 schizogenous intercellular spaces, clinical syndrome, 223 rnicroautoradiographv, 417 638-639 minimum infectious dose, 366 oxygen-based methods, 412-415 Plant infusion medium, protozoa, 84 subsurface transport, 877 photopigment radiolabeling, 416-417 PI Plant nutrients, wastewater, 335, 342 UV inactivation, 328-329 pigment-based estimates, 415-418 PI Plant pathogens waterborne, 223 regional and global studies, 417-418 PI airborne, 1031-1047 Pollutants, effect on viability of airborne stable isotope ratio, 409 active dispersal mechanisms, 1033 microorganisms, 962 uptake of HC-labeled carbon dioxide, anticrop biological warfare, Polychlorinated biphenyl, rnycorernedia­ 410-412 PI 1041-1042 tion, 1097 Winkler method, 413-414 bacteria, 1034-1036 Polychlorinated dibenzo-p-dioxms, see process and relevant microorganisms, disease forecasting and information PCDD 407 technology, 1042-1043 Polychlorinated dibenzufurans, see PCDF spatiotemporal interaction, 418 SUBJECT INDEX • 1281

Principal components analysis, 184, 208 cloning and sequencing of genes, source waters, 265-279 CLPP data, 133 461-462 subsurface transport, 877 functional gene array data, 1058 community structure, 454-468 viability markers, 275 PLFA fingerprints, 782-783, 786 denaturing gradient gel electrophore­ wastewater, oxygen consumption, 340 Pringsheim's solution, modified, 85 sis, 461 waterborne pathogens, 231, 234-237 Probability, 373-374 depth and seasonal distribution, Providencia, endophytic, 642 Probability of death, pathogens in drinking 463-464 Pseudoalteromonas, 566 water, 367,369,375-376 DNA fragment analysis, 461 biofilrn on U. lactuca, 569 Probability of illness, pathogens in drink­ freshwater vs. marine, 462-463 Pseudocercosporella, plant pathogens, 1033 ing water, 367-368, 376 future directions, 464 Pseudocoloring, CLSM systems, 45 Probability of infection, pathogens in immunological methods, 462 Pseudomonas drinking water, 365-367 microarrays, 462 airborne, 930, 989-992 Prochlorococcus, 394, 533 molecular approaches, 460-462 clinical syndrome, 225 Procurement system, 193 PCR-based methods, 461-462 endophytic, 642--643 Progressi ve sequence alignment, 161 species diversity, 454-456 morphology, 23 integration of structural information, temporal and spatial changes, naphthalene degradation, 1083 161 462-464 plant pathogens, 1034 "once a gap always a gap" problem, 161 terminal RFLP, 461-462 subsurface transport, 874-876, 878 "stripping of the alignment," 161 carbon-volume conversion factors, 456 waterborne, 225-226, 229, 251 Prokaryota (Procarva), 4 definition, 454 whole-genome probe, 143 Prokaryotic diversity, 20-34, seealso global distribution, 464 Pseudomonas aeruginosa, 251, 1138 Microbial diversity identification, 455 hiofilrnformation, 568 behavioral diversity, 28 marine environment, 455, 457, 462-463 lipids, 117 habitat diversity, 28-30 preservation and fixation, 455 metal interactions, 1202 limitations on our understanding, 20-22 prey type, 456-457, 459 waterborne, 222 macromolecular analysis, 26--27 sampling, 454-455 Pseudomonas cepacia, 117 metabolic flexibility, 21 sediment, 455, 464 Pseudomonas j!uorescens, 42, 117,962, morphology, 22-23 size classes, 454, 456-459 1035,1192 physiological, 21-26 trophic categories, 456, 458-460 Pseudomonas putida, 735, 1228 recognition, 20 Protocooperation, 10-11 Pseudomonas stutzeri, 117, 516 size of cells, 22-23 Protoctist, 79 Pseudomonas syringae, 735, 738-742 Promoter activity, from reporter activity, Protoperidinium, 457-458, 460 ice-minus, 1034-1035 743 Protoperidinium crassipes, 380, 382 Pseudo-nitzschia australis, 380, 382 Promoter trapping experiment, 737, 742 Protoslo, 266 Pseudo-nitzschia delicatula, 380, 382 Propagule, 8-9 Protozoa, seealso Microeukaryote assem­ Pseudo-nitzschia multiseries, 380, 382 arbuscular mycorrhizal fungi, 628--629 blage; Protist Pseudo-nitzschia pseudodelicatissma, 380, Propane torch, field sterilization of sam­ agar plating, 81 382 pling equipment, 294 airborne, 926, 928, 933 Pseudo-nitzschia pungens, 380, 382 Propidium iodide, 48, 55, 700 anaerobic, 85 Pseudo-nitzschia seriata, 380, 382 Prorocentrum lima, 381 biology, 266 Pseudoperonospora cubensis, 1043 Prorocentrum micans, 457-458 culture, 79-82, 266 Pseudorabies virus, 1020, 1024 Prosthecate bacteria, 28 limitation to cultivation procedures, Pseudoreplication, 203 Protease, landfill, 829 89 Psychrobacter, endophytic, 643 Protein(s) cysts, 85, 89, 231 Psychrophile, 25, 87 arbuscular mycorrhizal fungi, 631 definition, 454 Pvtest, seePhylogenetic test metal binding, 1167 detection, 266-275 Ptychodiscus, toxins, 219 microchemical analysis, 57 confocal microscopy, 274 Ptychodiscus brevis, 79 Protein folds, construction of genome trees, ELISA,274 Public building 164 FACS, 274 airborne bacteria and endotoxin, 992, Protein Prospector MS-Fit tool, 1095 FISH,274 995 Protein sequence, phylogenetic studies, 160 ICR method, 267 airborne microorganisms, 926, 929-930, Protein-based biosensor, 175 Method 1623, 267-274 974-975 Proteomics, 396 microscopic particulate analysis, 275 Public health, pathogens in drinking water, ecological, 709 PCR-based methods, 274-275 365-376 extracellular enzymes of P. solid-phase cytometry, 274 Puccinia coronata, 1039 chrysosporium, 1089-1096 drinking water, 265-279,365-376 Puccinia graminis, 1031, 1036, 1039, confirmation with reverse transcrip­ ecology, 266 1042-1043 rase PCR, 1096 electromigration, 81 Puccinia melanocephala, 1039 in-gel digestion, 1093 emerging diseases, 276 Puccinia striiformis, 1043 isolation of enzymes, 1091 enrichment culture, 80 Puccinia triticina, 1036, 1039, 1043 protein identification by MS, 1093­ free-living, 265 Puffball, 973 1095 detection, 266--267 Pulsed-field gel electrophoresis two-dimensional gels, 1091-1093 infection with Legionella, 1006-1007 fecal contamination of marine recre­ toxic-metal-resistant bacteria, 1178 isolation methods, 80-82 ational waters, 286 Proteose peptone glucose medium, 85 landfill, 820, 828 legionellae, 1011 Proteose peptone yeast extract medium, 84 long-term preservation methods, 89-90 microbial source tracking, 307 Proteus maintenance methods, 83-88 viruses in aquatic environment, 448 endophytic, 642 microscopy, 266, 272-273 Pump, groundwater sampling, 812 motility, 28 parasitic, 265-279 Pure culture, 9, 16,21,37,69,101-102 Protist, 79, seealso Microeukaryote assem­ detection, 267-275 community culture vs., 101-103 blage; Protozoa predatory, 11-12 natural, 6 aquatic environment sampling, 267, 270 Purple nonsulfur bacteria, 72, 505,1149 abundance and biomass, 456 shellfish, 311, 313-314, 316,318 Purple sulfur bacteria, 29, 497, 503, 505, benthic vs. pelagic, 463 signature lipids, 114 1149 1282 • SUBJECT INDEX

Push-pull test, aquifer biogeochemistry, isolation of bioactive compounds, 568 Recreational waters, 249, see also 851,853--854 selection of target organism, 568 Environmental freshwater Puumala virus, 1020 bacterial pathogens, 225 PYG medium, 1230 marine, seeMarine recreational waters PYNFH medium, 85 r growth strategy, 15-16 parasites, 225 Pyranose oxidase, 1089-1090 Rabies virus, airborne, 1024 protozoa, 231 Pvrene, mycoremediation, 1100-1102 Radioactive waste, 1198 viral pathogens, 225 Pyrenophora triticirepentis, 1043 Radiochemistry, 1198-1199 waterborne disease, 226-227 Pyricularia orrrae, 1042 Radioimmunoassay, airborne microorgan­ watershed management, 327 Pyridoxine, culture medium, 71 isms, 954 Rectangular bacteria, 23 Pyrite, nitrate-dependent microbial oxida­ Radiometric method Recycling facility tion, 1150 intracellular pH measurement, 58 airborne bacteria and endotoxin, 990 Pyrobaculum aerophilum, 1216 monitoring freshwaters and drinking airborne microorganisms, 926, 931 Pyrobaculum arsenaticum, 1216 waters, 259 Red fluorescent protein, 712, 736-737 Pyrodictium, 23 Radionuclides Red tide, 14, 79,378-379 P'Yrodinium bahamense, 380 annual limit of intake, 1198-1199 Redfield ratio, 517 Pyrolysis MS, wood degraded by brown rot measurement, 1199-1200 Redox indicator, culture medium, 74 R fungi, 1126 radiochemical techniques, 1198-1200 Redox potential, iron-reducing bacteria, Pyronema, airborne, 974 safety issues, 1198-1200 1244 Pyronema domesticum, 976 transformations Redox reactions R synchrotron-based techniques, aquifer, 845-849 R 1183-1194 high-pressure marine environment, 577 R Quadrat, 204 techniques for studying, 1195-1213 subsurface, 860 R Quality assurance, 39, 190-198 Raffinose, bioaerosol stabilizer, 966 Redundancy analysis, PLFA fingerprints, culture of algae and protozoa, 88-89 Rafting, 925 783-784 definition, 190 Rahnella, endophytic, 643 Reference materials, 196 Quality assurance program Rain splash, fungal spore dispersal, Reflection imaging, CLSM systems, 45 audits and assessments, 194 1032-1033 Refuse, see also Landfill costs, 190 RaLstonia, 1083 chemical measurements, 825, 831-832 document control, 193 endophytic,643 composition, 819 environmental microbiology and, 191 Raman spectroscopy, microbe-mineral decomposition in landfills, 818-842 F management, 191 interface, 1207-1208, 1241 excavated, 826 nonconformance and corrective action, Random amplification of polymorphic extraction of microbial cells, 827 194 DNA analysis, seeRAPD analysis microbiological measurements, 824-825, F organization, 191 Random sampling, 200-201 827-831 personnel qualifications and training, spatial sampling, 201 sample processing, 826-827 F 192 stratified sampling, 201 sampling, 823, 826-827 procurement system, 193 Random variable, 200 shredded, 823, 825 F record keeping, 193 continuous, 200, 204 Refuse metabolic capability, 824, 827--828 software and electronic data control, discrete, 200, 204 Relative humidity F 193-194 Randomization, experimental design, bioaerosol stability, 961-962 work processes, 192-193 202 fungal requirements, 973 Quality assurance record, 194-195 Ranking tests, 362 Released microorganisms, see also Quality assurance standards, 191 RAPD analysis Introduced microorganisms Quality control, 39, 190 arbuscular mycorrhizal fungi, 633 dilution, 355-356 culture of algae and protozoa, 88-89 arthropod pathogens in soil, 774 fate in water, wastewater, and soil, definition, 190-191 arthropod-associated microorganisms, 355-364 in field and laboratory, 196-197 777 microbial survival studies, 356-363 Method 1623 for protozoa, 267-270 monitoring freshwaters and drinking transport, 355-356 PCR-based methods, 305 waters, 259 Remote sensing, measurement of primary virus cell culture, 96 viruses in aquatic environment, 449 production, 417-418 Quality control standards, 197 Raphidopsis curvata, 385 Reovirus, 94, 964 Quality improvement, 190-191 Rarefaction analysis, denitrifying organ­ Rep proteins, 760 Quality planning, 191-192 isms, 516 Repeated-measures data, 203, 213 Quantal assay, viruses, 97 Rauscher murine leukemia virus, 1019 Repetitive intergenic palindromic sequence Quantile plot, 205-207 Real-time PCR, 320 PCR,679 Quantitative PCR arbuscular mycorrhizal fungi, 633 fecal contamination of marine recre­ airborne microorganisms, 956 arsenate-respiring bacteria, 1219 ational waters, 286 dye-based, 680 bacteria in aquatic environment, 439 monitoring freshwaters and drinking machines, 680 biofilm community, 566 waters, 259 methodology, 679-680 genes and genomes mediating biodegra­ soil isolates, 656 oil field microbes, 901 dation, 1083 Replicate, 200, 202 probe-based, 680 hyphomycetes, aquatic, 475 pseudoreplicate, 203 reagent kits, 680 legionellae, 1010 Replication, experimental design, 202 rRNA genes, 753 metal-reducing and metal-oxidizing bac­ Reporter gene system Quantum dots (Qdors), 46, 178 teria, 552 bioluminescent proteins, 170-171,736 Questionable research practices, 197 methanotrophs, 836 characteristics useful in microbial Quinones microeukaryote assemblages, 1116 ecology, 734-735 respiratory, 116 recA gene, phylogenetic studies, 158 data interpretation, 742-743 soil microbial community, 782 Recombinant yeast estrogen screen assay, detecrabilirv, 734 Quorum sensing, 28 350 dilution, maturation, and degradation of biofilm formation, 567-569 Records reporter gene, 743 quorum sensing antagonists dual storage, 194-195 endophytic bacteria, 645-646 assay, 568 quality assurance, 193-195 in environmental microbiology, 715-742 SUBJECT INDEX • 1283

fluorescent proteins, 170, 172-173, confirming proteomics of P. chryso­ phylogenetic relationships from, 26-27, 736-738 spoTium, 1096 140 gusA system, 735 genes and genomes mediating biodegra­ recovery from environmental samples, ice nucleation activity, 738-742 dation, 1083 139-140 inaZ gene, 738-742 iron-reducing bacteria, 1243 small-subunit, 140 lacZ gene, 735 toxic metal resistance genes, 1177 soil isolates, 655 lux genes, 170-171, 736 viruses in aquatic environment, 449-450 soil microbial community, 185 microbial activity in soil, 700-701, viruses in soil, 621 sulfate-reducing bacteria, 502 734-747 Reverse-osmosis filter, in-home water treat­ terminal RFLp, 147 plant-associated bacteria, 734-747 ment,228 Ribosomal RNA genets), 38, 679 quantification, 734 RFLP, see Restriction fragment length poly­ acidophiles, 1160-1162 response to changes in transcriptional morphism arbuscular mycorrhizal fungi, 632 activity, 735 Rhinovirus, 94 ARlSA,148 sensitivity, 734 airborne, 1021 bacteria in aquatic environment, 394, specific activity, 735 Rhizobium, 11, 638 436-438 xylE gene, 735 endophytic, 642-643 biodegradation microorganisms, Representational difference analysis, genes root colonization, 58 1080 and genornes mediating biodegra­ Rhizobium leguminosarum, 716, 718-720 biofilm community, 565 dation, 1082 Rhizoplane, direct examination of C,-metabolizing populations, 492 Representative sample, 200 microbes on roots, 718-720 correlation with functional parameters, Resazurin, 74 Rhizopus 749-751 Resonant-mirror biosensor, 176 airborne, 974, 978 denaturing gradient gel electrophoresis, Respiration water activity for growth, 973 149 aerobic, 23-24 Rhizosolenia clevei, 457-458 direct sequencing, 157 anaerobic, 23-24 Rhizosphere, 595 DNA hybridization, 157 aquifer, 845, 851 CLSM imaging, 58 indicator molecules in soil extracts, bacterial, 421 definition, 605, 697 657-658 community-level, 129-131 metabolic activity of microbes, 697 iron-oxidizing bacteria, 1152 substrate-induced, seeSubstrate-induced microbial community, 784-785 isolates from high-throughput culture, respiration plasmids, 763 403-404 Respiratory disease sampling, 605 landfill microbes, 830-831 airborne fungi, 976-978 Rhizosphere effect, 605 legionellae, 1010 airborne viruses, 1016-1030 Rhodamine,48,700 metal-reducing and metal-oxidizing bac­ Respiratory quinones, community meta­ geochemical tracer, 806-807 teria, 552, 554 bolic status, 116 Rhodamine isothiocyanate, 954 methanotrophs, 836 Respiratory syncytial virus, 94 Rhodazine-D test, oxygen in groundwater, microeukaryote assemblages, airborne, 1019-1020 863 1113-1116 Respiratory therapy equipment, legionellae, "Rhodobacter ferrooxidans," 1149 monitoring fresh waters and drinking 1007-1008, 1012 Rhodococcus waters, 259 Respirometry method airborne, 989 nitrogen-fixing organisms, 512 in situ, 698 endophytic, 643 oil field microbes, 901 INT-formazan method, 698-699 lipids, 114 PCR-ALH, 146, 148 isotopic methods, 698 subsurface transport, 874, 876 PCR-based cloning and sequencing, metabolic activity of soil- and plant­ Rhodoferax ferrireducens, 1138, 1141, 1240 436-438 associated microbes, 698-699 Rhodomicrobium vannielii, 1149 universal primers, 437 Restoration, soil, response of soil microbes, Rhodopseudomonas palustris, 545, 1149 phylogenetic studies, 157-159 785 Rhodopseudomonas viridis, 117 RFLP analysis, 142 Restriction enzymes, 142-143 RhodospiTillum, 23 rRNA gene-based population studies, Restriction fragment length polymorphism Rhodotorula, airborne, 930, 975-976 748-757 (RFLP),139 Rhodotorula rubra, 933 sequence alignment, 609 arbuscular mycorrhizal fungi, 633 Rhodovulum iodosum, 1149 sequence-selective PCR, 751-753 bacteria in aquatic environment, Rhodovulum robiginosum, 1149 sequence-selective regions, 751-752 437-438 Riboflavin, culture medium, 71 single-strand conformation polymor­ biodegradation microorganisms, 1083 Ribosomal RNA (rRNA) phism, 148-149 community structure analysis, 142-143 anammox bacteria, 516 soil isolates, 655 denitrifying bacteria, 516 bacteria in aquatic environment, soil microbial community, 608, 670 environmental DNA, 142 436-440 temperature gradient gel electrophoresis, hvphomvceres, aquatic, 474 cell growth rates from, 55 149 isolates from high-throughput culture, classification of prokaryotes, 21 Ribosomal RNA gene-based population 403-404 direct sequence analysis, 143 studies legionellae, 1011 evaluating contamination of subsurface correlation studies, 749-751 microeukaryote assemblages, 1113-1116 samples, 806 broad-range primer set and design, monitoring fresh waters and drinking FISH technique, 723 750-751 waters, 259 hyphomycetes, aquatic, 472-474 examining activity levels and func­ rRNA,142 indicator molecules in soil extracts, tional genes, 750-751 soil isolates, 655-656 657-658 multiple functional gradients, soil microbial community, 608 iron-reducing bacteria, 1242 749-750 terminal, seeTerminal RFLP large-subunit, 140 quantitative validation of rRNA gene Retrovirus, airborne, 1021 magnetotactic bacteria, 1132 correlates, 751-753 Reverse sample genome probing, 140 metabolic activity of soil- and plant- sequence-specific PCR, 751-753 community structure analysis, 143-144 associated microbes, 699 reintroduction of organisms to assess

sulfate-reducing bacteria, 502 nitrifying bacteria, 513-514 functions, 753 t· Reverse transcriptase PCR, 306, 318, 678 nucleic acid probes, 140-142 microbe isolation, 753 arsenate-respiring bacteria, 1219 phylogenetic oligonucleotide arrays, 150 microbe reintroduction, 753 1284 • SUBJECT INDEX

Ribotyping, 142, 147 Ruminococcus, 253 legionellae, 1007-1008 Sea: indication of fecal contamination, 326 Rust fungi, 1036, 1039-1041 microeukaryote assemblage, 1112 a marine recreational waters, 286 RVB medium, 302-303 mine, 800,810--811 p microbial source tracking, 307 oil field, 898 p monitoring freshwaters and drinking planktonic samples, 411--412 waters, 259 Sabouraud dextrose agar, 73 protists, 267, 270,454-455 Sea: Rift Valley fever virus, 1020 Saccharomonospora viridis, 989 refuse, 823, 826--827 Seal Right-skewed distribution, 204 Saccharomyces cerevisiae, tracing microbial rhizosphere, 605 ill Rinderpest virus, 1019 transport in groundwater, 805 rocks,811 c< Risk assessment Saccharopolyspora reerivirgula, 989-990 sediment, 497 UI infectious disease associated with drink­ Sacritoxin, 380, 382 sedimentary pore water, 497--498 Seav ing water, 365-376 Safe Drinking Water Act, 325, 914, 918 soil,597--607,618--626,652 Seav calculating risk estimation, 367-371 Salinity, culture medium, 75 sterilization of sampling equipment, m caveat emptor principle, 375-376 Salmonella 293-294 meaning of risk estimation, 371-375 airborne, 927, 989, 991 subsurface, 795-796, 799-817 se variables, 365-367 clinical syndrome, 223 surface sampling, 946--947 se waterborne-disease prevention and con­ culture media, 302-303 toxic-metal-resistant bacteria, Sea... trol,239 enrichment media, 301-302 1169-1173 Seall River, 393 shellfish, 227,312 tunnel, 800, 810--811 Seca RNA wastewater and sludge, 300-303, viruses in environmental waters, Seco extraction from environmental samples, 306-307 292-294 1219-1220 waterborne, 220, 223, 227, 229-230, viruses in soil, 618--626 Seco extraction from soil or microbes, 667 366-369 wastewater and sludge, 301 labeling for microarray experiment, Salmonella-shigella agar, 302 Sampling distribution, 211 Seco 667-668 Salt bridge Sampling frame, 200 Seco metabolic activity of soil- and plant­ bacterial electrode device, 1140 Sampling method aq associated microbes, 699 definition, 1138 bias, 200 hal "nonliving" nucleic acids in marine Sample processing study design, 195, 199-202 environment, 532-533 landfill, 826-827 Sampling site, 195 recovery from environmental samples, landfill cover, 834-835 Sand tank experiment, subsurface micro­ mE 139-140, 142 PCR-based methods, 955 bial transport, 888 ribosomal, seeRibosomal RNA soil, 604--606, 618--619 Sand-cartridge method, groundwater sam­ sample preparation for PCR, 305-306 for PCR amplifications, 684 pling,812 RNA probe, community structure analysis, study design, 195 Sapovirus 140-142 subsurface, 808-809 shellfish, 316 RNase H, 142-143 Sample selection protocol, 200 waterborne, 232 Robbins device, 106, 904 Sample storage Sapporo virus, shellfish, 313 Rockls) drinking water, 254 SARlI, see Pelagibaccer ubique collected underground, 811 environmental freshwaters, 254 Sarcina, 23 sampling, 811 soil, 601, 603, 605, 618-619 Sarcodine, 462 Sect« Rock crusher, 809 wastewater and sludge, 301 SARS coronavirus, airborne, 1016, 1022 Sedirr Rock splitter, 811 Sample transport Satellite-based remote sensing, mea­ nit Rod-shaped bacteria, 23 drinking water, 254 surement of primary production, pre Roots environmental freshwaters, 254 418 pro arbuscular mycorrhizal fungi, 627--637 federal regulations, 270 Satraroxin, 954, 980-981 res cell extraction and recovery soil, 605 Sawmill, airborne endotoxin, 994 san centrifugation method, 717 subsurface samples, 809--810 Saxitoxin, 235, 379-380, 384-386 Sedin flocculation method, 716-717 wastewater and sludge, 301 SC medium for fastidious bacteria, 644 Sedin colonization, 14 Sample unit, 200, 211 Scaling factor, 213-214 Sedin endophytic bacteria, 641 artificially defined, 200 Scanning electron microscopy enzyme production, 706 Sampling, 195 environmental, 1201 Seed( FISH technique, 723-728 airborne endotoxin, 996-997 metal-microbe interactions, 1201 Seed- immunofluorescence microscopy of root- airborne microorganisms, 939-951 rad ionuclides, 1200 associated microbes, 712-723 airborne viruses, 1017-1018 Scanning transmission X-ray microscopy, Selec Rose bengal-containing agar, 952 aquatic environment, 400--401, 497 59 Selec Rotary drilling, subsurface sampling, 796, aquifer, 846--847 Scanning tunneling microscopy, microbe­ 802-804, 807 arthropod-associated microbes, 772 mineral interface, 1208-1209 Selel1< Rotating annular bioreactor, 40--41, arthropods in soil, 771 Scanning-probe X-ray imaging microscopy, 105-106 benthic samples, 411--412 1191-1192 Selel1< Rotating drum bioreactor, 1111 bioaerosol, 939-946, 952, 1009-1010, Scatterplot, 205 Rotavirus, 94 1017-1018 Schistosoma Selen airborne, 964, 1018-1021 biofilrn, 564, 1112 clinical syndrome, 225 Selen clinical syndrome, 223 cave, 810-811 waterborne, 220, 225-226, 366 Selen detection, 237 drinking water, 254 Schizogenous intercellular spaces, plant, Selen drinking water, 367-369 environmental freshwaters, 254, 638--639 Selen group B, 237 292-294 Schizothrix, 235 aql minimum infectious dose, 366 groundwater, 796, 799-800, 811-813, Schizothrix calcicola, 383 COl shellfish, 319 846, 863 Schneeberg disease, 980 UV inactivation, 328 high-pressure marine environment School building, airborne bacteria and Seleru waterborne, 220, 223, 227, 230-231, background rationale, 576-579 endotoxin, 992 Self-< 237, 366 equipment, 579-580, 585 Scientific misconduct, 197-198 fur Roulette wheel selection, 1074 hyphomycercs, aquatic, 469--470 Scientific notebook, 192-193 Semi! Rous sarcoma virus, 964, 1019 landfill, 797, 823, 826-827 Sclerotium rot, 1042 Semi' rRNA, see Ribosomal RNA landfill cover, 834-835 Scopulariopsis, 973 Sem!: SUBJECT INDEX • 1285

Seasonal changes Seoul virus, 1020 ShewaneUa putrefaciens, 1137-1138, 1141, alpine tundra fungal communities, 615 Septata, waterborne, 232 1202, 1216 primary production, 408, 412 Septic tank, 229, 618 Shigella protists in aquatic environment, Septaria tritici, 1043 airborne, 927 463--464 Sequence-selective PCR clinical syndrome, 224 Seasonal migration, 12-13 assay optimization and validation, drinking water, 369 Seawater 752-753 endophytic, 642 artificial, 1231 genes and genomes mediating biodegra­ groundwater, 912 collection, 400--401 dation, 1082-1083 shellfish, 227, 312 uncultured organisms, 76 guidelines for optimizing and perform­ wastewater and sludge, 300, 303 Seawater medium, 75, 84 ing, 754 waterborne, 220, 224, 226--227, Seawater-based medium, 400--401 primer design, 752 229-230,238,366 nutrient, organic carbon, and vitamin quantitative, 753 ShigeUa sonnei, 226 additions, 401 rRNA genes, 751-753 Shipping regulations, 270 seawater collection, 400--401 Serial analysis of ribosomal sequence tags, Siderite, 1147 seawater processing, 401 143 nitrate-dependent microbial oxidation, Seaweed dermatitis, 383 Serology 1150 SeaWiFS remote-sensing platform, 418 arthropod pathogens in soil, 774 Siderophore, 543, 1122 Secalonic acid D, 980 legionellae, 1011 Sieving, soil sample, 604, 606 Second harmonic imaging microscopy, Serpula !acrymans, 974, 976, 978 Signature lipids, 113-115, 118-120 58-59 Serratia cellular location, 114 Secondary ion mass spectrometry, microbe­ endophytic, 642--643 Silicone oil plating, isolation of protists, 81 mineral interface, 1209-1210 motility, 28 Silver, toxic metal resistance, 1166--1182 Secondary metabolites, algae, 379-380 Serratia entomophila, 770, 772 Silver nanoparticle study, membrane trans­ Secondary production Serratia marcescens, 963 port, 178 aquatic environment, 421--433 biofllmformation, 568 Simian virus 40, 964 bacterial,421--422 tracing microbial transport in ground­ Similarity measures, 209 contribution of specific bacterial water, 805 SIMMAP,612 groups, 427--429 Setback distance, drinking water wells, Simplexvirus, 94 measurement state requirements, 916--917 Single-strand conformational polymor­ adenine incorporation into nucleic Settleable solids, wastewater, 335 phism acids, 427 Sewage, viruses, 290--299,618 arbuscular mycorrhizal fungi, 633 bromodeoxyuridine incorporation Sewage sludge, see Sludge community structure analysis, 146, into DNA, 427 Sewage treatment facility, airborne 148-149 FDC method, 427 microorganisms, 933 hvphomycetes, aquatic, 474 leucine incorporation into proteins, Shading correction, image processing, 49 Sinorhizobium meliloti, 671 422--423,425--426 Sheathed bacteria, 23 Sinusitis, allergic fungal, 978 thymidine incorporation into DNA, Shellfish, 227 Sipper (sampler), 498 422--425,429--430 amnesic shellfish poisoning, 380, 382 Sistotrema, 973 Sectioning methods, physical, 41 azaspiracid shellfish poisoning, 380, Sistotrema brinkmanii, 974, 976 Sediment 382-383 Skewed distribution, 204 nitrogen fixation, 512 bacteria, 311-312 Slaughterhouse facility, airborne bacteria preparation for microscopy, 41 conventional methods for detection, and endotoxin, 991 protists, 455, 464 314-315 Slime mold, airborne, 974, 976 reservoir of microorganisms, 356 molecular methods for detection, Slime-forming bacteria sampling, 497, 799 316-317,320 oil field, 900--901 Sediment fuel cell, 1140--1141 diarrheic shellfish poisoning, 380--381 oil field water system, 902 Sediment trap, 580 etiology of shellfish-associated out­ Slit impactor, 942 Sedimentary pore water, sampling, breaks, 311-314 Sludge 497--498 fecal contamination, 311-312 activated sludge processing, 672, 931 Seedts), endophytic bacteria, 640--641 neurotoxic shellfish poisoning, 380--381 bacteria, 300--310 Seed-processing industry, airborne bacteria paralytic shellfish poisoning, 379-380 beneficial uses, 351 and endotoxin, 991, 994 pathogen detection, selection and devel­ excellent-quality, 351 Selective filtration, isolation of protists, 81 opment of methods, 320--321 indicator organisms, 300 Selective medium, arthropod pathogens, protozoa, 311, 313-314 land application, 351, 355, 359-361 772-773 historical methods for concentration microbial source tracking, 307 Selenastrum capricamutum growth test, and detection, 315-316 monitoring 347-348 molecular methods for detection, ELISA, 306-307 Selenastrum capricamutum Printz algal assay 318 fluorescent-antibody methods, 306 bottle test, 342-343 viruses, 311-313, 319 molecular methods, 304-306 Selenite brilliant green, 302-303 historical methods for concentration most-probable-number method, 301 Selenite cysteine broth, 302-303 and detection, 315-316 plasmids, 763 Selenite dulcitol broth, 302-303 molecular methods for detection, Salmonella, 301-303, 306--307 Selenire-F broth, 302-303 317-319 sample collection, transport, and preser­ Selenium Shewanella vation, 301 aquatic environment, 541, 553 arsenate respiration, 1216, 1218-1219 viruses, 290-299, 359-361 connection to iron and manganese endophytic, 643 Sludge compost, airborne microorganisms, cycles, 553 iron reduction, 1242-1244 932 Selenomonas ruminantium, 115 manganese oxide reduction, 1233 Sludge digestion Self-organizing map, 669 metal cycling, 543 effectiveness, 336 functional gene array data, 1058 oil field, 900 wastewater treatment vs., 336 Seminested PCR, 677, 682--683 Shewanella algae, 117, 1243 Small round (featureless) virus, shellfish, Semivariogram plot, 786 ShewaneUa Federation medium, 1233 313,316 Semliki Forest virus, 964 Shewanella oneidensis, 1192, 1241-1244 Smallpox virus, 94, 1021 1286 • SUBJECT INDEX

SmartCET, 902 indicator molecules in soil extracts, bacteriophage, 623-624 Smoker poker, 580 656-660 concentration of viruses from soil elu­ Smut fungi, 1036, 1041 gene probes, 656-657 ates, 619-620 SNAP-BAC (selective nucleic acid poly­ lipid analysis, 656 elution of viruses from soil, 618-619 merase biotinvlation and capture) rapid screening methods, 658-659 plant pathogens, 624-625 method, contribution of major bac­ rRNA and rRNA genes, 657-658 reporting results, 619 terial groups to secondary produc­ stable-isotope probing, 659-660 sampling, 618-626 tivity, 427--428 isolate identification Soil block assay, brown rot fungi, 1123 Sneezing, 1018 colony morphology, 653-654 Soil core, 604-605 Snow Mountain agent, 223, 232 DNA fingerprinting, 655-656 arthropod collection, 771 Snowpack, long-time arctic research, 188 growth substrates, 654 Soil extract-based medium, protozoa, 84 Snow-shrub-soil-microbe feedback loop, lipid analysis, 654-655 Soil metagenomics, 660 188 rRNA,655 extraction and cloning of soil DNA, Sociomicrobiology, 28 landfill cover, 822 1063-1071 Sodium long-term research sites, 183, 185-188 library construction, 1063-1064 aquatic environment, 541 lysis of bacteria in, 684 bacterial artificial chromosome vec­ culture medium, 69 metabolic activity, 697-703, 748-757 tors, 1064 Sodium hypochlorite, water treatment, 329 metagenomics, see Soil metagenomics cosmid/fosmid vectors, 1064 Sodium thiosulfate, inactivation of halogen microarray analysis, 670-672 high-molecular-weight library, compounds, 254, 292, 294 functional genes in soil, 670-672 1063-1066 Software pathogen detection, 671-672 ligation of vector and insert DNA, image analysis, 48--49 rRNA genes, 670 1067 oligonucleotide probe design, microbial dispersal through, 14 low-molecular-weight library, 1054-1055 microhabitat, 652 1063-1066 primer prediction, 1082 mobile gene elements, 758-768 plasmid vectors, 1064, 1067 quality assurance, 193 modeling fate of microorganisms in, restriction digests, 1066 Soil, seealso Rhizosphere: Subsurface 355-364 transformation of E. coli, 1067 ammonia-oxidizing bacteria, 614-615 mycoremediation, 1097-1106 vector choice, 1064 anammox process, 693 nematodes, 772-77 5 vector preparation, 1064, 1066-1067 arbuscular mycorrhizal fungi, 627-637 nitrification, 690-691 library storage, 1067-1068 arthropod collection, 771 nitrogen cycling, 670, 687-696 Soil particulates, bacteria adherent to, 653 arthropod-microbe interactions, organic matter, 707, 770 Solar irradiance, viability of airborne 769-780 physical and biological complexity, 595 microbes, 961-962 carbon cycling, 707 reporter gene systems, 700-701 Solid-phase cytometry, protozoa, 274 cell extraction and recovery, 684 reporter gene systems for bacteria, Solid-state fermentation, 1107 centrifugation method, 717 734-747 fungal, see Fungal solid-state fermenta­ flocculation method, 716-717 sample processing, 604-606 tion system community structure, 595, 652-662, air drying, 604-606 Soluble reactive phosphorus 684, 777, 781-792 for microscopy, 41 marine environment, 523-527, 532-534 analysis of molecular data using tradi­ for PCR amplifications, 684 global patterns, 526-530 tional ecological approaches, sieving, 604, 606 12-MPA method, 523-524, 526 608-609 sample storage, 601, 603, 605, 618-619 Somatic coliphage, 251 assessing whether two communities sample transport, 605 Source waterfs), see also Surface waterls) differ, 611-613 sampling, 597-607, 618-626, 652 control of microorganisms, 325-333 constructing phylogenies, 609-611 bulk sample collection, 604-605 definition, 326 direct extraction of indicator mole­ coordinates of sampling site, 603 monitoring program, 327 cules, 656-660 equipment, 600, 603 protection and management, 325-328 DNA sequencing, 608-617 experimental design objectives, protozoa, 265-279 land use and, 785 598-599 sources of microbial contamination, metagenomic analysis, see Soil intact sample collection (soil core), 325-326 metagenomics 604-605 water treatment, 328 methods based on laboratory cultiva­ literature and internet resources, Source Water Assessment and Protection tion, 653-654 600-601 Programs (SWAPP), 914-921 phylogenetic analysis, 608-617 logistic needs, 598, 602-603 delineation of source water protection PLFA, 781-787 protocols, 600-601 areas, 914-918 processes governing community com­ sample containers, 605 determination of public water supply position and assembly, 613-614 site access considerations, 598 susceptibility, 919-921 sampling considerations, 652-653 site and scheduling needs, 598, 601 relationship to Groundwater Rule, strain identification, 654-656 soil collection approach, 599-601 920-921 cultivation of diverse strains, 654 statistical considerations, 598, source inventories in water protection denitrification, 692-693 601-602 areas, 918 DNA extraction from, 684 sterilization of sampling equipment, Souring, oil field, 898, 901-905 ecological proteornics, 709 603,619,771 nitrate to control, 904-905 enzymes, 704-711, see also Extracellular strategies, 598-599 Southampton virus, 232 enzymes, soil travel logistics, 603-604 Southern blotting, 142 FISH technique, 723-728 volumes of soil needed, 599 toxic metal resistance genes, 1174-1175 fungi, 787 strain isolation, 653 Soybean rust, 1032, 1036, 1040-1041, alpine tundra community, 615-616 substrate-induced respiration, 130-131 1043 horizontal gene transfer, 763-765 succession in microbial community, Soytone, 73 retrospective approaches, 763-765 706--707 Spartina altemij1ora, 474 identification of microbes involved in uncultured microorganisms, 654, 660 Spatial distribution pattern specific in situ functions, 748-757 variability over space and time, 652 modeling approaches, 214 immunofluorescence microscopy of soil­ viruses, 772-775 statistical analysis, 213-214 associated microbes, 712-723 animal viruses, 619-623 temporal-spatial correlations, 214 SUBJECT INDEX • 1287

Spatial sampling, 201 indicator molecules in soil extracts, StigmateUa, 23 Spearman rank order correlation, 207-208 659-660 Stimulated emission depletion microscopy, Species diversity, 9, 16 RNA-SIp, 1081 53,58-59 soil bacteria, 653 Staehybotrys Stomacher, 827 Species ecology, 6-7, 17 airborne, 975, 978 Storage rings, 1183-1184 Species evenness, 145-151 spore discharge, 974 Stover, substrate for fungal solid-state fer­ Species richness, 609 toxins, 979-981 mentation, 1109 molecular fingerprinting methods, Staehybotrys atra, 981 Stratified sampling, 201 145-151 Staehybotrys chartarum, 927, 929, 933, 955, Stratum, 201 soil bacteria, 653 973,975,980 Straw, substrate for fungal solid-state fer­ Sphacelotheca occidentalis, 1041 Staehybotrys microspora, 975 mentation, 1109 Sphaerotilus, 23 Staehybotrys nephrospora, 975 Stream, 393 Sphaerotilus-Leptothrix group, metal cycling, Stagonospora blotch, 1043 Streptococcus 545 Stalked bacteria, 23 airborne, 989, 991 Sphingobacterium, lipids, 114-115 Standard deviation, 204 morphology, 23 Sphingolipids, 115 Staphylococcus Streptococcus acidominimus, 250 Sphingomonas airborne, 989, 991 Streptococcus alactolyticus, 250 endophytic, 643 endophytic,642-643 Streptococcus bovis. 250, 253 lipids, 114-115, 117 freshwaters and drinking waters, Streptococcus equinus, 250 subsurface transport, 874-875 250-251 Streptococcus faecalis, 931 whole-genome probe, 143 Staphylococcus albus, 963 Streptococcus hyointestinalis, 250 Spiderweb, aerosol particles attached to, Staphylococcus aureus, 927, 956, 963, 989 Streptococcus intestinalis, 250 1017 freshwaters and drinking waters, Streptomyces Spinach white rust, 1043 250-251 airborne, 930, 933, 991 Spiral-shaped bacteria, 23 land-applied biosolids, 351 endophytic, 643 Spirochete, 28 marine recreational waters, 285 morphology, 23 Spirolactone, 980 waterborne, 226 Strombidium sulcacum, 457---458 Sponges, marine, biofilms on, 563-574 STARFISH (substrate-tracking autoradi­ Strontium Sporangiospore, 974 ographic FISH), 698-699 aquatic environment, 553 Sporets) Starvation mode, 13 connection to iron and manganese arbuscular mycorrhizal fungi, 627-628, Starvation response, 28 cycles, 553 631 Static column, subsurface microbial trans­ StructMiner, 161 environmental resistance, 13 port studies, 886-888 Structural equation models/path analysis, fungal, 75, 925,947,953-954,972,974, Station ALOHA (NPSG), 526-530, 208 977, 1032-1033, 1036-1041 533-536 Student's t distribution, 204-205, 211 allergens, 977 Statistical analysis, 39, 203-214 Study design, 199-203 discharge mechanisms, 973-974 assessing temporal and spatial patterns, associative study, 199,207-210 extraction from soil, 772 213-214 blocking, 202 inoculum for solid-state fermentation, comparative statistics, 202-203 comparative study, 199,202-203 1108 descriptive statistics, 199-207 controlled experimental protocols, P. chrysosporium, 1090-1091 exploring associations, 207-210 202-203 Spore trap sampler, 974 hypothesis testing, 210-213 descriptive study, 199-202 Sporobolomyces microbial survival studies, 356-357 measurement methods, 195 airborne, 975-976 PLFA fingerprints from soil microbial randomization, 202 spore discharge, 973 community, 782-784 replication, 202 Sporocytophaga, 23 risk of infectious disease from drinking sampling method, 195, 199-202 Sporomusa, 28 water, 365-376 Study factors, 202 Sporosarcina, 23, 28 selection of statistical test, 210 Study objectives, 199 Sporoschisma saccardoi, 975 soil sampling, 598, 601-602 Study quality, 195-197 Sporothrix schenckii, 977 Statistical model, 39 Subculture, isolates from high-throughput Sports facility, airborne viruses, 1024 Staurolite, nitrate-dependent microbial culture, 404---405 Spray-plating technique, 81 oxidation, 1151 Subjective determinations, 197 Spumella, 878 Steam sterilization, 73 Submersible operations, 580 Square bacteria, 23 Stemonitis, airborne, 976 Substrate-induced gene expression screen­ Squeezer (sampler), 498 Stemonitis ferruginea, 974 ing, soil microorganisms, 660 Sr. Louis encephalitis virus, 964 Stemphylium, plant pathogens, 1036 Substrate-induced respiration Stable isotope ratio, 395 Srenorropnomoncs CLPP based on, 129-131, 136 denitrification in subsurface, 864 airborne, 991 multiple, 130, 133-134 labeling strains for transport studies, endophytic, 643 Subsurface, see also Groundwater 880 subsurface transport, 873 aerobic respiration, 862-864 measurement of primary production, Stenotrophomonas maltophilia, 991 arsenic, 1214-1222 409 Stepwise multiple linear regression analy­ carbon dioxide, 861, 866 methanogenesis in subsurface, 866 sis, microbial survival calculations, chelators, 867 sulfate reduction in subsurface, 865 361 hydrogen gas, 866-867 Stable-isotope probing Stereological counting procedure, 42 interspecies hydrogen transfer, 866-867 aquifer microbes, 852-854 Sterigmatocystin, 980 metabolic activity, 795 arsenate-respiring bacteria, 1219 Sterilization microbial diversity, 795 biodegradation microorganisms, sampling equipment, 293-294,603,619 microbial transport, seeSubsurface 1081-1082 seawater, 401 microbial transport carbon metabolism in soils, 786 soil,771 modeling fate of microorganisms, CJ-metabolizing populations, 492 Sterols, see also Ergosterol 355-364 coupling with PLFA fingerprinting, community composition, 115 nitrate, 860-861, 864-865 786-787 indicators of fecal contamination, 252 organic compounds, 867-868 DNA-SIP, 1081 soil microbial community, 782 oxygen, 860,863-864 1288 • SUBJECT INDEX

Subsurface (continued) microprobe, 174 Suppressive subtraction hybridization, Tal redox reactions, 860 rate measurements genes and genomes mediating Ta sample processing, 808--809 jar technique, 498 biodegradation, 1082 To sampling, 795-796, 799---

Target statistic, 211 protists in aquatic environment, Thiosulfate Taxonomy, polyphasic, 157 461-462 electron donor fot photosynthesis, 505 Technetium soil microbial community, 608 measurement, 505 aquatic environment, 541 viruses in aquatic environment, 450 oxidation, 503-504 environmental chemistry and biogeo­ Terrestrial environment, long-term sulfur cycling in aquatic environment, chemistry, 1199-1200 research sites, 183, 185-188 497-510 measurement, 1199-1200 Terrestrial subsurface, seeSubsurface "Thiorurbo danicus," 503 oxidation states, 1199-1200 TES buffer, 74 Thiovulum, 23, 502 radiochemical techniques, 1198-1200 Test statistic, 210 Three-dimensional image reconstruction, Teflon ribbon, surface sampling, 947 Tetrachaetum elegans, 474 CLSM systems, 45,51-54,713 Teliospore, 1041 1.1,2,2-Tetrachloroethane, degradation in Thresholding, image processing, 49 Tellurium, toxic metal resistance, aquifer, 848 Thymidine incorporation into DNA 1166-1182 Tetrahymena. 265 deep-sea microorganisms. 585 Temperature culture, 84-85, 88 empirical conversion factor, 424, culture of algae, 83, 88 subsurface transport, 877 426-427 culture of amoebae, 86, 88 waterborne, 265 measurement of secondary production, culture of bacteria and fungi, 73 Tetrahymena rhermophila, 80 422-425,429-430 culture of flagellates and ciliates, 85, 88 Tetrathionate brilliant green broth, 302 rationale, advantages, and disadvan­ effect on viability of airborne microor­ Tetrathionate broth, 302 tages, 423-424 ganisms, 962 Tetrazolium salts, 55 TIck-borne virus, 927 high-pressure marine environment, Tetrazolium stain, endophytic bacteria, 645 TIFF file, 59 575-576 Texas Red, 713 Tilletia Temperature gradient gel electrophoresis Textile industry, airborne bacteria and plant pathogens, 1036, 1041-1042 arbuscular mycorrhizal fungi, 633 endotoxin, 991, 994 spore discharge, 973 bacteria in aquatic environment, 438 ThalassicoUa nucleara, 457-458.460 Time-of-flight neutron diffraction, man­ biodegradation microorganisms, 1080 Thallium. toxic metal resistance, ganese OXides, 1226 community structure analysis, 146, 149 1166-1182 Tin. toxic metal resistance, 1166-1182 hvphonwcetes, aquatic, 474 Thauera, 1081 Tintinnopsis pasva, 457-458, 460 indicator molecules in soil extracts. Thermoactinomyces, 23, 28 TItanium sampler, 580 658-659 Thermoactinomyces sacchari, 989 TItanium syringe, 580 methodology, 679 Thermoactinomyces rhalpophilus, 991 tmRNA, FISH targets, 725 Temperature gradient PCR, microeukarv­ Thennoactinomyces~garis,928.989, 991 Tobacco blue mold, 1036-1038, 1043 ote assemblages, 1113 Thermocyclet.676-677 Tobacco mosaic virus, 1034 Temporal distribution pattern Thermodesulfobacterium, 503 Toluene degradation modeling approaches, 214 Thennodesulfobacterium commune, 114 aquifer, 849-850 statistical analysis, 213-214 Thermodesulfovibrio, 503 landfill, 820 temporal-spatial correlations. 214 Themwmonas, iron-oxidizing, 1152 subsurface, 867 Terminal electron-accepting reaction Thermophile, 27 TO-PRO-l,47 aerobic respiration, 862-864 acidophiles, 1155, 1157 Toronto virus, 232 denitrification, 860--862, 864-865 culture, 87 Torula, plant pathogens, 1036 determination of electron-accepting Thermoplasma, 23. 1157 Total coliforms, 238-239 reaction. 863 Thermorogc, 27 definition, 249 humic acids, 867-868 morphology, 23 drinking water, 249-250, 255-256 hydrogen concentration, 866-867 signature lipids, 114 environmental freshwater, 249-250, iron reduction, 861-863, 865, 867-868, Thermotoga maritima, 117 255-256 1242 Thermorolerant coliforms, 250 marine recreational waters, 282 methanogenesis, 861-862, 866 definition, 250 membrane filtration method, 255-257 organic compounds, 867-868 drinking water, 250, 255-256, 258 most-probable-number method, 255-256 sequence of terminal electron acceptors, environmental freshwater, 250, presence-absence method, 257 860--861 255-256,258 Total dissolved phosphorus, marine envi­ subsurface, 796, 860--871 FC/FS ratio, 253-254 ronment.523-526,528,532 sulfate reduction, 861-862, 865-866 membrane filtration method, 255-257 Total organic carbon rest, wastewater treat­ Terminal RFLp, 184 most-probable-number method, 255-256 ment efficiency, 337, 341-342 aquifer microbes, 853 public health significance, 254 Total trihalomethanes, 330 arbuscular mycorrhizal fungi, 633 Thermus, arsenate respiration, 1216 Total viable microbial biomass, 112-113, bacteria in aquatic environment, Thiamine. culture medium, 71 120 437-438 Tbielaoia terrestris, 1107 TOTO-I,47 biofilm community, 564-565 Thin-section technology, soil, 700 Touchdown PCR, 677 community srructure analysis, 145-148, Thiobacillus denitri{icans, 1150 Tournament selection, 1074 186-187 "Thiobacillus !eTTooxidans," 1157 ToxAlerr, 346 denitrifying bacteria, 516 Thiobacillus thiooxidans, 117 Toxic metal resistance genes, 1167 endophytic bacteria, 645 Thioctic acid, culture medium, 71 DNA extraction from bacteria, 1173 fecal contamination of marine recre­ Thiodictyon, 1149 DNA extraction from environmental ational waters, 286 Thiomargarira, 23, 502-503 samples, 1172 hvphomvcetes, aquatic, 473-474 Thiomargarira namibiensis, 29 DNA hybridization, 1174-1175 indicator molecules in soil extracts, Thiomicrospira DNA sequencing, 1175-1177 658-659 oil field, 900-901, 905 gene function studies, 1177 iron-reducing bacteria. 1242 sulfur oxidation, 504-505 gene libraries, 1174 isolates from high-throughput culture, ThiomiCTospira denitri{icans, 900 gene regulation and expression studies, 404 Thiomonas. 1159-1160 1177 metal-reducing and metal-oxidizing bac­ Thiomonas cuprina, 1157 metal resistance operons, 1168 teria, 552 Thiomonasintenne~, 1157 PCR-based methods, 1175-1177 methodology. 679 ThiopWca, 29, 502-503 research strategies, 1168-1169 microeukaryote assemblages. 1116 Thiospirillum. 23 shotgun cloning, 1174 1290 • SUBJECT INDEX

Toxic metal resistance genes (continued) TEM-e1ectron energy loss spectroscopy, Ultrafiltration, virus concentration, Southern blotting, 1174-1175 1200, 1202 291 transfer of resistance to sensitive host viruses in aquatic environment, 445-447 Ultramicrobacteria, 22 strain, 1173-11 74 Transposase, 761 Ultrasonic mist machine, legionellae, transposition of resistance into plasmids, Transposition 1007-1008 1174 cut-and-paste, 761 Ulva lactuca, colonization ecology, 569 transposon mutagenesis, 1174 metal resistance genes into plasmids, Umezakia natans, 385 Toxic photosynthetic microbes, 378-390 1174 Unattended monitoring, measurement of Toxicity bioassay replicative, 761 primary production, 417--418 using algae, 347-349 Transposon Unbalanced growth, 426 using bacteria, 346-347 composite, 761 Unbiased estimation, 200-201 1 using fish or invertebrates, 345 conjugative, 763 Uncultured microorganisms, 21-22,37,76, , wastewater treatment efficiency, construction of inaZreporter gene sys­ 1079 , 335-336,342-349 tern, 740 airborne, 953-954 \ whole-effluent, see Whole-effluent toxi­ horizontal gene transfer, 761, 763 aquatic environment, 434--435 \ city bioassay mobilizable, 763 bioaerosols, 966 Toxicity identification evaluation, 346 noncomposite, 761 clone-FISH, 723-724 v Toxicity reduction evaluation, 346 Transposon mutagenesis, toxic metal resis­ magnetotactic bacteria, 1129-1132 Toxic-metal-resistant bacteria, 1166-1182 tance genes, 1174 seawater, 76 v cultivation, 1172-1173 Tray bioreactor, 1110 soil, 654, 660, 1063 V future directions, 1177-1178 Treatment (experimental protocol), 202 Undefined medium, 72-73 metagenomics, 1177-1178 Trehalose, bioaerosol stabilizer, 966 UNIFRAC, 613 metal toxicity, 1166-1167 Tribonema, culture, 88 United Nations Millennium Development postgenornic ("omic") technologies, Trichloroethene, degradation in landfill, Goals, 239 1178 820 United States, drinking water and recre­ VI research strategies, 1168-1169 Trichloroethylene, degradation in aquifer, ational freshwater standards, 254 resistance mechanisms, 1167-1168 848 Universal fast walking inverse PCR, genes "\ changes in cellular targets, 1168 TricluxJerma and genomes mediating biodegra­ efflux pump, 1168 airborne, 975-976, 978 dation, 1083 enzymatic reduction, 1168 spore discharge, 974 UPGMA,609 exclusion, 1168 toxins, 979-981 Upper quartile, 206-208 sequestration, 1168 water activity for growth, 973 Uranium sampling, 1169-1173 Trichoderma harzianum, 701 aquatic environment, 541, 553 Vi Toxin TricluxJerma viride, 1107 aqueous chemical speciation, 1197 avian vacuolar mvelinoparhv, 386 Trichodesmium, 387, 511-513, 518 aquifer, 854 cyanobacterial, 235, 383-386 Trichomonads, 27 connection to iron and manganese detection and identification, 387 Trichomonas hominis, 265 cycles, 553 Vic harmful algal bloom species, 379-383 Trichosporon cutaneum, 978 environmental chemistry and biogeo­ I removal from water, 235 Trichothecene, 980-982 chemistry, 1199-1200 Toxoplasma gondii, waterborne, 265, 276 Trichoverrol, 981 measurement, 1199-1200 ToxScreen-II, 346 Trickling filter, airborne microorganisms, oxidation states, 1199-1200 Trace metal solution, culture medium, 71 932 radiochemical techniques, 1198 Tracer Trimyema, maintenance methods, 85 Urea, culture medium, 72 aquifer biogeochemistry, 851 Trimyema minutum, 87 Uredospore, 1031, 1039 subsurface microbial transport studies, TRITC (rerramerhvl rhodamine isothio­ Urobilin, 252 881-882 cyanate), 46, 57, 713 Uronema marinum, 457--458 Trachipleistophora, 236, 266 Trophozoite, 266 Ustilago, plant pathogens, 1036, 1041 Training, to quality assurance require­ Trypanosoma, 14 Ustilago brumivora, 1041 ments, 192 Tryptic soy agar, 73, 953 Ustilago bullata, 1041 Vib Trajectory analysis, 1032 Tryptic soy broth, 73 Ustilago cynodontis, 1041 Vib Trametes oersicoior, 1102, 1107 Tryptone, 73 Ustilago kolleri, 1041 Vib Transcription-mediated amplification, Tullgren funnel, extraction of arthropods Ustilago maydis, 1041 ~ monitoring marine recreational from soil, 771 Ustilago mtici, 1041 c waters, 283-284 Tundra ecosystem, long-term research site, Ustulina vulgaris, 1107 d Transcriptomics, toxic-metal-resistant bac­ 188 UV light, water treatment, 228, 328-329 F teria, 1178 Tungsten carbide, geochemical tracer, 807 Uv-visible spectroscopy, radionuclides, sl Transduction, 759-760 Tunnel, sampling subsurface, 800, 810-811 1200 II generalized, 760 Turfgrass field, soil sampling, 599-604 II Transformation, bacterial, 759-760, 764 Tween 80, culture medium, 72 Vi!n natural,533 TWitching motility, 28 Vaccination, 374-375 Vi!n plants by endophytic bacteria, 647 Two-photon (2P) laser scanning Vaccinia virus, 94 Vi!n transfer of metal resistance genes, 1174 microscopy, 40, 43, 45--46 Vacuum sampling, 946-947, 997 Vi!n Transformation, biological, see Two-step PCR, 678 van Leeuwenhoek, Antony, 3 (I Biotransformation Two-way indicator species analysis Vanadium, aquatic environment, 541 w Transgenic crop, B. thuringiensis toxin, (TWINSPAN), 208-210 Variable, random, see Random variable 1035 Type I extreme value distribution, 204 Variance, 204 Vibr Transition metals, toxic-metal-resistant Type II extreme value distribution, 204 Varicella-zoster virus, 94 Vibr bacteria, 1166-1182 Tyromyces halsemeus, 1107 airborne, 1018 Vi!Jr, Transmission electron microscopy Varicellovirus, 94 Vilm cryo-TEM, 1203-1204 Variogram plot, 721, 786 Vi!m manganese-oxidizing bacteria, 1228 Ubiquinone, 116 Variola major virus, 927 sh metal-microbe interactions, 1201-1204, Ulocladium Variovorax, endophytic, 643 WI 1241 airborne, 927, 975 Vector, insect, see Insect vector Vibri radionuclides, 1200 water activity for growth, 973 Vector transmission, 13-14 bil SUBJECT INDEX • 1291

Vegetable-processing industry, airborne shellfish, 312, 314-317 nucleic acid probes, 94 bacteria and endotoxin, 991,994 waterborne, 366 ozone sensitivity, 331 Veillonella, 23 Vibroid,23 plaque assay, 96-97, 258, 298, 448-449, Veillonella parvula, 115 Vinyl chloride, degradation in subsurface, 620, 622--624 Venezuelan equine encephalitis virus, 964, 868 quantal assay, 97 1020 Virulence genes, microarray targeting, 671 macrotechnique (in flasks), 97 Venezuelan equine encephalomyelitis Virus, 12 microtechnique (multiwell plates), 97 virus, 927 airborne, 926,930-933, 1016-1030 safe handling, 93 Vent cap, 580 aerosol challenge studies, 1019-1021, sewage, 290-299 Vent catheter, 580 1024 shellfish, 311-313, 315-319 Venturia, plant pathogens, 1032, 1036 aerosol stability, 963-965 sludge, 290-299, 359-361 Venturia inaequalis, 1036, 1038 animal pathogens, 1022-1024 soil,772-775 Verrucomicrobia,76 bioaerosol generation, 1016-1017 animal viruses, 619--623 Verruculogen, 980 collection of naturally occurring bacteriophage, 623--624 VERTEX (Vertical Transport and aerosols, 1024 concentration of viruses from soil Exchange) research program, 531 exposing animal or human subjects eluates, 619--620 Verwey-Derjaguin-Landau-Overbeek to, 1018-1021 elution of viruses from soil, 618--619 theory, 873, 889 human pathogens, 1018-1022 plant pathogens, 624-625 Vesicular stomatitis virus, 964, 1019 long-distance transport, 1016, 1025 reporting results, 619 Viability indicators methods for study, 1016-1018 sampling, 618--626 analytical microscopy, 54--56 plant pathogens, 1033-1034 subsurface transport, 877 protozoa, 275 sampling, 1017-1018 UV inactivation, 328-329 soil microorganisms, 700 sources of viral aerosols, 1018 wastewater, 912-913 total viable microbial biomass, 112-113 aquatic environment waterborne Viability model, aerosolized microbes, abundance and diversity, 445-448 detection, 294--298 966-967 abundance of infectious viral popula­ pathogens, 223, 230-233 "Viable but nonculturable" microorgan­ tions, 448-449 sampling apparatus, 292-294 isms, 230 community structure, 445-453 Vitamin solution, culture medium, 70-71, aquatic environment, 434-435 denaturing gradient gel electrophore­ 401 drinking water, 375 sis, 450 Vitellogenin gene expression assay, 351 Vibrio, 570 DNA hybridization, 450-451 Vittaforma, 236, 266 wastewater, 349 fingerprinting of isolates, 449 Vivianite, 1147 Viable count genetic diversity, 447-450 Volatile organic compounds acidophiles, 1160 metagenomic analysis, 447-448 fungal, 972,982 airborne microorganisms, 953 nucleic acid staining, 445-446 microbial, 955 strains from transport studies, 878 PCR-based methods, 449-450 Volatile solids, landfill, 831 Vibrio population approaches, 448-451 Volcanic tuff, sampling, 810 biofilm formation, 570-571 pulsed-field gel electrophoresis, 448 Vomitoxin, seeDeoxynivalenol clinical syndrome, 225 terminal RFLP, 450 endophytic,642-643 total abundance, 445-446 lux genes, 170-171 transmission electron microscopy, Wallemia, 973 morphology, 23 445-447 Warts, 1021 motility, 28 assay, 298 Wastewater, 219 shellfish, 227,311-317,320 animal virus, 620-623 algae, 340-341 species identification, 158, 671 bacteriophage, see Bacteriophage antibiotic-resistant bacteria, 349-350 wastewater and sludge, 300 cell culture, 94--95, 316, 620--621, bacteria, 300-310 waterborne, 220, 222, 225-226, seealso Cell culture, virus assay enrichment and isolation, 301 229-230,366 chlorine inactivation, 330 bacteriophage, 913 Vibrio alginolyticus, 225, 570 concentration methods, 294--298 concentration methods, 301 Vibrio anguillarum, 570 affinity chromatography, 291 indicator organisms, 300 Vibrio cholerae, 927 cartridge filters, 292-293, 295-297 irrigation with, 618 biofilm formation, 570 directed adsorption, 291-292 land application, 912 clinical syndrome, 224 drinking water, 295-297 microbial source tracking, 307 drinking water, 367-369 environmental waters, 295-297 modeling fate of microorganisms in, PLFA,I13 flocculation and phase separation, 355-364 shellfish, 312, 314--315 291 monitoring wastewater and sludge, 303 passive adsorption, 291 ELISA, 306-307 waterborne, 224, 226, 229, 237, 366 sewage effluent, 295-297 fluorescent-antibody methods, 306 Vibrio cholerae, non-Ol , 312 ultrafiltration, 291 molecular methods, 304--306 Vibrio cholerae 01, 300 wastewater, 297-298 most-probable-number method, 301 Vibrio cholerae 0139, 237 wastewater sludge, 298 pathogens, 337,349,912 Vibrio fischeri cytopathic effect, 97, 298, 620-621 plant nutrients, 335, 342 colonization of light organ of squid, 570 detection methods, 93-96 protozoa, 340 whole-effluent toxicity bioassavs, disinfectant-related die-off, 292 Salmonella, 301-303, 306-307 346-347 drinking water, 365-376 sample collection, transport, and preser­ Vibrio fumissii, 570 electron microscopy, 93, 97, 445-447 vation, 301 Vibrio harveyi, 570 environmental waters, 290-299 virus concentration, 295, 297-298 Vibrio hollisae, 312 groundwater, 328, 812-813, 912 viruses, 618, 912-913 Vibrio mimicus, 225 identification, 98 Wastewater treatment, 221, 334--354 Vibrio parahaemolyticus, 225, 570 immunoassay, 93, 97-98 airborne bacteria and endotoxin, shellfish, 312, 314--317, 320 landfill, 912 990-992,994-995 waterborne, 366 marine environment, 450 airborne microorganisms, 926, 931-932 Vibrio vulnificus, 225-227, 259 marine recreational waters, 285-286 assessment of efficiency biofilms, 570 microarray detection, 671 algal growth test, 342-343 1292 • SUBJECT INDEX

Wastewater treatment (continued) protection of drinking water wells, peroxidases, 1108 biochemical oxygen demand test, 914-921 proteomic analysis, 1089-1096 335-341 protozoa, 231,234-237,265-279 WHO, drinking water and recreational chemical oxygen demand test, 337, recreational waters, 225-226, 280-289, freshwater standards, 254 341 365-366 Whole-effluent toxicity bioassay emerging issues, 349-351 routes of disease transmission, 219 biological end points, 344 indicator microorganisms, 335, 337, sewage, 290-299 flowthrough, 344 349 shellfish, seeShellfish interferences, 344-345 oxygen demand measurements, sludge, 300-310 static, 344 337-342 source waters, 325-333 using algae, 347-349 percent efficiency, 336 studies, 227-229 using bacteria, 346-347 total organic carbon test, 337, surveillance, 240 using fish or invertebrates, 345 341-342 toxic photosynthetic microbes, 378-390 variability, 344 toxicity bioassays,335-336, 342-349 United States, 1920-2001,912-913 wastewater treatment efficiency, waste load reduction, 336 unknown etiology, 237 343-349 biological, kinetic models, 338, 341 viruses, 223, 230-233, 290-299 Whole-genome DNA amplification, aquat­ objectives, 334-335 wastewater, 300--310 ic hyphomycetes, 474 pollutant removal and parameter reduc­ Waterborne infection, 225 Whole-genome shotgun sequencing, 394 tion, 335-336 Water-heating tank, 375 C)-metabolizing populations, 493 sludge digestion vs., 336 Water-immersible lens, CLSM, 46 targeted,493 Water, requirement of living things, 6 Waterloo sampler, 801-802 Widdel and Pfenning medium, 500--501 Water activity Watermelon anthracnose, 1043 Wind dispersal, fungi, 1032-1033 fungal growth and, 972-973 Watershed management, 326-327 Winkler iodometric method, oxygen in fungal solid-state fermentation system, Watershed Protection Approach (EPA), groundwater, 863 1108 325-326 Winkler method, measurement of primary high-pressure marine environment, Watershed quality assessment, 327 production, 413-414 577 Water-washed infection, 226 Winogradsky, S., 20 Water content, bioaerosols, viability of Weibull distribution, 204-205 Wire line rotary drilling, subsurface sam­ microbes and, 961-962 Well simulation, microbially enhanced oil pling, 802-804, 807 Water distribution system, 229 recovery, 906 Wolinella, arsenate respiration, 1216, 1219 legionellae, 1007 Well water, seealso Drinking water well; Wood water pressure in, 229 Groundwater degradation by brown rot fungi, Water indicator fungi, 975 arsenic, 1214-1222 1122-1128 Water resource management, 326 waterborne pathogens, 229, 237 structure, 1089 Water sampler, pressure-retaining, 579-580 Wellhead protection area, 914-918 substrate for fungal solid-state fermenta­ Water treatment delineation tion, 1109 advanced oxidation processes, 330-331 analytical method, 917-918, 921 Wood-degrading fungi, extracellular biological methods, 331 arbitrary-fixed-radius method, 915, enzymes, 1089-1096 chemical methods, 329-330 921 Work processes, quality assurance, 192-193 choosing treatment processes, 327-328 calculared-flxed-radius method, 915, Written procedures, 192 global problem, 239 921 inactivation of bacteria, 230 hydrogeologic mapping, 918, 921 inactivation of viruses, 230 numerical flow and transport models, x ravls), interactions with matter, 1185 in-home, 228, 238 918-919,921 X-ray absorption spectroscopy, 1184-1191 physical methods, 328-329 simplified variable shapes, 917 aqueous chemical speciation, 1197 Water-based infection, 226 source-driven radius, 915 data analysis, 1188-1191 Waterborne disease, 222-248 well-driven radius, 915-917 design of experiment, 1186-1190 aerosols, 227, 365-366 examples of wellhead protection regula­ EXAFS spectroscopy, 1185-1191, 1197, algae, 224,234-237 tions, 920 1206 bacteria, 223-224, 229-230, 233-234, sources of microbial contaminants, interactions of X rays with matter, 300--310 919 1185 body surface contact, 365-366 Western equine encephalomyelitis virus, microbe-mineral interface, 1206 classification, 226-227 927 optimizing XAS measurement clinical syndromes, 223-226 Wet sieving method, isolation of arbuscular data collection time, 1190 drinking water, 325-333, 365-376 mycorrhizal fungi from soil, 627 sample thickness, 1190 emerging infections, 231-237 Wheat leaf rust, 1036, 1039, 1043 radionuclide speciation, 1198 endemic, 228-229 Wheat stem rust, 1036, 1039 radionuclides, 1200 environmental waters, 290-299 Whirlpool spa, legionellae, 1007-1008, sample preparation, 1186 epidemic, 227-228 1012 synchrotron-based, 1184-1191, 1197 fungi, 234-237 White rot fungi, 1122, seealso XANES spectroscopy, 1185-1187, groundwater, 912-913 Phanerochaete chrysosporium 1190-1191, 1197,1206 helminths, 224 cytochrome P-450 monooxygenase, X-ray beamlines, 1184 ingestion of water, 223-224, 365-367 1100 X-ray diffraction marine waters, 280-289 laccase, 1101-1102 microbe-mineral interface, 1205-1206, outbreak surveillance, 227 lignin peroxidase, 1100 1241 parasites, 224, 226 lignin-degrading enzymes, 1098, powder, 1205-1206 prevention and control, 222, 237-240 1100--1101 X-ray fluorescence microprobe, 1191-1192 detection of infectious agents in manganese-dependent peroxidase, X-ray microscopy, synchrotron-based, water, 238 1100--1101, 1108 1191-1192 indicator organisms, 238-239 mycoremediation, 1097-11 06 X-ray photoelectron spectroscopy, microbe­ multiple-barrier approach, 239 PAH, 1100--1102 mineral interface, 1209, 1241 recommendations and research needs, PCDD/pcDF, 1098-1099 X-ray sources 239-240 tracking fungi in treated soils, storage rings, 1183-1184 risk assessment approach, 239 1102-1103 synchrotrons, 1183-1184

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