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Carbon Cycling CO Oxidation NitrogenNitrogen Fixation CyclingMetal Oxidation Biofilm/Quorum Phosphorus Solubulizing Phytohormone Producing Degrade Pesticides/Xenobiotics Domain Phylum Class Order Family Genus Species Compost TreatedControl Desert Total Count Specialty unclassified Antibiotic/Antimicrobial Production Archaea Thaumarchaeota Nitrosopumilales Nitrosopumilaceae Nitrosopumilus Nitrosopumilus maritimus 3,882 7,901 951 12,734 (Thaumarchaeota) Acidobacterium Acidobacterium capsulatum 2,631 3,534 1,147 7,312 Acidobacteria (class) Acidobacteriales Acidobacteriaceae Acidobacterium Acidobacterium sp. MP5ACTX8 1,418 1,639 254 3,311 Acidobacteria Solibacteres Solibacterales Solibacteraceae Candidatus Solibacter Candidatus Solibacter usitatus 17,913 22,435 9,691 50,039 Fe Cellulose Production unclassified unclassified unclassified Candidatus Koribacter Candidatus Koribacter versatilis 7,496 10,138 1,921 19,555 Acidothermaceae Acidothermus Acidothermus cellulolyticus 3,190 2,421 522 6,133 Actinomycetaceae Arcanobacterium Arcanobacterium haemolyticum 155 108 45 308 Cellulomonadaceae Cellulomonas Cellulomonas flavigena 2,226 1,255 19 3,500 Corynebacteriaceae Corynebacterium Corynebacterium glutamicum 767 481 38 1,286 Dermacoccaceae Dermacoccus Dermacoccus sp. Ellin185 684 424 9 1,117 Frankia sp. CcI3 2,895 2,157 229 5,281 F/S 15% of World Biologically Fixed N Frankia sp. EAN1pec 2,299 1,796 258 4,353 F Frankiaceae Frankia Frankia sp. EUN1f 1,148 822 70 2,040 F Frankia sp. EuI1c 1,685 1,434 243 3,362 F Frankia symbiont of Datisca glomerata 781 595 53 1,429 F Geodermatophilaceae Geodermatophilus Geodermatophilus obscurus 12,050 7,959 349 20,358 Mn Gordoniaceae Gordonia Gordonia bronchialis 1,006 588 30 1,624 Intrasporangiaceae Janibacter Janibacter sp. HTCC2649 2,792 1,921 70 4,783 Jonesiaceae Jonesia Jonesia denitrificans 909 457 5 1,371 Kineosporiaceae Kineococcus Kineococcus radiotolerans 4,486 2,799 92 7,377 Radiation Resistant/Self Re-assembling Clavibacter Clavibacter michiganensis 4,739 2,242 20 7,001 Microbacteriaceae Leifsonia Leifsonia xyli 4,001 1,679 46 5,726 Arthrobacter arilaitensis 1,042 377 31 1,450 Pesticides, Herbicides Degradation Arthrobacter aurescens 4,268 2,304 133 6,705 Atrazine Degradation Arthrobacter Arthrobacter chlorophenolicus 2,399 1,114 62 3,575 4-Chlorophenol Degradation Arthrobacter nitroguajacolicus 16 2 - 18 Cr Acrilonitrile Degradation Arthrobacter sp. FB24 4,837 2,635 160 7,632 Xylene Degradation Micrococcaceae Kocuria Kocuria rhizophila 1,928 752 23 2,703 Micrococcus Micrococcus luteus 1,440 565 24 2,029 Malathion & Chlopyriphos Degradation Renibacterium Renibacterium salmoninarum 1,593 847 14 2,454 Rothia Rothia dentocariosa 498 205 9 712 Rothia Rothia mucilaginosa 498 282 24 804 Micromonosporaceae Salinispora Salinispora tropica 7,392 6,293 176 13,861 Anti-cancer agents Mycobacterium abscessus 478 319 16 813 Actinomycetales Mycobacterium gilvum 1,371 906 84 2,361 Mycobacterium leprae 427 279 14 720 Actinobacteria Actinobacteria (class) Mycobacterium marinum 801 558 15 1,374 Mycobacteriaceae Mycobacterium Mycobacterium smegmatis 2,344 1,767 229 4,340 Mycobacterium sp. JLS 929 611 45 1,585 PAH & Pyrene Degradation w/ Humics Mycobacterium tuberculosis 1,783 1,284 59 3,126 Mycobacterium ulcerans 600 424 24 1,048 Mycobacterium vanbaalenii 1,957 1,315 149 3,421 PAH Degradation Nakamurellaceae Nakamurella Nakamurella multipartita 3,902 2,143 119 6,164 Nocardiaceae Rhodococcus Rhodococcus jostii 4,505 3,048 441 7,994 Toluene, Naphthalene,Herbicides, PCBs Degradation Aeromicrobium Aeromicrobium marinum 1,857 1,052 4 2,913 Alkanes Degradation Kribbella Kribbella flavida 4,524 2,998 280 7,802 Nocardioidaceae Nocardioides Nocardioides sp. JS614 11,260 7,472 1,126 19,858 Vinyl Chloride and Ethane Degradation Nocardiopsis Nocardiopsis dassonvillei 1,260 971 176 2,407 Antimicrobial, Anticancer, Immunomodulators Thermobifida Thermobifida fusca 2,926 2,290 308 5,524 Promicromonosporaceae Xylanimonas Xylanimonas cellulosilytica 1,783 834 49 2,666 Propionibacteriaceae Propionibacterium Propionibacterium freudenreichii 494 306 9 809 Cheese Production Amycolatopsis Amycolatopsis mediterranei 2,504 1,925 138 4,567 Saccharomonospora Saccharomonospora viridis 1,714 1,171 49 2,934 Pentachlorophenol Degradation Pseudonocardiaceae Saccharopolyspora Saccharopolyspora erythraea 5,922 4,329 372 10,623 Multidrug Resistant Thermobispora Thermobispora bispora 1,585 1,264 132 2,981 Sanguibacteraceae Sanguibacter Sanguibacter keddieii 2,005 893 14 2,912 Streptomyces albus 941 681 48 1,670 Streptomyces avermitilis 5,101 4,351 362 9,814 Streptomyces clavuligerus 694 583 75 1,352 Streptomycetaceae Streptomyces Streptomyces flavogriseus 613 306 25 944 Streptomyces lividans 3,100 2,757 151 6,008 Streptomyces sp. AA4 1,764 1,262 42 3,068 Streptomyces sp. ACT-1 1,471 828 23 2,322 Mycorrhiza Growth-Promoting Factor, Auxofuran Tsukamurellaceae Tsukamurella Tsukamurella paurometabola 650 414 9 1,073 Nematode Population Degrader Rubrobacterales Rubrobacteraceae Rubrobacter Rubrobacter xylanophilus 3,963 4,415 5,349 13,727 Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 6,844 6,453 1,330 14,627 unclassified (Actinobac.) unclassified (Actinobac.) unclassified (Actinobac.) marine actinobacterium PHSC20C1 2,876 1,509 16 4,401 Cyclobacteriaceae Algoriphagus Algoriphagus sp. PR1 8,013 6,073 80 14,166 Cytophagaceae Cytophaga Cytophaga hutchinsonii 6,961 8,711 1,150 16,822 Cytophagia Cytophagales Cytophagaceae Dyadobacter Dyadobacter fermentans 6,186 6,139 1,023 13,348 Flammeovirgaceae Marivirga Marivirga tractuosa 3,959 5,147 74 9,180 N2O Cytophagaceae Spirosoma Spirosoma linguale 6,158 7,098 999 14,255 UV and Gamma Radiation-Resistant Bacteroidetes Flavobacterium Flavobacterium johnsoniae 9,359 9,999 804 20,162 Bio-Control Phytophthora capsici Flavobacteria Flavobacteriales Flavobacteriaceae Flavobacterium Flavobacterium psychrophilum 3,390 3,356 147 6,893 Endophytic Gramella Gramella forsetii 3,890 3,514 495 7,899 Sphingobacteria Sphingobacteriales Sphingobacteriaceae Pedobacter Pedobacter saltans 1,157 1,069 175 2,401 Sphingobacteriaceae Pedobacter Pedobacter heparinus 3,890 3,510 1,502 8,902 N2O Sphingobacteria Sphingobacteriales Rhodothermaceae Rhodothermus Rhodothermus marinus 2,712 3,766 840 7,318 Chloroflexus Chloroflexus sp. Y-400-fl 3,352 3,341 481 7,174 Anaerobic Photosynthesis Chloroflexales Chloroflexaceae Roseiflexus Roseiflexus castenholzii 6,098 6,502 1,272 13,872 Anoxygenic Phototroph Chloroflexi (class) Roseiflexus Roseiflexus sp. RS-1 6,326 6,507 1,021 13,854 Chloroflexi Herpetosiphonales Herpetosiphonaceae Herpetosiphon Herpetosiphon aurantiacus 3,295 3,428 695 7,418 Ktedonobacteria Ktedonobacterales Ktedonobacteraceae Ktedonobacter Ktedonobacter racemifer 2,585 2,847 1,299 6,731 Sphaerobacterales Sphaerobacteraceae Sphaerobacter Sphaerobacter thermophilus 5,012 5,982 959 11,953 Thermomicrobia (class) Thermomicrobiales Thermomicrobiaceae Thermomicrobium Thermomicrobium roseum 2,740 3,204 796 6,740 unclassified Cyanobacteria Chroococcales unclassified Cyanothece Cyanothece sp. CCY0110 323 377 432 1,132 F (Cyanobacteria) Nostocales Nostocaceae Nodularia Nodularia spumigena 409 478 610 1,497 F Deinococcus-Thermus Deinococci Deinococcales Trueperaceae Truepera Truepera radiovictrix 1,790 1,543 251 3,584 Anoxybacillus Anoxybacillus flavithermus 904 715 74 1,693 Mn ≈ Ni < Zn < Cd < Pb ≈ Cu Bacillus megaterium 2,184 1,248 200 3,632 F BioControl/Endophyte Bacillus pumilus 1,027 803 83 1,913 Plant Growth Promoting/Endophyte Bacteria Bacillus Bacillus sp. B14905 833 384 14 1,231 Mosquito Control Bacillaceae Bacillus sp. SG-1 687 530 49 1,266 Mn Firmicutes Bacilli Bacillales Bacillus subtilis 2,572 1,991 169 4,732 Bo Lysinibacillus fusiformis 317 132 11 460 Bo Endophytic and Nematicidal Lysinibacillus Lysinibacillus sphaericus 965 448 14 1,427 Insecticidal/Mosquito Control Paenibacillus sp. JDR-2 1,081 795 74 1,950 Hardwood Depolymerization Paenibacillaceae Paenibacillus Paenibacillus sp. Y412MC10 906 704 111 1,721 Silicate, Phosphorus, Potassium Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatimonas Gemmatimonas aurantiaca 10,412 14,923 933 26,268 Nitrospira Candidatus Nitrospira defluvii 9,961 10,382 1,651 21,994 Perchlorate/Chlorate Reducing Nitrospirae Nitrospira (class) Nitrospirales Nitrospiraceae Thermodesulfovibrio Thermodesulfovibrio yellowstonii 748 977 1,183 2,908 Sulfate Reducing Blastopirellula Blastopirellula marina 6,496 7,657 778 14,931 Gemmata Gemmata obscuriglobus 7,971 7,884 1,849 17,704 Ammonium Oxidizers Pirellula Pirellula staleyi 8,414 10,167 913 19,494 Planctomycetes Planctomycetacia Planctomycetales Planctomycetaceae Planctomyces limnophilus 5,300 6,375 582 12,257 Planctomyces Planctomyces maris 4,392 5,111 271 9,774 Rhodopirellula Rhodopirellula baltica 8,791 10,463 1,534 20,788 Caulobacter Caulobacter sp. K31 2,041 2,313 4,564 8,918 Chlorophenol Degradation Caulobacterales Caulobacteraceae Caulobacter Caulobacter vibrioides 3,061 3,401 243 6,705 F Rhizobiaceae Agrobacterium Agrobacterium tumefaciens 2,895 2,820 352 6,067 Bradyrhizobium japonicum 5,036 5,346 1,453 11,835 Bradyrhizobiaceae Bradyrhizobium Bradyrhizobium sp. BTAi1 3,889 3,967 1,248 9,104 Chelativorans Chelativorans sp. BNC1 3,572 3,724 602 7,898 Phyllobacteriaceae Mesorhizobium Mesorhizobium loti 5,326 5,104 1,013 11,443 S Degrades Halogenated Aliphatic Pollutants Methylobacterium extorquens 1,922 1,706 364 3,992 Epiphyte Rhizobiales Methylobacteriaceae Methylobacterium Methylobacterium
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    Structural features of the vesicle of Frankia sp. CpIl in culture JOHNG. TORREYAND DALECALLAHAM Cabot Foundation, Harvard University, Petersham, MA, U.S.A.01366 and Department of Botany, University of Massachusetts, Amherst, MA, U.S.A.01003 Accepted March 16, 1982 TORREY,J. G., and D. CALLAHAM.1982. Structural features of the vesicle of Frankia sp. CpII inculture. Can. J. Microbiol. 28: 749-757. The filamentous bacterium Frankia sp. CpIl of the Actinomycetales, responsible for symbiotic nitrogen fixation in the nodules of certain woody dicots, also fixes dinitrogen when grown independently of the host in a nitrogen-free synthetic nutrient medium under aerobic conditions. In structural studies of Frankla grown in culture it has been shown that the bacterial filaments form vesicles, enlarged terminal endings in which the enzyme nitrogenase is formed. Microscopic examination of cultures shows that the vesicles possess a specialized envelope consisting of a number of thin layers or laminae which In polarized light show birefringence and in freeze-etch electron microscopy are resolved as multiple (12-15) laminae approximately 35-40 A (1 A = 0.1 nm) in thickness. Comparisons are made between the structure of the veslcle envelope in cultured Frankia and the ; strikingly similar innermost laminated layer in the dinitrogen-fixing heterocysts of the cyanobacterium Anabaena. Comparable protective functions in limiting oxygen to the dinitrogen-fixing sites are suggested for these similar structures in two quite unrelated microorganisms. 1 TORREY,J. G., et D. CALLAHAM.1982. Structural features of the vesicle of Frankia sp. CpIl in culture. Can. J. Microbiol. 28: 749-757. I La bactkrie filamenteuse Frankia sp.
  • UNIVERSITY of CALIFORNIA, SAN DIEGO the Comparative Genomics

    UNIVERSITY of CALIFORNIA, SAN DIEGO the Comparative Genomics

    UNIVERSITY OF CALIFORNIA, SAN DIEGO The Comparative Genomics of Salinispora and the Distribution and Abundance of Secondary Metabolite Genes in Marine Plankton A Dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Marine Biology by Kevin Matthew Penn Committee in charge: Paul R. Jensen, Chair Eric Allen Lin Chao Bradley Moore Brian Palenik Forest Rohwer 2012 UMI Number: 3499839 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent on the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. UMI 3499839 Copyright 2012 by ProQuest LLC. All rights reserved. This edition of the work is protected against unauthorized copying under Title 17, United States Code. ProQuest LLC. 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, MI 48106 - 1346 Copyright Kevin Matthew Penn, 2012 All rights reserved The Dissertation of Kevin Matthew Penn is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Chair University of California, San Diego 2012 iii DEDICATION I dedicate this dissertation to my Mom Gail Penn and my Father Lawrence Penn they deserve more credit then any person could imagine. They have supported me through the good times and the bad times. They have never given up on me and they are always excited to know that I am doing well. They just want the best for me.
  • Downloads (Downloaded on December Expected Length, 253 Bp) After Trimming Were Used for Further 04, 2014)

    Downloads (Downloaded on December Expected Length, 253 Bp) After Trimming Were Used for Further 04, 2014)

    fmicb-07-00579 April 21, 2016 Time: 15:32 # 1 View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Frontiers - Publisher Connector ORIGINAL RESEARCH published: 25 April 2016 doi: 10.3389/fmicb.2016.00579 Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem Eric R. Johnston1, Luis M. Rodriguez-R2,3, Chengwei Luo2, Mengting M. Yuan4, Liyou Wu4, Zhili He4, Edward A. G. Schuur5, Yiqi Luo4, James M. Tiedje6, Jizhong Zhou4,7,8* and Konstantinos T. Konstantinidis1,2,3* 1 School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA, 2 Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology, Atlanta, GA, USA, 3 School of Biology, Georgia Institute of Technology, Atlanta, GA, USA, 4 Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA, 5 Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA, 6 Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA, 7 Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA, 8 State Key Joint Laboratory of Environment Edited by: Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China Brett J. Baker, University of Texas at Austin, USA How soil microbial communities contrast with respect to taxonomic and functional Reviewed by: composition within and between ecosystems remains an unresolved question that M. J. L. Coolen, Curtin University, Australia is central to predicting how global anthropogenic change will affect soil functioning Kasthuri Venkateswaran, and services. In particular, it remains unclear how small-scale observations of soil NASA-Jet Propulsion Laboratory, USA communities based on the typical volume sampled (1–2 g) are generalizable to *Correspondence: ecosystem-scale responses and processes.