Index A Allium cepa, 244 Abelmoschus esculentus, 244 Amaranthus, 244, 279 Acacia, 244 A. hypochondriacus, 219 Acaciella angustissima, 167, 172 Amazon, 65, 310 Acaulospora, 124, 244 Ambrosia dumosa, 113 A. laevis, 244 Aminobacter, 167 A. scrobiculata, 244 Ammonia-oxidizing archaea (AOA), Acetobacter, 240 145, 149 Acid Ammonia-oxidizing bacteria (AOB), carboxylic, 97 145, 149 citric, 216 amoA gene, 145 gluconic, 130 Amplified ribosomal DNA restriction organic, 215–217 analysis (ARDRA), 146 Acidithiobacillus, 214, 221 Anabaena, 145, 147, 148, 151 A. ferroxidans, 214 Andropogon, 99 A. thiooxidans, 214 Arachis hypogaea, 88, 96, 98, 244 Acidobacteria, 152 Archaeopora, 124 Actinobacteria, 215 Artemisia Adesmia bedwellii, 115 A. herba-alba, 124 Aeschynomene, 172, 174 A. tridentata, 110, 123 Africa, sub-Saharan, 82 Arthrobacter, 141 Agave, 117 Ascomycetes, 121 A. datilyo, 112 Aspergillus, 242 A. deserti, 125 A. awamor, 220 Agriculture, 83, 185, 235, 299, 312 A. niger, 220 terrace, 304 Atlantic Coastal Rainforest, 65 Agrobacterium, 166 Atriplex A. rhizogenes, 246 A. confertifolia, 123 A. tumefaciens, 167 A. halimus, 124 Agroforestry, 73–75, 185–202 Axonopus, 99 Agromonas, 167 Azoarcus, 152, 154 Alcaligenes, 144 Azolla, 147, 148 317 318 Index Azorhizobium, 168 B. brasilensis, 240 A. caulinodans, 145, 172, 173 B. cepacia, 215 Azospirillum, 126, 144, 147, 152, 220 B. tropica, 69, 240 A. amazonense, 69, 240 B. vietnamiensis, 141, 241 A. brasilense, 129, 131, 240 A. lipoferum, 240, 241 Azotobacter, 144, 147, 220 C A. armeniacus, 147 Caatinga, 75 A. chroococcum, 219, 240 Calliandra calothyrsus, 192, 199 A. nigricans, 147 Calothrix elenkenii, 151 A. paspali, 240 Capsicum annuum, 244 Carbon cycling, 47, 194 B d13C composition, 18 Bacillus, 118, 141, 144, 175, 212 qCO2, 29, 34–36 B. circulans, 220 sequestration, 150–151, 194 B. coagulans, 222 Carica papaya, 245 B. fusiformis, 142 Carrichtera annua, 121 B. megaterium, 217, 218, 220, 221, 243 Cenchrus ciliaris, 191 B. subtilis, 220 Ceratocephalus testiculatus, 115 Beauveria, 98 Ceratoides lanata, 123 Beijerinckia fluminensis, 240 Cerrado, 11, 65, 75, 239 Beneficial microorganism, 87, 89, 97–100. Chara vulgaris, 149 See also Mycorrhizal fungi; Nitrogen- Chelator, 214–215 fixing bacteria; Phosphate-solubilizing Chorispora tenella, 115 bacteria; Plant growth-promoting Chroococcidiopsis, 125 bacteria Citrobacter, 144 Biofertilizer, 67, 69, 87, 100, 147, C. koseri, 222 211–215, 217, 226, 235, 238 Climate Biofilm, 214 change, 123 Biofuel, 174 pulsed, 195 Biogeography, 259–264 tropical, 2–3, 88 Biological crust, 118–123 Clostridium, 147 restoration, 128–129 C. bifermentans, 141 Bioremediation, 285–286 Coffea Biotechnology, 227 C. arabica, 88, 245 Blastobacter, 167 C. robusta, 88 Brachiaria, 99, 197, 239 Cola, 88 B. decumbens, 245 Coleogyne ramosissima, 121 B. humidicola, 74 Collema, 121 Bradyrhizobium, 145, 166, 168, 172, 237 Commission for Technical Co-operation B. betae, 167 in Africa, 8 B. elkanii, 72 Community B. japonicum, 35, 72, 173 composition, 59, 116, 265 Brazil, 65 distribution, 115, 259 Brucella, 167 diversity, 59, 66–67, 140–146, Burkholderia, 68, 144, 147, 152, 170, 263–264 172, 212 function, 51, 53, 85, 263 Index 319 resilience, 52 E response to disturbance, 51, 55, 57 Earth spirit, 299 structure, 51, 56 Echinocereus, 117 study by culture-independent methods, Ecosystem, 59 50, 141, 142, 146 Elaeis guineensis, 88, 97 turnover, 266 Elosine coracana, 219 Emericella, 242 Conservation. See Soil Endemism, 262 Cratylia argentea, 239 Endophyte, 117, 130, 174–176, 240 Crop diversity in rice, 142, 152–155 contamination, 279, 289, 291 Ensifer, 166 loss, 254 Enterobacter, 212 tropical, 253 E. absuriae, 222 Crotalaria, 95, 99 E. agglomerans, 215 Crust. See Biological crust Enterolobium, 172 Cryptosporidium, 278 Entrophospora, 124 Culture medium E. colombiana, 244 pH, 223 Enzyme P-solubilizing bacteria isolation, 222 chitinase, 154 Cupriavidus, 167, 170, 173 chitosanase, 151 Cyanobacteria, 120, 125, 129, 143, 145, endoglucanase, 155 147, 149, 151 extracellular activity, 54, 56 gluconokinase, 130 glucosidase, 54 D lignase, 56 Dacryodes edulis, 88 ligninase, 154 Dalbergia nigra, 199 nitrogenase, 116, 149, 151 Daucus carota, 70 phosphatase, 54, 196, 215, 242 Deforestation, 84 phosphogluconate dehydrogenase, 130 Deinococcus, 152 phytase, 217, 242 Denaturing gel gradient electrophoresis reductase, 56 (DGGE), 50, 57, 141 urease, 54 Denitrification, 56, 126 xylanase, 151 Derxia, 144 Epiphyte, 126 Desert, 109 Equatorial rainforest, 18 biota, 118, 132 Eremopyrum orientale, 115 restoration, 127–132 Erwinia, 175 Devosia, 168 Erythrina, 74 Diazotroph. See also Nitrogen-fixing Escherichia, 212 bacteria E. coli, 276, 279, 284 Ethnopedology, 304 diversity, 143–145 Eucalyptus grandis, 75 non-symbiotic, 240–241 Exopolysaccharide, 214 symbiotic, 237–239 Dichanthium aristatum, 190 Dioscorea, 88 F Disease, 277, 284 Fagopyrium esculentum, 219 Diversity. See Community Faidherbia albida, 198 Dolichos, 99 Fatty-acid methyl esters (FAME), 49–50, 52 320 Index Ferocactus acanthodes, 125 Herbaspirillum, 147, 153, 240 Fertility island. See Resource island H. rubrisubalbicans, 69, 240 Fertility management, 100, 237 H. seropedicae, 69, 154, 240, 241 integrated soil fertility management Hevea brasiliensis, 75 (ISFM), 84 Himalayas, 1 Ficus palmeri, 116 Horizon, 9 Fluorescent in situ hybridization (FISH), argic, 8, 11 141 argillic, 8, 11 Food insecurity, 82, 209 ferralic, 7, 10 Fouquieria columnaris, 124 nitic, 11 Fungi, 56. See also Mycorrhizal fungi oxic, 7, 10 Fusarium oxysporum, 76, 97 plinthic, 13 Human influence on ecosystems, 5, 18, 45 G knowledge, 299, 302, 312 Garcinia kola, 88 population, 45, 86 Gemmatimonadetes, 125 Humid forest, 83, 88, 91, 94, 99–100 Gigaspora G. gigantea, 245 G. margarita, 99 I Gliricidia sepium, 190 Innovation, 309 Glomalin-related soil protein (GRSP), Inoculant, 235 193, 197 commercial, 238, 242 Glomus, 124 field trial, 241 G. aggregatum, 245 multi-strain, 241 G. clarum, 99 mycorrhizal, 202, 243–245 G. constrictum, 115 production of, 245 G. deserticola, 98 rhizobia-based, 171–172, 237 G. etunicatum, 244, 245 Integrated pest management, 85, 251 G. fasciculatum, 221 International Center for Tropical G. intraradices, 244, 246 Agriculture (CIAT), 242, 244 G. manihotis, 220, 245 Ipomoea batatas, 88, 244 G. mosseae, 221, 245 Irrigation, 275, 288–289 G. proliferum, 246 Irvingia gabonensis, 88 G. spurcum, 245 G. vermiforme, 246 K Gluconacetobacter diazotrophicus, 69, 240 Klebsiella, 118 Glycine max, 66, 95 K. planticola, 141 Gnetum, 88 K. pneumoniae, 173 Greenhouse gas, 194 K-strategist, 192 Guadua angustifolia, 244 L H Lablab, 172 Health risk, 276–277, 279, 280, 283–285 Lactuca sativa, 70, 219 reduction of, 285–292 Land Helianthus annuus ssp. jaegeri, 126 agricultural superficies, 45, 46 Helminth, 278, 279, 287 arid, 109, 111 infection, 276, 283 grading, 286 Index 321 marginal, 209 Methylobacterium, 68, 146, 152, 168 use and conversion, 29, 32, 35, 45, 55, Methylocaldum, 146 81–102 Methylocella, 146 Lasiurus sindicus, 126 Methylococcus, 146 Laterite, 13. See also Plinthite Methylocystis, 146 Leeia oryzae, 142 Methylomicrobium, 146 Legume, 75, 93–97, 110, 147 Methylomonas, 146 domesticated species, 164 Methylosinus, 146 evolution, 163–165 Microcoleus, 129 seed protein content, 165 Micromonospora, 215 symbiosis establishment, 165–167, Mimosa caesalpinifolia, 72 239 Moss, 128 Lemaireocereus thurberi, 114 Mucuna, 93, 95, 99 Leucaena, 165, 172, 244 M. pruriens, 176 L. diversifolia, 166, 191 Musa, 88, 244, 246 Leymus secalinus, 127 Mycelium network, 189–191 Lichen, 118 Mycobacterium, 141 Ligand, 216 Mycoplasma, 167 lin genes, 264 Mycorrizal fungi, 87, 91–93, 186, 220, 243 Lophocereus schottii, 112, 131 within agroforestry system, 185–202 Lotus, 239 concept of parasitic behavior of, 189 L. japonicus, 173 density in soil, 91 Lycopersicum esculentum, 244 diversity, 90 effect on plant health, 197 effect on soil structure, 193–194 M impact on soil fertility, 53, 195 Machaerocereus gummosus, 114 inoculation assays, 89, 91–93, 98, 101, Macroptilium atropurpureum, 94 220, 244 Magic, 302 in vitro culture, 246 Mammillaria fraileana, 116–118, 130 within limiting environment, 123–125 Manguifera indica, 88 mycelium network, 189–191 Manihot esculenta, 75, 88, 244 within resource island, 113–115 Medicago truncatula, 173, 175 response of plant to, 91, 93, 192, 244 Medium. See Culture medium response to disturbance, 52 Melilotus, 239 restoration action, 129–132 Meloidogyne, 98, 155 Mythology, 302 Mesorhizobium M. loti, 10, 39, 166, 173 Metal N bioaccumulation, 280 nif genes, 120, 144, 155, 173 toxicity, 197, 280–281 Nitrification, 149 Metarhizium, 89, 98 Nitrogen Methane, 140, 146 biological fixation, 120, 147, 165, 188, emission reduction, 150 237–241 Methanogen, 145–146 contribution of biological crust to, 122 Methanomicrobiales, 146 cycling, 143–145 Methanotroph, 145–146, 150 excess, 282 Methylobacter, 146 15N abundance, 191, 240 322 Index soil content, 30 P. microphylla, 130 transfer between plants, 191 P. praecox, 116 Nitrogen-fixing bacteria, 67–69, 87, Passiflora edulis, 244 93–97, 168, 198, 211. See also Pathogen Diazotroph detection, 279 diversity, 96, 144, 168 level reduction methods, 286, 287, 291, inoculation assays, 89, 95, 96, 100, 292 219–220 survival, 277–279 Nitrosomonas europaea, 145 transfer to crops, 279 Nod factor, 172 wastewater contamination, 276–277, nod genes, 173 283 Nodulation, 172–174 Penicillium, 242 Nostoc, 119, 120, 145, 151 P. bilaii, 243 nosZ gene, 56 Pennisetum, 99 Nutrient Persea americana,