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, 88 balance, 88, 236 Peruvian Amazon, 263 cycling, 47, 53, 140 Pest, 253 microbial transformation, 140 Pesticide, 251 within rice rhizosphere, 147–152 biodegradation genes, 264 degradation, 251, 265 dissipation, 266–268 O fungicide, 256 Olneya tesota, 112 herbicide, 256 Ontology, 307 impact, 152, 253–254 opd gene, 264 insecticide, 256 Opuntia market, 256–259 O. cholla, 116 usage, 255–262 O. ficus-indica, 125 Phaseolus vulgaris, 167–171, 219, 239 O. sulphurea, 112 Phenolic compound, 217 Oryza O. officinalis, 155 Phormidium, 145 O. sativa, 142, 153–154 Phosphate rock, 100, 214, 221 Phosphate-solubilizing bacteria, 196, 212 inoculation assays, 97, 217–221, 224–226 P isolate, 212 Pachycereus pringlei, 114, 116, 128, 131 molecular detection, 224 Pachycormus discolor, 116 phenotype MPS+, 212, 224 Pachyrhizus erosus, 214, 221 Phosphate-solubilizing fungi, 220 Paenibacillus, 212 Phosphate-solubilizing micro-organisms, P. chitinolyticus, 131 87, 89, 97, 212, 242. See also P. polymyxa, 218 Mycorrizal fungi; Phosphate- Panicum, 99 solubilizing bacteria; Pantoea, 152, 212 Phosphate-solubilizing fungi P. agglomerans, 152, 155 Phospholipid, 49 Paraglomus, 124 fatty acids (PLFA), 50, 52, 57, 142 P. occultum, 245 Phosphorus, 210, 242 Parkinsonia acquisition by mycorrizal fungi, 194–197 P. florida, 130 fixation, 11, 12, 211 Index 323

mobilization mechanism, 213, 224 Pueraria, 172 organic mineralization, 215 P. lobata, 176 soil content, 30 P. phaseoloides, 221, 239, 245 transfer between plants, 191 Pythium, 155 Phyllobacterium, 169 P. aphanidermatum, 98, 151 Phytohormone, 212 P. myriotylum, 98 Phytophthora P. cinnamomi, 98 P. megakarya, 97 R Phytoremediation. See Bioremediation Radopholus similis, 98 Pinus radiata, 194 Rahnella, 212 Piptadenia, 172 Ralstonia Planctomycetes, 125, 144 R. solanacearum, 98 Plant R. taiwanensis, 167 health, 97–99, 197 Reboudia pinnata, 121 mycoheterotrophic, 190 Resource island, 109–118, 128 mycotrophic, 192 Restriction fragment length pioneer, 116 polymorphism (RFLP), 96, 141, 144 response to mycorrizal fungi, 91, 93, Revegetation, 111, 127, 131 192, 244 Rhizobia, 163 salt tolerance, 291 density in soil, 94, 116 systemic resistance, 212 diversity, 72, 166, 168–170 Plantago coronopus, 121 endophytic colonization, 155, Plant growth-promoting bacteria, 69–71, 174–176 129–132, 211, 218, 241 inoculation assays, 68, 145, 199, 218 Pleosporales, 121 legume symbiosis, 165–167, 239 Plinthite, 13 N fixation ability, 68, 144, 147, 237 pmoA gene, 146 nodulation genes, 172 Poaceae, 69 non-symbiotic strains, 167 Pongamia pinnata, 174 P-solubilizing ability, 212 Porlieria chilensis, 113 taxonomy, 166 Prosopis, 172 Rhizobium, 126, 152, 169, 198, 243 P. articulata, 112, 114, 130 R. cellulosilyticus, 167 P. chilensis, 130 R. daejeonense, 167 P. flexuosa, 110 R. etli, 171, 173, 175 P. glandulosa, 126 R. gallicum, 166 P. laevigata, 115 R. leguminosarum, 173, 175 P. velutina, 112 R. selenireducens, 167 Protozoa, 143, 287 R. tropici, 72, 166, 171, 176 Pseudomonas, 69, 98, 118, 141, 142, 144, Rhizoctonia solani, 70, 76, 152 212, 219, 220 Rhizodeposition, 223 P. alcaligenes, 142 Rhizosphere, 141, 211 P. fluorescens, 69, 70, 97, 216, 219 Rhizospheric micro-organism, 141 P. pseudoalcaligenes, 126, 142 associated with N plant nutrition, P. putida, 69, 70, 218 148 P. striata, 220 associated with P plant nutrition, P. stutzeri, 126, 144, 152 212, 213 324 Index

Rice, 139 fauna, 4, 71–72, 194 rhizosphere, 140–146 fertility, 17 r-strategist, 192, 223 flooded, 145, 215 forest, 25–26 formation, 1–2, 5–8 S Fragiudult, 221 Saccharum, 244 halomorphic, 13 Salinization, 282 hydraulic conductivity, 7, 10 Salmonella, 279 illuviation, 7, 11 Savanna, 11, 23–24, 239 leaching, 6, 11 Schinella, 167 microbial biomass, 20–29, 31, 32, Sclerotium rolfsii, 70 34–36, 47–49, 85, 126, 143, 186 Scutellospora, 124 microbial community, 17, 49–52, S. heterogama, 245 66–67, 85–86, 264–265 Scytonema, 119 moisture, 2, 6, 9, 13, 252, 265 Serratia, 212 organic carbon, 25–26, 29, 30, 34–36, S. marcescens, 152, 154 47, 48, 143 Sesbania, 175 organic matter, 30, 34, 47–49, 236 S. macrantha, 192 organization, 300 S. rostrata, 172 parent material, 3 S. sesban, 192 pH, 29, 265 S. virgata, 199 regolith, 4 Sesquioxide, 7, 211 respiration, 28, 29, 31, 33–34, 48, Shinella, 170 49, 56 Siderophore, 70, 214 rubefication, 12 Single strand conformation science, 300–301 polymorphisms (SSCP), 70 stability, 120 Sinorhizobium, 166, 169 structure, 193 S. chiapanecum, 172 temperature, 2, 262, 265 S. meliloti, 173 texture, 3 S. mexicanum, 172 traditional knowledge, 299–303 Slash-and-burn agriculture, 81–102 tropical, 1, 9–14, 20–26, 37, 202, Soil 236, 252 acid, 119, 210 Soil classification or taxonomy system, aggregation, 48, 193, 194 8–9, 303 alkaline, 126 CCTA Soil Map of Africa, 9, 11 ATP, 29, 31, 36–37 USDA Soil taxonomy system, 8 biological crust, 118–123 World Reference Base for Soils (WRB) burning, 84, 91 (see also Slash-and- system, 9 burn agriculture) Soil order/soil class calcimorphic, 13 Acrisols, 88 cation exchange capacity, 7, 10, 91 Alfisols, 11, 12, 222, 225 clay, 7, 29 Alisols, 12 conservation method, 67–76, 201, Andisols, 18, 34 304, 305 Andosols, 91 degradation, 46, 306 Argissols, 70 eluviation, 7 Ferralsols, 9, 88, 90, 95, 96, 98, 210 ergosterol, 29, 31, 36–37 Inceptisols, 34, 49, 219 Index 325

Latosols, 72 Tortula desertorum, 129 Lixisols, 12 Trichocereus pagacana, 117 Mollisols, 304 Trichoderma, 98, 243 Nitisols, 12 Tropics, 1, 18, 19, 29, 210, 252 Oxisols, 9, 18, 30, 91, 210, 214, 221 Planosols, 70 Ultisols, 11, 12, 18, 210, 219, 220 V Vertisols, 13, 34, 225 Veronica campylopoda, 115 Solanum, 99 Vigna, 172, 244 S. tuberosum, 220 V. subterranea, 94 Sorghum bicolor, 198, 214 V. unguiculata, 67, 94, 95 Sphenostylis stenocarpa, 244 Virus infection, 276, 284 Staphylococcus, 118 Visible-Near Infra Red (VIS-NIR), 143 S. gummosus, 112 S. thurberi, 112, 116, 131 Streptomyces, 116, 215 W Striga, 98 Wastewater S. hermonthica, 198 diseases associated, 277 Stylosanthes, 95, 99 field management, 286–287 Suillus luteus, 194 irrigation, 275, 288–290 Symbiosis, 165, 174, 201, 312 treatment, 285–292 Synergism, 199 Water. See also Wastewater Syntrophobacter fumaroxidans, 146 in biological crust, 119 Syzygium cumini, 72 infiltration, 121 salinity, 291 T in soil, 6 Tamarix, 115 Weathering, 6 Technology transfer, 101, 227, 236 Wetland, 140 Terminal restriction fragment length polymorphism (TRFLP), 50, 144, 146 Terra Preta do Indio, 304 X tfd genes, 264 Xanthosoma sagitifolia, 88 Theobroma cacao, 74, 88, 245 Thermus, 152 Thiobacillus thiooxidans, 214 Z Tillandsia recurvata, 126 Zea mays, 219 Topography, 4 Zygophyllum dumosum, 114