Beneficial microbes in agro-ecology. Bacteria and fungi

Front Cover......Page 1
BENEFICIAL MICROBES IN AGRO-ECOLOGY......Page 2
BENEFICIAL MICROBES IN AGRO-ECOLOGY......Page 4
Copyright......Page 5
Contents......Page 6
Contributors......Page 14
Preface......Page 22
I - Bacteria......Page 24
  1. Introduction......Page 26
  3. Isolation and identification of Arthrobacter genus......Page 27
  5. Siderophore production and metal solubilization by Arthrobacter......Page 28
  6. Role of Arthrobacter in bioremediation......Page 29
  8. Conclusion......Page 31
  References......Page 32
  1. Taxonomy......Page 36
   4.1 In vitro test of A. faecalis No. 4 against plant pathogens......Page 37
    4.2.1 Growth and products of A. faecalis No. 4......Page 38
    4.2.3 In vitro tests of the products......Page 40
    4.2.4 Production of a nonhydroxylamine-producing mutant of A. faecalis No. 4 and in vitro tests......Page 41
   4.3 Plant test using A. faecalis No. 4 and nonhydroxylamine-producing mutant, A. faecalis No. 4-1......Page 42
   4.5 Additional experiment......Page 45
   4.6 Harvesting of massive numbers of A. faecalis No. 4 from wastewater treatment......Page 46
  References......Page 48
  1. Introduction......Page 50
  2. Taxonomy of the genus Serratia......Page 51
  3. Isolation of the genus......Page 52
  4. Characterization and identification of the genus......Page 53
   5.1 Biological control potential......Page 54
   6.1 Other plant growth-promoting activities......Page 55
  References......Page 56
  1. Introduction......Page 60
  3. Physiologic aspects of rhizobia......Page 61
   4.1 Nitrogen fixation......Page 63
   4.2 Abiotic stress tolerance......Page 64
    4.3.1 Indole-3-acetic acid......Page 66
    4.3.3 Cytokinins......Page 67
   4.5 Phosphate solubilization......Page 68
   4.6 Siderophore production......Page 69
   4.7 Biocontrol abilities of rhizobia......Page 70
  References......Page 72
  2. Taxonomy of Streptomyces......Page 78
  3. Isolation of Streptomyces......Page 80
  4. Identification of Streptomyces......Page 81
  5. Beneficial role of Streptomyces in ago-ecology: in vitro PGP and biocontrol traits of the Streptomyces......Page 82
  6. In vitro physiologic traits of the Streptomyces......Page 83
  8. In planta biocontrol traits of the Streptomyces......Page 84
  10. Streptomyces research at ICRISAT......Page 85
  Acknowledgments......Page 90
  References......Page 91
 6 - Azospirillum......Page 96
  1. Taxonomy of Azospirillum......Page 97
  2. Isolation of Azospirillum......Page 98
  3. Biochemical and genetic methods for the identification of Azospirillum......Page 101
   4.1 Plant growth-promoting properties......Page 107
   4.2 Biofilm production and colonization of plant roots......Page 110
   4.3 Use as biofertilizer......Page 112
   4.4 Abiotic stress tolerance induction: salinity and water stress......Page 116
   4.6 Biofortification......Page 118
   4.7 Biocontrol......Page 119
  5. Concluding remarks......Page 120
  References......Page 121
 7 - Bacillus......Page 130
  1. Taxonomy of Bacillus......Page 131
   1.1 Bacillus taxonomy based on 16S rRNA gene......Page 132
   1.2 Bacillus taxonomy based on core genomes......Page 135
   2.1 History......Page 136
    2.1.2 Isolation of Bacillus anthracis (anthrax) by Robert Koch: the first pure culture of a bacterium......Page 137
    2.2.1 Soil and seawater......Page 138
    2.2.3 Plant inner tissues (endophytes)......Page 140
   3.1 Gram staining, morphology, and spore formation......Page 141
    3.1.1 Gram staining procedure......Page 142
    3.2.1 Motility......Page 146
    3.3.1 Yellow egg (lecithinase) reaction......Page 147
    3.4.3 Indole formation......Page 148
    3.6.1 Standard media......Page 149
     3.6.3.3 Citrate and propionate utilization medium......Page 150
   4.1 Plant and microbiota as a holobiont......Page 151
  References......Page 152
  1. Introduction......Page 156
  2. Historical perspective of Pseudomonas and their classification......Page 157
  3. Role of Pseudomonas as PGPR in agriculture......Page 158
    3.1.1 Nutrient mobilization......Page 159
    3.1.2 Production of plant growth regulators......Page 160
    3.2.2 Antibiotics production......Page 161
    3.2.4 Induced systemic resistance in host plant......Page 163
  4. Role of Pseudomonas in biodegradation of pesticides......Page 164
  References......Page 165
   1.1 Historical developments......Page 172
   1.2 Taxonomic structure......Page 173
   2.1 Underlying principle of enrichment and isolation......Page 176
   2.2 Selective media......Page 177
   3.1 Identification of the genus Brevibacillus......Page 178
   3.2 Polyphasic identification......Page 179
   4.1 Plant growth-promoting properties......Page 181
   4.2 Biocontrol agent......Page 182
   4.3 Bioremediation......Page 183
  References......Page 185
  1. Introduction/taxonomy......Page 192
   1.1 The genomes of Exiguobacterium......Page 193
  2. Isolation of the Exiguobacterium genus......Page 194
  3. Identification of the Exiguobacterium genus......Page 195
    3.1.1 Degradation of complex substances......Page 197
   4.1 Role of Exiguobacterium as plant growth enhancer......Page 198
    4.1.1 Interaction of bacteria with plant root......Page 199
    4.1.5 Siderophore production......Page 200
    4.2.2 Enhancement of plant antioxidant system......Page 201
  5. Future prospects......Page 202
  Acknowledgments......Page 203
  References......Page 204
  1. Introduction/taxonomy......Page 208
   1.2 Taxonomy of Frankia......Page 209
   2.1 Morphologic characteristics of Frankia spp.......Page 210
   2.4 Vesicles......Page 211
   2.6 Biochemical properties of Frankia......Page 212
   2.9 Isolation and cultivation of Frankia......Page 213
   2.11 Isolation on liquid medium......Page 214
    3.1.2 Scanning electron microscopy......Page 215
    3.1.6 Propagation of Casuarina......Page 217
    3.1.8 Benefits of Casuarina......Page 218
    3.2.1 Structure of root nodules using phase contrast microscope......Page 221
    3.2.2 Hydroponic conditions for root nodulation kinetics......Page 222
    3.2.4 Structure of root nodules......Page 223
    3.3.1 Screening of IAA......Page 224
    3.4.2 Quantification of siderophore......Page 225
    3.5.3 Siderophores......Page 226
   4.1 Nitrogen fixation......Page 227
   4.3 Erosion control......Page 228
   4.6 Fuel and timber production......Page 229
  References......Page 230
  1. The order Enterobacteriales......Page 236
   1.1 Enterobacteriaceae family......Page 237
   1.2 Kosakonia clade and Kosakonia genus......Page 239
  3. Participation of Kosakonia spp. as plant growth promoter......Page 240
   3.1 Kosakonia radicincitans......Page 243
   3.2 Kosakonia sacchari......Page 246
   3.3 Kosakonia arachidis......Page 249
  4. Other species of Kosakonia......Page 250
  References......Page 251
   1.1 Historical developments......Page 256
   1.2 Taxonomic structure......Page 259
   2.1 Underlying principles......Page 260
   2.2 Selective media......Page 261
   3.1 Identification of Klebsiella at the genus level......Page 262
   3.3 Identification based on molecular methods......Page 264
   4.1 Plant growth-promoting properties......Page 268
   4.2 Biocontrol......Page 270
   4.3 Phytoremediation......Page 271
   4.4 Bioremediation......Page 272
  References......Page 274
  2. Taxonomy......Page 282
  5. Characteristics of the Enterobacter as plant growth promoters......Page 285
   5.2 Nitrogen fixation......Page 286
   5.4 1-Aminocyclopropane-1-carboxylic acid deaminase......Page 287
  6. Bioremediation......Page 288
  8. Conclusions......Page 289
  References......Page 290
  1. Introduction......Page 294
  2. Taxonomy and some other features of Burkholderia sensu lato......Page 295
   3.1 Ecology and genome structure......Page 300
   4.1 General overview of the study of plant growth promotion abilities......Page 308
   4.2 Plant growth promotion abilities focused on members of the genus Paraburkholderia......Page 309
    4.3.1 Plant-Paraburkholderia interactions under gnotobiotic conditions......Page 317
    4.3.2 Paraburkholderia spp. growth chamber and greenhouse assays......Page 322
    4.3.3 Field trials with Paraburkholderia spp. as bioinput......Page 323
  References......Page 324
  1. Taxonomy of Lysobacter, a 40-year-old bacterial genus......Page 336
  2. Ubiquity of Lysobacter species and their ecology in the agroecosystem......Page 341
  3. Correlation of Lysobacter spp. with soil suppressiveness and isolation of bacterial strains belonging to plant beneficial s .........Page 342
  4. Plant beneficial role of Lysobacter spp. relies on multiple mechanisms of action......Page 346
  References......Page 354
  1. Introduction......Page 362
   2.1 A brief history......Page 363
   2.2 Reclassification of different genera......Page 364
   3.1 Nitrogen fixation......Page 365
   3.2 Phosphate solubilization......Page 366
   3.4 Production of siderophores......Page 367
   3.6 Biocontrol agent......Page 368
   3.7 Promotion of host defense mechanism......Page 369
  4. Paenibacillus sp. in Exopolysaccharide production......Page 370
  5. Genetic engineering-based modification of Paenibacillus......Page 371
  6. Paenibacillus in bioremediation of xenobiotics......Page 372
   6.1 Paenibacillus sp. for hydrocarbon bioremediation......Page 373
   6.2 Paenibacillus for removal of Polyaromatic hydrocarbons (PAHs)......Page 374
   6.3 Paenibacillus against heavy metal......Page 375
  References......Page 377
  1. Introduction......Page 386
   2.4 Beneficial role in agroecology......Page 387
   3.4 Beneficial role in agroecology......Page 400
   4.2 Isolation......Page 401
   4.4 Beneficial role in agroecology......Page 402
   5.3 Identification......Page 403
   6.2 Isolation......Page 404
   6.4 Beneficial role in agroecology......Page 405
   7.4 Beneficial role in agroecology......Page 406
   8.4 Beneficial role in agroecology......Page 407
   9.4 Beneficial role in agroecology......Page 408
   11.1 Taxonomy......Page 409
   12.1 Beneficial role in agroecology......Page 410
  Acknowledgments......Page 413
  References......Page 414
  1. Introduction......Page 420
   1.1 Azotobacter taxonomy......Page 421
   1.2 Distribution of Azotobacter......Page 422
   1.4 Molecular characterization......Page 423
   1.6 The general characteristic of Azotobacter......Page 424
  2. Isolation of the genus......Page 426
   2.1 Preservation of Azotobacter......Page 427
  3. Identification of the genus......Page 428
    3.1.2 Cyst induction and cyst staining......Page 429
   3.2 Confirmatory test for identification of Azotobacter sp.......Page 430
    3.2.1 Azotobacter chroococcum......Page 431
    3.2.2 Azotobacter vinelandii......Page 432
    3.2.3 Azotobacter beijerinckii......Page 434
    3.2.5 Azotobacter paspali......Page 435
    3.2.6 Azotobacter armeniacus......Page 436
   4.1 Mechanism of crop productivity benefit......Page 437
   4.2 Role of Azotobacter in crop productivity......Page 439
    4.2.5 Biopolymers as a soil conditioner......Page 440
    4.3.3 Siderophore production by Azotobacter......Page 443
  References......Page 444
  1. Introduction......Page 450
  3. Isolation and maintenance of Stenotrophomonas spp.......Page 451
  4. Morphological and biochemical properties of Stenotrophomonas spp.......Page 453
  5. Plant growth–promoting attributes of Stenotrophomonas spp.......Page 455
   5.2 Phosphate solubilization......Page 456
   5.3 Production of plant growth regulators......Page 457
   5.4 Siderophore production......Page 458
   5.6 Biocontrol potential......Page 459
  6. Bioremediation by Stenotrophomonas spp.......Page 460
  7. Biofortification......Page 461
  References......Page 462
  1. Introduction......Page 466
   2.1 Terrestrial environment......Page 467
   2.2 Aquatic environment......Page 468
   3.1 Substrate mycelia......Page 469
   3.2 Aerial mycelia......Page 470
   3.3 Spore chain morphology and spores......Page 472
  4. Taxonomy and molecular morphology of Actinobacteria......Page 474
  5. Isolation of Actinobacteria......Page 477
   5.2 Isolation of endophytic actinobacteria......Page 479
   6.1 Optimal temperature range......Page 480
   6.2 Optimal pH range......Page 482
   6.6 Enzyme production......Page 483
   6.8 Antibiotic susceptibility......Page 486
   7.1 Plant growth promotion......Page 487
      7.1.1.1.1 Indole acetic acid production......Page 488
      7.1.1.1.3 Nitrogen fixation......Page 489
     7.1.2.1 Siderophore production......Page 490
     7.1.2.4 Cell-wall degrading enzymes......Page 491
   7.2 Biocontrol agents......Page 492
  References......Page 493
  1. Introduction......Page 500
  2. Taxonomy of the Clostridium genus......Page 501
  3. Isolation and identification methods......Page 502
  4. Plant growth–promoting Clostridium......Page 503
   4.1 Nitrogen fixation......Page 504
   5.1 Bioethanol......Page 506
   5.2 Biohydrogen......Page 507
   5.3 Acetone and butanol......Page 508
  2. Taxonomy of the most agriculturally important entomophthoralean genera......Page 0
  References......Page 510
  1. Taxonomy......Page 516
  2. Ecology......Page 518
  3. Isolation procedures......Page 521
  4. Simple biochemical and molecular methods for identification......Page 522
  5. Beneficial roles in agroecology......Page 525
  References......Page 528
  1. Taxonomy of Methylobacterium......Page 532
  2. Methylobacterium interaction with plants......Page 533
  4. Selective media......Page 534
  5. General method for identification of Methylobacterium......Page 535
   8.1 Plant growth promotion by Methylobacterium......Page 536
   8.2 Biocontrol potential of Methylobacterium......Page 537
   8.3 Heavy metal tolerance and phytoremediation......Page 538
  References......Page 539
  1. Introduction......Page 544
  3. Isolation and growth of Gluconobacter......Page 545
  4. Taxonomy of Gluconobacter......Page 547
   4.2 Gluconobacter albidus sp. nov.......Page 548
   4.4 Gluconobacter cerinus sp. nov.......Page 549
   4.7 Gluconobacter kanchanaburiensis sp. nov.......Page 550
   4.8 Gluconobacter kondonii sp. nov.......Page 551
   4.10 Gluconobacter roseus sp. nov.......Page 552
   4.13 Gluconobacter oxydans subsp. industrius......Page 553
   4.16 Gluconobacter thailandicus sp. nov.......Page 554
   4.18 Gluconobacter wancherniae sp. nov.......Page 555
  5. Gluconacetobacter diazotrophicus......Page 556
  6. Role of Gluconobacter in the agroecosystem......Page 557
    6.1.2 Phytohormones production......Page 558
    6.1.4 Siderophore production......Page 559
   6.3 Gluconobacter as biocontrol agent......Page 560
    6.3.1 Antagonistic activity of G. diazotrophicus against phytopathogens......Page 561
  References......Page 562
  2. Taxonomy and reorganization of the genus Thiobacillus......Page 568
  3. Thiobacillus and its interactions with the physical environment......Page 569
   4.1 Thiobacillus and sulfur nutrition to crop plants......Page 572
   4.2 Thiobacillus and P nutrition in crop plants......Page 573
  5. Industrial importance......Page 574
   5.2 Bioflotation......Page 575
  6. Conclusion and future perspectives......Page 576
  References......Page 577
II - Fungi......Page 582
  2. Phylogenetic relationships......Page 584
  4. Identification of AM fungal spores......Page 585
  5. General morphological characters used for identification of AM fungal spores......Page 586
  6. Beneficial role......Page 588
  References......Page 589
  1. Introduction......Page 594
    1.1.1 Morphology-based taxonomic history of Trichoderma......Page 595
   2.1 Macroscopic characters......Page 596
  3. Isolation of Trichoderma spp.......Page 597
     4.1.1.1 Vegetable crops......Page 599
    4.1.2 Growth promotion by mineral solubilization and nutrient uptake......Page 600
    4.1.3 Growth promotion by secondary metabolites......Page 601
  5. Trichoderma used as biocontrol agent in agriculture......Page 602
   5.2 Antibiosis......Page 603
   5.3 Competition......Page 604
  6. Roles in biofortification......Page 605
  7. Roles in bioremediation......Page 606
  References......Page 607
   1.1 Entomopathogenic organisms......Page 616
   3.1 Culture plate method......Page 617
   3.2 Insect bait method......Page 619
   4.2 Spodoptera litura as model insect pest for bioassay......Page 620
   5.1 Destruxins......Page 621
  7. Mechanism of pathogenicity in insect......Page 624
  9. Characterization of cyclodepsipeptides......Page 625
   10.1 Biopesticide......Page 626
   10.2 Plant growth promoter activity......Page 627
  12. Conclusion......Page 628
  References......Page 629
  1. Introduction......Page 634
  2. The genus Aspergillus......Page 635
  3. Aflatoxins......Page 636
  4. The biocontrol......Page 638
   4.1 Biological control applied to peanut and corn crops......Page 639
  References......Page 642
  1. Introduction......Page 648
   1.1 Ganoderma species at a glance......Page 649
   2.1 Morphologic characters......Page 650
   2.2 Cultural characters......Page 651
   2.3 Identification key was prepared to differentiate the collected species of Ganoderma (Bhosle et al., 2010)......Page 654
  3. Diversity and distribution of Ganoderma......Page 655
  4. Host range......Page 657
   5.1 Subculturing (serial transfer)......Page 662
   6.1 Qualitative screening of fungal isolates for ligninolytic enzymes......Page 663
  7. Benefits......Page 664
   7.1 Commercial products of Ganoderma......Page 665
   7.2 Side effects......Page 667
  9. Future prospects......Page 668
  References......Page 669
  1. Introduction......Page 674
   2.1 Morphologic characterization......Page 675
   2.3 Chemotyping......Page 676
  4. Plant endophytic Penicillium......Page 677
  5. Phosphate solubilization by Penicillium......Page 678
   6.1 As antagonistic/biocontrol agent......Page 679
  7. Penicillium in soil suppressiveness......Page 680
  8. Penicillium in alleviation of abiotic stresses......Page 681
   9.1 Bioremediation......Page 682
  10. Bad members of Penicillium for human beings......Page 683
  References......Page 685
  1. Taxonomy......Page 692
  2. Isolation and mass production......Page 695
  3. Pochonia chlamydosporia for the control of nematodes......Page 697
  4. The plant-growth promotion by Pochonia chlamydosporia......Page 699
  5. Final considerations......Page 701
  References......Page 702
  1. Taxonomy......Page 706
  2. Isolation and mass production......Page 707
  3. The action of Duddingtonia flagrans on gastrointestinal nematodes......Page 708
  5. Duddingtonia flagrans promoting plant growth......Page 713
  6. Final considerations......Page 714
  References......Page 715
  1. Introduction......Page 718
  2. Distribution......Page 719
  5. Molecular identification......Page 720
     5.1.1.2 CTAB lysis buffer......Page 721
   6.1 Biological weathering and nutrients mobilization......Page 722
    6.2.1 Phytoremediation of cadmium......Page 723
    6.2.2 Phytoremediation of lead......Page 724
    6.4.1 Auxin......Page 726
  References......Page 727
  1. Introduction......Page 730
  2. Effect on plant growth, nutrition, and physiology......Page 732
  3. Response to drought......Page 738
  4. Response to soil contamination......Page 740
  References......Page 744
  2. Beauveria bassiana (Balsamo) Vuillemin......Page 750
  4. Beauveria bassiana in agriculture......Page 751
  5. Economic importance of pests in livestock and poultry production systems......Page 752
  6. Potential for biological control of livestock and poultry pests......Page 753
  8. Combinatorial studies of Beauveria bassiana with other entomopathogens for pest control......Page 754
  10. Beauveria bassiana as a biological control agent of pests of crops......Page 757
  12. Endophytic B. bassiana as a biological control agent of plant pests......Page 759
  14. Endophytic B. bassiana as a biological control of plant pathogens......Page 760
  15. Conclusions......Page 761
  References......Page 762
  1. Stropharia......Page 772
  2. Stropharia taxonomy......Page 773
  3. Isolation of Stropharia fungi......Page 774
  4. Beneficial uses of Stropharia......Page 775
  References......Page 776
  1. Introduction......Page 780
  4. Microbial control potential of entomophthoroid fungi......Page 783
   4.1 Batkoa spp.......Page 785
   4.2 Conidiobolus spp.......Page 786
   4.4 Entomophthora spp.......Page 787
   4.5 Neozygites spp.......Page 788
   4.7 Zoophthora spp.......Page 789
  5. Influence of environmental factors on fungal epizootics......Page 790
  6. Artificial introduction of entomophthoroid fungi......Page 791
  References......Page 792
  1. Introduction......Page 800
  2. Characteristic features, taxonomy, and identification of Pythium......Page 801
  3. Beneficial activities of Pythium spp.......Page 802
  5. Futuristic approach on Pythium spp.......Page 809
  References......Page 810
  1. Introduction......Page 816
  3. Taxonomy and phylogeny......Page 818
  5. Description of genus Purpureocillium......Page 821
  7. Colony morphological features......Page 822
  8. Key features......Page 823
  10. Biocontrol agent......Page 824
  11. Conclusion......Page 827
  References......Page 828
  1. Introduction......Page 832
  2. Taxonomy......Page 833
  3. Isolation of Dactylella......Page 834
   4.1 Biocontrol agent......Page 837
  References......Page 838
  2. Phylum ascomycota and dueteromycota......Page 840
    2.1.1 Taxonomy and Classification of Hirsutella spp.......Page 841
    2.1.2 Morphology......Page 842
    2.1.4 Isolation of Hirsutella thompsonii from the citrus rust mite......Page 843
    2.1.7 Phylogenetic analysis......Page 844
  3. Nutritional studies on the genus Hirsutella......Page 845
   3.1 Insecticide activity......Page 846
    3.1.1 Beneficial role......Page 847
    3.1.2 Mode of action of Hirsutella......Page 849
    4.1.1 Mass production......Page 850
    4.1.2 Formulation of fungal pesticides......Page 851
  5. Conclusion......Page 852
  References......Page 853
  1. Introduction......Page 856
  2. Historical developments in Ampelomyces research......Page 857
  3. Taxonomy of Ampelomyces......Page 858
   4.1 Identification of Ampelomyces......Page 860
   4.3 Cultivation of Ampelomyces......Page 861
  5. Biology and life cycle of mycoparasite......Page 863
   5.1 Overwintering of Ampelomyces quisqualis......Page 864
  6. Diversity of ampelomyces species and its host range......Page 865
  7. Applications of Ampelomyces in agriculture......Page 867
  8. Mode of action of Ampelomyces quisqualis on mycohost......Page 870
   8.1 Mycoparasitism/hyperparasitism of Ampelomyces quisqualis......Page 872
   8.3 In vivo biocontrol of powdery mildew......Page 873
  9. Ampelomyces quisqualis production and formulation development......Page 875
  11. Future prospects......Page 876
  References......Page 877
  A......Page 884
  B......Page 890
  C......Page 894
  D......Page 898
  E......Page 900
  F......Page 902
  G......Page 904
  H......Page 906
  I......Page 908
  K......Page 910
  L......Page 911
  M......Page 912
  N......Page 915
  P......Page 917
  R......Page 926
  S......Page 927
  T......Page 931
  V......Page 933
  Z......Page 934
Back Cover......Page 936