Effects of Soil Environment on Field Efficacy of Microbial Inoculants



Although many microorganisms show good performance in specific trials, this is often not translated into consistent, effective plant growth promotion and biocontrol in diverse field situations. The key factors involved in the lack of success are rapid decline in the size of populations of active cells to levels ineffective to achieve the objective and variable production of required metabolites or poor colonization, following the introduction into soil. The physical, chemical, and physicochemical nature of soil and its indigenous microorganisms and predators influence the microbial population both quantitatively and qualitatively. Soil abiotic factors (e.g., texture, pH, temperature, and moisture) exert their (direct) effect on inoculant population dynamics by imposing stresses. On the other side, trophic competitions and antagonistic/synergic and predatory interactions with the resident microbial and fauna populations determine the field efficiency of inoculants. The aim of this review is to throw light on different soil environmental conditions that affect the survival of inoculated microbial strains in the field. A proper characterization of target soils and rhizospheres as habitats for introduced microbes is a key to the development of bioformulations that support beneficial microorganisms in the soil.


Microbial Community Microbial Biomass Soil Microbial Community Osmotic Potential Arbuscular Mycorrhiza 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



EK is grateful to Vice Chancellor, Chhatrapati Shahu Ji Maharaj University, Kanpur, India, for providing facilities and support while NKA to VC, BBA University, Lucknow.


  1. Abd Alla MH, Abdel Wahab AM (1995) Survival of Rhizobium leguminosarum bv. viciae subjected to heat, drought and salinity in soil. Biol Plant 37:131–137Google Scholar
  2. Adl SM, Acosta-Mercado D, Anderson TR, Lynn DH (2006) Protozoa. In: Carter MR, Gregorich E (eds) Soil sampling and methods of analysis, 2nd edn. CRC Press, Boca RatonGoogle Scholar
  3. Allison SD, Wallenstein MD, Bradford MA (2010) Soil-carbon response to warming dependent on microbial physiology. Nat Geosci 3:336–340Google Scholar
  4. Al-Niemi TS, Kahn ML, McDermott TR (1997) P metabolism in the Rhizobium tropici-bean symbiosis. Plant Physiol 113:1233–1242PubMedPubMedCentralGoogle Scholar
  5. Antoun H, Prevost D (2005) Ecology of plant growth promoting rhizobacteria. In: Siddiqui ZA (ed) PGPR: biocontrol and biofertilization. Springer, Dordrecht, pp 1–38Google Scholar
  6. Arora NK, Singhal V, Maheshwari DK (2006) Salinity induced accumulation of poly-β-hydroxybutyrate in rhizobia indicating its role in cell protection. World J Microbiol Biotechnol 22:603–606Google Scholar
  7. Arora NK, Khare E, Singh S, Maheshwari DK (2009) Effect of Al and heavy metals on enzymes of nitrogen metabolism of fast and slow growing rhizobia under explanta conditions. World J Microbiol Biotechnol 26:811–816Google Scholar
  8. Ashman MR, Puri G (2002) Essential soil science: a clear and concise introduction to soil science. Blackwell Science Ltd., Oxford, p 208Google Scholar
  9. Baker GH (2007) Differences in nitrogen release from surface and incorporated plant residues by two endogeic species of earthworms (Lumbricidae) in a red-brown earth soil in southern Australia. Eur J Soil Biol 43:S165–S170Google Scholar
  10. Balser TC, Wixon DL (2009) Investigating biological control over soil carbon temperature sensitivity. Global Change Biol 15:2935–2949Google Scholar
  11. Bamforth SS (1997) Protozoa: recycling and indicators of agroecosystem quality. In: Benckiser G (ed) Fauna in soil ecosystems. Dekker, New York, pp 63–84Google Scholar
  12. Bardgett RD (2005) The biology of soil. Oxford University Press, OxfordGoogle Scholar
  13. Bashan Y (1998) Inoculants of plant growth-promoting bacteria for use in agriculture. Biotechnol Adv 15:729–770Google Scholar
  14. Beare MH, Coleman DC, Crossley DA Jr, Hendrix PF, Odum EP (1995) A hierarchical approach to evaluating the significance of soil biodiversity to biogeochemical cycling. Plant Soil 170:5–22Google Scholar
  15. Beltra R, Del-Solar G, Sanchez-Serrano JJ, Alonso E (1988) Mutants of Rhizobium phaseoli HM Mel(2) obtained by means of elevated temperatures. Zentbl Mikrobiol 143:529–532Google Scholar
  16. Berleman JE, Scott J, Chumley T, Kirby JR (2008) Predataxis behavior in Myxococcus xanthus. Proc Natl Acad Sci U S A 105:17127–17132PubMedPubMedCentralGoogle Scholar
  17. Bianciotto V, Bonfante P (2002) Arbuscular mycorrhizal fungi: a specialised niche for rhizospheric and endocellular bacteria. Antonie Leewvenhoek 81:365–371Google Scholar
  18. Bianciotto V, Genre A, Jargeat P, Lumini E, Bécard G, Bonfante P (2004) Vertical transmission of endobacteria in the arbuscular mycorrhizal fungus Gigaspora margarita through generation of vegetative spores. Appl Environ Microbiol 70:3600–3608PubMedPubMedCentralGoogle Scholar
  19. Bloem D, Hopkins W, Benedetti A (2006) Microbiological methods for assessing soil quality. CABI Publishing, CAB International, OxfordshireGoogle Scholar
  20. Bloemberg GV, Wijfjes AH, Lamers GE, Stuurman N, Lugtenberg BJJ (2000) Simultaneous imaging of Pseudomonas fluorescens WCS365 populations expressing three different autofluorescent proteins in the rhizosphere: new perspectives for studying microbial communities. Mol Plant Microbe In 13:1170–1176Google Scholar
  21. Bonkowski M, Brandt F (2002) Do soil protozoa enhance plant growth by hormonal effects? Soil Biol Biochem 34:1709–1715Google Scholar
  22. Boyle M, Frankenberger WT Jr, Stolzy JH (1989) The influence of organic on soil aggregation and water infiltration. J Prod Agr 2:209–299Google Scholar
  23. Bradford MA, Davies CA, Frey SD, Maddox TR, Melillo JM, Mohan JE, Reynolds JF, Treseder KK, Wallenstein MD (2008) Thermal adaptation of soil microbial respiration to elevated temperature. Ecol Lett 11:1316–1327PubMedGoogle Scholar
  24. Brady NC, Weil RR (1999) The nature and properties of soil, 12th edn. Prentice-Hall Inc., Upper Saddle RiverGoogle Scholar
  25. Brady NC, Weil R (2002) Elements of the nature and properties of soils. Prentice-Hall Inc., Upper Saddle RiverGoogle Scholar
  26. Bridges EM (1998) World soils. Cambridge University Press, CambridgeGoogle Scholar
  27. Brown GE, Trainor TP, Chaka AM (2008) Geochemistry of mineral surfaces and factors affecting their chemical reactivity. In: Nilsson A, Pettersson LGM, Norskov JK (eds) Chemical bonding at surfaces and interfaces. Elsevier, Amsterdam, pp 457–509Google Scholar
  28. Bürgmann H, Widmer F, Sigler WV, Zeyer J (2003) mRNA extraction and reverse transcription-PCR protocol for detection of nifH gene expression by Azotobacter vinelandii in soil. Appl Environ Microbiol 69:1928–1935PubMedPubMedCentralGoogle Scholar
  29. Busse MD, Bottomley PJ (1989) Growth and nodulation responses of Rhizobium meliloti to water stress induced by permeating and nonpermeating solutes. Appl Environ Microbiol 55:2431–2436PubMedPubMedCentralGoogle Scholar
  30. Cabeda MS (1984) Degradação física e erosão, In: I Simpósio de manejo do solo e plantio direito no sul do Brasil, 1, Simpósio de conservação de solos do planalto, 3. 1984, Passo Fundo, Anais, Passo Fundo: PIVCS e UPF – Faculdade de Agronomia, pp 28–33Google Scholar
  31. Capper AL, Higgin KP (1993) Application of Pseudomonas fluorescens isolates to wheat as potential biological control agents against take-all. Plant Pathol 42:560–567Google Scholar
  32. Chanway CP, Holl FB (1992) Influence of soil biota on Douglas-fir (Pseudotsuga menziesii) seedling growth: the role of rhizosphere bacteria. Can J Bot 70:1025–1031Google Scholar
  33. Chao WL, Nelson EB, Harman GE, Hoch HC (1986) Colonization of the rhizosphere by biological control agents applied to seeds. Phytopathology 76:60–65Google Scholar
  34. Chapin FSIII, Matson PA, Mooney HA (2002) Principles of terrestrial ecosystem ecology. Springer, New YorkGoogle Scholar
  35. Chater KF, Horinouchi S (2003) Signalling early developmental events in two highly diverged Streptomyces species. Mol Microbiol 48:9–15PubMedGoogle Scholar
  36. Chhabra SR, Philipp B, Eberl L, Givskov M, Williams P, Ca’ mara M (2005) Extracellular communication in bacteria. In: Schuz S (ed) Chemistry of pheromones and other semiochemicals 2. Springer, Berlin/Heidelberg, pp 279–315Google Scholar
  37. Chin-A-Woeng TFC, Bloemberg GV, van der Bij AJ, van der Drift KMGM, Schripsema J, Kroon B, Scheffer RJ, Keel C, Bakker PAHM, De Bruijn FJ, Thomas-Oates JE, Lugtenberg BJJ (1998) Biocontrol by phenazine-1-carboxamide producing Pseudomonas chlororaphis PCL1391 of tomato root rot caused by Fusarium oxysporum f. sp. radicis-lycopersici. Mol Plant Microbe In 10:79–86Google Scholar
  38. Chookietwattana K, Maneewan K (2012) Screening of efficient halotolerant phosphate solubilizing bacterium and its effect on promoting plant growth under saline conditions. World Appl Sci J 16(8):1110–1117Google Scholar
  39. Clarholm M, Bonkowski M, Griffiths BS (2006) Protozoa and other protists in soil. In: Van Elsas JD, Jansson JK, Trevors JT (eds) Modern soil microbiology, 2nd edn. CRC Press, Boca Raton, pp 147–176Google Scholar
  40. Coleman DC, Crossley DA Jr, Hendrix PF (2004) Fundamentals of soil ecology, 2nd edn. Elsevier, San DiegoGoogle Scholar
  41. Colores GM, Schmidt SK (2005) Recovery of microbially mediated processes in soil augmented with a pentachlorophenol-mineralizing bacterium. Environ Toxicol Chem 24:1912–1917PubMedGoogle Scholar
  42. Compant S, Duffy B, Nowak J, Clement C, Barka EA (2005) Use of plant-growth promoting bacteria for biocontrol of plant diseases: principles, mechanisms of action, and future prospects. Appl Environ Microbiol 71(9):4951–4959PubMedPubMedCentralGoogle Scholar
  43. Conn VM, Franco CMM (2004) Effect of microbial inoculants on the indigenous actinobacterial endophyte population in the roots of wheat as determined by terminal restriction fragment length polymorphism. Appl Environ Microbiol 70:6407–6413PubMedPubMedCentralGoogle Scholar
  44. Cruz AF, Hamel C, Hanson K, Selles F, Zentner RP (2009) Thirty-seven years of soil nitrogen and phosphorus fertility management shapes the structure and function of the soil microbial community in a Brown Chernozem. Plant Soil 315:73–184Google Scholar
  45. Dahlin S, Witter E, Martensson A, Turner A, Baath E (1997) Where’s the limit? Changes in the microbiological properties of agricultural soils at low levels of metal contamination. Soil Biol Biochem 29:1405–1415Google Scholar
  46. Das AC, Mukherjee D (2000) Soil application of insecticides influences microorganisms and plant nutrients. Appl Soil Ecol 14:55–62Google Scholar
  47. Davidson EA (1993) Soil water content and the ratio of nitrous oxide to nitric oxide emitted from soil. In: Oremland RS (ed) Biogeochemistry of global change. Chapman & Hall, New York, pp 369–386Google Scholar
  48. Dawid W (2000) Biology and global distribution of myxobacteria in soils. FEMS Microbiol Rev 24:403–427PubMedGoogle Scholar
  49. de Souza J, Arnould C, Deulvot C, Lamanceau P, Pearson VG, Raaijmakers JM (2003) Effect of 2,4 diacetylphloroglucinol on Pythium: cellular responses and variation in sensitivity among propagules and species. Phytopathology 93:966–975PubMedGoogle Scholar
  50. De’ziel E, Le’pine F, Milot S, He JX, Mindrinos MN, Tompkins RG, Rahme LG (2004) Analysis of Pseudomonas aeruginosa 4-hydroxy-2-alkylquinolines (HAQs) reveals a role for 4-hydroxy-2-heptylquinoline in cell-to-cell communication. Proc Natl Acad Sci U S A 101:1339–1344Google Scholar
  51. Degrassi G, Aguilar C, Bosco M, Zahariev S, Pongor S, Venturi V (2002) Plant growth-promoting Pseudomonas putida WCS358 produces and secretes four cyclic dipeptides: cross-talk with quorum sensing bacterial sensors. Curr Microbiol 45:250–254PubMedGoogle Scholar
  52. Dekkers LC, Mulders IH, Phoelich CC, Chin-A-Woeng TFC, Wijfjes AH, Lugtenberg BJ (2000) The sss colonization gene of the tomato-Fusarium oxysporum f. sp. radicis-lycopersici biocontrol strain Pseudomonas fluorescens WCS365 can improve root colonization of other wild-type Pseudomonas spp. Bacteria. Mol Plant Microbe In 13:1177–1183Google Scholar
  53. Demanou J, Monkiedje A, Njine T, Foto SM, Nola M, Serges H, Togouet Z, Kemka N (2004) Changes in soil chemical properties and microbial activities in response to the fungicide Ridomil gold plus copper. Int J Environ Res Public Health 1:26–34PubMedGoogle Scholar
  54. Devliegher W, Verstraete W (1995) Lumbricus terrestris in a soil core experiment—nutrient-enrichment processes (nep) and gut associated processes (gap) and their effect on. Soil Biol Biochem 27:1573–1580Google Scholar
  55. Diggle SP, Cornelis P, Williams P, Camara M (2006) 4-Quinolone signalling in Pseudomonas aeruginosa: old molecules, new perspectives. Int J Med Microbiol 296:83–91PubMedGoogle Scholar
  56. Doube BM, Stephens PM, Davoren CW, Ryder MH (1994) Earthworms and the introduction and management of beneficial soil microorganisms. In: Pankhurst C, Doube BM, Gupta VVSR, Grace PR (eds) Soil biota: management in sustainable farming systems. CSIRO, Melbourne, pp 32–41Google Scholar
  57. Drake HL, Horn MA (2006) Earthworms as a transient heaven for terrestrial denitrifying microbes: a review. Eng Life Sci 6:261–265Google Scholar
  58. Duffy BK, Défago G (1999) Environmental factors modulating antibiotic and siderophore biosynthesis by Pseudomonas fluorescens biocontrol strains. Appl Environ Microbiol 65:2429–2438PubMedPubMedCentralGoogle Scholar
  59. Dutta S, Podile AR (2010) Plant growth promoting rhizobacteria (PGPR): the bugs to debug the root zone. Crit Rev Microbiol 36(3):232–244PubMedGoogle Scholar
  60. Dwivedi D, Johri BN (2003) Antifungals from fluorescent pseudomonads: biosynthesis and regulation. Curr Sci 85(12):1693–1703Google Scholar
  61. Eaglesham ARJ, Ayanaba A (1984) Tropical stress ecology of rhizobia, root-nodulation and legume fixation. In: Subba Rao NS (ed) Current developments in biological nitrogen fixation. Edward Arnold Publishers, London, pp 1–35Google Scholar
  62. Eberhard AA, Burlingamme L, Eberhard C, Kenyon GL, Nealson KH (1981) Structural identification of autoinducer of Photobacterium fischeri luciferase. Biochemistry 20:2444–2449PubMedGoogle Scholar
  63. Edwards RA, Rodriguez-Brito B, Wegley L, Haynes M, Breitbart M, Peterson DM, Saar MO, Alexander S, Alexander EC Jr, Rohwer F (2006) Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics 7:57PubMedPubMedCentralGoogle Scholar
  64. Egert M, Marhan S, Wagner B, Scheu S, Friedrich MW (2004) Molecular profiling of 16S rRNA genes reveals diet-related differences of microbial communities in soil, gut, and casts of Lumbricus terrestris L(Oligochaeta:Lumbricidae). FEMS Microbiol Ecol 48(2):187–197PubMedGoogle Scholar
  65. Etebu E, Osborn AM (2012) A review of indicators of healthy agricultural soils with pea footrot disease suppression potentials. Sustain Agr Res 2:235–250Google Scholar
  66. Evans J, Wallace C, Dobrowolski N (1993) Interaction of soil type and temperature on the survival of Rhizobium leguminosarum bv. Viciae. Soil Biol Biochem 25:1153–1160Google Scholar
  67. Fabra A, Duffard R, de Duffard AE (1997) Toxicity of 2,4-Dichlorophenoxyacetic acid to Rhizobium sp. in pure culture. Bull Environ Contam Toxicol 59:645–652PubMedGoogle Scholar
  68. Fang M, Kremer RJ, Motavalli PP, Davis G (2005) Bacterial diversity in rhizospheres of nontransgenic and transgenic corn. Appl Environ Microbiol 71:4132–4136PubMedPubMedCentralGoogle Scholar
  69. Fernando WGD, Nakkeeran S, Zhang Y (2005) Biosynthesis of antibiotics by PGPR and its relation in biocontrol of plant diseases. In: Siddiqui ZA (ed) PGPR: biocontrol and biofertilization. Springer, Dordrecht, pp 67–109Google Scholar
  70. Fierer N, Jackson RB (2006) The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci 103:626–631PubMedPubMedCentralGoogle Scholar
  71. Flavier AB, Clough SJ, Schell MA, Denny TP (1997) Identification of 3-hydroxypalmitic acid methyl ester as a novel autoregulator controlling virulence in Ralstonia solanacearum. Mol Microbiol 26:251–259PubMedGoogle Scholar
  72. Foster RC (1988) Microenvironments of soil microorganisms. Biol Fertil Soils 6:189–203Google Scholar
  73. Francis CA, Flora CB, King LD (1990) Sustainable agriculture in temperate zones. Wiley, New York, p 487Google Scholar
  74. Garbeva P, van Veen JA, van Elsas JD (2004) Microbial diversity in soil: selection of microbial populations by plant and soil type and implications for disease suppressiveness. Ann Rev Phytopathol 42:243–270Google Scholar
  75. Garland JL (1996) Patterns of potential C source utilization by rhizosphere communities. Soil Biol Biochem 28:223–230Google Scholar
  76. Gaur AC (1980) Effect of pesticides on symbiotic nitrogen fixation by legumes. Indian J Microbiol 20:362–370Google Scholar
  77. Germida JJ, Siciliano SD, de Freitas JR, Seib AM (1998) Diversity of root-associated bacteria associated with field-grown canola (Brassica napus L.) and wheat (Triticum aestivum). FEMS Microbiol Ecol 26:43–50Google Scholar
  78. Giller KE, Witter E, McGrath SP (1998) Toxicity of heavy metals to microorganisms and microbial processes in agricultural soils a review. Soil Biol Biochem 30(10–11):1389–1414Google Scholar
  79. Gonzalez-lopez J, Martinez-Toledo MV, Salermon V, Rodelas B (1993) Studies on the effects of the insecticide phorate and malathion on soil microorganisms. Environ Toxicol Chem 12(7):1209–1214Google Scholar
  80. Govedarica M, Miloševiã N, Konstantinoviã B (2001) Uticaj dimetenamida i metalahlora na mikrobiološka svojstva zemljišta pod šeãernom repom, V jugoslovensko savetovanje o zaštiti bilja, Zlatibor, pp 3–8, 12Google Scholar
  81. Graham PH (1992) Stress tolerance in Rhizobium and Bradyrhizobium, and nodulation under adverse soil conditions. Can J Microbiol 38:475–484Google Scholar
  82. Griffiths BS (1990) Comparison of microbial-feeding nematodes and protozoa in the rhizosphere of different plants. Biol Fert Soils 9:83–88Google Scholar
  83. Griffiths BS, Bonkowski M, Dobson G, Caul S (1999) Changes in soil microbial community structure in the presence of microbial-feeding nematodes and protozoa. Pedobiologia 43:297–304Google Scholar
  84. Gross R, Arico B, Rappuoli R (1989) Families of bacterial signal-transducing proteins. Mol Microbiol 3:1661–1667PubMedGoogle Scholar
  85. Guaiquil VH, Luigi C (1992) Plant growth promoting rhizobacteria and their effect on rapeseed (Brassica napus L.) and potato seedlings. Microbiol Rev 23:264–273Google Scholar
  86. Guerinot ML, Ying Y (1994) Iron: nutritious, noxious, and not readily available. Plant Physiol 104:815–820PubMedPubMedCentralGoogle Scholar
  87. Gyaneshwar P, Kumar GN, Parekh LJ, Poole PS (2002) Role of soil microorganisms in improving P nutrition of plants. Plant Soil 245:83–93Google Scholar
  88. Haby VA (1993) Soil pH and plant nutrient availability. Ferti Gram, X(2)Google Scholar
  89. Hahn MW, Höfle MG (2001) Grazing of protozoa and its effect on populations of aquatic bacteria. FEMS Microbiol Ecol 35:113–121PubMedGoogle Scholar
  90. Hamarashid NH, Othman MA, Hussain MAH (2010) Effects of soil texture on chemical compositions, microbial populations and carbon mineralization in soil. Egypt J Exp Biol (Bot) 6(1):59–64Google Scholar
  91. Hammouda O (1999) Response of the paddy field cyanobacterium Anabaena doliolum to carbofuran. Ecotoxicol Environ Saf 44:215–219PubMedGoogle Scholar
  92. Harris RF (1981) Effect of water potential on microbial growth and activity. In: Parr JF, Gardner WR, Elliott LF (eds) Water potential relations in soil microbiology. Soil Science Society of America, Madison, pp 23–95Google Scholar
  93. Hartel PG, Alexander M (1984) Temperature and desiccation tolerance of cowpea rhizobia. Can J Microbiol 30:820–823Google Scholar
  94. Hassink J (1997) The capacity of soils to preserve organic C and N by their association with clay and silt particles. Plant Soil 191:77–87Google Scholar
  95. Hattori T, Hattori R (1976) The physical environment in soil microbiology: an attempt to extend principles of microbiology to soil microorganisms. CRC Crit Rev Microbiol 4:423–461PubMedGoogle Scholar
  96. Hausmann K, Hülsmann N (1996) Ecology of protozoa. In: Hausmann K, Hülsmann N (eds) Protozoology. Georg Thieme Verlag, Stuttgart, pp 272–300Google Scholar
  97. Herron PM, Stark JM, Holt C, Hooker T, Cardon ZG (2009) Microbial growth efficiencies across a soil moisture gradient assessed using 13C-acetic acid vapor and 15N-ammonia gas. Soil Biol Biochem 41:1262–1269Google Scholar
  98. Hochella MF (2002) Sustaining earth: thoughts on the present and future roles in mineralogy in environmental science. Mineral Mag 66:627–652Google Scholar
  99. Hol WHG, Bezemer TM, Biere A (2013) Getting the ecology into interactions between plants and the plant growth-promoting bacterium Pseudomonas fluorescens. Front Plant Sci 4(81):1–9Google Scholar
  100. Holden MT, Chhabra SR, de Nys R, Stead P, Bainton NJ, Hill PJ, Manefield M, Kumar N, Labatte M, England D, Rice S, Givskov M, Salmond GP, Stewart GS, Bycroft BW, Kjelleberg S, Williams P (1999) Quorum-sensing cross talk: isolation and chemical characterization of cyclic dipeptides from Pseudomonas aeruginosa and other Gram-negative bacteria. Mol Microbiol 33:1254–1266PubMedGoogle Scholar
  101. Horn MA, Mertel R, Gehre M, Kaestner M, Drake HL (2006) In vivo emission of dinitrogen by earthworms via denitrifying bacteria in the gut. Appl Environ Microbiol 72:1013–1018PubMedPubMedCentralGoogle Scholar
  102. Huang JS, Barker KR, Van Dyke CG (1984) Suppression of binding between rhizobia and soybean roots by Heterodera glycines. Phytopathology 74:1381–1384Google Scholar
  103. Hungria M, Franco AA (1993) Effects of high temperature on nodulation and nitrogen fixation by Phaseolus vulgaris L. Plant Soil 149:95–102Google Scholar
  104. Hunt PG, Wollum AG, Matheny TA (1981) Effects of soil water on Rhizobium japonicum infection nitrogen accumulation and yield in bragg soybean. Agron J 73:501–505Google Scholar
  105. Ingham ER, Trofymow JA, Ames RN, Hunt HW, Morley CR, Moore LC, Coleman DC (1986) Trophic interactions and nitrogen cycling in a semi-arid grassland soil II system responses to removal of different groups of soil microbes or fauna. J Appl Ecol 23:615–630Google Scholar
  106. Jayaraman S, Rangarajan M, Jayachandran S (1985) Metabolism of antibiotic resistant mutants of Rhizobium sp. as influenced by different temperature regimes. Hindustan Antibiot Bull 27:38–41PubMedGoogle Scholar
  107. Jensen A, Jakobsen I (1980) The occurrence of vesicular-arbuscular mycorrhiza in barley and wheat grown in some Danish soils with different fertilizer treatments. Plant Soil 55:403–414Google Scholar
  108. Jensen LS, McQueen DJ, Ross DJ, Tate KR (1996) Effect of soil composition on N-mineralization and microbial-C and -N II: laboratory simulation. Soil Till Res 38:189–202Google Scholar
  109. Jensen LE, Kragelund L, Nybroe O (1998) Expression of a nitrogen regulated lux gene fusion in Pseudomonas fluorescens DF57 studied in pure culture and in soil. FEMS Microbiol Ecol 25:23–32Google Scholar
  110. Jiang H, Dong H, Yu B, Liu X, Li Y, Ji S, Zhang CL (2007) Microbial response to salinity change in Lake Chaka, a hypersaline lake on Tibetan plateau. Environ Microbiol 9(10):2603–2621PubMedGoogle Scholar
  111. Jørgensen F, Nybroe O, Knøchel S (1994) Effects of starvation and osmotic stress on viability and heat resistance of Pseudomonas fluorescens AH9. J Appl Bacteriol 77:340–347Google Scholar
  112. Jousset A (2012) Ecological and evolutive implications of bacterial defences against predators. Environ Microbiol 14:1830–1843PubMedGoogle Scholar
  113. Jousset A, Scheu S, Bonkowski M (2008) Secondary metabolite production facilitates establishment of rhizobacteria by reducing both protozoan predation and the competitive effects of indigenous bacteria. Funct Ecol 22:714–719Google Scholar
  114. Jürgens K, Güde H (1994) The potential importance of grazing-resistant bacteria in planktonic systems. Mar Ecol Prog Ser 112:169–188Google Scholar
  115. Jürgens K, Pernthaler J, Schalla S, Amann R (1999) Morphological and compositional changes in a planktonic bacterial community in response to enhanced protozoan grazing. Appl Environ Microbiol 65:1241–1250PubMedPubMedCentralGoogle Scholar
  116. Kalam A, Mukherjee AK (2001) Influence of hexaconazole, carbofuran and ethion on soil microflora and dehydrogenase activities in soil and intact cell. Indian J Exp Biol 39:90–94PubMedGoogle Scholar
  117. Karanja NK, Wood M (1988) Selecting Rhizobium phaseoli strains for use with beans (Phaseolus vulgaris L.) in Kenya, Tolerance of high temperature and antibiotic resistance. Plant Soil 112:15–22Google Scholar
  118. Khan MS, Zaid A, Rizvi PQ (2006) Biotoxic effects of herbicides on growth, nodulation, nitrogenase activity, and seed production in chickpeas. Commun Soil Sci Plant Anal 37:1783–1793Google Scholar
  119. Khare E, Arora NK (2011) Dual activity of pyocyanin from Pseudomonas aeruginosa: antibiotic against phytopathogen and signal molecule for biofilm development by rhizobia. Can J Microbiol 57(9):708–713PubMedGoogle Scholar
  120. Khare E, Singh S, Maheshwari DK, Arora NK (2011) Suppression of charcoal rot of chickpea by fluorescent pseudomonas under saline stress condition. Curr Microbiol 62:1548–1553PubMedGoogle Scholar
  121. Khare E, Chopra J, Arora NK (2014) Screening for MCL-PHA producing fluorescent pseudomonads and comparison of MCL-PHA production under iso-osmotic conditions induced by PEG and NaCl. Curr Microbiol 68(4):457–462PubMedGoogle Scholar
  122. Killham K (1994) Soil ecology. Cambridge University Press, Cambridge, p 242Google Scholar
  123. Kim Y-G, Lee J-H, Cho MH, Lee J (2011) Indole and 3-indolylacetonitrile inhibit spore maturation in Paenibacillus alvei. BMC Microbiol 11:119PubMedPubMedCentralGoogle Scholar
  124. Kluepfel DA (1993) The behaviour and tracking of bacteria in the rhizosphere. Ann Rev Phytopathol 31:441–472Google Scholar
  125. Kong P, Lee BWK, Zhou ZS, Hong C (2010) Zoosporic plant pathogens produce bacterial autoinducer-2 that affects Vibrio harveyi quorum sensing. FEMS Microbiol Lett 303(1):55–60PubMedPubMedCentralGoogle Scholar
  126. Kosinkievicz B (1984) Interaction between bacterial metabolites and some pesticides, I Interaction between the phenolic compounds produced by Pseudomonas acidovorans and the herbicide Venzar. Acta Microbiol Pol 33(12):103–110Google Scholar
  127. Kumar H, Arora NK, Kumar V, Maheshwari DK (1999) Isolation, characterization and selection of salt tolerant rhizobia nodulating Acacia catechu and A. nilotica. Symbiosis 26:279–288Google Scholar
  128. Kumar B, Trivedi P, Pandey A (2007) Pseudomonas corrugata: a suitable bioinoculant for maize grown under rainfed conditions of Himalayan region. Soil Biol Biochem 39:3093–3100Google Scholar
  129. Kyei-Boahen S, Slinkard AE, Walley FL (2001) Rhizobial survival and nodulation of chickpea as influenced by fungicide seed treatment. Can J Microbiol 47:585–589PubMedGoogle Scholar
  130. Lambert C, Morehouse KA, Chang CY, Sockett RE (2006) Bdellovibrio: growth and development during the predatory cycle. Curr Opin Microbiol 9:639–644PubMedGoogle Scholar
  131. Latour X, Delorme S, Mirleau P, Lemanceau P (2003) Identification of traits implicated in the rhizosphere competence of fluorescent pseudomonads: description of a strategy based on population and model strain studies. Agronomie 23:397–405Google Scholar
  132. Linderman RG, Paulitz TC (1990) Mycorrhizal-rhizobacterial interactions. In: Hornby D, Cook RJ, Henis Y, Ko WH, Rovira AD, Schippers B, Scott PR (eds) Biological control of soil-borne plant pathogens. CAB International, Wallingford, pp 261–283Google Scholar
  133. Lipson DA, Monson RK, Schmidt SK, Weintraub MN (2009) The trade-off between growth rate and yield in microbial communities and the consequences for under-snow soil respiration in a high elevation coniferous forest. Biogeochemistry 95:23–35Google Scholar
  134. Loh J, Carlson RW, York WS, Stacey G (2002) Bradyoxetin, a unique chemical signal involved in symbiotic gene regulation. Proc Natl Acad Sci U S A 99:14446–14451PubMedPubMedCentralGoogle Scholar
  135. Loper JE, Haack C, Schroth MN (1985) Population dynamics of soil pseudomonads in the rhizosphere of potato (Solanum tuberosum L.). Appl Environ Microbiol 49:416–422PubMedPubMedCentralGoogle Scholar
  136. Lugtenberg B, Kamilova F (2009) Plant-growth-promoting rhizobacteria. Annu Rev Microbiol 63:541–556PubMedGoogle Scholar
  137. Lynch JM (1983) Microorganisms and enzymes in the soil. In: Marumoto T, Watanabe I, Satoh K, Kanazawa S (eds) Soil biotechnology, microbiological factors in crop productivity. Blackwell Science Publications, London, p. 185Google Scholar
  138. Ma JF (2005) Plant root responses to three abundant soil minerals: silicon, aluminum and iron. Crit Rev Plant Sci 24:267–281Google Scholar
  139. Madsen EL, Alexander M (1982) Transport of Rhizobium and Pseudomonas through soil. Soil Sci Soc Am J 46:557–560Google Scholar
  140. Magasanik B (1996) Regulation of nitrogen utilization, Escherichia coli and Salmonella: cellular and molecular biology, 2nd edn. American Society of Microbiology, Washington, DC, pp 1345–1356Google Scholar
  141. Malcolm GM, López-Gutiérrez JC, Koide RT, Eissenstat DM (2008) Acclimation to temperature and temperature sensitivity of metabolism by ectomycorrhizal fungi. Global Change Biol 14:1–12Google Scholar
  142. Malus’a E, Sas-Paszt L, Ciesielska J (2012) Technologies for beneficial microorganisms inocula used as biofertilizers. Sci World J 2012:491206Google Scholar
  143. Marhan M, Scheu S (2006) Mixing of different mineral soil layers by endogeic earthworms affects carbon and nitrogen mineralization. Biol Fertil Soils 32:308–314Google Scholar
  144. Marhan S, Kandeler E, Scheu S (2007) Phospholipid fatty acid profiles and xylanase activity in particle size fractions of forest soil and casts of Lumbricus terrestris L. (Oligochaeta, Lumbricidae). Appl Soil Ecol 35:412–422Google Scholar
  145. Marshall K (1975) Clay mineralogy in relation to survival of soil bacteria. Annu Rev Phytopathol 13:357–373Google Scholar
  146. Martinez-Toledo MV, Salermon V, Rodelas B, Pozo C, Gonzalez-Lopez J (1998) Effects of the fungicide captan on some functional groups of soil microflora. Appl Soil Ecol 7:245–255Google Scholar
  147. Mascher F, Hase C, Moënne-Loccoz Y, De’fago (2000) The viable-but-nonculturable state induced by abiotic stress in the biocontrol agent Pseudomonas fluorescens CHA0 does not promote strain persistence in soil. Appl Environ Microbiol 66(4):1662–1667PubMedPubMedCentralGoogle Scholar
  148. Mavi MS, Marschner P (2013) Salinity affects the response of soil microbial activity and biomass to addition of carbon and nitrogen. Soil Res 51(1):68–75Google Scholar
  149. McBride MJ, Zusman DR (1996) Behavioral analysis of single cells of Myxococcus xanthus in response to prey cells of Escherichia coli. FEMS Microbiol Lett 137:227–231PubMedGoogle Scholar
  150. Mclachlan JA (2001) Environmental signaling: what embryos and evolution teach us about endocrine disrupting chemicals. Endocr Rev 22:319–341PubMedGoogle Scholar
  151. Michiels J, Verreth C, Vanderleyden J (1994) Effects of temperature stress on bean nodulating Rhizobium strains. Appl Environ Microbiol 60:1206–1212PubMedPubMedCentralGoogle Scholar
  152. Miller RW, Donahue RL (1995) Soils in our environment, 7th edn. Prentice-Hall, Inc., Upper Saddle RiverGoogle Scholar
  153. Miller KJ, Wood JM (1996) Osmoadaptation by rhizosphere bacteria. Annu Rev Microbiol 50:101–136PubMedGoogle Scholar
  154. Millner JL, Silo-Suh L, Lee JC, He HY, Clardy J, Handelsman J (1996) Production of kanosamine by Bacillus cereus UW85. Appl Environ Microbiol 62:3061–3065Google Scholar
  155. Miloševiã N, Govedarica M (2000) Effect of some herbicides on microbial properties of soil. In: Albanis T (ed) Proceedings of the 1st European conferences on pesticides and related organic micropollutants in the environment, Ioannina, Greece, pp 61–62Google Scholar
  156. Miloševiã N, Govedarica M (2001) Uticaj prometrina na mikrobiološka svojstva zemljišta pod sojom i suncokretom, V jugoslovensko savetovanje o zaštiti bilja, Zlatibor, pp 3–7Google Scholar
  157. Miloševiã N, Govedarica M, Jarak M, Konstantinoviã B, Miletiã S (1995) Effect of herbicides on the number of microorganisms and dehydrogenase activity in soil under soybean, I Regional symposium: chemistry and environment, 25–29 Sept, Vr. Banja, Proceedings II, pp 551–554Google Scholar
  158. Miloševiã N, Govedarica M, Jarak M, Ðuriã S, Kon-stantinoviã B (1998) Uticaj herbicida na brojnost i dehidrogenaznu aktivnost mikroorganizama u zemljištu pod usevom soje. IV Jugoslovenski kongres o zaštiti bilja, Vrnjaåka Banja 9:21–26Google Scholar
  159. Miloševiã N, Govedarica M, Konstantinoviã B (2000) Uticaj herbicida na nodulaciju soje i mikrobiološku aktivnost zemljišta, Šesti kongres o korovima. Zbornik radova, Banja Koviljaåa, pp 455–460Google Scholar
  160. Miloševiã N, Govedarica M, Jarak M, DÐorðeviã S (2001) Pesticidi i mikroorganizmi. In: Konstatinoviã A (ed) Zaštita šeãerne repe od štetoåina, bolesti I korova. Stylos, Novi Sad, pp 109–149Google Scholar
  161. Min H, Ye YF, Chen ZY, Wu WX, Yufeng D (2001) Effects of butachlor on microbial populations and enzymes activities in paddy soil. J Environ Sci Health B 36:581–595PubMedGoogle Scholar
  162. Misaghi IJ, Olsen MW, Billotte JM, Sonoda RM (1992) The importance of rhizobacterial mobility in biocontrol of bacterial wilt of tomato. Soil Biol Biochem 24:287–293Google Scholar
  163. Monkiedje A, Ilori MO, Spiteller M (2002) Soil quality changes resulting from the application of the fungicides mefenoxam and metalaxyl to a sandy loam soil. Soil Biol Biochem 34:1939–1948Google Scholar
  164. Moore JC, Walter DE, Hunt HW (1988) Arthropod regulation of micro- and mesobiota in below-ground detrital food webs. Ann Rev Entomol 33:419–439Google Scholar
  165. Morgan AD, MacLean RC, Hillesland KL, Velicer GJ (2010) Comparative analysis of Myxococcus predation on soil bacteria. Appl Environ Microbiol 76(20):6920–6927PubMedPubMedCentralGoogle Scholar
  166. Mummey DL, Rillig MC, Six J (2006) Endogeic earthworms differentially influence bacterial communities associated with different soil aggregate size fractions. Soil Biol Biochem 38:1608–1614Google Scholar
  167. Musarrat J, Haseeb A (2000) Agrichemicals as antagonist of lectin-mediated Rhizobium–legume symbiosis: paradigms and prospects. Curr Sci 78(7):793–797Google Scholar
  168. Nakkeeran S, Dilantha Fernando WG, Siddiqui WA (2005) Plant growth promoting rhizobacteria formulations and its scope in commercialization for the management of pests and diseases. In: Siddiqui ZA (ed) PGPR: biocontrol and biofertilization. Springer, Dordrecht, pp 257–296Google Scholar
  169. Nannipieri P, Ascher J, Ceccherini MT, Landi L, Pietramellara G, Renella G (2003) Microbial diversity and soil functions. Eur J Soil Sci 54:655–670Google Scholar
  170. Narasimhan K, Basheer C, Bajic VB, Swarup S (2003) Enhancement of plant-microbe interactions using a rhizosphere metabolomics driven approach and its application in the removal of polychlorinated biphenyls. Plant Physiol 132:146–153PubMedPubMedCentralGoogle Scholar
  171. Natsch A, Keel C, Troxler J, Zala M, Von Albertini N, De’fago G (1996) Importance of preferential flow and soil management in vertical transport of a biocontrol strain of Pseudomonas fluorescens in structured field soil. Appl Environ Microbiol 62:33–40PubMedPubMedCentralGoogle Scholar
  172. Neidig N, Paul RJ, Scheu S, Jousset A (2011) Secondary metabolites of Pseudomonas fluorescens CHA0 drive complex non-trophic interactions with bacterivorous nematodes. Microb Ecol 61:853–859PubMedPubMedCentralGoogle Scholar
  173. Neilands JB (1981) Iron adsorption and transport in microorganisms. Annu Rev Nutr 1:27–46PubMedGoogle Scholar
  174. Niewiadomska A (2004) Effect of carbendazim, imazetapir and thiramon nitrogenase activity, the number of microorganisms in soil and yield of red clover (Trifolium pretense L). Pol J Environ Stud 13:403–410Google Scholar
  175. Niewiadomska A, Klama J (2005) Pesticide side effect on the symbiotic efficiency and nitrogenase activity of rhizobiaceae bacteria family. Polish J Microbiol 54(1):43–48Google Scholar
  176. Nimmo JR, Perkins KS (2002) Aggregate stability and size distribution. In: Dane JH, Topp GC (eds) Methods of soil analysis, Part 4: Physical methods: Soil Science Society of America Book Series No. 5. Soil Science Society of America, Madison, pp 317–328Google Scholar
  177. Noble AD, Randall PJ (1999) Alkalinity effects of different tree litters incubated in an acid soil of NSW. Aust Agrofor Syst 46:147–160Google Scholar
  178. Notz R, Maurhofer M, Schnider-Keel U, Duffy B, Haas D, Défago G (2001) Biotic factors affecting expression of the 2,4-diacetylpholoroglucinol biosynthesis gene phlA in Pseudomonas fluorescens biocontrol strain CHA0 in the rhizosphere. Phytopathology 91:873–881PubMedGoogle Scholar
  179. Nowak A, Nowak J, Klodka D, Pryzbulewska K, Telesinski A, Szopa E (2004) Changes in the microflora and biological activity of the soil during the degradation of isoproturon. J Plant Dis Prot 19:1003–1016Google Scholar
  180. Nowak-Thompsan B, Gould SJ, Kraus J, Loper JE (1994) Production of 2,4-diacetylphloroglucinol by the biocontrol agent Pseudomonas fluorescens Pf-5. Can J Microbiol 40:1064–1066Google Scholar
  181. Ogunseitan OA, Odeyemi O (1985) Effect of lindane, captan and malathion on nitrification, sulphur oxidation, phosphate aerobic heterotrophic soil bacteria to the generic level by solubilization and respiration in tropical soil. Environ Pollut 37:343–354Google Scholar
  182. Okada M, Sato I, Cho SJ, Iwata H, Nishio T, Dubnau D, Sakagami Y (2005) Structure of the Bacillus subtilis quorum-sensing peptide pheromone ComX. Nat Chem Biol 1:23–24PubMedGoogle Scholar
  183. Orchard VA, Cook FG (1983) Relation between soil respiration and soil moisture. Soil Biol Biochem 15:447–453Google Scholar
  184. Oren A (1999) Bioenergetic aspects of halophilism. Microbiol Mol Biol Rev 63:334–348PubMedPubMedCentralGoogle Scholar
  185. Pandey A, Sharma E, Palni LMS (1998) Influence of bacterial inoculation on maize in upland farming systems of the Sikkim Himalaya. Soil Biol Biochem 30:379–384Google Scholar
  186. Pankhurst CE, Yu S, Hawke BG, Harch BD (2001) Capacity of fatty acid profiles and substrate utilization patterns to describe differences in soil microbial communities associated with increased salinity or alkalinity at three locations in South Australia. Biol Fert Soils 33:204–217Google Scholar
  187. Papendick RI, Campbell GS (1981) Theory and measurement of water potential. In: Parr JF, Gardner WR, Elliott LF (eds) Water potential relations in soil microbiology, Soil Science Society of America Special Publication Number 9. Soil Science Society of America, Madison, pp 1–22Google Scholar
  188. Parke JL, Moen R, Rovira AD, Bowen GD (1986) Soil water flow affects the rhizosphere distribution of a seed-borne biological control agent, Pseudomonas fluorescens. Soil Biol Biochem 18:583–588Google Scholar
  189. Parmar N, Dadarwal KR (1997) Rhizobacteria from rhizosphere and rhizoplane of chick pea (Cicer arietinum L.). Indian J Microbiol 37:205–210Google Scholar
  190. Parmar N, Dufresne J (2011) Beneficial interactions of plant growth promoting rhizosphere microorganisms. In: Singh A, Parmar N, Kuhad RC (eds) Bioaugmentation, biostimulation and biocontrol, vol 28, Soil Biology., pp 27–42Google Scholar
  191. Pedersen AL, Nybroe O, Winding A, Ekelund F, Bjornlund L (2009) Bacterial feeders, the nematode Caenorhabditis elegans and the flagellate Cercomonas longicauda, have different effects on outcome of competition among the Pseudomonas biocontrol strains CHA0 and DSS73. Microb Ecol 57:501–509PubMedGoogle Scholar
  192. Pernthaler J, Posch T, Simek K, Vrba J, Amann R (1997) Contrasting bacterial strategies to coexist with a flagellate predator in an experimental microbial assemblage. Appl Environ Microbiol 63:596–601PubMedPubMedCentralGoogle Scholar
  193. Pietikäinen J, Pettersson M, Bååth E (2005) Comparison of temperature effects on soil respiration and bacterial and fungal growth rates. FEMS Microbiol Ecol 52(1):49–58PubMedGoogle Scholar
  194. Piha MI, Munnus DN (1987) Sensitivity of the common bean (Phaseolus vulgaris L.) symbiosis to high soil temperature. Plant Soil 98:183–194Google Scholar
  195. Pocknee S, Sumner ME (1997) Cation and nitrogen contents of organic matter determine its soil liming potential. Soil Sci Soc Am J 61:86–92Google Scholar
  196. Posch T, Simek K, Vrba J, Pernthaler J, Nedoma J, Sattler B, Sonntag B, Psenner R (1999) Predator-induced changes of bacterial size-structure and productivity studied on an experimental microbial community. Aquat Microb Ecol 18:235–246Google Scholar
  197. Post E (1922) Etiquette in society, in business, in politics and at home. New York: Funk & Wagnalls. Bartleby.com, www.bartleby.com/95/37
  198. Postma J, Walter S, van Veen JA (1989) Influence of different initial soil moisture contents on the distribution and population dynamics of introduced Rhizobium leguminosarum biovar trifolii. Soil Biol Biochem 21:437–444Google Scholar
  199. Pugashetti BK, Angle JS, Wagner GH (1992) Soil microorganism antagonistic towards Rhizobium japonicum. Soil Biol Biochem 14:45–47Google Scholar
  200. Raiesi F (2006) Carbon and N mineralization as affected by soil cultivation and crop residue in a calcareous wetland ecosystem in Central Iran. Agr Ecosyst Environ 112:13–20Google Scholar
  201. Rengasamy P (2006) Soil salinity and sodicity. In: Stevens D, Kelly J, McLaughlin M, Unkovich M (eds) Growing crops with reclaimed wastewater. CSIRO Publishing, Collingwood, pp 125–138Google Scholar
  202. Rieu M, Sposito G (1991) Fractal fragmentation, soil porosity, and soil water properties- I, theory. Soil Sci Soc Am J 55:1233–1238Google Scholar
  203. Robin A, Mougel C, Siblot S, Vansuyt G, Mazurier S, Lemanceau P (2006) Effect of ferritin overexpression in tobacco on the structure of bacterial and pseudomonad communities associated with the roots. FEMS Microbiol Ecol 58:492–502PubMedGoogle Scholar
  204. Robleto EA, Borneman J, Triplett EW (1998) Effects of bacterial antibiotic production on rhizosphere microbial communities from a culture-independent perspective. Appl Environ Microbiol 64(12):5020–5022PubMedPubMedCentralGoogle Scholar
  205. Romheld V, Kirkby E (2010) Research on potassium in agriculture: needs and prospects. Plant Soil 335:155–180Google Scholar
  206. Rønn R, Mc Caig AE, Griffiths BS, Prosser JI (2002) Impact of protozoan grazing on bacterial community structure in soil microcosms. Appl Environ Microbiol 68:6094–6105PubMedPubMedCentralGoogle Scholar
  207. Rosenberg K (2008) Interactions in the rhizosphere of Arabidopsis thaliana: effects of protozoa on soil bacterial communities, Dissertation, Technical University of DarmstadtGoogle Scholar
  208. Roth WG, Leckie MP, Dietzler DN (1988) Restoration of colony forming activity in osmotically stressed Escherichia coli by betaine. Appl Environ Microbiol 54:3142–3146PubMedPubMedCentralGoogle Scholar
  209. Roughley RJ (1970) The influence of root temperature, Rhizobium strain and host selection on the structure and nitrogen-fixing efficiency of the root nodules of Trifolium subterraneum. Ann Bot 34:631–646Google Scholar
  210. Rousk J, Brookes PC, Bååth E (2009) Contrasting soil pH effects on fungal and bacterial growth suggest functional redundancy in carbon mineralization. Appl Environ Microbiol 75(6):1589–1596PubMedPubMedCentralGoogle Scholar
  211. Rowell DL (1994) Soil science: methods and applications. Longman, London, p 350Google Scholar
  212. Ryan RP, Dow JM (2008) Diffusible signals and interspecies communication in bacteria. Microbiology 154:1845–1858PubMedGoogle Scholar
  213. Sakala GM, Rowell DL, Pilbeam CJ (2004) Acid-base reactions between an acidic soil and plant residues. Geoderma 123:219–232Google Scholar
  214. Sardinha M, Müller T, Schmeisky H, Joergensen RG (2003) Microbial performance in soils along a salinity gradient under acidic conditions. Appl Soil Ecol 23:237–244Google Scholar
  215. Sato K (1983) Effect of pesticide, pentachlorophenol (PCP) on soil microflora. Plant Soil 75:417–426Google Scholar
  216. Scheu S, Ruess L, Bonkowski M (2005) Interactions between microorganisms and soil micro- and mesofauna. In: Buscot F, Varma A (eds) Microorganisms in soils: roles in genesis and functions. Springer, Germany, pp 253–275Google Scholar
  217. Schimel J, Balser TC, Wallenstein M (2007) Microbial stress-response physiology and its implications for ecosystem function. Ecology 88:1386–139PubMedGoogle Scholar
  218. Schindlbacher A, Rodler A, Kuffner M, Kitzler B, Sessitsch A, Zechmeister-Boltenstern S (2011) Experimental warming effects on the microbial community of a temperate mountain forest soil. Soil Biol Biochem 43(7):1417–1425PubMedPubMedCentralGoogle Scholar
  219. Scott J, Robert J (2006) Soil texture and nitrogen mineralization potential across a riparian toposequence in a semi-arid savanna. Soil Boil Biochem 38(6):1325–1333Google Scholar
  220. Scullion J, Malik A (2000) Earthworm activity affecting organic matter, aggregation and microbial activity in soils restored after open cast mining for coal. Soil Biol Biochem 32:119–126Google Scholar
  221. Seymour NP (2002) Responses of linseed to vesicular-arbuscular mycorrhizae, phosphorus and zinc in a vertisol, Doctor of Philosophy, University of Queensland, p 263Google Scholar
  222. Shoushtari NH, Pepper IL (1985) Mesquite rhizobia isolated from the Sonoran desert: competitiveness and survival in soil. Soil Biol Biochem 17:803–806Google Scholar
  223. Silveira APD, Freitas SS, Silva LRC, Lombardi MLCO, Cardoso EJBN (1995) Interactions between arbuscular mycorrhizas and plant-growth promoting rhizobacteria in beans. Rev Bras Ciênc Solo 19:205–211Google Scholar
  224. Silver WL, Neff J, McGroddy M, Veldkamp E, Keller M, Cosme R (2000) Effects of soil texture on belowground carbon and nutrient storage in a lowland Amazonian forest ecosystem. Ecosystems 3:193–209Google Scholar
  225. Singleton PW, El Swaify SA, Bohlool BB (1982) Effect of salinity on Rhizobium growth and survival. Appl Environ Microbiol 44:884–890PubMedPubMedCentralGoogle Scholar
  226. Six J, Conant RT, Paul EA, Paustian K (2002) Stabilization mechanisms of soil organic matter: Implications for C-saturation of soils. Plant Soil 241:155–176Google Scholar
  227. Slininger PJ, Jackson MA (1992) Nutritional factors regulating growth and accumulation of phenazine-1-carboxylic acid by Pseudomonas fluorescens 2–79. Appl Microbiol Biotech 37:388–392Google Scholar
  228. Smalla K, Wieland G, Buchner A, Zock A, Parzy J, Kaiser S, Roskot N, Heuer H, Berg G (2001) Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed. Appl Environ Microbiol 67:4742–4751PubMedPubMedCentralGoogle Scholar
  229. Somerville L, Greaves MP, Domsch KH, Verstraete W, Poole NJ, van Dijk H, Anderson JPE (1987) Recommended laboratory tests for assessing the side effects of pesticides on soil microflora. In: Somerville L, Greaves MP (eds) Pesticide effects on soil microflora. Taylor and Francis, London, pp 205–219Google Scholar
  230. Sood SG (2003) Chemotactic response of plant-growth-promoting bacteria towards roots of vesicular-arbuscular mycorrhizal tomato plants. FEMS Microbiol Ecol 45:219–227Google Scholar
  231. Soto MJ, van Dillewijn P, Martı’nez-Abarca F, Jime’nez-Zurdo JI, Toro N (2004) Attachment to plant roots and nod gene expression are not affected by pH or calcium in the acid-tolerant alfalfa-nodulating bacteria Rhizobium sp. LPU83. FEMS Microbiol Ecol 48:71–77PubMedGoogle Scholar
  232. Spormann AM (1999) Gliding motility in bacteria: insights from studies of Myxococcus xanthus. Microbiol Mol Biol Rev 63:621–641PubMedPubMedCentralGoogle Scholar
  233. Stark JM, Firestone MK (1995) Mechanisms for soil-moisture effects on activity of nitrifying bacteria. Appl Environ Microbiol 61:218–221PubMedPubMedCentralGoogle Scholar
  234. Stengel P, Gelin S (2003) Soil, fragile interface. Science Publishers, Inc., New HampshireGoogle Scholar
  235. Stephens PM, Davoren CW, Doube BM, Ryder MH, Benger AM, Neate SM (1993) Reduced severity of Rhizoctonia solani disease on wheat seedlings associated with the presence of the earthworm Aporrectodea trapezoids (Lumbricidae). Soil Biol Biochem 25:1477–1484Google Scholar
  236. Stevenson FJ (1982) Humus chemistry. Wiley, New YorkGoogle Scholar
  237. Stevenson FJ (1994) Humus chemistry: genesis, composition, reactions. Wiley, New YorkGoogle Scholar
  238. Subba Rao NS (1993) Biofertilizers in agriculture and forestry. Oxford and IBH publishing Co. Pvt. Ltd., New Delhi, p 242Google Scholar
  239. Sudo S, Dworkin M (1972) Bacteriolytic enzymes produced by Myxococcus xanthus. J Bacteriol 110:236–245PubMedPubMedCentralGoogle Scholar
  240. Sumathi T, Janardhan A, Srilakhmi A, Sai Gopal DVR, Narasimha G (2012) Impact of indigenous microorganisms on soil microbial and enzyme activities. Arch Appl Sci Res 4(2):1065–1073Google Scholar
  241. Sumner ME, Rengasamy P, Naidu R (1998) Sodic soils: a reappraisal. In: Sumner ME, Naidu R (eds) Sodic soils: distribution, properties, management and environmental consequences. Oxford University Press, New York, pp 3–17Google Scholar
  242. Suslow TV (1982) Role of root colonising bacteria in plant growth. In: Mount MS, Lary GH (eds) Phytopathogenic Prokaryotes, vol 2. Academic, London, pp 187–223Google Scholar
  243. Sylvia DM, Fuhrmann JF, Hartel PG, Zuberer DA (2005) Principles and applications of soil microbiology. Pearson Education Inc., Upper Saddle RiverGoogle Scholar
  244. Tang C, Yu Q (1999) Impact of chemical composition of legume residues and initial soil pH on pH change of a soil after residue incorporation. Plant Soil 215:29–38Google Scholar
  245. Tang C, Sparling GP, McLay CDA, Raphael C (1999) Effect of short-term legume residue decomposition on soil acidity. Aust J Soil Res 37:561–573Google Scholar
  246. Theng BKG (1979) Formation and properties of clay-polymer complexes. Elsevier, New YorkGoogle Scholar
  247. Tisdale SL, Nelson WL, Beaton JD (1985) Soil fertility and fertilizers, 4th edn. MacMillan Publishing Company, New York, p 754Google Scholar
  248. Trabelsi D, Mhamdi R (2013) Microbial inoculants and their impact on soil microbial communities: a review. BioMed Res Int. doi: 10.1155/2013/863240 PubMedPubMedCentralGoogle Scholar
  249. Treonis AM, Wall DH (2005) Soil nematodes and desiccation survival in the extreme arid environment of the antarctic dry valleys. Integr Comp Biol 45:741–750PubMedGoogle Scholar
  250. Trivedi P, Pandey A, Palni LMS, Bag N, Tamang MB (2005) Colonization of rhizosphere of tea by growth promoting bacteria. Int J Tea Sci 4:19–25Google Scholar
  251. Trivedi P, Pandey A, Palni LMS (2012) Bacterial inoculants for field applications under mountain ecosystem: present initiatives and future prospects. In: Maheshwari DK (ed) Bacteria in agrobiology: plant probiotics. Springer, Berlin/Heidelberg, pp 15–44Google Scholar
  252. Tunlid A, White D (1992) Biochemical analysis of biomass, community structure, nutritional status, and metabolic activity of microbial communities in soil. In: Stotzky G, Bollag JM (eds) Soil biochemistry. Marcel Dekker, New York, pp 229–262Google Scholar
  253. Turnbull GA, Morgan JAW, Whipps JM, Saunders JR (2001) The role of bacterial motility in the survival and spread of Pseudomonas fluorescens in soil and in the attachment and colonisation of wheat roots. FEMS Microbiol Ecol 36(1):21–31PubMedGoogle Scholar
  254. van Elsas JD, Heijnen CE, van Veen JA (1991) The fate of introduced genetically engineered microorganisms in soil, in microcosms and the field: impact of soil textural aspects. In: MacKenzie DR, Henry SC (eds) Biological monitoring of genetically engineered plants and microbes. Agricultural Research Institute, Bethesda, pp 67–79Google Scholar
  255. van Overbeek LS, van Elsas JD, van Veen JA (2006) Pseudomonas fluorescens Tn5-B20 mutant RA92 responds to carbon limitation in soil. FEMS Microbiol Ecol 24(1):57–71Google Scholar
  256. van Veen JA, van Overbeek LS, van Elsas JD (1997) Fate and activity of microorganisms introduced into soil. Microbiol Mol Biol Rev 61(2):121–135PubMedPubMedCentralGoogle Scholar
  257. Vaughan DJ, Pattrick RAD, Wogelius RA (2002) Minerals, metals and molecules: ore and environmental mineralogy in the new millennium. Mineral Mag 66:653–676Google Scholar
  258. Velasco R, Burgoa R, Flores E, Hernandez E, Villa A, Vaca S (1995) Osmoregulation in Pseudomonas aeruginosa under hyperosmotic shock. Rev Lat Am Microbiol 37:209–216Google Scholar
  259. Velicer GJ, Vos M (2009) Sociobiology of the myxobacteria. Annu Rev Microbiol 63:599–623PubMedGoogle Scholar
  260. Vendeville A, Winzer K, Heurlier K, Tang CM, Hardie KR (2005) Making sense of metabolism: autoinducer-2, LuxS and pathogenic bacteria. Nature Rev 3:383–396Google Scholar
  261. Wang LH, He Y, Gao Y, Wu JE, Dong YH, He C, Wang SX, Weng LX, Xu JL, Tay L, Fang RX, Zhang LH (2004) A bacterial cell-cell communication signal with cross-kingdom structural analogues. Mol Microbiol 51:903–912PubMedGoogle Scholar
  262. Wardle DA (2002) Linking the aboveground and belowground components. Princeton University Press, PrincetonGoogle Scholar
  263. Wichern J, Wichern F, Joergensen RG (2006) Impact of salinity on soil microbial communities and the decomposition of maize in acidic soils. Geoderma 137:100–108Google Scholar
  264. Wididana GN (1990) Inducing disease suppressive soil through “effective microorganisms” (EM), M.S. Thesis. Department of Agriculture, University of the Ryukyus, OkinawaGoogle Scholar
  265. Williams P, Winzer K, Chan W, Camara M (2007) Look who’s talking: communication and quorum sensing in the bacterial world. Philos Trans R Soc Lond B Biol Sci 362:1119–1134PubMedPubMedCentralGoogle Scholar
  266. Worrall VS, Roughley RJ (1976) The effect of moisture stress on infection of Trifolium subterraneum L. by Rhizobium trifolii Dang. J Exp Bot 27:1233–1241Google Scholar
  267. Wu Y, Yu X, Wang H, Ding N, Xu J (2010) Does history matter? Temperature effects on soil microbial biomass and community structure based on the phospholipid fatty acid (PLFA) analysis. J Soils Sediments 10(2):223–230Google Scholar
  268. Xavier KB, Bassler BL (2003) LuxS quorum sensing: more than just a numbers game. Curr Opin Microbiol 6:191–197PubMedGoogle Scholar
  269. Xu RK, Coventry DR (2003) Soil pH changes associated with lupin and wheat plant materials incorporated in a red-brown earth soil. Plant Soil 250:113–119Google Scholar
  270. Xu JM, Tang C, Chen ZL (2006a) Chemical composition controls residue decomposition in soils differing in initial pH. Soil Biol Biochem 38:544–552Google Scholar
  271. Xu JM, Tang C, Chen ZL (2006b) The role of plant residues in pH change of acid soils differing in initial pH. Soil Biol Biochem 38:709–719Google Scholar
  272. Yan F, Schubert S, Mengel K (1996) Soil pH increase due to biological decarboxylation of organic anions. Soil Biol Biochem 28:617–624Google Scholar
  273. Yeates GW, Bongers T, de Goede RGM, Freckman DW, Georgieva SS (1993) Feeding habits in soil nematode families and genera—an outline for soil ecologists. J Nematol 25:315–331PubMedPubMedCentralGoogle Scholar
  274. Zhang F, Dashti N, Hynes RK, Smith DL (1996) Plant growth promoting rhizobacteria and soybean [Glycine max (L.) Merr.] nodulation and nitrogen fixation at suboptimal root zone temperatures. Ann Bot 77:453–459Google Scholar
  275. Zhang F, Dashti N, Hynes RK, Smith DL (1997) Plant growth promoting rhizobacteria and soybean [Glycine max (L.) Merr.] growth and physiology at suboptimal root zone temperatures. Ann Bot 79:243–249Google Scholar
  276. Zogg GP, Zak DR, Ringelberg DB, MacDonald NW, Pregitzer KS, White DC (1997) Compositional and functional shifts in microbial communities due to soil warming. Soil Sci Soc Am J 61:475–481Google Scholar

Copyright information

© Springer India 2015

Authors and Affiliations

  1. 1.Department of Microbiology, Institute of Biosciences and BiotechnologyChhatrapati Shahu Ji Maharaj UniversityKanpurIndia
  2. 2.Department of Environmental MicrobiologyBabasaheb Bhimrao Ambedkar UniversityLucknowIndia

Personalised recommendations