Skip to main content

Diversity, Functions, and Stress Responses of Soil Microorganisms

  • Chapter
  • First Online:
Plant Microbiome: Stress Response

Part of the book series: Microorganisms for Sustainability ((MICRO,volume 5))

Abstract

Plant-associated soil microorganisms colonize the rhizosphere, face many stresses, and play the significant role in the functioning of plants by influencing their growth and metabolism. Microorganisms are beneficial to decompose organic matter, for mineralization, and for the availability of plant nutrients in the soil. They also maintain the soil ecosystem and biogeochemical cycle. The soil microflora and microfauna cause synergistic or antagonistic effects on plants and face various biotic and abiotic stresses in the rhizosphere. Soil microbes make a gene pool involved in microbes-plant interactions. The main categories of soil microorganisms are bacteria, algae, protozoa, fungi, viruses, and multicellular animal parasites. The activities of soil microorganisms are influenced by interactions between soil physicochemical properties and environmental conditions. Bacteria are present in all types of soil and play their roles in atmospheric nitrogen fixation. In this review, the stress conditions in the rhizosphere, diversity of microorganisms, and their role in increasing soil fertility have been emphasized. Most of the microflora and microfauna are pathogenic in nature, but their positive interactions into the soil (in the rhizosphere) are very significant. Therefore, review of recent studies on diversity, stresses, and functions of soil microorganisms are described in this article.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  • Aneja KR, Pray J, Raman J (2008) Soil microbiology. In: Basic and applied microbiology. New Age International Publishers, New Delhi, pp 379–400

    Google Scholar 

  • ASA (1980) Nitrification inhibitors-potentials and limitations, ASA special publication no. 38. American Society of Agronomy/Soil Science Society of America, Midison

    Google Scholar 

  • Augustine SK, Bhavsar SP, Baserisalehi M, Kapadnis BP (2004) Isolation and characterization of antifungal activity of an actinomycete of soil origin. Indian J Exp Biol 42:928–932

    CAS  PubMed  Google Scholar 

  • Avis PG (2008) Ectomycorrhizal fungal communities in two North American oak forests respond to nitrogen addition. New Phytol 179(2):472–483

    Article  CAS  PubMed  Google Scholar 

  • Ayalaja CF, Pedro A (2012) Stress response in microbiology. In: Jose M. Reguena (ed) Caister Academic Press, Madrid

    Google Scholar 

  • Bardgett RD, Putten WH (2014) Belowground biodiversity and ecosystem functioning. Nature 515:505–511

    Article  CAS  PubMed  Google Scholar 

  • Barret M, Morrissey JP, O’Gara F (2011) Functional genomics analysis of plant growth-promoting rhizobacterial traits involved in rhizosphere competence. Biol Fertil Soils 47:729–747

    Article  CAS  Google Scholar 

  • Beijerinck MW (1901) UberoligonitrophileMikroben.zbl.Backt 7:561–582

    Google Scholar 

  • Berdy J (2005) Bioactive microbial metabolites. J Antibiot (Tokyo) 58:1–26

    Article  CAS  Google Scholar 

  • Berg G, Alvi M, Schmidt C, Zachow C, Egamberdieva D, Kamilova F, Lugtenberg B (2013) Biocontrol and osmoprotection for plants under salinated conditions. In: de Bruijn FJ (ed) Molecular microbiology, ecology of the rhizosphere. Wiley, Blackwell. https://doi.org/10.1002/9781118297674.ch55

    Google Scholar 

  • Bhat AK (2013) Preserving microbial diversity of soil ecosystem: a key to sustainable productivity. Int J Curr Microbiol App Sci 2(8):85–101

    Google Scholar 

  • Bibb MJ (2005) Regulation of secondary metabolism in Streptomycetes. Curr Opin Microbiol 8:208–215

    Article  CAS  PubMed  Google Scholar 

  • Borken W, Matzner E (2009) Reappraisal of drying and wetting effects on C and N mineralization and fluxes in soils. Glob Chang Biol 15:808–824

    Article  Google Scholar 

  • Brady NC (1995) The nature and properties of soils, 10th edn. Prentice-Hall, New Delhi

    Google Scholar 

  • Brady NC (2001) The nature and properties of soils, 10th edn. Prentice-Hall, New Delhi

    Google Scholar 

  • Brady NC, Weil RR (2008) The nature and properties of soils, 14th edn. Printice Hall, Upper Saddle River

    Google Scholar 

  • Broadbent FE, Nakashima T, Chang GY (1982) Estimation of nitrogen fixation by Isotope dilution in field and green house experiments. Agron J 74:625–628

    Article  Google Scholar 

  • Burns RC, Hardy RWF (1975) Nitrogen fixation in bacteria and higher plants. Springer, Berlin

    Book  Google Scholar 

  • Chanthasena P, Nantapong N (2016) Biodiversity of antimicrobial-producing actinomycetes strains isolated from dry Dipterocarp forest soil in Northeast Thailand. Braz Arch Biol Technol 59:145–151

    Article  CAS  Google Scholar 

  • Deshmukh AA, Vidhale NN (2015) Characterization of novel antibacterial Actinomycetes strain N8 from saline soil of Vidarbha region. Int J Life Sci Biotechnol Pharma Res 4(1):22–25

    CAS  Google Scholar 

  • Doi T, Matsumoto H, Oshita N, Takemoto Y, Shinada T (2006) Microflora analysis on hydrogen fermentation of feedstock wastes. J Water Waste 48:784–790

    CAS  Google Scholar 

  • Doi T, Hagiwara Y, Abe J, Morita S (2007) Analysis of rhizosphere bacteria of rice cultivated in Andisol lowland and upland fields using molecular biological methods. Plant Roots 1:66–74

    Article  CAS  Google Scholar 

  • Druzhinina IS, Seidl-Seiboth V, Herrera-Estrella A et al (2011) Trichoderma: the genomics of opportunistic success. Nat Rev Microbiol 9:896

    Article  CAS  Google Scholar 

  • Du L, Liu W (2012) Occurrence, fate and ecotoxicity of antibiotics in agroecosystems. A review. Agron Sustain Dev 32:309–327

    Article  CAS  Google Scholar 

  • Ferrer VR, Voinnet O (2009) Roles of plant small RNAs in biotic stress responses. Annu Rev Plant Biol 60:485–510

    Article  CAS  Google Scholar 

  • Garland JL (1997) Analysis and interpretation of community-level physiological profile in microbial ecology. FEMS Microb Ecol 24:289–300

    Article  CAS  Google Scholar 

  • George M, George G, Hatha AM (2011) Diversity and antibacterial activity of actinomycetes from wetland soil. South Pac J Nat Appl Sci 28(1):52–57

    Article  Google Scholar 

  • Griffith P, Shiah FK, Gloersen K, Ducklow HW, Fletcher M (1994) Activity and distribution of attached bacteria in Chesapeake Bay. Mar Ecol Prog Ser 108:1–10

    Article  Google Scholar 

  • Griffiths BS (1994) Microbial-feeding nematodes and protozoa in soil: their effects on microbial activity and nitrogen mineralization in decomposition hotspots and the rhizosphere. Plant Soil 164:25–33

    Article  CAS  Google Scholar 

  • Gul S, Whalen JK (2016) Biochemical cycling of nitrogen and phosphorus in biochar-amended soils. Soil Biol Biochem 103:1–15

    Article  CAS  Google Scholar 

  • Hakemian AS, Rosenzweig AC (2007) The biochemistry of methane oxidation. Annu Rev Biochem 76:223–241

    Article  CAS  PubMed  Google Scholar 

  • Hartmann FE, Vallet AS, McDonald BA, Croll D (2017) A fungal wheat pathogen evolved host specialization by extensive chromosomal rearrangements. ISME J 11:1189–1204. https://doi.org/10.1038/15mej.2016.196

    Article  CAS  PubMed  Google Scholar 

  • Herron PM, Gage DJ, Cardon ZG (2010) Microscale water potential gradients visualized in soil around plant root tips using microbiosensors. Plant Cell Environ 33:199–210

    Article  CAS  PubMed  Google Scholar 

  • Hiinninghaus M, Koller R, Kramer S, marhan S, Ellen K, Bonkowski M (2017) Changes in bacterial community composition and soil respiration indicate rapid successions of protest grazers during mineralization of maize crop residues. Pedobiologia 62:1–8

    Article  Google Scholar 

  • Hoffmeister D, Keller NP (2007) Natural products of filamentous fungi: enzymes, genes and their regulation. Nat Prod Rep 24:393–416

    Article  CAS  PubMed  Google Scholar 

  • Hooks CRR, Wang KH, Ploeg A, McSorley R (2010) Using marigold (Tagetes spp.) as a cover crop to protect crops from plant parasitic nematodes. Appl Soil Ecol 46:307–320

    Article  Google Scholar 

  • Hoorman JJ (2011) The role of soil protozoa and nematodes. Agriculture and Natural resources, Ohio State University, Columbus, pp 1–4

    Google Scholar 

  • Howell DM, Kenzie DM (2017) Using bioavailable nutrients and microbial dynamics to assess soil type and placement depth in reclamation. Appl Soil Ecol 116:87–95

    Article  Google Scholar 

  • Hoyle FC, Baldock JA, Murphy DV (2011) Soil organic carbon-role in rainfed farming systems with particular reference to Australian conditions. Springer, Dordrecht

    Google Scholar 

  • Hui D, Deng Q, Tian H, Luo Y (2016) Climate change and carbon sequestration in forest ecosystems. In: Suzuki T, Lackner M (eds) Handbook of climate change migration and application. Springer, Berlin, pp 555–594

    Google Scholar 

  • Ingham ER (2009) Soil biology primer, chapter 4: soil fungus. Soil and Water Conservation Society, Ankeny, pp 22–23

    Google Scholar 

  • IPCC (2006) IPCC guidelines for national greenhouse gas inventories. In: Egghleston HS, Bunendia L, Miwa K, Ngara T and Tanabe K (eds). Tokyo

    Google Scholar 

  • Islam KR (2008) Lecture on soil physics, personal collection of K. Islam. Ohio State University, School of natural resources, Columbus, Ohio

    Google Scholar 

  • Janga MR, Raoof MA, Ulaganthan K (2017) Effective biocontrol of Fusarium wilt in castor (Ricinuscommunis L.) with Bacillus sp., in pot experiment. Rhizosphere 3(1):50–52

    Article  Google Scholar 

  • Jeya K, Kiruthika K, Veerapagu M (2013) Isolation of antibiotic producing Streptomyces sp. from soil of Perambalur district and a study on the antibacterial activity against clinical pathogens. Int J Pharm Tech Res 5:1207–1211

    Google Scholar 

  • Jimtha CJ, Jishma P, Shreelekha S, Chitra S, Radhekrishnan EK (2017) Antifungal properties prodigiosin producing rhizospheric serratia sp. Rhizosphere 3(1):105–108

    Article  Google Scholar 

  • Jorquera MA, Shaharoona B, Nadeem SM, de La Luz Mora M, Crowley DE (2012) Plant growth-promoting rhizobacteria associated with ancient clones of creosote bush (Larrea tridentata). Microb Ecol 64:1008–1017

    Google Scholar 

  • Kaiser K, Kalbitz K (2012) Cycling downwards- dissolved organic matter in soils. Soil Biol Biochem 52:29–32

    Article  CAS  Google Scholar 

  • Kamble PN, Baath E (2016) Comparison of fungal and bacterial growth after alleviating induced N-limitation in soil. Soil Biol Biochem 103:97–105

    Article  CAS  Google Scholar 

  • Kar G, Hilger D, Schoenau JJ, Peak D (2017) Effect of plant growth and time on phosphorus speciation in a manure-amended prairie soil under controlled conditions. Rhizosphere. https://doi.org/10.1016/j.rhisph.2017.05.004

  • Kashaija IN, Mcintyre BD, Ssali H, Kizito F (2004) Spatial distribution of roots, nematode populations and root necrosis in highland banana in Uganda. Nematology 6:7–12

    Article  Google Scholar 

  • Kawasaki A, Watson ER, andKertesz MA (2012) Indirect effect of polycyclic aromatic hydrocarbon contamination on microbial communities in legume and grass rhizospheres. Plant Soil 358:169–182

    Article  CAS  Google Scholar 

  • Klumpp K, Fontaine S, Attard E, Le Roux X, Gleixner G, Soussana JF (2009) Grazing triggers soil carbon loss by altering plant roots and their control on soil microbial community. J Ecol 97:876–885

    Article  CAS  Google Scholar 

  • Koch B, Worm J, Jonson LE, Hojberg O, Nymbroe O (2001) Carbon limitation induces sigma (S)-dependent gene expression in Pseudomonas fluorescens in soil. Appl Environ Microbiol 67:3363–3370

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Koele N, Turpanlt MP, Hildebrand EE, Uroz S, Klett EF (2009) Interaction between mycorrhizal fungi and mycorrhizosphere bacteria during mineral weathering. Soil Biol Biochem 9:1935–1942

    Article  CAS  Google Scholar 

  • Koenning SR, Overstreet C, Noling JW, Donald PA, Becker JO, Fortnum BA (1999) Survey of crop losses in response to phytoparasitic nematodes in the United States in 1999. Suppl J Nematol 31:587–618

    CAS  Google Scholar 

  • Kogel KH, Franken P, Huckelhoven R (2006) Endophyte or parasite-what decides? Curr Opin Plant Biol 9:358–363

    Article  PubMed  Google Scholar 

  • Kohout P, Tedersoo L (2017) Effect of soil moisture on root-associated fungal communities of Erica dominans in Drakensberg mountains in South Africa. Micorrhiza 27:1–10

    Article  CAS  Google Scholar 

  • Kowalchuk G, Buma DS, de Boer W, Klinkhamer PGL, van Veen JA (2002) Effects of above- ground plant species composition and diversity on the diversity of soil borne microorganisms. Anton Leeuw Int J Gen Mol Microbiol 81:509–520

    Article  Google Scholar 

  • Kuzyakov Y (2010) Primary effects: interactions between living and dead organic matter. Soil Biol Biochem 42(9):1363–1371

    Article  CAS  Google Scholar 

  • Lal R (1987) Tropical ecology and physical Edaphology. Wiley, New York

    Google Scholar 

  • Lal R (2004) Soil carbon sequestration impacts on global climate change and global security. Science 403:1623–1627

    Article  CAS  Google Scholar 

  • Lambert DH, Baker DE, Cole Jr H (1979) The role of mycorrhizae in the interactions of phosphorus with zinc, copper, and other elements. Soil Sci Soc Amer 43:976–980

    Article  CAS  Google Scholar 

  • Latge JP (2017) Immune evasion: face changing in the fungal opera. Nat Microbiol 2:16266–16269

    Article  CAS  PubMed  Google Scholar 

  • Lavelle P, Spain A (2001) Soil Ecology. Kluwer Academic Publishers, Dordrecht

    Book  Google Scholar 

  • Leckie SE, Prescott CE, Grayston SJ, Neufeld JD, Mohn WW (2004) Comparison of chloroform fumigation extraction, phospholipid fatty acid and DNA methods to determine microbial biomass in forest humus. Soil BiolBiochem 36:532–536

    Article  CAS  Google Scholar 

  • Leffelaar PA (1986) Dynamics of anaerobiosis, denitrification and water in a soil aggregate. Soil Sci 142:352–366

    Article  CAS  Google Scholar 

  • Lugtenberg B, Kamilova F (2009) Plant growth promoting rhizobacteria. Annu Rev Microbiol 63:541–558

    Article  CAS  PubMed  Google Scholar 

  • Ma Z, Jacobson FE, Geidroc DP (2009) Coordination chemistry of bacterial metal transport and sensing. Chem Rev 109:4644–4681

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • MacFadyen A (1963) Soil Organisms. In: Doekson J, Drift JV (eds). North-Holland Public Co., Amsterdam

    Google Scholar 

  • Manzoni S, Schimel JP, Porporato A (2012) Responses of soil microbial communities to water stress: results from a meta-analysis. Ecology 93(4):930–938

    Article  PubMed  Google Scholar 

  • Mela F, Fritsche K, de Boer W, van Veen JA, de Graaff LH, van den Berg M, andLeveau JHJ (2011) Dual transcriptional profiling of a bacterial/fungal confrontation: Collimonas fungivorans versus Aspergillus niger. ISME J 5:1494–1504

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mendes R, Garbeva P, Raaijmakers JM (2013) The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol Rev 37(5):634–663

    Article  CAS  PubMed  Google Scholar 

  • Miransari M (2013) Soil microbes and the availability of soil nutrients. Acta Physiol Plant 35(11):3075–3084

    Article  CAS  Google Scholar 

  • Moore-Kucera J, Dick RP (2008) PLFA profiling of microbial community structure and seasonal shifts in soils of a Douglas- fir chronosequence. Microb Ecol 55(3):500–511

    Article  PubMed  Google Scholar 

  • Neufeld JD, Mohn WW (2005) Unexpectedly high bacterial diversity in arctic tundra relative to boreal forest soils, revealed by serial analysis of ribosomal sequence tags. Appl Environ Microbiol 71:5710–5718

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Newman MM, Hoilett N, Lorenz N, Dick RP, Liles MR, Ramsier C, Kloepper JW (2016) Glyphosate effects on soil rhizosphere-associated bacterial communities. Sci Total Environ 543:155–160

    Article  CAS  PubMed  Google Scholar 

  • Nicolas V, Platsaki S, Basle A, Allen SJ, Peterson NG, Crombie AT, Deninson C (2015) A four helix bundle stores copper for methane oxidation. Nature 525:140–143

    Article  CAS  Google Scholar 

  • Oka Y, Shapira N, Fine P (2007) Control of root-knot nematodes in organic farming systems by organic amendments and soil solarization. Crop Prot 26:1556–1565

    Article  Google Scholar 

  • Panagos P, Borrell P, Meusburger K, Alewell C, Lugato E, Montanarella L (2015) Estimating the soil erosion cover-management factor at European scale. Land Use Policy 48:38–50

    Article  Google Scholar 

  • Pandey P, Chauhan D, Pandey B (2017) Isolation, identification and seasonal distribution of soil fungi in Achanakmar Bilaspur. Indian J Sci Res 13(2):51–56

    Google Scholar 

  • Panikov NS, Flanagan PW, Oechel WC, Mastepanov MA, Christenson TR (2006) Microbial activity in soils frozen to below -39 degrees C. Soil BiolBiochem 38:3520

    Article  CAS  Google Scholar 

  • Parungao MM, Maceda EBG, Villano MAF (2007) Screening of antibiotic-producing actinomycetes from marine, brackish and terrestrial sediments of Samal Island. Philipp J Res Sci Comput Eng 4(3):29–38

    Google Scholar 

  • Patrick WH Jr (1982) Nitrogen transformations in submerged soils. In: Stevenson FJ (ed) Nitrogen in agricultural soils, Agronomy series no. 22. American Society of Agronomy/Soil Science Society of America, Midison

    Google Scholar 

  • Penman TD, Pike DA, Webb JK, Shine R (2010) Predicting the impact of climate change on Australia’s most endangered snake, Hoplocephalus bungaroides. Diver Distribut 16:109–118

    Article  Google Scholar 

  • Pieterse CMJ (2012) Prime time for transgenerational defense. Plant Physiol 158:545

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Poomthongdee N, Daungmal K, Panthom-aree W (2015) Acidophilic actinomycetes from rhizosphere soil: diversity and properties beneficial to plants. J Antibiot 68:106–114. https://doi.org/10.1111/1574-6976.12028

    Article  CAS  PubMed  Google Scholar 

  • Qiang X, Weiss M, Kogel KH, Schafer P (2012) Piriformospora indica and mutualistic basidiomycete with an exceptionally large plant host range. Mol Plant Pathol 13:508–518

    Article  CAS  PubMed  Google Scholar 

  • Rainey PB (1999) Adaptation of Pseudomonas fluorescens to the plant rhizosphere. Environ Microbiol 1:243–257

    Article  CAS  PubMed  Google Scholar 

  • Raudales RE, Stone E, McSpadden Gardener BB (2009) Seed treatment with 2, 4 diacetylphloroglucinol-producing pseudomonads improves crop health in low pH soils by altering pattern of nutrients uptake. Phytology 99:506–511

    CAS  Google Scholar 

  • Reader JS, Ordoukhanian PT, Kim JG, de Crecy-Lagard V, Hwang I, Farrand S, Schimmel P (2005) Major biocontrol of plant tumors targets tRNA synthetase. Science 309:1533

    Article  CAS  PubMed  Google Scholar 

  • Romero-Olivares L, Allison SD, Treseder KK (2017) Soil microbes and their response to experimental warming over time: a meta-analysis of field studies. Soil Biol Biochem 107:32–40

    Article  CAS  Google Scholar 

  • Sanaullah M, Blagodatskaya E, Chabbi A, Rumpel C, Kuzyakov Y (2011) Drought effects on microbial biomass and enzyme activities in rhizosphere of grasses depend on plant community composition. Appl Soil Ecol 48:38–44

    Article  Google Scholar 

  • Schmidt MWI, Torn MS, Abivens S, Dittmar T, Guggenberger G, Janssens IA, Kleber M, Kögel-Knabner I, Lehmann J, Manning DA, Nannipieri P, Rasse DP, Weiner S, Trumbore SE (2011) Persistence of soil organic matter as an ecosystem property. Nature 478:49–56

    Article  CAS  PubMed  Google Scholar 

  • Selvameenal L, Radhakrishnan M, Balagurunathan R (2009) Antibiotic pigment from desert soil actinomycetes; biological activity, purification and chemical screening. Indian J Pharm 71(5):499–504

    Article  CAS  Google Scholar 

  • Sharma CP (2006) Plant Micronutrients, 1st edn. Science, Enfield, pp 5–15

    Google Scholar 

  • Sharma N, Sudarshan Y, Sharma R, Singh G (2008) RAPD analysis of soil microbial diversity in Western Rajasthan. Curr Sci 94(8):1058–1061

    CAS  Google Scholar 

  • Shetty PR, Buddana SK, Tatipamula VB, Naga YVV, Ahmad J (2014) Production of polypeptide antibiotic from Streptomyces parvulus and its antibacterial activity. Braz J Microbiol 45(1):303–312

    Article  PubMed  PubMed Central  Google Scholar 

  • Siddikee M, Chauhan P, Anandham R, Han GH, Sa T (2010) Isolation, characterization and use for plant growth promotion under salt stress, of ACC deaminase-producing halotolerant bacteria derived from coastal soil. J Microbiol Biotechnol 20:1577–1584

    Article  CAS  PubMed  Google Scholar 

  • Singh A, Bahel GS (1993) Phosphate equilibria in soils in relation to added phosphorus, Sesbania aculeate incorporation and cropping- a study of solubility relationship. J Indian Soc Soil Sci 41:233–237

    CAS  Google Scholar 

  • Singh BK, Bardgett RD, Smith P, Dave S (2010) Microorganisms and climate change: Terrestrial feedbacks and mitigation options. Nat Rev Microbiol 8:779–790

    Article  CAS  PubMed  Google Scholar 

  • Singh K, Pandey SN, Mishra A (2015) Preference of heavy metals accumulation, tolerance limit and biochemical responses of Eichhornia crassipes (Mart.) exposed to industrial waste water. Int J Curr Res 7(1):11818–11822

    Google Scholar 

  • Smith KP, Goodman RM (1999) Host variation for interactions with beneficial plant-associated microbes. Annu Rev Phytopathol 37:473–491

    Article  CAS  PubMed  Google Scholar 

  • Smith ML, Bruhn JN, Anderson JB (1992) The fungus Armillaria bulbosa is among the largest and oldest living organism. Nature 356:428–431

    Article  Google Scholar 

  • Stipanuk MH (1986) Metabolism of sulfur-containing amino acids. Annu Rev Nutr 6:179–209

    Article  CAS  PubMed  Google Scholar 

  • Stotzky G (1997) Soil as an environment for microbial life. In: JDV E (ed) Modern soil microbiology. Trevors JT and Wellington/Marcel Dekker, New York, pp 20–28

    Google Scholar 

  • Sturz AV, Kimpinski J (2004) Endoroot bacteria derived from marigold (Tagetes spp.) can decrease soil population densities of root-lesion nematodes in the potato root zone. Plant Soil 262:241–249

    Article  CAS  Google Scholar 

  • Subramani R, Aalbersberg W (2012) Marine actinomycetes: an ongoing source of novel bioactive metabolites. Microbiol Res 167:571–580

    Article  CAS  PubMed  Google Scholar 

  • Sylvia DM, Hartel PG, FuhrmannJJ JDA (2005) In: David MS (ed) Principals and applications of microbiology, 2nd edn. Pearson Printice hall, Upper Saddle River

    Google Scholar 

  • Thilakrathana MS, Raizada MN (2017) A meta-analysis of the effectiveness of diverse rhizobia inoculants on soybean traits under field conditions. Soil BiolBiochem 105:177–196

    Article  CAS  Google Scholar 

  • Tilman D, Dowing JA (1994) Biodiversity and stability in grasslands. Nature 367:363–365

    Article  Google Scholar 

  • Tongway D, Ludwig J (1996) Rehabilitation of semiarid landscapes in Australia, restoring productive soil patches. Restora Ecol 4:388–397

    Article  Google Scholar 

  • Tongway DJ, Ludwig JA (2005) Heterogeneity in arid and semi-arid lands. In: Lovett GM, Turner MG, Jones GG, Weathers KC (eds) Ecosystem function in heterogeneous landscapes. Springer, New York, pp 189–205

    Chapter  Google Scholar 

  • Torsvik V, Ovreas I (2002) Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 5:240–245

    Article  CAS  PubMed  Google Scholar 

  • Unkovich (2003) Symbiotic nitrogen fixation and fertilizers in Australian agriculture. In: Proceedings of the 12th Australian nitrogen fixation conference, Glenelg

    Google Scholar 

  • Upadhyay SK, Singh DP, Saikia R (2009) Genetic diversity of plant growth promoting rhizobacteria isolated from rhizospheric soil of wheat under saline condition. Curr Microbiol 59:489–496

    Article  CAS  PubMed  Google Scholar 

  • Uphoff N, Ball AS, Fernandes E, Herren H, Husson O, Laing M, Palm C, Pretty J, Sanchez P, Sanginga N, Thies J (2006) Biological approaches to sustainable soil systems. CRC Press/Francis & Taylor, London

    Book  Google Scholar 

  • Verma P, Pandey SN (2016) Effect of integrated nutrient management in alluvial soil on growth and biochemical responses of radish. J Biol Chem Res 33(1):34–39

    Google Scholar 

  • Vyas RK, Mathus K (2002) Trichoderma spp. in cumin rhizosphere and their potential in suppression of wilt. Indian Phytopathol 55:455–457

    Google Scholar 

  • Waldrop MP, Firestone MK (2006) Response of microbial community composition and function to soil climate change. MicrobEcol 52:716–724

    CAS  Google Scholar 

  • Wall DH, Virginia RA (1999) Controls on soil biodiversity: insights from extreme environments. Appl Soil Ecol 13:137–150

    Article  Google Scholar 

  • Watt M, Kirkegaard JA, Passioura J (2006a) Rhizosphere biology and crop productivity- a review. Aust J Soil Res 44:299–317

    Article  Google Scholar 

  • Watt M, Silk W, Passioura J (2006b) Rates of root and organism growth, soil conditions and temporal and spatial development of the rhizosphere. Ann Bot 97:839–855

    Article  PubMed  PubMed Central  Google Scholar 

  • White PM, Charls WR (2009) Tillage effects on microbial and carbon dynamics during plant residue decomposition. Soil Sci Soc Am J 73:138–145. https://doi:10.2136/sssaj2007.0384

    Google Scholar 

  • Wolters V (2001) Biodiversity of soil animal and its function. Eur J Soil Biol 37:221–227

    Article  Google Scholar 

  • Yadav A, Pandey SN (2015) Effect of integrated nutrient management on the growth, biochemical constituents and yield of tomato (Lycopersicon esculentum Mill.) J Biol Chem Research 32(2):835–838

    Google Scholar 

  • Young IM, Crawford JW (2004) Interactions and self-organization in the soil-microbe complex. Science 304:1634–1637

    Article  CAS  PubMed  Google Scholar 

  • Zhou X, Guo Z, Chen C, Jia Z (2017) Soil microbial community structure and diversity are largely influenced by soil pH and nutrient quality in 78-year-old tree plantations. Biogeosciences 14:2101–2111

    Article  Google Scholar 

Download references

Acknowledgment

I acknowledge Dr. Shalini Srivastava, Department of Botany, University of Lucknow, Lucknow, for the suggestions and providing reference materials during the preparation of the article.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Mirza Mohammad Abid Ali Khan .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Pandey, S.N., Abid, M., Abid Ali Khan, M.M. (2018). Diversity, Functions, and Stress Responses of Soil Microorganisms. In: Egamberdieva, D., Ahmad, P. (eds) Plant Microbiome: Stress Response. Microorganisms for Sustainability, vol 5. Springer, Singapore. https://doi.org/10.1007/978-981-10-5514-0_1

Download citation

Publish with us

Policies and ethics