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Soil Microbiome for Enhanced Crop Productivity

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Mining of Microbial Wealth and MetaGenomics

Abstract

Current agricultural practices demand for low-input technologies with an objective to scale down the synthetic fertilizers and pesticides usage in order to enhance the sustainability in food production and restore ecosystem functioning. Regardless of much understanding of the essential role played by the soil microbiome in agriculture, we still have a limited knowledge of the multifarious response of microbial heterogeneity. To explore this covert attribute of soil microbial diversity, there is a need to focus upon the infinite ways by virtue of which soil microbiome helps in sustainable agriculture. There is limited access to highly diverse and dynamic communities of microbiome in soil due to inability of culture techniques in laboratory. With the advent of next-generation sequencing (NGS) techniques and high-throughput analysis, researchers gained new opportunities to investigate undetermined composition of soil microorganisms. Among rapidly growing field of research, the role of metagenomics is crucial in studying uncultured microbes to comprehend the actual microbial diversity and pertinent cooperation, evolution, and functions in diverse environment. Soil microbiologists are putting efforts in analyzing the phylogenetic diversity of soil niches and subsequently attempting to describe the functions of these soil inhabitants at trophic levels for improvement of soil fertility and productivity for the future generation.

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References

  • Adesemoye AO, Torbert HA, Kloepper JW (2008) Enhanced plant nutrient use efficiency with PGPR and AMF in an integrated nutrient management system. Can J Microbiol 54:876–886. doi:10.1139/w08-081

    Article  CAS  PubMed  Google Scholar 

  • Aguirre-Garrido JF, Montiel-Lugo D, Rodríguez CH, Torres-Cortes G, Millán V, Toro N, Abarca FM, Ramírez-Saad HC (2012) Bacterial community structure in the rhizosphere of three cactus species from semi-arid highlands in central Mexico. Antonie Van Leeuwenhoek 101:891–904. doi:10.1007/s10482-012-9705-3

    Article  PubMed  Google Scholar 

  • Ahmad F, Ahmad I, Khan MS (2008) Screening of free-living rhizospheric bacteria for their multiple plant growth promoting activities. Microbiol Res 163:173–181. doi:10.1016/j.micres.2006.04.001

    Article  CAS  PubMed  Google Scholar 

  • Alabouvette C, Hoper H, Lemanceau P, Steinberg C (1996) Soil suppressiveness to diseases induced by soil-borne plant pathogens. In: Stotzky G, Bollag JM (eds) Soil biochemistry. Marcel Dekker, New York, pp 371–413

    Google Scholar 

  • Alagawadi AR, Gour AC (1988) Associative effect of Rhizobium and phosphate solubilizing bacteria on the yield and nutrient uptake of chickpea. Plant Soil 105:241–246. doi:10.1007/bf02376788

    Article  Google Scholar 

  • Amellal N, Burtin G, Bartoli F, Heulin T (1998) Colonization of wheat roots by an exopolysaccharide producing Pantoea agglomerans strain and its effect on rhizosphere soil aggregation. Appl Environ Microbiol 64:3740–3747

    CAS  PubMed  PubMed Central  Google Scholar 

  • Aroca R, Porcel R, Ruiz Lozano JM (2012) Regulation of root water uptake under abiotic stress conditions. J Exp Bot 63:43–57. doi:10.1093/jxb/err266

    Article  CAS  PubMed  Google Scholar 

  • Asaka O, Shoda M (1996) Biocontrol of Rhizoctonia solani damping-off of tomato with Bacillus subtilis RB14. Appl Environ Microbiol 62:4081–4085

    CAS  PubMed  PubMed Central  Google Scholar 

  • Atamna IN, Finkel OM, Glaser F, Sharon I, Schneider R, Post AF (2012) Microbial rhodopsins on leaf surfaces of terrestrial plants. Environ Microbiol 14:140–146. doi:10.1111/j.1462-2920.2011.02554

    Article  CAS  Google Scholar 

  • Audenaert K, Pattery T, Cornelis P, Höfte M (2002) Induction of systemic resistance to Botrytis cinerea in tomato by Pseudomonas aeruginosa 7NSK2: role of salicylic acid, pyochelin and pyocyanin. Mol Plant-Microbe Interact 15:1147–1156. doi:10.1094/MPMI.2002.15.11.1147

    Article  CAS  PubMed  Google Scholar 

  • Azcón R, Barea JM (2010) Mycorrhizosphere interactions for legume improvement. In: Khan MS, Zaidi A, Musarrat J (eds) Microbes for legume improvement. Springer, Vienna, pp 237–271

    Chapter  Google Scholar 

  • Babana AH, Antoun H (2006) Effect of Tilemsi phosphate rock solubilizing microorganisms on phosphorus uptake and yield of field grown wheat (Triticum aestivum L.) in Mali. Plant Soil 287:51–58. doi:10.1007/s11104-006-9060-0

    Article  CAS  Google Scholar 

  • Bardi L, Malusà E (2012) Drought and nutritional stresses in plant: alleviating role of rhizospheric microorganisms. In: Haryana N, Punj S (eds) Abiotic stress: new research. Nova Science, Hauppauge, pp 1–57

    Google Scholar 

  • Barea JM, Pozo MJ, Azcón R, Azcón Aguilar C (2013) Microbial interactions in the rhizosphere. In: de Bruijn FJ (ed) Molecular microbial ecology of the rhizosphere. Wiley, Hoboken, pp 29–44

    Chapter  Google Scholar 

  • Barrios E (2007) Soil biota, ecosystem services and land productivity. Ecol Econ 64:269–285. doi:10.1016/j.ecolecon.2007.03.004

    Article  Google Scholar 

  • Barzana G, Aroca R, Bienert GP, Chaumont F, Ruiz-Lozano JM (2014) New insights into the regulation of aquaporins by the arbuscular mycorrhizal symbiosis in maize plants under drought stress and possible implications for plant performance. Mol Plant-Microbe Interact 27:349–363. doi:10.1094/MPMI-09-13-0268-R

    Article  CAS  PubMed  Google Scholar 

  • Bashan Y, de-Bashan LE, Prabhu SR, Hernandez JP (2014) Advances in plant growth-promoting bacterial inoculant technology: formulations and practical perspectives (1998–2013). Plant Soil 378:1–33. doi:10.1007/s11104-013-1956-x

    Article  CAS  Google Scholar 

  • Berg G (2009) Plant-microbe interactions promoting plant growth and health: perspectives for controlled use of microorganisms in agriculture. Appl Microbiol Biotechnol 84:11–18. doi:10.1007/s00253-009-2092-7

    Article  CAS  PubMed  Google Scholar 

  • Bhattacharyya PN, Jha DK (2012) Plant growth-promoting rhizobacteria (PGPR): emergence in agriculture. World J Microbiol Biotechnol 28:1327–1350. doi:10.1007/s11274-011-0979-9

    Article  CAS  PubMed  Google Scholar 

  • Borie F, Rubio R, Morales A, Curaqueo G, Cornejo P (2010) Arbuscular mycorrhizae in agricultural and forest ecosystems in Chile. J Soil Sci Plant Nutr 10:185–206. doi:10.4067/S0718-95162010000100001

    Article  Google Scholar 

  • Brodie EL, DeSantis TZ, Parker JP, Zubietta IX, Piceno YM, Andersen GL (2007) Urban aerosols harbor diverse and dynamic bacterial populations. Proc Natl Acad Sci U S A 104:299. doi:10.1073/pnas.0608255104

    Article  CAS  PubMed  Google Scholar 

  • de Bruijn FJ (2011) Handbook of molecular microbial ecology I: metagenomics and complementary approaches. Wiley, Hoboken

    Book  Google Scholar 

  • Buée M, De Boer W, Martin F, van Overbeek L, Jurkevitch E (2009) The rhizosphere zoo: an overview of plant-associated communities of microorganisms, including phages, bacteria, archaea, and fungi, and of some of their structuring factors. Plant Soil 321:189–212. doi:10.1007/s11104-009-9991-3

    Article  CAS  Google Scholar 

  • Bulgarelli D, Rott M, Schlaeppi K, Ver Loren van Themaat E, Ahmadinejad N, Assenza F, Rauf P, Huettel B, Reinhardt R, Schmelzer E (2012) Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 488:91–95. doi:10.1038/nature11336

    Article  CAS  PubMed  Google Scholar 

  • Bulgarelli D, Oter RG, McHardy AC, Lefert PS (2015) Structure and function of the bacterial root microbiota in wild and domesticated barley. Cell Host Microbe 17:392–403. doi:10.1016/j.chom.2015.01.011

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Calvo P, Nelson L, Kloepper JW (2014) Agricultural uses of plant biostimulants. Plant Soil 383:3–41. doi:10.1007/s11104-014-2131-8

    Article  CAS  Google Scholar 

  • Calvo-Polanco M, Sánchez-Romera B, Aroca R (2013) Arbuscular mycorrhizal fungi and the tolerance of plants to drought and salinity. In: Aroca R (ed) Symbiotic endophytes. Springer, Berlin, pp 271–288

    Chapter  Google Scholar 

  • Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M, Gormley N, Gilbert JA, Smith G, Knight R (2012) Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 6:1621–1624. doi:10.1038/ismej.2012.8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Carvalhais LC, Dennis PG, Tyson GW, Schenk PM (2013) Rhizosphere metatranscriptomics: challenges and opportunities. In: de Bruijn FJ (ed) Molecular microbial ecology of the rhizosphere. Wiley, Hoboken, pp 1137–1144. ISBN: 978-0-470-64479-9

    Google Scholar 

  • Chaudhry V, Rehman A, Mishra A, Chauhan PS, Nautiyal CS (2012) Changes in bacterial community structure of agricultural land due to long term organic and chemical amendments. Microb Ecol 64:450–460. doi:10.1007/s00248-012-0025-y

    Article  PubMed  Google Scholar 

  • Chauhan PS, Chaudhry V, Mishra S, Nautiyal CS (2011) Uncultured bacterial diversity in tropical maize (Zea mays L.) rhizosphere. J Basic Microbiol 51:15–32. doi:10.1002/jobm.201000171

    Article  CAS  PubMed  Google Scholar 

  • Chernin L, Ismailov Z, Haran S, Chet I (1995) Chitinolytic Enterobacter agglomerans antagonistic to fungal plant pathogens. Appl Environ Microbiol 61:1720–1726

    CAS  PubMed  PubMed Central  Google Scholar 

  • Compant S, Reiter B, Sessitsch A, Nowak J, Clément C, Barka EA (2005) Endophytic colonization of Vitis vinifera L. by plant growth-promoting bacterium Burkholderia sp. strain PsJN. Appl Environ Microbiol 71:1685–1693. doi:10.1128/AEM.71.4.1685-1693.2005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • De Angelis KM, Brodie EL, DeSantis TZ, Andersen GL, Lindow SE, Firestone MK (2009) Selective progressive response of soil microbial community to wild oat roots. ISME J 3:168–178. doi:10.1038/ismej.2008.103

    Article  CAS  Google Scholar 

  • De Roy K, Marzorati M, Van den Abbeele P, Van de Wiele T, Boon N (2013) Synthetic microbial ecosystems: an exciting tool to understand and apply microbial communities. Environ Microbiol 16:1472–1481. doi:10.1111/1462-2920.12343

    Article  PubMed  Google Scholar 

  • Delmotte N, Knief C, Chaffron S, Innerebner G, Roschitzki B, Schlapbach R, von Mering C, Vorholt JA (2009) Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc Natl Acad Sci U S A 106:16428–16433. doi:10.1073/pnas.0905240106

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Donn S, Kirkegaard JA, Perera G, Richardson AE, Watt M (2014) Evolution of bacterial communities in the wheat crop rhizosphere. Environ Microbiol 17:610–621. doi:10.1111/1462-2920.12452

    Article  PubMed  Google Scholar 

  • Doran JW, Zeiss MR (2000) Soil health and sustainability: managing the biotic component of soil quality. Appl Soil Ecol 15:3–11. doi:10.1016/S0929-1393(00)00067-6

    Article  Google Scholar 

  • Downey J, van Kessel C (1990) Dual inoculation of Pisum sativum with Rhizobium leguminosarum and Penicillium bilaji. Biol Fertil Soils 10:194–196. doi:10.1007/bf00336135

    Article  Google Scholar 

  • Duijff BJ, Bakker PAHM, Schippers B (1994) Suppression of Fusarium wilt of carnation by Pseudomonas putida WCS358 at different levels of disease incidence and iron availability. Biocontrol Sci Tech 4:279–288. doi:10.1080/09583159409355336

    Article  Google Scholar 

  • Dunne C, Crowley JJ, Moënne-Loccoz Y, Dowling DN, de Bruijn FJ, O’Gara F (1997) Biological control of Pythium ultimum by Stenotrophomonas maltophilia W81 is mediated by an extracellular proteolytic activity. Microbiology 143:3921–3391. doi:10.1099/00221287-143-12-3921

    Article  CAS  Google Scholar 

  • Egamberdieva D, Jabborova D, Berg G (2016) Synergistic interactions between Bradyrhizobium japonicum and the endophyte Stenotrophomonas rhizophila and their effects on growth, nodulation and nutrition of soybean under salt stress. Plant Soil 405:35. doi:10.1007/s11104-015-2661-8

    Article  CAS  Google Scholar 

  • Eilers KG, Lauber CL, Knight R, Fierer N (2010) Shifts in bacterial community structure associated with inputs of low molecular weight carbon compounds to soil. Soil Biol Biochem 42:896–903. doi:10.1016/j.soilbio.2010.02.003

    Article  CAS  Google Scholar 

  • El-Tarabily KA (2006) Rhizosphere competent isolates of Streptomycete and non-streptomycete Actinomycetes capable of producing cell-wall degrading enzymes to control Pythium aphanidermatum damping off disease of cucumber. Can J Bot 84:211–222. doi:10.1139/b05-153

    Article  CAS  Google Scholar 

  • El-Tarabily KA (2008) Promotion of tomato (Lycopersicon esculentum Mill.) plant growth by rhizosphere competent 1-aminocyclopropane-1-carboxylic acid deaminase producing streptomycete Actinomycetes. Plant Soil 308:161–174. doi:10.1007/s11104-008-9616-2

    Article  CAS  Google Scholar 

  • Frankowski J, Lorito M, Scala F, Schmidt R, Berg G, Bahl H (2001) Purification and properties of two chitinolytic enzymes of Serratia plymuthica HRO-C48. Arch Microbiol 176:421–426. doi:10.1007/s002030100347

    Article  CAS  PubMed  Google Scholar 

  • Gamalero E, Lingua G, Berta G, Lemanceau P (2009) Methods for studying root colonization by introduced beneficial bacteria. In: Lichtfouse E, Navarrete M, Debaeke P, Souchere V, Alberola C (eds) Sustainable agriculture. Springer, New York, pp 601–615. doi:10.1007/978-90-481-2666-8_37

    Chapter  Google Scholar 

  • Gloor GB, Hummelen R, Macklaim JM, Dickson RJ, Fernandes AD, MacPhee R, Reid G (2010) Microbiome profiling by illumina sequencing of combinatorial sequence-tagged PCR products. PLoS One 5:e15406. doi:10.1371/journal.pone.0015406

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Groppa MD, Benavides MP, Zawoznik MS (2012) Root hydraulic conductance, aquaporins and plant growth promoting microorganisms: a revision. Appl Soil Ecol 61:247–254. doi:10.1016/j.apsoil.2011.11.013

    Article  Google Scholar 

  • van der Heijden MGA, Bardgett RD, van Straalen NM (2008) The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecol Lett 11:296–310. doi:10.1111/j.1461-0248.2007.01139.x

    Article  PubMed  Google Scholar 

  • van der Heijden MGA, Martin FM, Selosse MA, Sanders IR (2015) Mycorrhizal ecology and evolution: the past, the present, and the future. New Phytol 205:1406–1423. doi:10.1111/nph.13288

    Article  PubMed  CAS  Google Scholar 

  • Hirsch PR, Mauchline TH, Clark IM (2010) Culture independent molecular techniques for soil microbial ecology. Soil Biol Biochem 42:878–887. doi:10.1016/j.soilbio.2010.02.019

    Article  CAS  Google Scholar 

  • Howie WJ, Cook RJ, Weller DM (1987) Effects of soil matrix potential and cell motility on wheat root colonization by fluorescent pseudomonads suppressive to take-all. Phytopathology 77:286–292

    Article  Google Scholar 

  • Jeffries P, Barea JM (2012) Arbuscular mycorrhiza—a key component of sustainable plant-soil ecosystems. In: Hock B (ed) The Mycota, a comprehensive treatise on fungi as experimental systems for basic and applied research. Springer, Berlin, pp 51–75

    Google Scholar 

  • Jeffries P, Gianinazzi S, Perotto S, Turnau K, Barea JM (2003) The contribution of arbuscular mycorrhizal fungi in sustainable maintenance of plant health and soil fertility. Biol Fertil Soils 37:1–16. doi:10.1007/s00374-002-0546-5

    Google Scholar 

  • Johnson KB (2010) Pathogen refuge: a key to understanding biological control. Annu Rev Phytopathol 48:141–160. doi:10.1146/annurev.phyto.112408.132643

    Article  CAS  PubMed  Google Scholar 

  • Jung SC, Martinez-Medina A, Lopez Raez JA, Pozo MJ (2012) Mycorrhiza induced resistance and priming of plant defences. J Chem Ecol 38:651–664. doi:10.1007/s10886-012-0134-6

    Article  CAS  PubMed  Google Scholar 

  • Khamna S, Yokota A, Lumyong S (2009) Actinomycetes isolated from medicinal plant rhizosphere soils: diversity and screening of antifungal compounds, indole-3-acetic acid and siderophore production. World J Microbiol Biotechnol 25:649–655. doi:10.1007/s11274-008-9933-x

    Article  CAS  Google Scholar 

  • Khan MH, Meghvansi MK, Gupta R, Chaudhary KK, Prasad K, Siddiqui S, Veer V, Varma A (2015) Combining application of vermiwash and Arbuscular Mycorrhizal fungi for effective plant disease suppression. In: Varma A, Meghvansi MK (eds) Organic amendments and soil suppressiveness in plant disease management. Springer, Basel, pp 479–493. doi:10.1007/978-3-319-23075-7_23

    Chapter  Google Scholar 

  • Klein E, Ofek M, Katan J, Minz D, Gamliel A (2013) Soil suppressiveness to Fusarium disease: shifts in root microbiome associated with reduction of pathogen root colonization. Phytopathology 103:23–33. doi:10.1094/PHYTO-12-11-0349

    Article  PubMed  Google Scholar 

  • Kumar BSD (1999) Fusarial wilt suppression and crop improvement through two rhizobacterial strains in chick pea growing in soils infested with Fusarium oxysporum f. sp. ciceris. Biol Fertil Soils 29:87–91. doi:10.1007/s003740050529

    Article  Google Scholar 

  • Kumar M, Mishra S, Dixit V, Kumar M, Agarwal L, Chauhan PS, Nautiyal CS (2016) Synergistic effect of Pseudomonas putida and Bacillus amyloliquefaciens ameliorates drought stress in chickpea (Cicer arietinum L.) Plant Signal Behav 11:e1071004. doi:10.1080/15592324.2015.1071004

    Article  PubMed  CAS  Google Scholar 

  • Landa BB, Mavrodi OV, Raaijmakers JM, McSpadden-Gardener BB, Thomashow LS, Weller DM (2002) Differential ability of genotypes of 2,4-diacetylphloroglucinol producing Pseudomonas fluorescens to colonize the roots of pea. Appl Environ Microbiol 68:3226–3237. doi:10.1128/AEM.68.7.3226-3237.2002

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li X, Rui J, Xiong J, Li J, He Z, Zhou J, Anthony C, Yannarell MR (2014) Functional potential of soil microbial communities in the maize rhizosphere. PLoS One 9:e112609. doi:10.1371/journal.pone.0112609

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lisette JXC, Germida JJ (2003) Selective interactions between arbuscular mycorrhizal fungi and Rhizobium leguminosarum bv. viceae enhance pea yield and nutrition. Biol Fertil Soils 37:261–267. doi:10.1007/s00374-003-0605-6

    Google Scholar 

  • Loper JE, Buyer JS (1991) Siderophores in microbial interactions on plant surfaces. Mol Plant-Microbe Interact 4:5–13

    Article  CAS  Google Scholar 

  • López-Ráez JA, Bouwmeester H, Pozo MJ (2012) Communication in the rhizosphere, a target for pest management. In: Lichtfouse E (ed) Agroecology and strategies for climate change. Springer, Dordrecht, pp 109–133. doi:10.1007/978-94-007-1905-7_5

    Chapter  Google Scholar 

  • Lugtenberg B (2015) Life of microbes in the rhizosphere. In: Lugtenberg B (ed) Principles of plant-microbe interactions. Springer, Heidelberg, pp 7–15. doi:10.1007/978-3-319-08575-3_3

    Google Scholar 

  • Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, Tremblay J, Engelbrektson A, Kunin V, del Rio TG, Edgar RC, Eickhorst T, Ley RE, Hugenholtz P, Tringe SG, Dangl JL (2012) Defining the core Arabidopsis thaliana root microbiome. Nature 488:86–90. doi:10.1038/nature11237

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Malusà E, Vassilev N (2014) A contribution to set a legal framework for biofertilizers. Appl Microbiol Biotechnol 98:6599–6607. doi:10.1007/s00253-014-5828-y

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Malusa E, Sas-Paszt L, Popinska W, Zurawicz E (2007) The effect of a mycorrhiza-bacteria substrate and foliar fertilization on growth response and rhizosphere pH of three strawberry cultivars. Int J Fruit Sci 6:25–41. doi:10.1126/science.1203980

    Article  Google Scholar 

  • Marques JM, da Silva TF, Vollu RE, Blank AF, Ding GC, Seldin L, Smalla K (2014) Plant age and genotype affect the bacterial community composition in the tuber rhizosphere of field-grown sweet potato plants. FEMS Microbiol Ecol 88:424–435. doi:10.1111/1574-6941.12313

    Article  CAS  PubMed  Google Scholar 

  • Mendes R, Kruijt M, de Bruijn I, Dekkers E, van der Voort M, Schneider JHM, Piceno YM, DeSantis TZ, Anderson GL, Bakker PAHM, Raaijmakers JM (2011) Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 332:1097–1100. doi:10.1126/science.1203980

    Article  CAS  PubMed  Google Scholar 

  • Meziane H, Van der Sluis I, Van Loon LC, Höfte M, Bakker PAHM (2005) Determinants of Pseudomonas putida WCS358 involved in inducing systemic resistance in plants. Mol Plant Pathol 6:177–185. doi:10.1111/j.1364-3703.2005.00276.x

    Article  PubMed  Google Scholar 

  • Micallef SA, Channer S, Shiaris MP, Colón-Carmona A (2009) Plant age and genotype impact the progression of bacterial community succession in the Arabidopsis rhizosphere. Plant Signal Behav 4:777–780. doi:10.4161/psb.4.8.9229

    Article  PubMed  PubMed Central  Google Scholar 

  • Michiels KW, Croes CL, Vanderleyden J (1991) Two different modes of attachment of Azospirillum brasilense Sp7 to wheat roots. J Gen Microbiol 137:2241–2246. doi:10.1099/00221287-137-9-2241

    Article  CAS  Google Scholar 

  • Nautiyal CS, Chauhan PS, Bhatia CR (2010) Changes in soil physicochemical properties and microbial functional diversity due to 14 years of conversion of grassland to organic agriculture in semi-arid agro-ecosystem. Soil Tillage Res 109:55–60. doi:10.1016/j.still.2010.04.008

    Article  Google Scholar 

  • Nichols D (2007) Cultivation gives context to the microbial ecologist. FEMS Microbiol Ecol 60:351–357. doi:10.1111/j.1574-6941.2007.00332.x

    Article  CAS  PubMed  Google Scholar 

  • Notz R, Maurhofer M, Schnider-Keel U, Duffy B, Haas D, Défago G (2001) Biotic factors affecting expression of the 2, 4-diacetylphloroglucinol biosynthesis gene phl A in Pseudomonas fluorescens biocontrol strain CHA0 in the rhizosphere. Phytopathology 91:873–881. doi:10.1094/PHYTO.2001.91.9.873

    Article  CAS  PubMed  Google Scholar 

  • Nunes da Rocha U, Andreote FD, De Azevedo JL, Van Elsas JD, Van Overbeek LS (2010) Cultivation of hitherto-uncultured bacteria belonging to the Verrucomicrobia subdivision 1 from the potato (Solanum tuberosum L.) rhizosphere. J Soils Sediments 10:326–339. doi:10.1007/s11368-009-0160-3

    Article  CAS  Google Scholar 

  • Osorio NW, Habte M (2001) Synergistic influence of an arbuscular mycorrhizal fungus and P solubilizing fungus on growth and plant P uptake of Leucaena leucocephala in an Oxisol. Arid Land Res Manag 15:263–274. doi:10.1080/15324980152119810

    Article  CAS  Google Scholar 

  • Owen D, Williams AP, Griffith GW, Withers PJA (2015) Use of commercial bio-inoculants to increase agricultural production through improved phosphorus acquisition. Appl Soil Ecol 86:41–54. doi:10.1016/j.apsoil.2014.09.012

    Article  Google Scholar 

  • Pace NR, Sapp J, Goldenfeld N (2012) Phylogeny and beyond: scientific, historical, and conceptual significance of the first tree of life. Proc Natl Acad Sci U S A 109:1011–1018. doi:10.1073/pnas.1109716109

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pangesti N, Pineda A, Pieterse CMJ, Dicke M, van Loon JJA (2013) Two-way plant-mediated interactions between root-associated microbes and insects: from ecology to mechanisms. Front Plant Sci 4:414. doi:10.3389/fpls.2013.00414

    Article  PubMed  PubMed Central  Google Scholar 

  • Paterson E, Gebbing T, Abel C, Sim A, Telfer G (2007) Rhizodeposition shapes rhizosphere microbial community structure in organic soil. New Phytol 173:600–610. doi:10.1111/j.1469-8137.2006.01931.x

    Article  CAS  PubMed  Google Scholar 

  • Pérez-García A, Romero D, de Vicente A (2011) Plant protection and growth stimulation by microorganisms: biotechnological applications of Bacilli in agriculture. Curr Opin Biotechnol 22:187–193. doi:10.1016/j.copbio.2010.12.003

    Article  PubMed  CAS  Google Scholar 

  • Perotto S, Bonfante P (1997) Bacterial associations with mycorrhizal fungi: close and distant friends in the rhizosphere. Trends Microbiol 5:496–501. doi:10.1016/s0966-842x(97)01154-2

    Article  CAS  PubMed  Google Scholar 

  • Phelan VV, Liu WT, Pogliano K, Dorrestein PC (2012) Microbial metabolic exchange—the chemotype phenotype link. Nat Chem Biol 8:26–35. doi:10.1038/nchembio.739

    Article  CAS  Google Scholar 

  • Pozo MJ, Azcón Aguilar C (2007) Unraveling mycorrhiza-induced resistance. Curr Opin Plant Biol 10:393–398. doi:10.1016/j.pbi.2007.05.004

    Article  CAS  PubMed  Google Scholar 

  • Pozo MJ, Jung SC, Martínez-Medina A, López-Ráez JA, Azcón-Aguilar C, Barea JM (2013) Root allies: arbuscular mycorrhizal fungi help plants to cope with biotic stresses. In: Aroca R (ed) Symbiotic endophytes. Springer, Berlin, pp 289–307. doi:10.1007/978-3-642-39317-4_15

    Chapter  Google Scholar 

  • Pozo MJ, López-Ráez JA, Azcón-Aguilar C, García-Garrido JM (2015) Phytohormones as integrators of environmental signals in the regulation of mycorrhizal symbioses. New Phytol 205:1431–1436. doi:10.1111/nph.13252

    Article  CAS  PubMed  Google Scholar 

  • Raaijmakers JM, Weller DM (1998) Natural plant protection by 2,4-diacetylphloroglucinol producing Pseudomonas spp. in take-all decline soils. Mol Plant-Microbe Interact 11:144–152

    Article  CAS  Google Scholar 

  • Raaijmakers JM, Paulitz TC, Steinberg C, Alabouvette C, Moënne-Loccoz Y (2009) The rhizosphere: a playground and battlefield for soil borne pathogens and beneficial microorganisms. Plant Soil 321:341–361. doi:10.1007/s11104-008-9568-6

    Article  CAS  Google Scholar 

  • Ram RJ, VerBerkmoes NC, Thelen MP, Tyson GW, Baker BJ, Blake RC II, Shah M, Hettich RL, Banfield JF (2005) Community proteomics of a natural microbial biofilm. Science 308:1915–1920. doi:10.1126/science. 1109070

    Article  CAS  PubMed  Google Scholar 

  • Rice WA, Lupwayi NZ, Olsen PE, Schlechte D, Gleddie SC (2000) Field evaluation of dual inoculation of alfalfa with Sinorhizobium meliloti and Penicillium bilaii. Can J Plant Sci 80:303–308. doi:10.4141/p99-055

    Article  Google Scholar 

  • Ritz K (2007) The plate debate: cultivable communities have no utility in contemporary environmental microbial ecology. FEMS Microbiol Ecol 60:358–362. doi:10.1111/j.1574-6941.2007.00331.x

    Article  CAS  PubMed  Google Scholar 

  • Ruiz-Lozano JM, Porcel R, Azcón C, Aroca R (2012) Regulation by arbuscular mycorrhizae of the integrated physiological response to salinity in plants: new challenges in physiological and molecular studies. J Exp Bot 63:4033–4044. doi:10.1093/jxb/ers126

    Article  CAS  PubMed  Google Scholar 

  • Schüßler A, Schwarzott D, Walker C (2001) A new fungal phylum, the Glomeromycota, phylogeny and evolution. Mycol Res 105:1413–1421. doi:10.1017/S0953756201005196

    Article  Google Scholar 

  • Selosse MA, Bessis A, Pozo MJ (2014) Microbial priming of plant and animal immunity: symbionts as developmental signals. Trends Microbiol 22:607–613. doi:10.1016/j.tim.2014.07.003

    Article  CAS  PubMed  Google Scholar 

  • Sergeeva E, Hirkala DLM, Nelson LM (2007) Production of indole-3-acetic acid, aromatic amino acid aminotransferase activities and plant growth promotion by Pantoea agglomerans rhizosphere isolates. Plant Soil 297:1–13. doi:10.1007/s11104-007-9314-5

    Article  CAS  Google Scholar 

  • Sessitsch A, Hardoim P, Döring J, Weilharter A, Krause A, Woyke T, Mitter B, Hauberg-Lotte L, Friedrich F, Rahalkar M, Hurek T, Sarkar A, Bodrossy L, van Overbeek L, Brar D, van Elsas JD, Reinhold-Hurek B (2012) Functional characteristics of an endophyte community colonizing rice roots as revealed by metagenomic analysis. Mol Plant-Microbe Interact 25:28–36. doi:10.1094/MPMI-08-11-0204

    Article  CAS  PubMed  Google Scholar 

  • Singh JS, Pandey VC, Singh DP (2011) Efficient soil microorganisms: a new dimension for sustainable agriculture and environmental development. Agric Ecosyst Environ 140:339–353. doi:10.1016/j.agee.2011.01.017

    Article  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 SE, Read DJ (2008) Mycorrhizal symbiosis, 3rd edn. Elsevier, New York

    Google Scholar 

  • Someya N, Tsuchiya K, Yoshida T, Noguchi MT, Akutsu K, Sawada H (2007) Co-inoculation of an antibiotic-producing bacterium and a lytic enzyme-producing bacterium for the biocontrol of tomato wilt caused by Fusarium oxysporum f. sp. lycopersici. Biocontrol Sci 12:1–6. doi:10.4265/bio.12.1

    Article  CAS  PubMed  Google Scholar 

  • de Souza JTA, Arnould C, Deulvot C, Lemanceau P, Gianinazzi-Pearson V, Raaijmakers JM (2003) Effect of 2,4-diacetylphloroglucinol on Pythium: cellular responses and variation in sensitivity among propagules and species. Phytopathology 93:966–975. doi:10.1094/PHYTO.2003.93.8.966

    Article  PubMed  Google Scholar 

  • Spence C, Alff E, Johnson C, Ramos C, Donofrio N, Sundaresan V, Bais H (2014) Natural rice rhizospheric microbes suppress rice blast infections. BMC Plant Biol 14:130. doi:10.1186/1471-2229-14-130

    Article  PubMed  PubMed Central  Google Scholar 

  • Sturz AV, Christie BR, Nowak J (2000) Bacterial endophytes: potential role in developing sustainable systems of crop production. CRC Crit Rev Plant Sci 19:1–30. doi:10.1080/07352680091139169

    Article  Google Scholar 

  • Sugiyama A, Ueda Y, Zushi T, Takase H, Yazaki K (2014) Changes in the bacterial community of soybean rhizospheres during growth in the field. PLoS One 9:e100709. doi:10.1371/journal.pone.0100709

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Taberlet P, Prud’homme SM, Campione E, Roy J, Miquel C, Shehzad W, Gielly L, Rioux D, Choler P, Clément JC, Melodelima C, Pompanon F, Coissac E (2012) Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies. Mol Ecol 21:1816–1820. doi:10.1111/j.1365-294X.2011.05317.x

    Article  CAS  PubMed  Google Scholar 

  • Thomashow LS, Weller DM (1988) Role of a phenazine antibiotic from Pseudomonas fluorescens in biological control of Gaeumannomyces graminis var. tritici. J Bacteriol 170:3499–3508

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Uroz S, Buée M, Murat C, Frey-Klett P, Martin F (2010) Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil. Environ Microbiol Rep 2:281–288. doi:10.1111/j.1758-2229.2009.00117.x

    Article  CAS  PubMed  Google Scholar 

  • Van Loon LC, Bakker PAHM (2003) Signalling in rhizobacteria-plant interactions. In: De Kroon H, Visser EJW (eds) Root ecology (Ecological studies). Springer, Berlin, pp 297–330. doi:10.1007/978-3-662-09784-7_12

    Chapter  Google Scholar 

  • Vassilev N, Franco I, Vassileva M, Azcon R (1996) Improved plant growth with rock phosphate solubilized by Aspergillus niger grown on sugar beet waste. Bioresour Technol 55:237–241. doi:10.1016/0960-8524(96)00008-9

    Article  CAS  Google Scholar 

  • Vassilev N, Medina A, Azcon R, Vassileva M (2006) Microbial solubilization of rock phosphate media containing agro-industrial wastes and effect of the resulting products on plant growth and P uptake. Plant Soil 287:77–84. doi:10.1007/s11104-006-9054-y

    Article  CAS  Google Scholar 

  • Vassilev N, Martos E, Mendes G, Martos V, Vassileva M (2013) Biochar of animal origin: a sustainable solution of the high grade rock phosphate scarcity? J Sci Food Agric 93:1799–1804. doi:10.1002/jsfa.6130

    Article  CAS  PubMed  Google Scholar 

  • Velazhahan R, Samiyappan R, Vidhyasekaran P (1999) Relationship between antagonistic activities of Pseudomonas fluorescens isolates against Rhizoctonia solani and their production of lytic enzymes. Z Pflanz Pflanzen 106:244–250

    CAS  Google Scholar 

  • Wang HX, Geng ZL, Zeng Y, Shen YM (2008) Enriching plant microbiota for a metagenomic library construction. Environ Microbiol 10:2684–2691. doi:10.1111/j.1462-2920.2008.01689.x

    Article  CAS  PubMed  Google Scholar 

  • Wang X, Pan Q, Chen F, Yan X, Liao H (2011) Effects of co-inoculation with arbuscular mycorrhizal fungi and rhizobia on soybean growth as related to root architecture and availability of N and P. Mycorrhiza 21:173–181. doi:10.1007/s00572-010-0319-1

    Article  PubMed  CAS  Google Scholar 

  • Weinert N, Piceno Y, Ding GC, Meincke R, Heuer H, Berg G, Schloter M, Andersen G, Smalla K (2011) PhyloChip hybridization uncovered an enormous bacterial diversity in the rhizosphere of different potato cultivars: many common and few cultivar-dependent taxa. FEMS Microbiol Ecol 75:497–506. doi:10.1111/j.1574-6941.2010.01025.x

    Article  CAS  PubMed  Google Scholar 

  • Weller DM, Cook RJ (1983) Suppression of take-all of wheat by seed treatments with fluorescent pseudomonads. Phytopathology 73:463–469

    Article  Google Scholar 

  • Woeng TFCCA, Bloemberg GV, Mulders IHM, Dekkers LC, Lugtenberg BJJ (2000) Root colonization by phenazine-1-carboxamide-producing bacterium Pseudomonas chlororaphis PCL1391 is essential for biocontrol of tomato root rot. Mol Plant-Microbe Interact 12:1340–1345. doi:10.1094/MPMI.2000.13.12.1340

    Article  Google Scholar 

  • Woeng TFCCA, Bloemberg GV, Lugtenberg BJJ (2003) Phenazines and their role in biocontrol by Pseudomonas bacteria. New Phytol 157:503–523. doi:10.1046/j.1469-8137.2003.00686.x

    Article  Google Scholar 

  • Wu SC, Cao ZH, Li ZG, Cheung KC, Wong MH (2005) Effects of biofertilizer containing N-fixer, P and K solubilizers and AM fungi on maize growth: a greenhouse trial. Geoderma 125:155–166. doi:10.1016/j.geoderma.2004.07.003

    Article  Google Scholar 

  • Zachow C, Müller H, Tilcher R, Berg G (2014) Differences between the rhizosphere microbiome of Beta vulgaris ssp. maritima—ancestor of all beet crops and modern sugar beets. Front Microbiol 5:415. doi:10.3389/fmicb.2014.00415

    Article  PubMed  PubMed Central  Google Scholar 

  • Zarraonaindia I, Owens SM, Weisenhorn P, West K, Hampton-Marcell J, Lax S, Bokulich NA, Mills DA, Martin G, Taghavi S, van der Lelie D, Gilberta JA (2015) The soil microbiome influences grapevine-associated microbiota. mBio 6:e02527-14. doi:10.1128/mBio.02527-14

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zolla G, Badri DV, Bakker MG, Manter DK, Vivanco JM (2013) Soil microbiomes vary in their ability to confer drought tolerance to Arabidopsis. Appl Soil Ecol 68:1–9. doi:10.1016/j.apsoil.2013.03.007

    Article  Google Scholar 

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Acknowledgments

The study was supported by New Initiative (as a Cross Flow Technology project) “Root Biology and Its Correlation to Sustainable Plant Development and Soil Fertility” (RootSF; BSC0204) from the Council of Scientific and Industrial Research (CSIR), New Delhi, India.

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  1. CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226 001, Uttar Pradesh, India

    Sankalp Misra, Swapnil Pandey, Vijaykant Dixit, Shashank Kumar Mishra, Mohammad Haneef Khan, Lalit Agarwal & Puneet Singh Chauhan

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  1. Sankalp Misra
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Correspondence to Puneet Singh Chauhan .

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  1. Microbial Biotechnology and Genomics, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India

    Vipin Chandra Kalia

  2. Microbial Culture Collection, National Centre for Cell Science, Pune, India

    Yogesh Shouche

  3. Environmental Biotechnology and Genomics Division, National Environmental Engineering Research Institute (CSIR), Nagpur, India

    Hemant J. Purohit

  4. Microbial Culture Collection, National Centre for Cell Science, Pune, India

    Praveen Rahi

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Misra, S. et al. (2017). Soil Microbiome for Enhanced Crop Productivity. In: Kalia, V., Shouche, Y., Purohit, H., Rahi, P. (eds) Mining of Microbial Wealth and MetaGenomics. Springer, Singapore. https://doi.org/10.1007/978-981-10-5708-3_14

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