Abstract
In interactions between plants and soil, microorganisms have significant roles. Ecological stability is contributed by the biogeochemical cycling of elements. An emerging body of research is distinguishing the impacts that root-associated microbial communities can have on plant fitness and growth. Rocks and minerals are weathered by the activities of plants, which exude various types of hormones, with a crucial role in the supply of organic matter and formation of soils. Various types of plant species have distinctive biological characteristics that show constraint to precise soil types. Plant–microbe interactions in soil are contributing to a new, microbially based perspective on plant community and ecology. These microorganisms are soil dwellers, diverse, and their interactions with plants vary with respect to specificity, environmental heterogeneity, and fitness impact. The key influences on plant community structure and dynamics are effected by two microbial procedures: microbial intervention of niche diversity in resource use and response dynamics among the soil community and plants. The hypothesis of niche diversity is based on various interpretations that the nutrients of soil are found in different chemical forms: the plant requires accessing these enzymes and nutrients, and the microorganisms of the soil are a major source of these enzymes. Plant–microbe interactions are a significant establishing force for extensive spatial gradients in species abundance. The positive response (a homogenizing force) and negative response (a diversifying force) of virtual balance may contribute to detected latitudinal (and altitudinal) diversity patterns. The microbially based perception for the ecology of plants promises to contribute to our understanding of long-standing issues in ecology and to disclose new areas of future investigation.
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References
Araújo WL, Creason AL, Mano ET, Camargo-Neves AA, Minami SN, Chang JH, Loper JE (2016) Genome sequencing and transposon mutagenesis of Burkholderia seminalis TC3.4.2 R3 identify genes contributing to suppression of orchid necrosis caused by B. gladioli. Mol Plant Microbe Interact 29:435–446
Ardanov P, Sessitsch A, Häggman H, Kozyrovska N, Pirttilä AM (2012) Methylobacterium-induced endophyte community changes correspond with protection of plants against pathogen attack. PLoS One 7:1–8
Bäckhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI (2005) Host-bacterial mutualism in the human intestine. Science 307:1915–1920
Badri DV, Vivanco JM (2009) Regulation and function of root exudates. Plant Cell Environ 32:666–681
Badri DV, Weir TL, van der Lelie D, Vivanco JM (2009) Rhizosphere chemical dialogues: plant–microbe interactions. Curr Biotechnol 20:642–650
Baetz U, Martinoia E (2014) Root exudates: the hidden part of plant defense. Trends Sci 19(2):90–98
Bais HP, Park SW, Weir TL, Callaway RM, Vivanco JM (2004) How plants communicate using the underground information superhighway. Trends Sci 9:26–32
Bais HP, Weir TL, Perry LG, Gilroy S, Vivanco JM (2006) The role of root exudates in rhizosphere interactions with plants and other organisms. Annu Rev Plant Biol 57:233–266
Balendres MA, Nichols DS, Tegg RS, Wilson CR (2016) Metabolomes of potato root exudates: compounds that stimulate resting spore germination of the soil-borne pathogen Spongospora subterranea. J Agric Food Chem 64:7466–7474
Bardgett RD, Freeman C, Ostle NJ (2008) Microbial contributions to climate change through carbon cycle feedbacks. ISME J 2:805–814
Barrière Q, Guefrachi I, Gully D, Lamouche F, Pierre O, Fardoux J, Mergaert P (2017) Integrated roles of BclA and DD-carboxypeptidase 1 in Bradyrhizobium differentiation within NCR-producing and NCR-lacking root nodules. Sci Rep 7:1–13
Barsainya M, Chandra P, Singh DP (2016) Investigation of Cr (VI) uptake in saline condition using psychrophilic and mesophilic Penicillium sp. Int J Curr Microbiol App Sci 5(1):274–288
Baudoin E, Benizri E, Guckert A (2003) Impact of artificial root exudates on the bacterial community structure in bulk soil and maize rhizosphere. Soil Biol Biochem 35:1183–1192
Beattie GA (2007) Plant-associated bacteria: survey, molecular phylogeny, genomics and recent advances. In: Plant-associated bacteria. Springer, Dordrecht, pp 1–56
Bentley SD, Chater KF, Cerdeño-Tárraga AM, Challis GL, Thomson NR, James KD, Bateman A (2002) Complete genome sequence of the model actinomycete Streptomyces coelicolor A3 (2). Nature 417:141–147
Berendsen RL, Pieterse CM, Bakker PA (2012) The rhizosphere microbiome and plant health. Trends Sci 17:478–486
Berg G, Smalla K (2009) Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. FEMS Microbiol Ecol 68:1–13
Bertrand S, Bohni N, Schnee S, Schumpp O, Gindro K, Wolfender JL (2014) Metabolite induction via microorganism co-culture: a potential way to enhance chemical diversity for drug discovery. Biotechnol Adv 32:1180–1204
Bever JD (2003) Soil community feedback and the coexistence of competitors: conceptual frameworks and empirical tests. New Phytol 157:465–473
Bever JD, Schultz PA, Pringle A, Morton JB (2001) Arbuscular mycorrhizal fungi: more diverse than meets the eye, and the ecological tale of why. BioScience 51:923–931
Bever JD, Dickie IA, Facelli E, Facelli JM, Klironomos J, Moora M, Zobel M (2010) Rooting theories of plant community ecology in microbial interactions. Trends Ecol Evol 25:468–478
Björkman M, Klingen I, Birch AN, Bones AM, Bruce TJ, Johansen TJ, Stewart D (2011) Phytochemicals of Brassicaceae in plant protection and human health: influences of climate, environment and agronomic practice. Phytochemistry 72:538–556
Bloemberg GV, Lugtenberg BJ (2001) Molecular basis of plant growth promotion and biocontrol by rhizobacteria. Curr Biol 4:343–350
Bobbink R, Hornung M, Roelofs JG (1998) The effects of air-borne nitrogen pollutants on species diversity in natural and semi-natural European vegetation. J Ecol 86:717–738
Bodenhausen N, Bortfeld-Miller M, Ackermann M, Vorholt JA (2014) A synthetic community approach reveals plant genotypes affecting the phyllosphere microbiota. PLoS Genet 10:1–12
Boer WD, Folman LB, Summerbell RC, Boddy L (2005) Living in a fungal world: impact of fungi on soil bacterial niche development. FEMS Microbiol Rev 29:795–811
Bogino P, Abod A, Nievas F, Giordano W (2013) Water-limiting conditions alter the structure and biofilm-forming ability of bacterial multispecies communities in the alfalfa rhizosphere. PLoS One 8:1–17
Bongers T, Ferris H (1999) Nematode community structure as a bioindicator in environmental monitoring. Trends Ecol Evol 14:224–228
Bourgaud F, Gravot A, Milesi S, Gontier E (2001) Production of plant secondary metabolites: a historical perspective. Plant Sci 161:839–851
Braga RM, Dourado MN, Araújo WL (2016) Microbial interactions: ecology in a molecular perspective. Braz J Microbiol 47(suppl 1):86–98
Brooker RW, Bennett AE, Cong WF, Daniell TJ, George TS, Hallett PD, Li L (2015) Improving intercropping: a synthesis of research in agronomy. New Phytol 206:107–117
Brundrett MC (2002) Coevolution of roots and mycorrhizas of land plants. New Phytol 154:275–304
Burr TJ, Schroth MN, Suslow T (1978) Increased potato yields by treatment of seed pieces with specific strains of Pseudomonas fluorescens and P. putida. Phytopathology 68:1377–1383
Calvo P, Nelson L, Kloepper JW (2014) Agricultural uses of plant biostimulants. Plant Soil 383:3–41
Certini G (2005) Effects of fire on properties of forest soils: a review. Oecologia (Berl) 143:1–10
Chamoun R, Aliferis KA, Jabaji S (2015) Identification of signatory secondary metabolites during mycoparasitism of Rhizoctonia solani by Stachybotrys elegans. Front Microbiol 6:1–11
Chandra P, Enespa (2017) Microbial volatiles as chemical weapons against pathogenic fungi. In: Volatiles and food security. Springer, Singapore, pp 227–254
Chandra P, Enespa (2019) Fungal Community for Novel Secondary Metabolites. In: Recent advancement in white biotechnology through fungi. Springer, Cham, pp 249–283
Chandra P, Singh E (2016) Applications and mechanisms of plant growth-stimulating rhizobacteria. In: Plant–microbe interaction: an approach to sustainable agriculture. Springer, Singapore, pp 37–62
Chandra P, Enespa, Mukesh K (2019) Contribution of microbes in the renovation of wetlands. Springer Nature, Singapore, pp 105–026
Chapin FS, Matson PA, Mooney HA (2002) Terrestrial decomposition. Springer, New York, pp 151–175
Choudhary DK, Johri BN (2009) Interactions of Bacillus spp. and plants–with special reference to induced systemic resistance (ISR). Microbiol Res 164:493–513
Choudhary DK, Prakash A, Wray V, Johri BN (2009) Insights of the fluorescent pseudomonads in plant growth regulation. Curr Sci 97:170–179
Codispoti LA, Brandes JA, Christensen JP, Devol AH, Naqvi SWA, Paerl HW, Yoshinari T (2001) The oceanic fixed nitrogen and nitrous oxide budgets: moving targets as we enter the anthropocene. Sci Mar (Barc) 65:85–105
Compant S, Clément C, Sessitsch A (2010) Plant growth-promoting bacteria in the rhizo- and endosphere of plants: their role, colonization, mechanisms involved and prospects for utilization. Soil Biol Biochem 42:669–678
Cray JA, Bell AN, Bhaganna P, Mswaka AY, Timson DJ, Hallsworth JE (2013) The biology of habitat dominance: can microbes behave as weeds. Microb Biotechnol 6:453–492
Curl EA, Truelove B (2012) The rhizosphere. Advanced Series in Agricultural Sciences, vol 15. Springer Science, Berlin
Davis MA, Chew MK, Hobbs RJ, Lugo AE, Ewel JJ, Vermeij GJ, Thompson K (2011) Don’t judge species on their origins. Nature 474:153–154
Dawson TE, Mambelli S, Plamboeck AH, Templer PH, Tu KP (2002) Stable isotopes in plant ecology. Annu Rev Ecol Syst 33:507–559
De Coninck B, Timmermans P, Vos C, Cammue BP, Kazan K (2015) What lies beneath: belowground defense strategies in plants. Trends Sci 20:91–101
De Deyn GB, Raaijmakers CE, Van Ruijven J, Berendse F, Van Der Putten WH (2004) Plant species identity and diversity effects on different trophic levels of nematodes in the soil food web. Oikos 106:576–586
Delgado-Baquerizo M, Maestre FT, Reich PB, Jeffries TC, Gaitan JJ, Encinar D, Singh BK (2016) Microbial diversity drives multifunctionality in terrestrial ecosystems. Nat Commun 7:1–8
Depoorter E, Bull MJ, Peeters C, Coenye T, Vandamme P, Mahenthiralingam E (2016) Burkholderia: an update on taxonomy and biotechnological potential as antibiotic producers. Appl Microbiol Biotechnol 100:5215–5229
Downer CC (2014) The horse and burro as positively contributing returned natives in North America. Am Life Sci 2:5–23
Enespa, Chandra P (2017) Microbial volatiles as chemical weapons against pathogenic fungi. In: Choudhary D, Sharma A, Agarwal P, Varma A, Tuteja N (eds) Volatiles and food security. Springer, Berlin
Enespa, Dwivedi SK (2014) Effectiveness of some antagonistic fungi and botanicals against Fusarium solani and Fusarium oxysporum f. sp. lycopersici infecting Brinjal and tomato plants. Asian J Plant Patho 8(1):18–25
Fiehn O, Wohlgemuth G, Scholz M, Kind T, Lee DY, Lu Y, Nikolau B (2008) Quality control for plant metabolomics: reporting MSI-compliant studies. Plant J 53:691–704
Fuqua WC, Winans SC, Greenberg EP (1994) Quorum sensing in bacteria: the LuxR-LuxI family of cell density-responsive transcriptional regulators. J Bacteriol 176:269
Gaiero JR, McCall CA, Thompson KA, Day NJ, Best AS, Dunfield KE (2013) Inside the root microbiome: bacterial root endophytes and plant growth promotion. Am Bot 100:1738–1750
Gemperline E, Horn HA, DeLaney K, Currie CR, Li L (2017) Imaging with mass spectrometry of bacteria on the exoskeleton of fungus-growing ants. ACS Chem Biol 12:1980–1985
Gilbert GS (2002) Evolutionary ecology of plant diseases in natural ecosystems. Annu Rev Phytopathol 40:13–43
Gonzalez JE, Marketon MM (2003) Quorum sensing in nitrogen-fixing rhizobia. Microbiol Mol Biol Rev 67:574–592
Gougoulias C, Clark JM, Shaw LJ (2014) The role of soil microbes in the global carbon cycle: tracking the below-ground microbial processing of plant-derived carbon for manipulating carbon dynamics in agricultural systems. J Sci Food Agric 94:2362–2371
Gravel V, Antoun H, Tweddell RJ (2007) Growth stimulation and fruit yield improvement of greenhouse tomato plants by inoculation with Pseudomonas putida or Trichoderma atroviride: possible role of indole acetic acid (IAA). Soil Biol Biochem 39:1968–1977
Haas D, Défago G (2005) Biological control of soil-borne pathogens by fluorescent pseudomonads. Nat Rev Microbiol 3:307
Hacquard S, Garrido-Oter R, González A, Spaepen S, Ackermann G, Lebeis S, Schulze-Lefert P (2015) Microbiota and host nutrition across plant and animal kingdoms. Cell Host Microbe 17:603–616
Hansen EM, Goheen EM (2000) Phellinus weirii and other native root pathogens as determinants of forest structure and process in western North America. Annu Rev Phytopathol 38:515–539
Hardoim PR, Van Overbeek LS, Berg G, Pirttilä AM, Compant S, Campisano A, Sessitsch A (2015) The hidden world within plants: ecological and evolutionary considerations for defining functioning of microbial endophytes. Microbiol Mol Biol Rev 79:293–320
Harrier LA, Watson CA (2004) The potential role of arbuscular mycorrhizal (AM) fungi in the bioprotection of plants against soil-borne pathogens in organic and/or other sustainable farming systems. Pest Manag Sci 60:149–157
Hartmann A, Schmid M, Van Tuinen D, Berg G (2009) Plant-driven selection of microbes. Plant Soil 321:235–257
Hausch S, Vamosi SM, Fox JW (2018) Effects of intraspecific phenotypic variation on species coexistence. Ecology 99:1453–1462
Herbst FA, Lünsmann V, Kjeldal H, Jehmlich N, Tholey A, von Bergen M, Nielsen PH (2016) Enhancing metaproteomics: the value of models and defined environmental microbial systems. Proteomics 16:783–798
Hibbing ME, Fuqua C, Parsek MR, Peterson SB (2010) Bacterial competition: surviving and thriving in the microbial jungle. Nat Rev Microbiol 8:15–25
Hierro JL, Maron JL, Callaway RM (2005) A biogeographical approach to plant invasions: the importance of studying exotics in their introduced and native range. J Ecol 93:5–15
Hodge A (2004) The plastic plant: root responses to heterogeneous supplies of nutrients. New Phytol 162:9–24
Hoitink HA, Fahy PC (1986) Basis for the control of soilborne plant pathogens with composts. Annu Rev Phytopathol 24:93–114
Igiehon NO, Babalola OO (2018) Below-ground-above-ground plant-microbial interactions: focusing on soybean, rhizobacteria and mycorrhizal fungi. Microbiol J 12:261–279
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 Soil 37:1–16
Jenny H (1980) The soil resource: origin and behavior. Ecological studies, vol 37. Springer, New York
Jentsch A, Kreyling J, Beierkuhnlein C (2007) A new generation of climate-change experiments: events, not trends. Front Ecol Environ 5:365–374
Jessup CM, Kassen R, Forde SE, Kerr B, Buckling A, Rainey PB, Bohannan BJ (2004) Big questions, small worlds: microbial model systems in ecology. Trends Ecol Evol 19:189–197
Jimenez PN, Koch G, Thompson JA, Xavier KB, Cool RH, Quax WJ (2012) The multiple signaling systems regulating virulence in Pseudomonas aeruginosa. Microbiol Mol Biol Rev 76:46–65
Johansson JF, Paul LR, Finlay RD (2004) Microbial interactions in the mycorrhizosphere and their significance for sustainable agriculture. FEMS Microbiol Ecol 48:1–13
Johnson NC (2010) Resource stoichiometry elucidates the structure and function of arbuscular mycorrhizas across scales. New Phytol 185:631–647
Jones DL, Hodge A, Kuzyakov Y (2004) Plant and mycorrhizal regulation of rhizodeposition. New Phytol 163:459–480
Jones JT, Haegeman A, Danchin EG, Gaur HS, Helder J, Jones MG, Perry RN (2013) Top 10 plant-parasitic nematodes in molecular plant pathology. Mol Plant Pathol 14:946–961
Jones MG, Iqbal S, Fosu-Nyarko J (2016) Belowground defence strategies against migratory nematodes. In: Belowground defence strategies in plants. Springer, Cham, pp 253–278
Kanoh K, Kamino K (2001) Effect of exogenous siderophores on iron uptake activity of marine bacteria under iron-limited conditions. Appl Environ Microl 67:1710–1717
Khan MR (2015) Nematode diseases of crops in India. In: Recent advances in the diagnosis and management of plant diseases. Springer India, Cham, pp 183–224
Kim ES, Trisurat Y, Muraoka H, Shibata H, Amoroso V, Boldgiv B, Ohte N (2018) The International Long-Term Ecological Research-East Asia-Pacific Regional Network (ILTER-EAP): history, development, and perspectives. Ecol Res 33:19–34
Kliebenstein DJ (2004) Secondary metabolites and plant/environment interactions: a view through Arabidopsis thaliana tinged glasses. Plant Cell Environ 27:675–684
Kõljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AF, Bahram M, Douglas B (2013) Towards a unified paradigm for sequence-based identification of fungi. Mol Ecol 22:5271–5277
Kong C, Liang W, Xu X, Hu F, Wang P, Jiang Y (2004) Release and activity of allelochemicals from allelopathic rice seedlings. J Agric Food Chem 52:2861–2865
Korhonen A, Lehto T, Repo T (2015) Frost hardiness of mycorrhizal and non-mycorrhizal Scots pine under two fertilization treatments. Mycorrhiza 25(5):377–386
Koutsoudis MD, Tsaltas D, Minogue TD, von Bodman SB (2006) Quorum-sensing regulation governs bacterial adhesion, biofilm development, and host colonization in Pantoea stewartii subspecies stewartii. Proc Natl Acad Sci U S A 103:5983–5988
Kulmatiski A, Beard KH, Stevens JR, Cobbold SM (2008) Plant–soil feedbacks: a meta-analytical review. Ecol Lett 11:980–992
Lacava PT, Araújo WL, Marcon J, Maccheroni W Jr, Azevedo JL (2004) Interaction between endophytic bacteria from citrus plants and the phytopathogenic bacteria Xylella fastidiosa, causal agent of citrus-variegated chlorosis. Lett Appl Microbiol 39:55–59
Laliberté E, Grace JB, Huston MA, Lambers H, Teste FP, Turner BL, Wardle DA (2013) How does pedogenesis drive plant diversity. Trends Ecol Evol 28:331–340
Lambers H, Chapin FS, Pons TL (2008) Interactions among plants. In: Plant physiological ecology. Springer, New York, pp 505–531
Lambers H, Mougel C, Jaillard B, Hinsinger P (2009) Plant–microbe–soil interactions in the rhizosphere: an evolutionary perspective. Plant Soil 321:83–115
Langley JA, Hungate BA (2003) Mycorrhizal controls on belowground litter quality. Ecology 84:2302–2312
Lanoue A, Burlat V, Henkes GJ, Koch I, Schurr U, Röse US (2010) De novo biosynthesis of defense root exudates in response to Fusarium attack in barley. New Phytol 185:577–588
Lareen A, Burton F, Schäfer P (2016) Plant root-microbe communication in shaping root microbiomes. Plant Mol Biol 90:575–587
Lattanzio V, Lattanzio VM, Cardinali A (2006) Role of phenolics in the resistance mechanisms of plants against fungal pathogens and insects. Phytol Adv Res 661:23–67
Lee KJ, Oh B, Seralathan KK (2013) Advances in plant growth promoting rhizobacteria for biological control of plant diseases. In: Bacteria in agrobiology: disease management. Springer, Berlin, pp 1–13
Li XG, Zhang TL, Wang XX, Hua K, Zhao L, Han ZM (2013) The composition of root exudates from two different resistant peanut cultivars and their effects on the growth of soil-borne pathogen. Int J Biol Sci 9:164–173
Lindsay WL, Norvell WA (1978) Development of a DTPA soil test for zinc, iron, manganese, and copper. Soil Sci Am J 42:421–428
Lloyd-Price J, Abu-Ali G, Huttenhower C (2016) The healthy human microbiome. Gen Med 8:1–11
Lugtenberg B, Kamilova F (2009) Plant-growth-promoting rhizobacteria. Annu Rev Microbiol 63:541–556
Lynch JM, Benedetti A, Insam H, Nuti MP, Smalla K, Torsvik V, Nannipieri P (2004) Microbial diversity in soil: ecological theories, the contribution of molecular techniques and the impact of transgenic plants and transgenic microorganisms. Biol Fertil Soil 40:363–385
Mansfield J, Genin S, Magori S, Citovsky V, Sriariyanum M, Ronald P, Toth IAN (2012) Top 10 plant pathogenic bacteria in molecular plant pathology. Mol Plant Pathol 13:614–629
Marschner H (2011) Marschner’s mineral nutrition of higher plants. Academic press, London
Marschner P (2012) Rhizosphere biology. In: Marschner’s mineral nutrition of higher plants, 3rd edn. Springer, New York, pp 369–388
Massalha H, Korenblum E, Tholl D, Aharoni A (2017) Small molecules below-ground: the role of specialized metabolites in the rhizosphere. Plant J 90:788–807
Mauch-Mani B, Baccelli I, Luna E, Flors V (2017) Defense priming: an adaptive part of induced resistance. Annu Rev Plant Bio 68:485–512
McCann KS (2000) The diversity stability debate. Nature 405:228–233
Mendes R, Garbeva P, Raaijmakers JM (2013) The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol Rev 37:634–663
Mueller UG, Sachs JL (2015) Engineering microbiomes to improve plant and animal health. Trends Microbiol 23:606–617
Nega A (2014) Review on concepts in biological control of plant pathogens. J Biol Agric Health 4:33–54
Nicol JM, Turner SJ, Coyne DL, Den Nijs L, Hockland S, Maafi ZT (2011) Current nematode threats to world agriculture. In: Genomics and molecular genetics of plant-nematode interactions. Springer, Dordrecht, pp 21–43
Öpik M, Vanatoa A, Vanatoa E, Moora M, Davison J, Kalwij JM, Zobel M (2010) The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota). New Phytol 188:223–241
Packer A, Clay K (2003) Soil pathogens and Prunus serotina seedling and sapling growth near conspecific trees. Ecology 84:108–119
Palacios OA, Bashan Y, de-Bashan LE (2014) Proven and potential involvement of vitamins in interactions of plants with plant growth-promoting bacteria: an overview. Biol Fertil Soils 50:415–432
Parnell JJ, Berka R, Young HA, Sturino JM, Kang Y, Barnhart DM, DiLeo MV (2016) From the lab to the farm: an industrial perspective of plant beneficial microorganisms. Front Sci 7:1–12
Peix A, Ramírez-Bahena MH, Velázquez E, Bedmar EJ (2015) Bacterial associations with legumes. Crit Rev Sci 34:17–42
Pérez-Jaramillo JE, Mendes R, Raaijmakers JM (2016) Impact of plant domestication on rhizosphere microbiome assembly and functions. Plant Mol Biol 90:635–644
Pérez-Montaño F, Alías-Villegas C, Bellogín RA, Del Cerro P, Espuny MR, Jiménez-Guerrero I, Cubo T (2014) Plant growth promotion in cereal and leguminous agricultural important plants: from microorganism capacities to crop production. Microbiol Res 169:325–336
Pieterse CM, Leon-Reyes A, Van der Ent S, Van Wees SC (2009) Networking by small-molecule hormones in plant immunity. Nat Chem Biol 5:308–316
Pieterse CM, Van der Does D, Zamioudis C, Leon-Reyes A, Van Wees SC (2012) Hormonal modulation of plant immunity. Annu Rev Cell Biol 28:489–521
Pineda A, Zheng SJ, Van Loon JJ, Pieterse CM, Dicke M (2010) Helping plants to deal with insects: the role of beneficial soil-borne microbes. Trends Sci 15:507–514
Polke M, Sprenger M, Scherlach K, Albán-Proaño MC, Martin R, Hertweck C, Jacobsen ID (2017) A functional link between hyphal maintenance and quorum sensing in Candida albicans. Mol Microbiol 103:595–617
Prasad R, Kumar M, Varma A (2015) Role of PGPR in soil fertility and plant health. In: Egamberdieva D, Shrivastava S, Varma A (eds) Plant growth-promoting rhizobacteria (PGPR) and medicinal plants. Springer International, Switzerland, pp 247–260
Pringle A, Bever JD, Gardes M, Parrent JL, Rillig MC, Klironomos JN (2009) Mycorrhizal symbioses and plant invasions. Annu Rev Ecol Evol Syst 40:699–715
Quiñones B, Dulla G, Lindow SE (2005) Quorum sensing regulates exopolysaccharide production, motility, and virulence in Pseudomonas syringae. Mol Interact 18:682–693
Raaijmakers JM, Vlami M, De Souza JT (2002) Antibiotic production by bacterial biocontrol agents. Antonie van Leeuwenhoek 81:537–547
Ramaswamy AV, Sorrels CM, Gerwick WH (2007) Cloning and biochemical characterization of the hectochlorin biosynthetic gene cluster from the marine cyanobacterium Lyngbya majuscula. J Nat Prod 70:1977–1986
Rapparini F, Peñuelas J (2014) Mycorrhizal fungi to alleviate drought stress on plant growth. In: Use of microbes for the alleviation of soil stresses, vol 1. Springer, New York, pp 21–42
Rasolomampianina R, Bailly X, Fetiarison R, Rabevohitra R, Béna G, Ramaroson L, Avarre JC (2005) Nitrogen-fixing nodules from rose wood legume trees (Dalbergia spp.) endemic to Madagascar host seven different genera belonging to α-and β-Proteobacteria. Mol Ecol 14:4135–4146
Ratnadass A, Blanchart É, Lecomte P (2013) Ecological interactions within the biodiversity of cultivated systems. In: Cultivating biodiversity to transform agriculture. Springer, Dordrecht, pp 141–179
Read DJ, Duckett JG, Francis R, Ligrone R, Russell A (2000) Symbiotic fungal associations in ‘lower’ land plants. Philos Trans R Soc Lond B Biol Sci 355:815–831
Redecker D, Schüßler A, Stockinger H, Stürmer SL, Morton JB, Walker C (2013) An evidence-based consensus for the classification of arbuscular mycorrhizal fungi (Glomeromycota). Mycology 23:515–531
Reynolds HL, Packer A, Bever JD, Clay K (2003) Grassroots ecology: plant–microbe-soil interactions as drivers of plant community structure and dynamics. Ecology 84:2281–2291
Richardson AE, Barea JM, McNeill AM, Prigent-Combaret C (2009) Acquisition of phosphorus and nitrogen in the rhizosphere and plant growth promotion by microorganisms. Plant Soil 32:305–339
Rodrıguez-Echeverrıa S, Costa SR, Freitas H (2007) Biodiversity and interactions in the rhizosphere: effects on ecosystem functioning. In: Functional plant ecology. 7488. CRC Press, Boca Raton, FL, pp 581–595
Romero IG, Ruvinsky I, Gilad Y (2012) Comparative studies of gene expression and the evolution of gene regulation. Nat Rev Genet 13(7):505–516
Römheld V, Kirkby EA (2010) Research on potassium in agriculture: needs and prospects. Plant Soil 335:155–180
Salas-Marina MA, Silva-Flores MA, Uresti-Rivera EE, Castro-Longoria E, Herrera-Estrella A, Casas-Flores S (2011) Colonization of Arabidopsis roots by Trichoderma atroviride promotes growth and enhances systemic disease resistance through jasmonic acid/ethylene and salicylic acid pathways. Eur J Plant Pathol 131:15–26
Sawada H, Kuykendall LD, Young JM (2003) Changing concepts in the systematics of bacterial nitrogen-fixing legume symbionts. J Appl Microbiol 49:155–179
Schmidt MW, Torn MS, Abiven S, Dittmar T, Guggenberger G, Janssens IA, Nannipieri P (2011) Persistence of soil organic matter as an ecosystem property. Nature 478:49–56
Schoener TW (1974) Resource partitioning in ecological communities. Science 185:27–39
Selosse MA, Richard F, He X, Simard SW (2006) Mycorrhizal networks: des liaisons dangereuses? Trends Ecol Evol 21:621–628
Shade A, Peter H, Allison SD, Baho D, Berga M, Bürgmann H, Matulich KL (2012) Fundamentals of microbial community resistance and resilience. Front Microbiol 3:1–19
Shamseldin A (2013) The role of different genes involved in symbiotic nitrogen fixation. Review. J Biotechnol Biochem 8:84–94
Sharpley AN, Chapra SC, Wedepohl R, Sims JT, Daniel TC, Reddy KR (1994) Managing agricultural phosphorus for protection of surface waters: issues and options. J Environ Qual 23:437–451
Shoresh M, Harman GE, Mastouri F (2010) Induced systemic resistance and plant responses to fungal biocontrol agents. Annu Rev Phytopathol 48:21–43
Shrivastava S, Prasad R, Varma A (2014) Anatomy of root from eyes of a microbiologist. In: Morte A, Varma A (eds) Root engineering. Springer, Berlin, pp 3–22
Shtark OY, Borisov AY, Zhukov VA, Provorov NA, Tikhonovich IA (2010) Intimate associations of beneficial soil microbes with host plants. In: Soil microbiology and sustainable crop production. Springer, Dordrecht, pp 119–196
Sikkema J, de Bont JA, Poolman B (1995) Mechanisms of membrane toxicity of hydrocarbons. Microbiol Rev 59:201–222
Simard S, Asay A, Beiler K, Bingham M, Deslippe J, He X, Teste F (2015) Resource transfer between plants through ectomycorrhizal fungal networks. In: Horton TR (ed) Mycorrhizal networks. Ecological studies, vol 224. Analysis and synthesis. Springer, Dordrecht, pp 133–176
Singh D, Raina TK, Kumar A, Singh J, Prasad R (2019) Plant microbiome: a reservoir of novel genes and metabolites. Plant Gene. https://doi.org/10.1016/j.plgene.2019.100177
Six J, Bossuyt H, Degryze S, Denef K (2004) A history of research on the link between (micro) aggregates, soil biota, and soil organic matter dynamics. Soil Res 79:7–31
Smith SE, Read DJ (2010) Mycorrhizal symbiosis. Academic Press, New York
Smith SE, Smith FA (2012) Fresh perspectives on the roles of arbuscular mycorrhizal fungi in plant nutrition and growth. Mycologia 104:1–13
Smith SE, Facelli E, Pope S, Smith FA (2010) Plant performance in stressful environments: interpreting new and established knowledge of the roles of arbuscular mycorrhizas. Plant Soil 326:3–20
Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR, Herndl GJ (2006) Microbial diversity in the deep sea and the underexplored “rare biosphere.”. Proc Natl Acad Sci U S A 103:12115–12120
Somers E, Vanderleyden J, Srinivasan M (2004) Rhizosphere bacterial signalling: a love parade beneath our feet. Crit Rev Microbiol 30:205–240
Sparbier K, Schubert S, Weller U, Boogen C, Kostrzewa M (2012) Matrix-assisted laser desorption ionization–time of flight mass spectrometry-based functional assay for rapid detection of resistance against β-lactam antibiotics. J Clin Microbiol 50:927–937
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 9:1–9
Swamy MK, Akhtar MS, Sinniah UR (2016) Root exudates and their molecular interactions with rhizospheric microbes. In: Hakeem KR, Akhtar MS (eds) Plant, soil and microbes: vol 2. Mechanisms and molecular interactions. Springer, Cham, pp 59–77
Taylor JH, Peterson CA (2005) Ectomycorrhizal impacts on nutrient uptake pathways in woody roots. New For 30:203–214
Taylor MW, Radax R, Steger D, Wagner M (2007) Sponge-associated microorganisms: evolution, ecology, and biotechnological potential. Microbiol Mol Biol Rev 71:295–347
Tewari S, Arora NK (2013) Transactions among microorganisms and plant in the composite rhizosphere habitat. In: Plant microbe symbiosis: fundamentals and advances. Springer, New Delhi, pp 1–50
Toby Kiers E, Palmer TM, Ives AR, Bruno JF, Bronstein JL (2010) Mutualisms in a changing world: an evolutionary perspective. Ecol Lett 13:1459–1474
Toljander JF, Santos-González JC, Tehler A, Finlay RD (2008) Community analysis of arbuscular mycorrhizal fungi and bacteria in the maize mycorrhizosphere in a long-term fertilization trial. FEMS Microbiol Ecol 65:323–338
Torsvik V, Øvreås L (2002) Microbial diversity and function in soil: from genes to ecosystems. Currt Opin Microbiol 5:240–245
Van Der Heijden MG, Horton TR (2009) Socialism in soil. The importance of mycorrhizal fungal networks for facilitation in natural ecosystems. J Ecol 97:1139–1150
Van Der Heijden MG, 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
Venturi V, Keel C (2016) Signaling in the rhizosphere. Trends Sci 21:187–198
Vigo C, Norman JR, Hooker JE (2000) Biocontrol of the pathogen Phytophthora parasitica by arbuscular mycorrhizal fungi is a consequence of effects on infection loci. Plant Pathol 49:509–514
Vovlas N, Rapoport HF, Jiménez Díaz RM, Castillo P (2005) Differences in feeding sites induced by root-knot nematodes, Meloidogyne sp., in chickpea. Phytopathology 95:368–375
Walker AW, Duncan SH, Louis P, Flint HJ (2014) Phylogeny, culturing, and metagenomics of the human gut microbiota. Trends Microbiol 22:267–274
Wang M, Zheng Q, Shen Q, Guo S (2013) The critical role of potassium in plant stress response. Int J Mol Sci 14(4):7370–7390
Wardle DA, Karban R, Callaway RM (2011) The ecosystem and evolutionary contexts of allelopathy. Trends Ecol Evol 26:655–662
Wassmann R, Jagadish SVK, Sumfleth K, Pathak H, Howell G, Ismail A, Heuer S (2009) Regional vulnerability of climate change impacts on Asian rice production and scope for adaptation. Adv Agron 102:91–133
Waters CM, Bassler BL (2005) Quorum sensing: cell-to-cell communication in bacteria. Annu Rev Cell Dev Biol 21:319–346
Weller DM (1988) Biological control of soilborne plant pathogens in the rhizosphere with bacteria. Annu Rev Phytopathol 26:379–407
West SA, Diggle SP, Buckling A, Gardner A, Griffin AS (2007) The social lives of microbes. Annu Rev Ecol Evol Syst 38:53–77
Whitham TG, Bailey JK, Schweitzer JA, Shuster SM, Bangert RK, LeRoy CJ, Wooley SC (2006) A framework for community and ecosystem genetics: from genes to ecosystems. Nat Rev Genet 7:510–523
Wright JS (2002) Plant diversity in tropical forests: a review of mechanisms of species coexistence. Oecologia (Berl) 130:1–14
Xu J (2006) Invited review: microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances. Mol Ecol 15:1713–1731
Yuan J, Zhang N, Huang Q, Raza W, Li R, Vivanco JM, Shen Q (2015) Organic acids from root exudates of banana help root colonization of PGPR strain Bacillus amyloliquefaciens NJN-6. Sci Rep 5:1–8
Zhao J, Davis LC, Verpoorte R (2005) Elicitor signal transduction leading to production of plant secondary metabolites. Biotechnol Adv 23:283–333
Zornoza R, Acosta JA, Bastida F, Domínguez SG, Toledo DM, Faz A (2015) Identification of sensitive indicators to assess the interrelationship between soil quality, management practices and human health. Soil 1:173–185
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Chandra, P., Enespa (2019). Soil–Microbes–Plants: Interactions and Ecological Diversity. In: Varma, A., Tripathi, S., Prasad, R. (eds) Plant Microbe Interface. Springer, Cham. https://doi.org/10.1007/978-3-030-19831-2_6
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