Abstract
The research related to belowground ecology is a fascinating field and gaining immense attention currently. A multitude of interactions operating in the rhizosphere has been revealed by recent boom in the studies exploring the underlying mechanism of the communications between plant and microbial communities. These interactions are mediated by root exudates released by plant roots controlling numerous ecological processes. The ecological functions based on root-microbe interactions include nutrient cycling, decomposition, and maintenance of soil structure, disease suppression, bioremediation, biomass production, soil carbon sequestration and regulation of microbial communities. A greater understanding of these root-microbe interactions is strongly required to exploit the soil microbiota for plant development from applied perspective.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Abdel-Lateif K, Bogusz D, Hocher V (2012) The role of flavonoids in the establishment of plant roots endosymbioses with arbuscular mycorrhiza fungi, rhizobia and Frankia bacteria. Plant Signal Behav 7:636–641. https://doi.org/10.4161/psb.20039
Alavi P, Starcher MR, Zachow C, Müller H, Berg G (2013) Root-microbe systems: the effect and mode of interaction of stress protecting agent (SPA) Stenotrophomonas rhizophila DSM14405T. Front Plant Sci 4:141
Badri DV, Vivanco JM (2009) Regulation and function of root exudates. Plant Cell Environ 32:666–681. https://doi.org/10.1111/j.1365-3040.2009.01926.x
Badri DV, Chaparro JM, Zhang R, Shen Q, Vivanco JM (2013a) Application of natural blends of phytochemicals derived from the root exudates of Arabidopsis to the soil reveal that phenolic-related compounds predominantly modulate the soil microbiome. J Biol Chem 288:4502–4512. https://doi.org/10.1074/jbc.M112.433300
Badri DV, Zolla G, Bakker MG, Manter DK, Vivanco JM (2013b) Potential impact of soil microbiomes on the leaf metabolome and on herbivore feeding behavior. New Phytol 198:264–273. https://doi.org/10.1111/nph.12124
Baetz U (2016) Root exudates as integral part of belowground plant defence. In: CNF V, Kazan K (eds) Belowground defence strategies in plants. Springer, Berlin, pp 45–67. https://doi.org/10.1007/978-3-319-42319-7_3
Baetz U, Martinoia E (2014) Root exudates: the hidden part of plant defense. Trends Plant Sci 19:90–98. https://doi.org/10.1016/j.tplants.2013.11.006
Bakker M, Manter D, Sheflin A, Weir T, Vivanco J (2012) Harnessing the rhizosphere microbiome through plant breeding and agricultural management. Plant Soil 360:1–13. https://doi.org/10.1007/s11104-012-1361-x
Barea JM, Azcón R, Azcón-Aguilar C (2002) Mycorrhizosphere interactions to improve plant fitness and soil quality. Anton Leeuw 81:343–335
Bever JD (2003) Soil community feedback and the coexistence of competitors: conceptual framework and empirical tests. New Phytol 157:465–473
Bisht S, Pandey P, Bhargava B, Sharma S, Kumar V, Sharma KD (2015) Bioremediation of polyaromatic hydrocarbons (PAHs) using rhizosphere technology. Braz J Microbiol 46:7–21
Bonkowski M, Villenage C, Griffiths B (2009) Rhizosphere fauna: the functional and structural diversity of intimate interactions of soil fauna with plant roots. Plant Soil 321:213–233
Bouwmeester HJ, Roux C, López Ráez JA, Bécard G (2007) Rhizosphere communication of plants, parasitic plants and AM fungi. Trends Plant Sci 12:224–230. https://doi.org/10.1016/j.tplants.2007.03.009
Cai T, Cai W, Zhang J, Zheng H, Tsou AM, Xiao L, Zhong Z, Zhu J (2009) Host legume-exuded antimetabolites optimize the symbiotic rhizosphere. Mol Microbiol 73:507–517. https://doi.org/10.1111/j.1365-2958.2009.06790.x
Cannesan MA, Durand C, Burel C, Gangneux C, Lerouge P, Ishii T, Laval K, Follet-Gueye ML, Driouich A, Vicré-Gibouin M (2012) Effect of arabinogalactan proteins from the root caps of pea and Brassica napus on Aphanomyces euteiches zoospore chemotaxis and germination. Plant Physiol 159:1658–1670. https://doi.org/10.1104/pp.112.198507
Cardinale M (2014) Scanning a microhabitat: plant-microbe interactions revealed by confocal laser microscopy. Front Microbiol 5:94. https://doi.org/10.3389/fmicb.2014.00094
Carvalhais LC, Dennis PG, Fan B, Fedoseyenko D, Kierul K, Becker A, Wiren N, Borriss R, Baxter I (2013) Linking plant nutritional status to plant-microbe interactions. PLoS One 8(7):e68555
Chaparro J, Sheflin A, Manter D, Vivanco J (2012) Manipulating the soil microbiome to increase soil health and plant fertility. Biol Fertil Soils 48:489–499. https://doi.org/10.1007/s00374-012-0691-4
Chaparro JM, Badri DV, Bakker MG, Sugiyama A, Manter DK, Vivanco JM (2013) Root exudation of phytochemicals in Arabidopsis follows specific patterns that are developmentally programmed and correlate with soil microbial functions. PLoS One 8:e55731. https://doi.org/10.1371/journal.pone
Cheng F, Cheng Z (2015) Research progress on the use of plant allelopathy in agriculture and the physiological and ecological mechanisms of allelopathy. Front Plant Sci 6:1020. https://doi.org/10.3389/fpls.2015.01020
Chomel M, Guittonny-Larchevêque M, Fernandez C, Gallet C, Des Rochers A, Paré D, Jackson BG, Baldy V (2016) Plant secondary metabolites: a key driver of litter decomposition and soil nutrient cycling. J Ecol 104:1527–1541. https://doi.org/10.1111/1365-2745.12644
Cocking EC (2003) Endophytic colonisation of plant roots by nitrogen-fixing bacteria. Plant Soil 252:169–175
Cordero OX, Datta MS (2016) Microbial interactions and community assembly at microscales. Curr Opin Microbiol 31:227–234
De Hoff P, Brill L, Hirsch A (2009) Plant lectins: the ties that bind in root symbiosis and plant defense. Mol Genet Genomics 282:1–15. https://doi.org/10.1007/s00438-009-0460-8
De-la-Pena C, Vivanco JM (2010) Root-microbe interactions: the importance of protein secretion. Curr Proteonomics 7:265–274
De-la-Pena C, Badri DV, Lei Z, Watson BS, Brandão MM, Silva-Filho MC, Sumner LW, Vivanco JM (2010) Root secretion of defense-related proteins is development-dependent and correlated with flowering time. J Biol Chem 285:30654–30666
Dighton J (2014) Introduction: soils and their promotion of plant growth. In: Dighton J, Krumins JA (eds) Interactions in soil: promoting plant growth, biodiversity, community and ecosystems. Springer, Berlin, pp 1–26. https://doi.org/10.1007/978-94-017-8890-8_1
Fang W, St. Leger RJ (2010) Mrt, a gene unique to fungi, encodes an oligosaccharide transporter and facilitates rhizosphere competency in Metarhizium robertsii. Plant Physiol 154:1549–1557. https://doi.org/10.1104/pp.110.163014
Fang C, Zhuang Y, Xu T, Li Y, Li Y, Lin W (2013) Changes in rice allelopathy and rhizosphere microflora by inhibiting rice phenylalanine ammonia-lyase gene expression. J Chem Ecol 39:204–212. https://doi.org/10.1007/s10886-013-0249-4
Finkel OM, Castrillo G, Paredes SH, González IS, Dang JL (2017) Understanding and exploiting plant beneficial microbes. Curr Opin Plant Biol 38:155–163
Gao X, Wu M, Xu R, Wang X, Pan R, Kim H-J, Liao H (2014) Root interactions in a Maize/Soybean intercropping system control soybean soil-borne disease, red crown rot. PLoS One 9(5):e95031. https://doi.org/10.1371/journal.pone.0095031
Gera Hol WH, de Boer W, Medina A (2014) Beneficial interactions in the rhizosphere. In: Dighton J, Krumins JA (eds) Interactions in soil: promoting plant growth, biodiversity, community and ecosystems 1. Springer, Berlin, pp 59–80. https://doi.org/10.1007/978-94-017-8890-8_3
Grayston SJ, Vaughan D, Jones D (1996) Rhizosphere carbon flow in trees, in comparison with annual plants: the importance of root exudation and its impact on microbial activity and nutrient availability. Appl Soil Ecol 5:29–56
Havlicek E, Mitchell EAD (2014) Soils supporting biodiversity. In: Dighton J, Krumins JA (eds) Interactions in soil: promoting plant growth, biodiversity, community and ecosystems. Springer, Berlin, pp 27–58. https://doi.org/10.1007/978-94-017-8890-8_2
Hayat R, Ali S, Amara U, Khalid R, Ahmed I (2010) Soil beneficial bacteria and their role in plant growth promotion: a review. Ann Microbiol 60:579–598. https://doi.org/10.1007/s13213-010-0117-1
Houlden A, Timms-Wilson TM, Day MJ, Bailey MJ (2008) Influence of plant developmental stage on microbial community structure and activity in the rhizosphere of three field crops. FEMS Microbiol Ecol 65(2):193–201. https://doi.org/10.1111/j.1574-6941.2008.00535.x
Johnson SN, Rasmann S (2015) Root-feeding insects and their interactions with organisms in the rhizosphere. Annu Rev Entomol 60:517–535
Johnson SN, Erb M, Hartley SE (2016) Roots under attack: contrasting plant responses to below- and aboveground insect herbivory. New Phytol 210:413–418
Jones DL, Hodge A, Kuzyakov Y (2004) Plant and mycorrhizal regulation of rhizodeposition. New Phytol 163:459–480. https://doi.org/10.1111/j.1469-8137.2004.01130.x
Kiers ET, Duhamel M, Beesetty Y, Mensah JA, Franken O, Verbruggen E, Fellbaum CR, Kowalchuk GA, Hart MM, Bago A, Palmer TM, West SA, Vandenkoornhuyse P, Jansa J, Bücking H (2011) Reciprocal rewards stabilize cooperation in the mycorrhizal symbiosis. Science 333:880–882. https://doi.org/10.1126/science.1208473
Krumins JA (2014) The positive effects of trophic interactions in soil. In: Dighton J, Krumins JA (eds) Interactions in soil: promoting plant growth, biodiversity, community and ecosystems 1. Springer, Berlin, pp 81–94. https://doi.org/10.1007/978-94-017-8890-8_4
Kumar AS, Lakshmanan V, Caplan JL, Powell D, Czymmek KJ, Levia DF, Bais HP (2012) Rhizobacteria Bacillus subtilisrestricts foliar pathogen entry through stomata. Plant J 72:694–706. https://doi.org/10.1111/j.1365-313X.2012.05116.x
Lal R (2003) Global potential of soil carbon sequestration to mitigate the greenhouse effect. Crit Rev Plant Sci 22:151–184
Lambers H, Clements JC, Nelson MN (2013) How a phosphorus-acquisition strategy based on carboxylate exudation powers the success and agronomic potential of lupines (Lupinus, Fabaceae). Am J Bot 100:263–288. https://doi.org/10.3732/ajb.1200474
Lareen A, Burton F, Schäfer P (2016) Plant root-microbe communication in shaping root microbiomes. Plant Mol Biol 90:575–587
Lavelle P, Spain AV (2005) Soil ecology. Springer, Dordrecht, pp 1–654
Li B, Li Y-Y, Wu H-M, Zhang F-F, Li C-J, Li X-X, Lambers H, Li L (2016) Root exudates drive interspecific facilitation by enhancing nodulation and N2 fixation. PNAS 113:6496–6501
Ma Y, Zhang M, Li Y, Shui J, Zhou Y (2014) Allelopathy of rice (Oryza sativa L.) root exudates and its relations with Orobanche Cumana Wallr. and Orobanche minor Sm. germination. J Plant Interact 9:722–730. https://doi.org/10.1080/17429145.2014.912358.
Matilla MA, Ramos JL, Bakker PAHM, Doornbos R, Badri DV, Vivanco JM, Ramos-González MI (2010) Pseudomonas putida KT2440 causes induced systemic resistance and changes in Arabidopsis root exudation. Environ Microbiol Rep 2:381–388. https://doi.org/10.1111/j.17582229.2009.00091.x
Mendes R, Kruijt M, de Bruijn I, Dekkers E, van der Voort M, Schneider JH, Piceno YM, DeSantis TZ, Andersen GL, Bakker PA, Raaijmakers JM (2011) Deciphering the rhizosphere microbiome for disease suppressive bacteria. Science 332:1097–1100. https://doi.org/10.1126/science.1203980
Mezzari MP, Zimermann DMH, Corseuil HX, Nogueira AV (2011) Potential of grasses and rhizosphere bacteria for bioremediation of diesel-contaminated soils. Rev Bras Ciênc Solo 35:2227–2236
Michalet S, Rohr J, Warshan D, Bardon C, Roggy J-C, Domenach A-M, Czarnes S, Pommier T, Combourieu B, Guillaumaud N, Bellvert F, Comte G, Poly F (2013) Phytochemical analysis of mature tree root exudates in situ and their role in shaping soil microbial communities in relation to tree N-acquisition strategy. Plant Physiol Biochem 72:169–177. https://doi.org/10.1016/j.plaphy.2013.05.003
Morrissey JP, Dow JM, Mark GL, O’Gara F (2004) Are microbes at the root of a solution to world food production? EMBO Rep 5:922–926. https://doi.org/10.1038/sj.embor.7400263
Narula N, Kothe E, Behl RK (2009) Role of root exudates in plant-microbe interactions. J Appl Bot Food Qual 82:122–130
Naznin HA, Kiyohara D, Kimura M, Miyazawa M, Shimizu M, Hyakumachi M, Yang C-H (2014) Systemic resistance induced by volatile organic compounds emitted by plant growth-promoting fungi in Arabidopsis thaliana. PLoS One 9(1):e86882. https://doi.org/10.1371/journal.pone.0086882
Neal AL, Ahmad S, Gordon-Weeks R, Ton J (2012) Benzoxazinoids in root exudates of maize attracts Pseudomonas putida to the rhizosphere. PLoS One 7:e35498. https://doi.org/10.1371/journal.pone.0035498
Nguema-Ona E, Vicré-Gibouin M, Cannesan M-A, Driouich A (2013) Arabinogalactan proteins in root–microbe interactions. Trends Plant Sci 18(8):440–449. https://doi.org/10.1016/j.tplants.2013.03.006
Olson PE, Reardon KF, Pilon-Smits EAH (2003) Ecology of rhizosphere bioremediation. In: McCutcheon SC, Schnoor JL (eds) Phytoremediation: transformation and control of contaminants. Wiley, Hoboken, pp 317–357. https://doi.org/10.1002/047127304X.ch10
Orgiazzi A, Bardgett RD, Barrios E, Behan-Pelletier V, Briones MJI, Chotte J-L, De Deyn GB, Eggleton P, Fierer N, Fraser T, Hedlund K, Jeffery S, Johnson NC, Jones A, Kandeler E, Kaneko N, Lavelle P, Lemanceau P, Miko L, Montanarella L, Moreira FMS, Ramirez KS, Scheu S, Singh BK, Six J, van der Putten WH, Wall DH (2016) Global soil biodiversity Atlas. European Commission, Publications Office of the European Union, Luxembourg, 176 pp
Pavlović P, Muscolo A, Sidari M, Mitrović M (2014) Non-trophic interactions: allelopathy. In: Dighton J, Krumins JA (eds) Interactions in soil: promoting plant growth, biodiversity, community and ecosystems 1. Springer, Berlin, pp 139–162. https://doi.org/10.1007/978-94-017-8890-8_7
Pereg L, McMillan M (2015) Scoping the potential uses of beneficial microorganisms for increasing productivity in cotton cropping systems. Soil Biol Biochem 80:349–358
Pérès G (2014) Soils suppressing biodiversity. In: Dighton J, Krumins JA (eds) Interactions in soil: promoting plant growth, biodiversity, community and ecosystems 1. Springer, Berlin, pp 95–118. https://doi.org/10.1007/978-94-017-8890-8_5
Pieterse CMJ, Zamioudis C, Berendsen RL, Weller DM, Van Wees SC, Bakker PA (2014) Induced systemic resistance by beneficial microbes. Annu Rev Phytopathol 52:347–375
Pineda A, Zheng SJ, Van Loon JJA, Pieterse CMJ, Dicke M (2010) Helping plants to deal with insects: the role of beneficial soil-borne microbes. Trends Plant Sci 15:507–514
Pineda A, Soler R, Pozo MJ, Rasmann S, Turlings TCJ (2015) Editorial: Above-belowground interactions involving plants, microbes and insects. Front Plant Sci 6:318. https://doi.org/10.3389/fpls.2015.00318
Pinton R, Varanini Z, Nannipieri P (2001) The rhizosphere. Biochemistry and organic substances at the soil-plant interface. Marcel Dekker, New York, pp 1–472
Rasmann S, Bennett A, Biere A, Karley A, Guerrieri E (2017) Root symbionts: powerful drivers of plant above- and belowground indirect defences. Insect Sci 24:1–14. https://doi.org/10.1111/1744-7917.12464
Read DS, Matzke M, Gweon HS, Newbold LK, Heggelund L, Ortiz MD, Lahive E, Spurgeon D, Svendsen C (2016) Soil pH effects on the interactions between dissolved zinc, non-nano- and nano-ZnO with soil bacterial communities. Environ Sci Pollut Res 23:4120–4128. https://doi.org/10.1007/s11356-015-4538-z
Reich PB, Tilman D, Naeem S, Ellsworth DS, Knops J, Craine J, Wedin D, Trost J (2004) Species and functional group diversity independently influence biomass accumulation and its response to CO2 and N. Proc Natl Acad Sci USA 101:10101–10106. https://doi.org/10.1073/pnas.0306602101
Rudrappa T, Czymmek KJ, Paré PW, Bais HP (2008) Root-secreted malic acid recruits beneficial soil bacteria. Plant Physiol 148(3):1547–1556. https://doi.org/10.1104/pp.108.127613
Rugova A, Puschenreiter M, Koellensperger G, Hanna S (2017) Elucidating rhizosphere processes by mass spectrometry – a review. Anal Chim Acta 956:1–13
Schmelz EA (2015) Impacts of insect oral secretions on defoliation-induced plant defense. Curr Opin Insect Sci 9:7–15
Sen R (2003) The root–microbe–soil interface: new tool for sustainable plant production. New Phytol 157:391–398
Singh BK, Millard P, Whiteley AS, Murrell JC (2004) Unravelling rhizosphere-microbial interactions: opportunities and limitations. Trends Microbiol 12:386–393. https://doi.org/10.1016/j.tim.2004.06.008
Steinkellner S, Lendzemo V, Langer I, Schweiger P, Khaosaad T, Toussaint J-P, Vierheilig H (2007) Flavonoids and strigolactones in root exudates as signals in symbiotic and pathogenic plant–fungus interactions. Molecules 12:1290–1306. https://doi.org/10.3390/12071290
Termorshuizen AJ (2014) Root pathogens. In: Dighton J, Krumins JA (eds) Interactions in soil: promoting plant growth, biodiversity, community and ecosystems 1. Springer, Berlin, pp 119–138. https://doi.org/10.1007/978-94-017-8890-8_6
Trolove SN, Hedley MJ, Kirk GJD, Bolan NS, Loganathan B (2003) Progress in selected areas of rhizosphere on P acquisition. Aust J Soil Res 41:471–499
Tsunoda T, Kachi N, Suzuki J-I (2014a) Availability and temporal heterogeneity of water supply affect the vertical distribution and mortality of a belowground herbivore and consequently plant growth. PLoS One 9:e100437. https://doi.org/10.1371/journal.pone.0100437
Tsunoda T, Kachi N, Suzuki J-I (2014b) Effects of belowground vertical distribution of a herbivore on plant biomass and survival in Lolium perenne. Ecol Res 29:351–355. https://doi.org/10.1007/s11284-014-1133-6
Tsunoda T, Kachi N, Suzuki J-I (2014c) Effects of belowground herbivory on the survival and biomass of Lolium perenne and Plantago lanceolata plants at various growth stages. Botany 92:737–741. https://doi.org/10.1139/cjb-2014-0045
Tsunoda T, Kachi N, Suzuki J-I (2017) Belowground herbivory decreases shoot water content and biomass of Lolium perenne seedlings under nutrient-poor conditions. Botany 95:29–36. https://doi.org/10.1139/cjb-2016-0076
Van der Ent S, Van Wees SCM, Pieterse CMJ (2009) Jasmonate signaling in plant interactions with resistance-inducing beneficial microbes. Phytochemistry 70:1581–1588. https://doi.org/10.1016/j.phytochem.2009.06.009
Velmourougane K, Prasanna R, Saxena AK (2017) Agriculturally important microbial biofilms: present status and future prospects. J Basic Microbiol 57:548–573. https://doi.org/10.1002/jobm.201700046
Vos CNF, Kazan K (2016) Belowground defence strategies in plants. Springer, Berlin
Wen F, Van Etten HD, Tsaprailis G, Hawes MC (2007) Extracellular proteins in pea root tip and border cell exudates. Plant Physiol 143:773–783. https://doi.org/10.1104/pp.106.091637
Weyens N, van der Lelie D, Taghavi S, Newman L, Vangronsveld J (2009a) Exploiting plant–microbe partnerships for improving biomass production and remediation. Trends Biotechnol 27:591–598
Weyens N, van der Lelie D, Taghavi S, Vangronsveld J (2009b) Phytoremediation: Plant-endophyte partnerships take the challenge. Curr Opin Biotechnol 20:248–254
Weyens N, Thijs S, Popek R, Witters N, Przybysz A, Espenshade J, Gawronska H, Vangronsveld J, Gawronski SW (2015) The role of plant–microbe interactions and their exploitation for phytoremediation of air pollutants. Int J Mol Sci 16:25576–25604. https://doi.org/10.3390/ijms161025576
Xie F, Williams A, Edwards A, Downie JA (2012) A plant arabinogalactan like glycoprotein promotes a novel type of polar surface attachment by Rhizobium leguminosarum. Mol Plant Microbe Interact 25:250–258. https://doi.org/10.1094/MPMI-08-11-0211
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. https://doi.org/10.1016/j.apsoil.2013.03.007
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer International Publishing AG, part of Springer Nature
About this chapter
Cite this chapter
Sharma, A., Verma, R.K. (2018). Root–Microbe Interactions: Understanding and Exploitation of Microbiome. In: Giri, B., Prasad, R., Varma, A. (eds) Root Biology. Soil Biology, vol 52. Springer, Cham. https://doi.org/10.1007/978-3-319-75910-4_13
Download citation
DOI: https://doi.org/10.1007/978-3-319-75910-4_13
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-75909-8
Online ISBN: 978-3-319-75910-4
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)