Abstract
The classical view on plant diseases represented by a triangle where the host, the pathogen, and the environment interact with each other resulting in disease or not is recently challenged by a more complex holistic view including the presence of complex microbial communities in the pathosystem. The plant and soil microbiomes are closely connected with all three causal factors of the classical “disease triangle.” The environment, especially the soil characteristics, determines the source of microbes recruited by plant roots, which in turn directly affect the success of given pathogen to cause disease. In the plant, the microbiome impacts host development and health and its assembling and functioning is to some extend controlled by the host genetic traits. The pathogen, as member of the soil microbiome, also interacts and competes with a complex microbial community striving to invade the rhizosphere microbiome and reach the root system to infect and cause disease. Here, we discuss the interactions on the rhizosphere microbiome in the context of soil-borne diseases, highlighting the microbiome as a key player in pathosystems, acting as first line of defense in the rhizosphere. We also discuss strategies to identify plant genetic traits involved in recruitment of beneficial microorganisms and the potential to explore it in the breeding programs to promote plant health and productivity.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Abawi GS, Widmer TL (2000) Impact of soil health management practices on soilborne pathogens, nematodes and root diseases of vegetable crops. Appl Soil Ecol 15:37–47. https://doi.org/10.1016/S0929-1393(00)00070-6
Arnold AE, Mejía LC, Kyllo D et al (2003) Fungal endophytes limit pathogen damage in a tropical tree. Proc Natl Acad Sci 100:15649–15654. https://doi.org/10.1073/pnas.2533483100
Badri DV, Weir TL, van der Lelie D, Vivanco JM (2009) Rhizosphere chemical dialogues: plant-microbe interactions. Curr Opin Biotechnol 20:642–650. https://doi.org/10.1016/j.copbio.2009.09.014
Bais HP, Walker TS, Schweizer HP, Vivanco JM (2002) Root specific elicitation and antimicrobial activity of rosmarinic acid in hairy root cultures of Ocimum basilicum. Plant Physiol Biochem 40:983–995. https://doi.org/10.1016/S0981-9428(02)01460-2
Bais HP, Weir TL, Perry LG et al (2006) The role of root exudates in rhizosphere interactions with plants and other organisms. Annu Rev Plant Biol 57:233–266. https://doi.org/10.1146/annurev.arplant.57.032905.105159
Baker KF, Cook RJ (1974) Biological control of plant pathogens. American Phytopathological Society, Saint Paul
Bakker MG, Sheflin AM, Weir TL (2012) Harnessing the rhizosphere microbiome through plant breeding and agricultural management. Plant Soil. https://doi.org/10.1007/s11104-012-1361-x
Bakker MG, Chaparro JM, Manter DK, Vivanco JM (2015) Impacts of bulk soil microbial community structure on rhizosphere microbiomes of Zea mays. Plant Soil 392:115–126. https://doi.org/10.1007/s11104-015-2446-0
Berendsen RL, Pieterse CMJ, Bakker PHM (2012) The rhizosphere microbiome and plant health. Trends Plant Sci 17:478–486. https://doi.org/10.1016/j.tplants.2012.04.001
Berendsen RL, Vismans G, Yu K et al (2018) Disease-induced assemblage of a plant-beneficial bacterial consortium. ISME J 12:1496–1507. https://doi.org/10.1038/s41396-018-0093-1
Berg G, Raaijmakers JM (2018) Saving seed microbiomes. ISME J 12:1167–1170. https://doi.org/10.1038/s41396-017-0028-2
Bordiec S, Paquis S, Lacroix H et al (2011) Comparative analysis of defence responses induced by the endophytic plant growth-promoting rhizobacterium Burkholderia phytofirmans strain PsJN and the non-host bacterium Pseudomonas syringae pv. pisi in grapevine cell suspensions. J Exp Bot 62:595–603. https://doi.org/10.1093/jxb/erq291
Bressan M, Achouak W, Berge O (2013) Exogenous glucosinolate produced by transgenic arabidopsis thaliana has an impact on microbes in the rhizosphere and plant roots. Mol Microb Ecol Rhizosph 2:1173–1179. https://doi.org/10.1002/9781118297674.ch112
Bulgarelli D, Rott M, Schlaeppi K et al (2012) Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 488:91–95. https://doi.org/10.1038/nature11336
Bulgarelli D, Garrido-Oter R, Münch PC et al (2015) Structure and function of the bacterial root microbiota in wild and domesticated barley. Cell Host Microbe 17:392–403. https://doi.org/10.1016/j.chom.2015.01.011
Carvalhais LC, Dennis PG, Fedoseyenko D et al (2011) Root exudation of sugars, amino acids, and organic acids by maize as affected by nitrogen, phosphorus, potassium, and iron deficiency. J Plant Nutr Soil Sci 174:3–11. https://doi.org/10.1002/jpln.201000085
Cavaglieri L, Orlando J, Rodríguez MI et al (2005) Biocontrol of Bacillus subtilis against Fusarium verticillioides in vitro and at the maize root level. Res Microbiol 156:748–754. https://doi.org/10.1016/j.resmic.2005.03.001
Chaparro JM, Badri DV, Vivanco JM (2014) Rhizosphere microbiome assemblage is affected by plant development. ISME J 8:790–803. https://doi.org/10.1038/ismej.2013.196
Chapelle E, Mendes R, Bakker PH, Raaijmakers JM (2015) Fungal invasion of the rhizosphere microbiome. ISME J 82:1–4. https://doi.org/10.1038/ismej.2015.82
Chowdhury AK, Singh G, Tyagi BS et al (2013) Spot blotch disease of wheat – a new thrust area for sustaining productivity. J Wheat Res 5:1–11. https://doi.org/10.1029/2004JD005373
Coakley SM (1988) Prediction of disease in plants. Annu Rev Phytopathol 26:163–181. https://doi.org/10.2307/1940036
Coleman-Derr D, Tringe SG (2014) Building the crops of tomorrow: advantages of symbiont-based approaches to improving abiotic stress tolerance. Front Microbiol 5:1–6. https://doi.org/10.3389/fmicb.2014.00283
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. https://doi.org/10.1016/j.soilbio.2009.11.024
Conrath U, Beckers GJM, Flors V, García-Agustín P, Jakab G, Maunch F, Newman M-A, CMJ P, Poinssot B, Pozo MJ et al (2006) Priming: getting ready for battle. Mol Plan-Mic Interac 19:1062–1071. https://doi.org/10.1094/MPMI-19-1062
Cook RJ, Thomashow LS, Weller DM et al (1995) Molecular mechanisms of defense by rhizobacteria against root disease. Proc Natl Acad Sci 92:4197–4201. https://doi.org/10.1073/pnas.92.10.4197
Diehl JA, Kochhann RA, et al (1982) The effects of fallow periods on common rot of wheat in Rio Grande do Sul, Brazil.PDF. pp 1297–1301
Doebley JF, Gaut BS, Smith BD (2006) Review the molecular genetics of crop domestication. Cell 127:1309–1321
Doornbos RF, Van Loon LC, Bakker PAHM (2012) Impact of root exudates and plant defense signaling on bacterial communities in the rhizosphere. A review. Agron Sustain Dev 32:227–243. https://doi.org/10.1039/c6dt04275a
Edwards J, Johnson C, Santos-Medellín C et al (2015) Structure, variation, and assembly of the root-associated microbiomes of rice. Proc Natl Acad Sci 112:E911–E920. https://doi.org/10.1073/pnas.1414592112
Etalo DW, Jeon J-S, Raaijmakers JM (2018) Modulation of plant chemistry by beneficial root microbiota. Nat Prod Rep 35:398–409. https://doi.org/10.1039/c7np00057j
Francl LJ (2001) The disease triangle: a plant pathological paradigm revisited. The Plant Health Instructor. https://doi.org/10.1094/PHI-T-2001-0517-01
Gepts P (2010) Crop domestication as a long-term selection experiment. In: Plant breeding reviews. Wiley-Blackwell, Hoboken, pp 1–44
Gómez Expósito R, de Bruijn I, Postma J, Raaijmakers JM (2017) Current insights into the role of rhizosphere bacteria in disease suppressive soils. Front Microbiol 8:2529. https://doi.org/10.3389/fmicb.2017.02529
Guo XW, Fernando WGD, Entz M (2005) Effects of crop rotation and tillage on blackleg disease of canola. Can J Plant Pathol 27:53–57. https://doi.org/10.1080/07060660509507193
Hallmann J, Quadt-Hallmann A, Mahaffee WF, Kloepper JW (1997) Bacterial endophytes in agricultural crops. Can J Microbiol 43:895–914. https://doi.org/10.1139/m97-131
Hardoim PR, van Overbeek LS, Berg G et al (2015) The hidden world within plants: ecological and evolutionary considerations for defining functioning of microbial endophytes. Microbiol Mol Biol Rev 79:293–320. https://doi.org/10.1128/MMBR.00050-14
Higginbotham SJ, Arnold AE, Ibañez A et al (2013) Bioactivity of fungal endophytes as a function of endophyte taxonomy and the taxonomy and distribution of their host plants. PLoS One 8. https://doi.org/10.1371/journal.pone.0073192
Hiltner L (1904) Über neure Erfahrungen und Probleme auf dem Gebiet der Bodenbackteriologie und unter besonderer Berücksichtigung der Gründüngung und Brache. Arb Deut Landwirsch Ges 98:59–78
Lebeis SL, Paredes SH, Lundberg DS et al (2015) Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa. Science 349:860–864. https://doi.org/10.1126/science.aaa8764
Mallon CA, van Elsas JD, Salles JF (2015) Microbial invasions: the process, patterns, and mechanisms. Trends Microbiol 23:719–729. https://doi.org/10.1016/j.tim.2015.07.013
Maloy OC, Burkholder WH (1959) Some effects of crop rotation on Fusarium root rot of bean. Phytopathology 49:583–587
Manghwar H, Hussain A, Ullah A et al (2018) Expression analysis of defense related genes in wheat and maize against Bipolaris sorokiniana. Physiol Mol Plant Pathol 103:36–46. https://doi.org/10.1016/j.pmpp.2018.04.002
Mendes R, Kruijt M, de Bruijn I et al (2011) Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 332:1097–1100. https://doi.org/10.1126/science.1203980
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. https://doi.org/10.1111/1574-6976.12028
Mendes LW, Kuramae EE, Navarrete AA et al (2014) Taxonomical and functional microbial community selection in soybean rhizosphere. ISME J 8:1577–1587. https://doi.org/10.1038/ismej.2014.17
Mendes LW, Mendes R, Raaijmakers JM, Tsai SM (2018a) Breeding for soil-borne pathogen resistance impacts active rhizosphere microbiome of common bean. ISME J 1:12. https://doi.org/10.1038/s41396-018-0234-6
Mendes LW, Raaijmakers JM, De Hollander M et al (2018b) Influence of resistance breeding in common bean on rhizosphere microbiome composition and function. ISME J 12:212–224. https://doi.org/10.1038/ismej.2017.158
Mercado-Blanco J, Prieto P (2012) Bacterial endophytes and root hairs. Plant Soil 361:301–306. https://doi.org/10.1007/s11104-012-1212-9
Monchgesang S, Strehmel N, Schmidt S et al (2016) Natural variation of root exudates in arabidopsis thaliana-linking metabolomic and genomic data. Sci Rep 6:1–11. https://doi.org/10.1038/srep29033
Peiffer JA, Spor A, Koren O et al (2013) Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proc Natl Acad Sci 110:6548–6553. https://doi.org/10.1073/pnas.1302837110
Pérez-Jaramillo JE, Mendes R, Raaijmakers JM (2016) Impact of plant domestication on rhizosphere microbiome assembly and functions. Plant Mol Biol 90:635–644. https://doi.org/10.1007/s11103-015-0337-7
Pérez-Jaramillo JE, Carrión VJ, Bosse M et al (2017) Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits. ISME J 11:2244–2257. https://doi.org/10.1038/ismej.2017.85
Philippot L, Raaijmakers JM, Lemanceau P, Van Der Putten WH (2013) Going back to the roots: the microbial ecology of the rhizosphere. Nat Rev Microbiol 11:789–799. https://doi.org/10.1038/nrmicro3109
Raaijmakers JM, Mazzola M (2016) Soil immune responses. Science 352:1392–1393. https://doi.org/10.1126/science.aaf3252
Raaijmakers JM, Paulitz TC, Steinberg C et al (2009) The rhizosphere: a playground and battlefield for soilborne pathogens and beneficial microorganisms. Plant Soil 321:341–361. https://doi.org/10.1007/s11104-008-9568-6
Robertson-Albertyn S, Alegria Terrazas R, Balbirnie K et al (2017) Root hair mutations displace the barley rhizosphere microbiota. Front Plant Sci 8:1–15. https://doi.org/10.3389/fpls.2017.01094
Smith KP, Handelsman J, Goodman RM (1999) Genetic basis in plants for interactions with disease-suppressive bacteria. Proc Natl Acad Sci U S A 96:4786–4790. https://doi.org/10.1073/pnas.96.9.4786
Sun J, Peng M, Wang Y et al (2013) The effects of different disease-resistant cultivars of banana on rhizosphere microbial communities and enzyme activities. FEMS Microbiol Lett 345:121–126. https://doi.org/10.1111/1574-6968.12192
Tawaraya K, Horie R, Saito S et al (2014) Metabolite profiling of root exudates of common bean under phosphorus deficiency. Metabolites 4:599–611. https://doi.org/10.3390/metabo4030599
Tejesvi MV, Segura DR, Schnorr KM et al (2013) An antimicrobial peptide from endophytic Fusarium tricinctum of Rhododendron tomentosum Harmaja. Fungal Divers 60:153–159. https://doi.org/10.1007/s13225-013-0227-8
Torsvik V, Øvreås L (2002) Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 5:240–245. https://doi.org/10.1016/S1369-5274(02)00324-7
Turner TR, James EK, Poole PS (2013) The plant microbiome. Genome Biol 14:209. https://doi.org/10.1186/gb-2013-14-6-209
Van der Putten WH, Van Dijk C, Peters BM (1993) Plant-specific soil-borne diseases contribute to succession in foredune vegetation. Nature 362:53–56. https://doi.org/10.1038/362053a0
van Elsas JD, Chiurazzi M, Mallon CA et al (2012) Microbial diversity determines the invasion of soil by a bacterial pathogen. Proc Natl Acad Sci U S A 109:1159–1164. https://doi.org/10.1073/pnas.1109326109
Venturi V, Keel C (2016) Signaling in the Rhizosphere. Trends Plant Sci 21:187–198. https://doi.org/10.1016/j.tplants.2016.01.005
Weinert N, Piceno Y, Ding G, et al (2011) PhyloChip hybridization uncovered an enormous bacterial diversity in the rhizosphere of different potato cultivars: many common and few cultivar-dependent taxa. https://doi.org/10.1111/j.1574-6941.2010.01025.x
Weller DM, Raaijmakers JM, Gardener BBM, Thomashow LS (2002) Microbial populations responsible for specific soil suppressiveness to plant pathogens. Annu Rev Phytopathol 40:309–348. https://doi.org/10.1146/annurev.phyto.40.030402.110010
Yao H, Wu F (2010) Soil microbial community structure in cucumber rhizosphere of different resistance cultivars to fusarium wilt. FEMS Microbiol Ecol 72:456–463. https://doi.org/10.1111/j.1574-6941.2010.00859.x
Zhang S, Zhu W, Wang B et al (2011) Secondary metabolites from the invasive Solidago canadensis L. accumulation in soil and contribution to inhibition of soil pathogen Pythium ultimum. Appl Soil Ecol 48:280–286. https://doi.org/10.1016/j.apsoil.2011.04.011
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2021 Springer Nature Singapore Pte Ltd.
About this chapter
Cite this chapter
Chiaramonte, J.B., Mendes, L.W., Mendes, R. (2021). Rhizosphere Microbiome and Soil-Borne Diseases. In: Gupta, V.V.S.R., Sharma, A.K. (eds) Rhizosphere Biology: Interactions Between Microbes and Plants. Rhizosphere Biology. Springer, Singapore. https://doi.org/10.1007/978-981-15-6125-2_7
Download citation
DOI: https://doi.org/10.1007/978-981-15-6125-2_7
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-15-6124-5
Online ISBN: 978-981-15-6125-2
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)