Abstract
The rhizosphere provides a home to numerous (micro)organisms that in turn may affect plant growth, development, and tolerance to abiotic and biotic stresses. How plants shape the rhizosphere microbiome has been subject of many past and present studies with the ultimate goal to identify plant genetic traits that select and support beneficial microorganisms. Novel ‘omics technologies have provided more in-depth knowledge of the diversity and functioning of the rhizosphere microbiome and significant advances are being made to uncover mechanisms, genes and metabolites involved in the multitrophic interactions in the rhizosphere. To better understand this intriguing complexity, both reductionists’ and systems ecology approaches are needed to identify the biotic and abiotic factors involved in microbiome assembly. Here, different strategies are discussed to re-shape the rhizosphere microbiome in favour of microbial consortia that promote root development and plant growth, and that prevent the proliferation of pests and diseases.
Keywords
- Microbial Consortium
- Induce Systemic Resistance
- Disease Suppression
- Rhizosphere Microorganism
- Beneficial Microorganism
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
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
Bakker MG, Manter DK, Sheflin AM et al (2012) Harnessing the rhizosphere microbiome through plant breeding and agricultural management. Plant Soil 360:1–13
Berendsen RL, Pieterse CMJ, Bakker P (2012) The rhizosphere microbiome and plant health. Trends Plant Sci 17:478–486
Boon E, Meehan CJ, Whidden C et al (2013) Interactions in the microbiome: communities or organisms and communities of genes. FEMS Microbiol Rev 38:90–118.
Buee M, De Boer W, Martin F et al (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
Burke C, Steinberg P, Rusch D, Kjelleberg S,Thomas T (2011) Bacterial community assembly based on functional genes rather than species. Proc Natl Acad Sci U S A 108:14288–14293
Cook RJ, Thomashow LS, Weller DM et al. (1995) Molecular mechanisms of defense by rhizobacteria against root disease. Proc Natl Acad Sci U S A 92:4197
De Roy K, Marzorati M, Van den Abbeele P et al. (2013) Synthetic microbial ecosystems: an exciting tool to understand and apply microbial communities. Environ Microbiol doi:10.1111/1462–2920.12343
Garbeva P, de Boer W (2009) Inter-specific interactions between carbon-limited soil bacteria affect behavior and gene expression. Microb Ecol 58:36–46
Garbeva P, Silby MW, Raaijmakers JM et al (2011) Transcriptional and antagonistic responses of Pseudomonas fluorescens Pf0–1 to phylogenetically different bacterial competitors. ISME J 5:973–985
Grosskopf T, Soyer OS (2014) Synthetic microbial communities. Curr Opin Microbiol 18:72–77
Hannula SE, de Boer W, van Veen JA (2010) In situ dynamics of soil fungal communities under different genotypes of potato, including a genetically modified cultivar. Soil Biol Biochem 42:2211–2223.
Juhas M, Eberl L, Glass JI (2011) Essence of life: essential genes of minimal genomes. Trends Cell Biol 21:562–568
Kinkel LL, Bakker MG, Schlatter DC (2011) A coevolutionary framework for managing disease-suppressive soils. Annu Rev Phytopathol 49:47–67
Kyselková M, Kopecký J, Frapolli M et al (2009) Comparison of rhizobacterial community composition in soil suppressive or conducive to tobacco black root rot disease. ISME J 3:1127–1138
Lugtenberg B, Kamilova F (2009) Plant-growth-promoting rhizobacteria. Annu Rev Microbiol 63: 541–556
Lynch JM (1990) The rhizosphere. Wiley, New York
Mendes R, Kruijt M, de Bruijn I et al (2011) Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 332:1097–1100
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
Moya A, Gil R, Latorre A et al (2009) Toward minimal bacterial cells: evolution vs. design. FEMS Microbiol Rev 33:225–235
Neal AL, Ahmad S, Gordon-Weeks R, Ton J (2012) Benzoxazinoids in root exudates of maize attract Pseudomonas putida to the rhizosphere. PLOS One 7:e35498
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
Prosser JI, Rangel-Castro JI, Killham K (2006) Studying plant-microbe interactions using stable isotope technologies. Curr Opin Biotechnol 17:98–102
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
Raaijmakers J, Mazzola M (2012) Diversity and natural functions of antibiotics produced by beneficial and pathogenic soil bacteria. Annu Rev Phytopathol 50:403–424
Rosenzweig N, Tiedje JM, Quensen JF et al (2012) Microbial communities associated with potato common scab-suppressive soil determined by pyrosequencing analyses. Plant Dis 96:718–725
Rudrappa T, Czymmek KJ, Pare PW, Bais HP (2008) Root-secreted malic acid recruits beneficial soil bacteria. Plant Physiol 148:1547–1556
Scheuring I, Yu DW (2012) How to assemble a beneficial microbiome in three easy steps. Ecol Lett 15:1300–1307
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
Wang HB, Zhang ZX, Li H et al (2011) Characterization of metaproteomics in crop rhizospheric soil. J Proteome Res 10:932–940
Weller DM, Raaijmakers JM, Gardener BBMS, Thomashow LS (2002) Microbial populations responsible for specific soil suppressiveness to plant pathogens. Annu Rev Phytopathol 40:309–348
Zengler K, Palsson BO (2012) A road map for the development of community systems (CoSy) biology. Nat Rev Microbiol 10:366–372
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer International Publishing Switzerland
About this chapter
Cite this chapter
Raaijmakers, J. (2015). The Minimal Rhizosphere Microbiome. In: Lugtenberg, B. (eds) Principles of Plant-Microbe Interactions. Springer, Cham. https://doi.org/10.1007/978-3-319-08575-3_43
Download citation
DOI: https://doi.org/10.1007/978-3-319-08575-3_43
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-08574-6
Online ISBN: 978-3-319-08575-3
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)