Abstract
We examined succession of the rhizosphere microbiota of three model plants (Arabidopsis, Medicago and Brachypodium) in compost and sand and three crops (Brassica, Pisum and Triticum) in compost alone. We used serial inoculation of 24 independent replicate microcosms over three plant generations for each plant/soil combination. Stochastic variation between replicates was surprisingly weak and by the third generation, replicate microcosms for each plant had communities that were very similar to each other but different to those of other plants or unplanted soil. Microbiota diversity remained high in compost, but declined drastically in sand, with bacterial opportunists and putative autotrophs becoming dominant. These dramatic differences indicate that many microbes cannot thrive on plant exudates alone and presumably also require carbon sources and/or nutrients from soil. Arabidopsis had the weakest influence on its microbiota and in compost replicate microcosms converged on three alternative community compositions rather than a single distinctive community. Organisms selected in rhizospheres can have positive or negative effects. Two abundant bacteria are shown to promote plant growth, but in Brassica the pathogen Olpidium brassicae came to dominate the fungal community. So plants exert strong selection on the rhizosphere microbiota but soil composition is critical to its stability. microbial succession/ plant–microbe interactions/rhizosphere microbiota/selection.
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Acknowledgements
The research was funded by Zuckerman Endowment Fund and UK Biotechnology and Biological Sciences Research Council (BBSRC) grant BB/K001868/1. We thank Darren Heavens (The Genome Analysis Centre) and John Walshaw (John Innes Centre) for sequencing and initial data analysis, Rob Green (John Innes Centre) for help with figures, Alison East (John Innes Centre) for help with the manuscript and Peter Sterk (EMBL-EBI) for data submission. Metagenomic sequence data have been submitted to the EMBL databases under accession PRJEB7318.
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Tkacz, A., Cheema, J., Chandra, G. et al. Stability and succession of the rhizosphere microbiota depends upon plant type and soil composition. ISME J 9, 2349–2359 (2015). https://doi.org/10.1038/ismej.2015.41
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DOI: https://doi.org/10.1038/ismej.2015.41
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