Multicellular organisms, including plants, are colonized by microorganisms, some of which are beneficial to growth and health. The assembly rules for establishing plant microbiota are not well understood, and neither is the extent to which their members interact. We conducted drop-out and late introduction experiments by inoculating Arabidopsis thaliana with synthetic communities from a resource of 62 native bacterial strains to test how arrival order shapes community structure. As a read-out we tracked the relative abundance of all strains in the phyllosphere of individual plants. Our results showed that community assembly is historically contingent and subject to priority effects. Missing strains could, to various degrees, invade an already established microbiota, which was itself resistant and remained largely unaffected by latecomers. Additionally, our results indicate that individual strains of Proteobacteria (Sphingomonas, Rhizobium) and Actinobacteria (Microbacterium, Rhodococcus) have the greatest potential to affect community structure as keystone species.
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Raw data can be found in the European Nucleotide Archive under accession number PRJEB32997.
The code used to analyse all data and generate figures can be found at https://github.com/cmfield/carlstrom2019. No unpublished algorithms or methods were used.
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DNA sequencing was performed at the Functional Genomics Centre Zurich. We thank D. Müller and C. Vogel for helpful discussions and support with initial strain selection. This work was funded through a European Research Council Advanced Grant (PhyMo; grant number 668991) to J.A.V. and by ETH Zurich. S.S. is grateful for financial support by the Helmut Horten Foundation.
The authors declare no competing interests.
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Supplementary Figs. 1–12 and Tables 1 and 2.
Relative abundance (median and interquartile range) of all strains in the control community (1 independent replicate, n = 48).
Relative abundance of all strains in all samples of the control community (1 independent replicate, n = 48).
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Carlström, C.I., Field, C.M., Bortfeld-Miller, M. et al. Synthetic microbiota reveal priority effects and keystone strains in the Arabidopsis phyllosphere. Nat Ecol Evol 3, 1445–1454 (2019) doi:10.1038/s41559-019-0994-z