Synthetic microbiota reveal priority effects and keystone strains in the Arabidopsis phyllosphere

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Abstract

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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Fig. 1: Concept of drop-out and late introduction experiments using synthetic microbiota.
Fig. 2: Relative abundance in control community.
Fig. 3: Proteobacteria class drop-out and late introduction experiment.
Fig. 4: Single-strain drop-outs.
Fig. 5: Causal network (P ≤ 0.01) based on single-strain drop-outs.
Fig. 6: Correlation between node out degree and effect size following node removal.

Data availability

Raw data can be found in the European Nucleotide Archive under accession number PRJEB32997.

Code availability

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 No unpublished algorithms or methods were used.

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Acknowledgements

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.

Author information

C.I.C. and J.A.V. conceived the project. C.I.C., M.B.-M. and B.M. carried out the plant experiments. C.I.C. and M.B.-M. extracted DNA from samples. C.I.C. prepared DNA libraries for sequencing. C.M.F. wrote the code for data analysis and visualization. S.S. guided data analysis. C.I.C., C.M.F. and J.A.V. wrote the manuscript with input from S.S. All authors read the manuscript and approved it.

Correspondence to Julia A. Vorholt.

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Supplementary Information

Supplementary Information

Supplementary Figs. 1–12 and Tables 1 and 2.

Reporting Summary

Supplementary Dataset 1

Relative abundance (median and interquartile range) of all strains in the control community (1 independent replicate, n = 48).

Supplementary Dataset 2

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

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