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Bipartite interactions, antibiotic production and biosynthetic potential of the Arabidopsis leaf microbiome

Nature Microbiology volume 3, pages 909–919 (2018)Cite this article

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Abstract

Plants are colonized by phylogenetically diverse microorganisms that affect plant growth and health. Representative genome-sequenced culture collections of bacterial isolates from model plants, including Arabidopsis thaliana, have recently been established. These resources provide opportunities for systematic interaction screens combined with genome mining to discover uncharacterized natural products. Here, we report on the biosynthetic potential of 224 strains isolated from the A. thaliana phyllosphere. Genome mining identified more than 1,000 predicted natural product biosynthetic gene clusters (BGCs), hundreds of which are unknown compared to the MIBiG database of characterized BGCs. For functional validation, we used a high-throughput screening approach to monitor over 50,000 binary strain combinations. We observed 725 inhibitory interactions, with 26 strains contributing to the majority of these. A combination of imaging mass spectrometry and bioactivity-guided fractionation of the most potent inhibitor, the BGC-rich Brevibacillus sp. Leaf182, revealed three distinct natural product scaffolds that contribute to the observed antibiotic activity. Moreover, a genome mining-based strategy led to the isolation of a trans-acyltransferase polyketide synthase-derived antibiotic, macrobrevin, which displays an unprecedented natural product structure. Our findings demonstrate that the phyllosphere is a valuable environment for the identification of antibiotics and natural products with unusual scaffolds.

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Fig. 1: Bacillales and Pseudomonadales dominate the binary interaction network.
Fig. 2: Biosynthetic potential of the At-LSPHERE strain collection.
Fig. 3: BiG-SCAPE analysis of BGCs detected by antiSMASH in 207 genomes of the At-LSPHERE strain collection and comparison with the MIBiG database of characterized BGCs.
Fig. 4: MALDI imaging results of selected top inhibitors against different sensitive strains and antibiotics isolated from Brevibacillus sp. Leaf182.

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Acknowledgements

This work was financially supported by SNF grant NRP72 to J.P. and J.A.V. and by European Research Council Advanced Grants (PhyMo to J.A.V. and SynPlex to J.P.).

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  1. These authors contributed equally: Eric J. N. Helfrich, Christine M. Vogel.

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  1. Institute of Microbiology, ETH Zurich, Zurich, Switzerland

    Eric J. N. Helfrich, Christine M. Vogel, Reiko Ueoka, Martin Schäfer, Florian Ryffel, Daniel B. Müller, Silke Probst, Markus Kreuzer, Jörn Piel & Julia A. Vorholt

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Contributions

E.J.N.H., C.M.V., R.U., M.S., F.R., D.B.M., J.P. and J.A.V. designed the research. C.M.V., M.S., F.R., D.B.M. and M.K. performed binary interaction screens. E.J.N.H., C.M.V., F.R. and S.P. performed genome mining studies. C.M.V. and D.B.M. conducted statistical analyses. E.J.N.H., C.M.V. and M.S. conducted MALDI imaging experiments. E.J.N.H., C.M.V., M.S., F.R. and S.P. conducted bioassays. E.J.N.H., C.M.V., R.U., F.R. and S.P. isolated and structure-elucidated metabolites. M.S. generated Brevibacillus knockout mutants. E.J.N.H., C.M.V., D.B.M., J.P. and J.A.V. wrote the manuscript with contributions from all authors.

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Correspondence to Jörn Piel or Julia A. Vorholt.

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Helfrich, E.J.N., Vogel, C.M., Ueoka, R. et al. Bipartite interactions, antibiotic production and biosynthetic potential of the Arabidopsis leaf microbiome. Nat Microbiol 3, 909–919 (2018). https://doi.org/10.1038/s41564-018-0200-0

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