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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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 No unpublished algorithms or methods were used.
References
Fischbach, M. A. Microbiome: focus on causation and mechanism. Cell 174, 785–790 (2018).
Vorholt, J. A., Vogel, C., Carlstrom, C. I. & Müller, D. B. Establishing causality: opportunities of synthetic communities for plant microbiome research. Cell Host Microbe 22, 142–155 (2017).
Venturelli, O. S. et al. Deciphering microbial interactions in synthetic human gut microbiome communities. Mol. Syst. Biol. 14, e8157 (2018).
Friedman, J., Higgins, L. M. & Gore, J. Community structure follows simple assembly rules in microbial microcosms. Nat. Ecol. Evol. 1, 0109 (2017).
Müller, D. B., Schubert, O. T., Röst, H., Aebersold, R. & Vorholt, J. A. Systems-level proteomics of two ubiquitous leaf commensals reveals complementary adaptive traits for phyllosphere colonization. Mol. Cell Proteom. 15, 3256–3269 (2016).
Gourion, B., Rossignol, M. & Vorholt, J. A. A proteomic study of Methylobacterium extorquens reveals a response regulator essential for epiphytic growth. Proc. Natl Acad. Sci. USA 103, 13186–13191 (2006).
Abreu, C., Ortiz Lopez, A. & Gore, J. Pairing off: a bottom-up approach to the human gut microbiome. Mol. Syst. Biol. 14, e8425 (2018).
Brugiroux, S. et al. Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium. Nat. Microbiol. 2, 16215 (2016).
Goodman, A. L. et al. Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice. Proc. Natl Acad. Sci. USA 108, 6252–6257 (2011).
Bonilla-Rosso, G. & Engel, P. Functional roles and metabolic niches in the honey bee gut microbiota. Curr. Opin. Microbiol. 43, 69–76 (2018).
Rawls, J. F., Samuel, B. S. & Gordon, J. I. Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota. Proc. Natl Acad. Sci. USA 101, 4596–4601 (2004).
Bodenhausen, N., Bortfeld-Miller, M., Ackermann, M. & Vorholt, J. A. A synthetic community approach reveals plant genotypes affecting the phyllosphere microbiota. PLoS Genet. 10, e1004283 (2014).
Lebeis, S. et al. Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa. Science 349, 860–864 (2015).
Niu, B., Paulson, J. N., Zheng, X. & Kolter, R. Simplified and representative bacterial community of maize roots. Proc. Natl Acad. Sci. USA 114, E2450–E2459 (2017).
Herrera Paredes, S. et al. Design of synthetic bacterial communities for predictable plant phenotypes. PLoS Biol. 16, e2003962 (2018).
Bai, Y. et al. Functional overlap of the Arabidopsis leaf and root microbiota. Nature 528, 364–369 (2015).
Müller, D. B., Vogel, C., Bai, Y. & Vorholt, J. A. The plant microbiota: systems-level insights and perspectives. Annu. Rev. Genet. 50, 211–234 (2016).
Vorholt, J. A. Microbial life in the phyllosphere. Nat. Rev. Microbiol. 10, 828–840 (2012).
Meyer, K. M. & Leveau, J. H. Microbiology of the phyllosphere: a playground for testing ecological concepts. Oecologia 168, 621–629 (2012).
Woodward, F. I. & Lomas, M. R. Vegetation dynamics—simulating responses to climatic change. Biol. Rev. 79, 643–670 (2004).
Innerebner, G., Knief, C. & Vorholt, J. A. Protection of Arabidopsis thaliana against leaf-pathogenic Pseudomonas syringae by Sphingomonas strains in a controlled model system. Appl. Environ. Microbiol. 77, 3202–3210 (2011).
Ritpitakphong, U. et al. The microbiome of the leaf surface of Arabidopsis protects against a fungal pathogen. New Phytol. 210, 1033–1043 (2016).
Busby, P. E. et al. Research priorities for harnessing plant microbiomes in sustainable agriculture. PLoS Biol. 15, e2001793 (2017).
Knief, C., Ramette, A., Frances, L., Alonso-Blanco, C. & Vorholt, J. A. Site and plant species are important determinants of the Methylobacterium community composition in the plant phyllosphere. ISME J. 4, 719–728 (2010).
Laforest-Lapointe, I. & Whitaker, B. K. Decrypting the phyllosphere microbiota: progress and challenges. Am. J. Bot. 106, 171–173 (2019).
Copeland, J. K., Yuan, L., Layeghifard, M., Wang, P. W. & Guttman, D. S. Seasonal community succession of the phyllosphere microbiome. Mol. Plant Microbe Interact. 28, 274–285 (2015).
Laforest-Lapointe, I., Messier, C. & Kembel, S. W. Host species identity, site and time drive temperate tree phyllosphere bacterial community structure. Microbiome 4, 27 (2016).
Kembel, S. W. et al. Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest. Proc. Natl Acad. Sci. USA 111, 13715–13720 (2014).
Horton, M. W. et al. Genome-wide association study of Arabidopsis thaliana leaf microbial community. Nat. Commun. 5, 5320 (2014).
Redford, A. J., Bowers, R. M., Knight, R., Linhart, Y. & Fierer, N. The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves. Environ. Microbiol. 12, 2885–2893 (2010).
Finkel, O. M., Burch, A. Y., Lindow, S. E., Post, A. F. & Belkin, S. Geographical location determines the population structure in phyllosphere microbial communities of a salt-excreting desert tree. Appl. Environ. Microbiol. 77, 7647–7655 (2011).
Fukami, T. Historical contingency in community assembly: integrating niches, species pools, and priority effects. Annu. Rev. Ecol. Evol. Syst. 46, 1–23 (2015).
Chase, J. M. Community assembly: when should history matter? Oecologia 136, 489–498 (2003).
Peay, K. G., Belisle, M. & Fukami, T. Phylogenetic relatedness predicts priority effects in nectar yeast communities. Proc. Biol. Sci. 279, 749–758 (2012).
Werner, G. D. & Kiers, E. T. Order of arrival structures arbuscular mycorrhizal colonization of plants. New Phytol. 205, 1515–1524 (2015).
Fukami, T. et al. Assembly history dictates ecosystem functioning: evidence from wood decomposer communities. Ecol. Lett. 13, 675–684 (2010).
Hiscox, J. et al. Priority effects during fungal community establishment in beech wood. ISME J. 9, 2246–2260 (2015).
van Gremberghe, I. et al. Priority effects in experimental populations of the cyanobacterium Microcystis. Environ. Microbiol. 11, 2564–2573 (2009).
Adame-Alvarez, R. M., Mendiola-Soto, J. & Heil, M. Order of arrival shifts endophyte-pathogen interactions in bean from resistance induction to disease facilitation. FEMS Microbiol. Lett. 355, 100–107 (2014).
Braun-Kiewnick, A., Jacobsen, B. & Sands, D. Biological control of Pseudomonas syringae pv. syringae, the causal agent of basal kernel blight of barley, by antagonistic Pantoea agglomerans. Phytopathology 90, 368–375 (2000).
Wilson, M. & Lindow, S. E. Interactions between the biological control agent Pseudomonas fluorescens A506 and Erwinia amylovora in pear blossoms. Phytopathology 83, 117–123 (1992).
Maignien, L., DeForce, E. A., Chafee, M. E., Eren, A. M. & Simmons, S. L. Ecological succession and stochastic variation in the assembly of Arabidopsis thaliana phyllosphere communities. mBio 5, e00682–00613 (2014).
Delmotte, N. et al. Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc. Natl Acad. Sci. USA 106, 16428–16433 (2009).
Bodenhausen, N., Horton, M. W. & Bergelson, J. Bacterial communities associated with the leaves and the roots of Arabidopsis thaliana. PLoS ONE 8, e56329 (2013).
Rottjers, L. & Faust, K. From hairballs to hypotheses—biological insights from microbial networks. FEMS Microbiol. Rev. 42, 761–780 (2018).
Duran, P. et al. Microbial interkingdom interactions in roots promote Arabidopsis survival. Cell 175, 973–983 (2018).
Agler, M. T. et al. Microbial hub taxa link host and abiotic factors to plant microbiome variation. PLoS Biol. 14, e1002352 (2016).
Faust, K. et al. Microbial co-occurrence relationships in the human microbiome. PLoS Comput. Biol. 8, e1002606 (2012).
Faust, K. & Raes, J. Microbial interactions: from networks to models. Nat. Rev. Microbiol. 10, 538–550 (2012).
Rottjers, L. & Faust, K. Can we predict keystones? Nat. Rev. Microbiol. 17, 193 (2019).
Huse, S. M., Ye, Y., Zhou, Y. & Fodor, A. A. A core human microbiome as viewed through 16S rRNA sequence clusters. PLoS ONE 7, e34242 (2012).
Wu, G. D. et al. Linking long-term dietary patterns with gut microbial enterotypes. Science 334, 105–108 (2011).
Hall, A. B., Tolonen, A. C. & Xavier, R. J. Human genetic variation and the gut microbiome in disease. Nat. Rev. Genet. 18, 690–699 (2017).
Martinez, I. et al. Experimental evaluation of the importance of colonization history in early-life gut microbiota assembly. eLife 7, e36521 (2018).
Kinkel, L. L. & Lindow, S. E. Invasion and exclusion among coexisting Pseudomonas syringae strains on leaves. Appl. Environ. Microbiol. 59, 3447–3454 (1993).
Lindow, S. E., Arny, D. C. & Upper, C. D. Biological control of frost injury: an isolate of Erwinia herbicola antagonistic to ice nucleation active bacteria. Phytopathology 73, 1097–1102 (1983).
Jousset, A. et al. Where less may be more: how the rare biosphere pulls ecosystems strings. ISME J. 11, 853–862 (2017).
Sogin, M. L. et al. Microbial diversity in the deep sea and the underexplored “rare biosphere”. Proc. Natl Acad. Sci. USA 103, 12115–12120 (2006).
Lynch, M. D. & Neufeld, J. D. Ecology and exploration of the rare biosphere. Nat. Rev. Microbiol. 13, 217–229 (2015).
Shade, A. et al. Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity. mBio 5, e01371–01314 (2014).
Chelius, M. K. & Triplett, E. W. The diversity of Archaea and bacteria in association with the roots of Zea mays L. Microb. Ecol. 41, 252–263 (2001).
Bulgarelli, D. et al. Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 488, 91–95 (2012).
Schloss, P. D. et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537–7541 (2009).
Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461 (2010).
Edgar, R. C. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat. Methods 10, 996–998 (2013).
Pruesse, E., Peplies, J. & Glockner, F. O. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28, 1823–1829 (2012).
Guindon, S. et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307–321 (2010).
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
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.
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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.
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Supplementary Figs. 1–12 and Tables 1 and 2.
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). https://doi.org/10.1038/s41559-019-0994-z
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DOI: https://doi.org/10.1038/s41559-019-0994-z
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