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Strain-level diversity drives alternative community types in millimetre-scale granular biofilms

Nature Microbiology volume 3, pages 1295–1303 (2018)Cite this article

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Abstract

Microbial communities are often highly diverse in their composition, both at a coarse-grained taxonomic level, such as genus, and at a highly resolved level, such as strains, within species. This variability can be driven by either extrinsic factors such as temperature and or by intrinsic ones, for example demographic fluctuations or ecological interactions. The relative contributions of these factors and the taxonomic level at which they influence community composition remain poorly understood, in part because of the difficulty in identifying true community replicates assembled under the same environmental parameters. Here, we address this problem using an activated granular sludge reactor in which millimetre-scale biofilm granules represent true community replicates. Differences in composition are then expected to be driven primarily by biotic factors. Using 142 shotgun metagenomes of single biofilm granules we found that, at the commonly used genus-level resolution, community replicates varied much more in their composition than would be expected from neutral assembly processes. This variation did not translate into any clear partitioning into discrete community types, that is, distinct compositional states, such as enterotypes in the human gut. However, a strong partition into community types did emerge at the strain level for the dominant organism: genotypes of Candidatus Accumulibacter that coexisted in the metacommunity (the reactor) excluded each other within community replicates (granules). Individual granule communities maintained a significant lineage structure, whereby the strain phylogeny of Accumulibacter correlated with the overall composition of the community, indicating a high potential for co-diversification among species and communities. Our results suggest that due to the high functional redundancy and competition between close relatives, alternative community types are most probably observed at the level of recently differentiated genotypes but not at higher orders of genetic resolution.

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Fig. 1: High degree of variability among replicate communities at the genus level.
Fig. 2: Strains of Accumulibacter segregate among community replicates.
Fig. 3: Accumulibacter strain-level phylogeny correlates with compositional structure.
Fig. 4: Schematic view of the relationship between phylogenetic depth and community structure.

Data availability

Raw sequencing reads are available on the European Nucleotide Archive (project PRJEB24825). Granule metadata and a list of the accession numbers of the genomes in the reference database are provided as Supplementary Data.

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Acknowledgements

We thank A. Adler and A. Gelb for help with sampling and the provision of images/videos. We also thank T. de Wouters and S. Kuehn for comments on an early draft of the paper. G.E.L. was supported by the Swiss National Science Foundation (grant no. 162251) and the Human Frontiers Science Program (grant no. LT000643/2016-L). O.X.C. was supported by a grant from the Simons Foundation (grant no. 542395).

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Authors and Affiliations

  1. Department of Civil and Environmental Engineering, Massachusetts Institute of Technology , Cambridge, MA, USA

    Gabriel E. Leventhal, Carles Boix, Tim N. Enke & Otto X. Cordero

  2. Department of Environmental System Sciences, ETH Zurich, Zurich, Switzerland

    Urs Kuechler, Tim N. Enke, Elzbieta Sliwerska & Otto X. Cordero

  3. Laboratory for Environmental Biotechnology, École Polytechnique Fédéral de Lausanne, Lausanne, Switzerland

    Christof Holliger

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Contributions

C.H. operated the reactors and sampled granules. T.N.E. and E.S. extracted DNA and prepared the samples for sequencing. G.E.L. and O.X.C. designed the methodology. G.E.L., C.B., U.K., T.N.E. and O.X.C. performed computational analyses. G.E.L., C.H. and O.X.C. wrote the paper.

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Correspondence to Otto X. Cordero.

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Supplementary information

Supplementary Information

Supplementary Table 1, Supplementary Figures 1–19.

Reporting Summary

Supplementary Data 1

Granule metadata.

Supplementary Data 2

Reference database accession numbers.

Supplementary Video 1

Granular reactor operation.

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Leventhal, G.E., Boix, C., Kuechler, U. et al. Strain-level diversity drives alternative community types in millimetre-scale granular biofilms. Nat Microbiol 3, 1295–1303 (2018). https://doi.org/10.1038/s41564-018-0242-3

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