Abstract

Recent diversity studies have revealed that microbial communities of natural environments are dominated by species-like, sequence-discrete populations. However, how stable the sequence and gene-content diversity are within these populations and especially in highly dynamic lotic habitats remain unclear. Here we quantified the dynamics of intra-population diversity in samples spanning two years and five sites in the Kalamas River (Northwest Greece). A significant positive correlation was observed between higher intra-population sequence diversity and longer persistence over time, revealing that more diverse populations tended to represent more autochthonous (vs. allochthonous) community members. Assessment of intra-population gene-content changes caused by strain replacement or gene loss over time revealed different profiles with the majority of populations exhibiting gene-content changes close to 10% of the total genes, while one population exhibited ~21% change. The variable genes were enriched in hypothetical proteins and mobile elements, and thus, were probably functionally neutral or attributable to phage predation. A few notable exceptions to this pattern were also noted such as phototrophy-related proteins in summer vs. winter populations. Taken together, these results revealed that some freshwater genomes are remarkably dynamic, even across short time and spatial scales, and have implications for the bacterial species concept and microbial source tracking.

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Acknowledgements

This research was supported, in part, by the US National Science Foundation (award DEB 1241046 to KTK), the European Union (European Regional Development Fund- ERDF), and Greek national funds through the Operational Program “THESSALY- MAINLAND GREECE AND EPIRUS-2007-2013” of the National Strategic Reference Framework (NSRF 2007–2013) (2012–2015). We are grateful to the Management Body of Straits and Estuaries of the Rivers Acheron and Kalamas and to Theofilos Vanikiotis for providing helpful information on the sampling area as well as sampling facilities, and to an anonymous reviewer for providing useful suggestions regarding the manuscript.

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Author notes

  1. These authors contributed equally: Alexandra Meziti, Despina Tsementzi and Luis M. Rodriguez-R

Affiliations

  1. Department of Biological Applications and Technology, University of Ioannina, 45110, Ioannina, Greece

    • Alexandra Meziti
    •  & Hera Karayanni
  2. School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science & Technology Building, 311 Ferst Drive, 30332, Atlanta, GA, Georgia

    • Alexandra Meziti
    • , Despina Tsementzi
    • , Luis M. Rodriguez-R
    • , Janet K. Hatt
    •  & Konstantinos T. Konstantinidis
  3. Department of Ichthyology and Aquatic Environment, University of Thessaly, 38446, Volos, Greece

    • Konstantinos A. Kormas
  4. School of Biological Sciences, Georgia Institute of Technology, Ford Environmental Sciences & Technology Building, 311 Ferst Drive, 30332, Atlanta, GA, Georgia

    • Konstantinos T. Konstantinidis

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The authors declare that they have no conflict of interest.

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Correspondence to Konstantinos T. Konstantinidis.

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DOI

https://doi.org/10.1038/s41396-018-0307-6