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Taxonomic and metabolic shifts in the Coorong bacterial metagenome driven by salinity and external inputs

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Abstract

The Coorong estuary lies at the terminus of Australia’s largest river system, the Murray-Darling; both are strongly influenced by human activities; including farming and extensive flow modification. Metagenomic approaches were used to determine the planktonic bacterial community composition and potential metabolic function at two extremes in the Coorong, the river mouth which exhibits marine-like salinity, and the hypersaline upper-reaches of the estuary. Significant shifts in taxa and metabolic function were seen between the two sites. The river mouth exhibited an increase in abundance of Rhodobacteriaceae and Alteromonadaceae; families readily able to adapt to change in nutrient conditions; and the potentially pathogenic families Brucellaceae, Enterobacteriaceae and Vibrionaceae. Metabolisms over-represented include motility and chemotaxis, RNA metabolism and membrane transport, all of which are involved in actively searching for and obtaining nutrients. Also over-represented were metabolisms involved in population succession and stress response. An over-representation of taxa and metabolisms indicative of environmental change is reflective of anthropogenically affected riverine input. In the hypersaline upper reaches of the estuary, the halophilic family Ectothiorhodospiraceae was over-represented, as were the families Flavobacteriaceae, Cytophagaceae and Nocardioidaceae, members of which are able to survive over a wide salinity range. Metabolisms over-represented here were reflective of increased bacterial growth, characteristic of hypersaline environments, and included DNA metabolism, nucleotide and nucleoside synthesis and cell cycle. Coorong metagenomes clustered taxonomically and metabolically with other planktonic metagenomes, but remained an outlier of this group with only 71% and 84% similarity, respectively. This indicates that the Coorong exhibits a unique planktonic bacterial community that is influenced by riverine input at the river mouth and salinity in the upper-reaches.

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Acknowledgement

The authors gratefully acknowledge B. Roudnew and T. Lavery for informative discussions, A. Burley and E. Alvino for editorial assistance. We sincerely thank A. Fitch from the School of Biological Sciences, Flinders University for technical support and guidance during laboratory work and S. Bailey and E. Ng from the Flow Cytometry Unit of the Flinders Medical Centre for providing technical support during flow cytometry sessions. We would like to especially thank the two anonymous reviewers whose comments and insights improved this manuscript. We also thank the Department of Environment and Natural Resources (DENR) for allowing us access to the Coorong National Park (permit number G25583-2). This research was supported by the Australian Research Council and by Flinders University. K. Newton was in recipient of a Flinders University Research Scholarship (FURS) at the time the research was undertaken.

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Authors and Affiliations

  1. School of Biological Sciences, Flinders University, PO Box 2100, Bedford Park, SA, 5042, Australia

    Kelly Newton, Thomas C. Jeffries, Renee J. Smith, Justin R. Seymour, Laurent Seuront & James G. Mitchell

  2. School of Science and Health, Western Sydney University, Richmond, NSW, 2753, Australia

    Thomas C. Jeffries

  3. Flinders Centre for Innovation in Cancer, Flinders University, Bedford Park, SA, 5042, Australia

    Renee J. Smith

  4. Climate Change Cluster, University of Technology Sydney, Sydney, NSW, 2007, Australia

    Justin R. Seymour

  5. Centre National de la Recherche Scientifique, Laboratoire d’Océanologie et de Géosciences, CNRS UMR 8187 LOG, Wimereux, France

    Laurent Seuront

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  6. James G. Mitchell
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Correspondence to Kelly Newton.

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Newton, K., Jeffries, T.C., Smith, R.J. et al. Taxonomic and metabolic shifts in the Coorong bacterial metagenome driven by salinity and external inputs. J. Ocean. Limnol. 36, 2033–2049 (2018). https://doi.org/10.1007/s00343-018-7387-z

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  • DOI: https://doi.org/10.1007/s00343-018-7387-z

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