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Bioprospecting and Biotechnology of Extremophiles

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Front. Bioeng. Biotechnol. | doi: 10.3389/fbioe.2019.00032

Anadromous Arctic Char Microbiomes: Bioprospecting in the High Arctic

 Erin F. Hamilton1,  Geraint Element1, Peter van Coeverden de Groot1, Katja Engel2, Josh D. Neufeld2,  Vishal Shah3 and  Virginia K. Walker1*
  • 1Queen's University, Canada
  • 2University of Waterloo, Canada
  • 3West Chester University, United States

Northern populations of Arctic char (Salvelinus alpinus) can be anadromous, migrating annually from the ocean to freshwater lakes and rivers in order to escape sub-zero temperatures. Such seasonal behaviour demands that these fish and their associated microbiomes adapt to changes in salinity, temperature, and other environmental challenges. We characterized the microbial community composition of anadromous S. alpinus, netted by Inuit fishermen at freshwater and seawater fishing sites in the high Arctic, both under ice and in open water. Bacterial profiles were generated by DNA extraction and high-throughput sequencing of PCR-amplified 16S ribosomal RNA genes. Results showed that microbial communities on the skin and intestine of Arctic char were statistically different when sampled from freshwater or saline water sites. This association was tested using hierarchical Ward’s linkage clustering, showing eight distinct clusters in each of the skin and intestinal microbiomes, with the clusters reflecting sampling location between fresh and saline environments, confirming a salinity-linked turnover. This analysis also provided evidence for a core composition of skin and intestinal bacteria, with the phyla Proteobacteria, Firmicutes, and Cyanobacteria presenting as major phyla within the skin-associated microbiomes. The intestine-associated microbiome was characterized by unidentified genera from families Fusobacteriaceae, Comamonadaceae, Pseudomonadaceae, and Vibrionaceae. The salinity-linked turnover was further tested through ordinations that showed samples grouping based on environment for both skin- and intestine-associated microbiomes. This finding implies that core microbiomes between fresh and saline conditions could be used to assist in regulating optimal fish health in aquaculture practices. Furthermore, identified taxa from known psychrophiles and with nitrogen cycling properties suggest that there is additional potential for biotechnological applications for fish farm and waste management practices.

Keywords: Arctic char (Salvelinus alpinus), Salmonid fish, Anadromous, microbiomes, Bioprospecting, Aquaculture, Arctic Ocean, aquatic biotechnology

Received: 15 Oct 2018; Accepted: 05 Feb 2019.

Edited by:

Steffen P. Graether, University of Guelph, Canada

Reviewed by:

Nadia Solovieva, University College London, United Kingdom
Ashok K. Dubey, Netaji Subhas Institute of Technology, India  

Copyright: © 2019 Hamilton, Element, van Coeverden de Groot, Engel, Neufeld, Shah and Walker. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Virginia K. Walker, Queen's University, Kingston, Canada, walkervk@queensu.ca