Distinct oceanic microbiomes from viruses to protists located near the Antarctic Circumpolar current

Flavia Flaviani, Declan C. Schroeder, Karen Lebret, Cecilia Balestreri, Andrea C. Highfield, Joanna L. Schroeder, Sally E. Thorpe, Karen Moore, Konrad Pasckiewicz, Maya C. Pfaff, Edward P. Rybicki

Research output: Contribution to journalArticlepeer-review

7 Scopus citations

Abstract

Microbes occupy diverse ecological niches and only through recent advances in next generation sequencing technologies have the true microbial diversity been revealed. Furthermore, lack of perceivable marine barriers to genetic dispersal (i.e., mountains or islands) has allowed the speculation that organisms that can be easily transported by currents and therefore proliferate everywhere. That said, ocean currents are now commonly being recognized as barriers for microbial dispersal. Here we analyzed samples collected from a total of six stations, four located in the Indian Ocean, and two in the Southern Ocean. Amplicon sequencing was used to characterize both prokaryotic and eukaryotic plankton communities, while shotgun sequencing was used for the combined environmental DNA (eDNA), microbial eDNA (meDNA), and viral fractions. We found that Cyanobacteria dominated the prokaryotic component in the South-West Indian Ocean, while γ-Proteobacteria dominated the South-East Indian Ocean. A combination of γ- and α-Proteobacteria dominated the Southern Ocean. Alveolates dominated almost exclusively the eukaryotic component, with variation in the ratio of Protoalveolata and Dinoflagellata depending on station. However, an increase in haptophyte relative abundance was observed in the Southern Ocean. Similarly, the viral fraction was dominated by members of the order Caudovirales across all stations; however, a higher presence of nucleocytoplasmic large DNA viruses (mainly chloroviruses and mimiviruses) was observed in the Southern Ocean. To our knowledge, this is the first that a statistical difference in the microbiome (from viruses to protists) between the subtropical Indian and Southern Oceans. We also show that not all phylotypes can be found everywhere, and that meDNA is not a suitable resource for monitoring aquatic microbial diversity.

Original languageEnglish (US)
Article number1474
JournalFrontiers in Microbiology
Volume9
Issue numberJUL
DOIs
StatePublished - Jul 17 2018

Bibliographical note

Funding Information:
Computations were performed using facilities provided by the University of Cape Town's ICTS High Performance Computing team: http://hpc.uct.ac.za. We would like to thank Barney Balch for the opportunity to join the Coccolithophore Belt cruise. The altimeter products were produced by Ssalto/Duacs and distributed by Aviso, with support from Cnes. The OSTIA sea surface temperature product was derived by the UK Met Office and at the time of access was made available through the MyOcean follow-on project. Both datasets are now available from www.marine.copernicus.eu. We acknowledge M. Niccoli for the colour palette used in Figure 1. The project was funded by a South African National Research Foundation (NRF) grant to ER (CPR20110717000020991). DS was funded by the FP7-OCEAN-2011 call, MicroB3 (grant number 287589) and the NERC eDNA award (grant number NE/N006151/1). ST was funded through the Ocean Ecosystems Program at the British Antarctic Survey (NERC, United Kingdom).

Keywords

  • Antarctic Polar Front
  • EDNA
  • Marine microbes
  • MeDNA
  • Microbiome
  • Viruses

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