Long-read powered viral metagenomics in the oligotrophic Sargasso Sea

Joanna Warwick-Dugdale (), Funing Tian, Michelle L. Michelsen, Dylan R. Cronin, Karen Moore, Audrey Farbos, Lauren Chittick, Ashley Bell, Ahmed A. Zayed, Holger H. Buchholz, Luis M. Bolanos, Rachel J. Parsons, Michael J. Allen, Matthew B. Sullivan and Ben Temperton ()
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Joanna Warwick-Dugdale: University of Exeter
Funing Tian: Ohio State University
Michelle L. Michelsen: University of Exeter
Dylan R. Cronin: Ohio State University
Karen Moore: University of Exeter
Audrey Farbos: University of Exeter
Lauren Chittick: Ohio State University
Ashley Bell: University of Exeter
Ahmed A. Zayed: Ohio State University
Holger H. Buchholz: University of Exeter
Luis M. Bolanos: University of Exeter
Rachel J. Parsons: Bermuda Institute of Ocean Sciences
Michael J. Allen: University of Exeter
Matthew B. Sullivan: Ohio State University
Ben Temperton: University of Exeter

Nature Communications, 2024, vol. 15, issue 1, 1-15

Abstract: Abstract Dominant microorganisms of the Sargasso Sea are key drivers of the global carbon cycle. However, associated viruses that shape microbial community structure and function are not well characterised. Here, we combined short and long read sequencing to survey Sargasso Sea phage communities in virus- and cellular fractions at viral maximum (80 m) and mesopelagic (200 m) depths. We identified 2,301 Sargasso Sea phage populations from 186 genera. Over half of the phage populations identified here lacked representation in global ocean viral metagenomes, whilst 177 of the 186 identified genera lacked representation in genomic databases of phage isolates. Viral fraction and cell-associated viral communities were decoupled, indicating viral turnover occurred across periods longer than the sampling period of three days. Inclusion of long-read data was critical for capturing the breadth of viral diversity. Phage isolates that infect the dominant bacterial taxa Prochlorococcus and Pelagibacter, usually regarded as cosmopolitan and abundant, were poorly represented.

Date: 2024
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DOI: 10.1038/s41467-024-48300-6

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