Roux, S., J. R. Brum, B. E. S. Roux, J.R. Brum, B.E. Dutilh, S. Sunagawa, M.B. Duhaime, A. Loy, B.T. Poulos, N. Solonenko, E. Lara, J. Poulain, S. Pesant, S. Kandels-Lewis, C. Dimier, M. Picheral, S. Searson, C. Cruaud, A. Alberti, C.M. Duarte, ...
Nature 537, 689-693, (2016)
Water microbiology, Phage biology, Metagenomics, Microbial biooceanography, Marine biology
Ocean microbes drive biogeochemical cycling on a global scale1.
However, this cycling is constrained by viruses that affect community
composition, metabolic activity, and evolutionary trajectories2, 3.
Owing to challenges with the sampling and cultivation of viruses,
genome-level viral diversity remains poorly described and grossly
understudied, with less than 1% of observed surface-ocean viruses known4. Here we assemble complete genomes and large genomic fragments from both surface- and deep-ocean viruses sampled during the Tara Oceans and Malaspina research expeditions5, 6,
and analyse the resulting ‘global ocean virome’ dataset to present a
global map of abundant, double-stranded DNA viruses complete with
genomic and ecological contexts. A total of 15,222 epipelagic and
mesopelagic viral populations were identified, comprising 867 viral
clusters (defined as approximately genus-level groups7, 8). This roughly triples the number of known ocean viral populations4 and doubles the number of candidate bacterial and archaeal virus genera8,
providing a near-complete sampling of epipelagic communities at both
the population and viral-cluster level. We found that 38 of the 867
viral clusters were locally or globally abundant, together accounting
for nearly half of the viral populations in any global ocean virome
sample. While two-thirds of these clusters represent newly described
viruses lacking any cultivated representative, most could be
computationally linked to dominant, ecologically relevant microbial
hosts. Moreover, we identified 243 viral-encoded auxiliary metabolic
genes, of which only 95 were previously known. Deeper analyses of four
of these auxiliary metabolic genes (dsrC, soxYZ, P-II (also known as glnB) and amoC)
revealed that abundant viruses may directly manipulate sulfur and
nitrogen cycling throughout the epipelagic ocean. This viral catalog and
functional analyses provide a necessary foundation for the meaningful
integration of viruses into ecosystem models where they act as key
players in nutrient cycling and trophic networks.