Abstract
Microbes drive myriad ecosystem processes, and their viruses modulate microbial-driven processes through mortality, horizontal gene transfer, and metabolic reprogramming by viral-encoded auxiliary metabolic genes (AMGs). However, our knowledge of viral roles in the oceans is primarily limited to surface waters. Here we assess the depth distribution of protein clusters (PCs) in the first large-scale quantitative viral metagenomic data set that spans much of the pelagic depth continuum (the Pacific Ocean Virome; POV). This established ‘core’ (180 PCs; one-third new to science) and ‘flexible’ (423K PCs) community gene sets, including niche-defining genes in the latter (385 and 170 PCs are exclusive and core to the photic and aphotic zones, respectively). Taxonomic annotation suggested that tailed phages are ubiquitous, but not abundant (<5% of PCs) and revealed depth-related taxonomic patterns. Functional annotation, coupled with extensive analyses to document non-viral DNA contamination, uncovered 32 new AMGs (9 core, 20 photic and 3 aphotic) that introduce ways in which viruses manipulate infected host metabolism, and parallel depth-stratified host adaptations (for example, photic zone genes for iron–sulphur cluster modulation for phage production, and aphotic zone genes for high-pressure deep-sea survival). Finally, significant vertical flux of photic zone viruses to the deep sea was detected, which is critical for interpreting depth-related patterns in nature. Beyond the ecological advances outlined here, this catalog of viral core, flexible and niche-defining genes provides a resource for future investigation into the organization, function and evolution of microbial molecular networks to mechanistically understand and model viral roles in the biosphere.
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Acknowledgements
We thank Tucson Marine Phage Lab members for comments on the manuscript; Matt Kane for suggesting the designation of two classes of AMGs; UITS Research Computing Group and the ARL Biotechnology Computing for HPCC access and support. Funding was provided by NSF (DBI-0850105 and OCE-0961947), BIO5 and Gordon and Betty Moore Foundation grants (GBMF2631 and GBMF3790) to MBS, and an NSF Integrative Graduate Education and Research Training Fellowship and NSF Graduate Research Fellowship to BLH.
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Hurwitz, B., Brum, J. & Sullivan, M. Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome. ISME J 9, 472–484 (2015). https://doi.org/10.1038/ismej.2014.143
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DOI: https://doi.org/10.1038/ismej.2014.143
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