ArticleThe ISME journal2015
Depth-stratified functional and taxonomic niche specialization in the 'core' and 'flexible' Pacific Ocean Virome.
Article in The ISME journal, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 101 papers.
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101 citing papers in PubMed, 201 citations in OpenAlex.
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- High niche specificity and host genetic diversity of groundwater viruses.The ISME journal · 2024Article
- Genomic and transcriptomic insights into complex virus-prokaryote interactions in marine biofilms.The ISME journal · 2023Article
- Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition.Scientific data · 2023Article
- Water mass age structures the auxiliary metabolic gene content of free-living and particle-attached deep ocean viral communities.Microbiome · 2023Article
- Characterization and genomic analysis of a novel Synechococcus phage S-H9-2 belonging to Bristolvirus genus isolated from the Yellow Sea.Virus research · 2023Article
- Depth-driven patterns in lytic viral diversity, auxiliary metabolic gene content, and productivity in offshore oligotrophic waters.Frontiers in microbiology · 2023Article
- Viruses of sulfur oxidizing phototrophs encode genes for pigment, carbon, and sulfur metabolisms.Communications earth & environment · 2023Article
- Characterization and genomic analysis of an oceanic cyanophage infecting marineFrontiers in microbiology · 2023Article
41 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.