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1. Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters

   https://doi.org/10.1038/s41396-020-00825-6  

   Gazitúa, M. Consuelo; Vik, Dean R.; Roux, Simon; Gregory, Ann C.; Bolduc, Benjamin; Widner, Brittany; Mulholland, Margaret R.; Hallam, Steven J.; Ulloa, Osvaldo; Sullivan, Matthew B. (April 2021, The ISME Journal)

   null (Ed.)

   Abstract Viruses play an important role in the ecology and biogeochemistry of marine ecosystems. Beyond mortality and gene transfer, viruses can reprogram microbial metabolism during infection by expressing auxiliary metabolic genes (AMGs) involved in photosynthesis, central carbon metabolism, and nutrient cycling. While previous studies have focused on AMG diversity in the sunlit and dark ocean, less is known about the role of viruses in shaping metabolic networks along redox gradients associated with marine oxygen minimum zones (OMZs). Here, we analyzed relatively quantitative viral metagenomic datasets that profiled the oxygen gradient across Eastern Tropical South Pacific (ETSP) OMZ waters, assessing whether OMZ viruses might impact nitrogen (N) cycling via AMGs. Identified viral genomes encoded six N-cycle AMGs associated with denitrification, nitrification, assimilatory nitrate reduction, and nitrite transport. The majority of these AMGs (80%) were identified in T4-like Myoviridae phages, predicted to infect Cyanobacteria and Proteobacteria , or in unclassified archaeal viruses predicted to infect Thaumarchaeota . Four AMGs were exclusive to anoxic waters and had distributions that paralleled homologous microbial genes. Together, these findings suggest viruses modulate N-cycling processes within the ETSP OMZ and may contribute to nitrogen loss throughout the global oceans thus providing a baseline for their inclusion in the ecosystem and geochemical models. 

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2. OUP accepted manuscript

   https://doi.org/10.1093/bioinformatics/btaa490  

   Antipov, Rayko (May 2020, Bioinformatics)

   metaviralSPAdes: Assembly of Viruses From Metagenomic Data Abstract Motivation: Although the set of currently known viruses has been steadily expanding, only a tiny fraction of the Earth's virome has been sequenced so far. Shotgun metagenomic sequencing provides an opportunity to reveal novel viruses but faces the computational challenge of identifying viral genomes that are often difficult to detect in metagenomic assemblies. Results: We describe a metaviralSPAdes tool for identifying viral genomes in metagenomic assembly graphs that is based on analyzing variations in the coverage depth between viruses and bacterial chromosomes. We benchmarked metaviralSPAdes on diverse metagenomic datasets, verified our predictions using a set of virus-specific Hidden Markov Models, and demonstrated that it improves on the state-of-the-art viral identification pipelines. Availability: metaviralSPAdes includes viralAssembly, viralVerify, and viralComplete modules that are available as standalone packages: https://github.com/ablab/spades/tree/metaviral_publication, https://github.com/ablab/viralVerify/ and https://github.com/ablab/viralComplete/. Supplementary information: Supplementary data are available at Bioinformatics online. 

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3. Data Proliferation, Reconciliation, and Synthesis in Viral Ecology

   https://doi.org/10.1093/biosci/biab080  

   Gibb, Rory; Albery, Gregory F; Becker, Daniel J; Brierley, Liam; Connor, Ryan; Dallas, Tad A; Eskew, Evan A; Farrell, Maxwell J; Rasmussen, Angela L; Ryan, Sadie J; et al (August 2021, BioScience)

   Abstract The fields of viral ecology and evolution are rapidly expanding, motivated in part by concerns around emerging zoonoses. One consequence is the proliferation of host–virus association data, which underpin viral macroecology and zoonotic risk prediction but remain fragmented across numerous data portals. In the present article, we propose that synthesis of host–virus data is a central challenge to characterize the global virome and develop foundational theory in viral ecology. To illustrate this, we build an open database of mammal host–virus associations that reconciles four published data sets. We show that this offers a substantially richer view of the known virome than any individual source data set but also that databases such as these risk becoming out of date as viral discovery accelerates. We argue for a shift in practice toward the development, incremental updating, and use of synthetic data sets in viral ecology, to improve replicability and facilitate work to predict the structure and dynamics of the global virome. 

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4. Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology

   https://doi.org/10.1186/s40168-024-01905-x  

   Kosmopoulos, James C; Klier, Katherine M; Langwig, Marguerite V; Tran, Patricia Q; Anantharaman, Karthik (December 2024, Microbiome)

   Abstract BackgroundViruses, the majority of which are uncultivated, are among the most abundant biological entities on Earth. From altering microbial physiology to driving community dynamics, viruses are fundamental members of microbiomes. While the number of studies leveraging viral metagenomics (viromics) for studying uncultivated viruses is growing, standards for viromics research are lacking. Viromics can utilize computational discovery of viruses from total metagenomes of all community members (hereafter metagenomes) or use physical separation of virus-specific fractions (hereafter viromes). However, differences in the recovery and interpretation of viruses from metagenomes and viromes obtained from the same samples remain understudied. ResultsHere, we compare viral communities from paired viromes and metagenomes obtained from 60 diverse samples across human gut, soil, freshwater, and marine ecosystems. Overall, viral communities obtained from viromes had greater species richness and total viral genome abundances than those obtained from metagenomes, although there were some exceptions. Despite this, metagenomes still contained many viral genomes not detected in viromes. We also found notable differences in the predicted lytic state of viruses detected in viromes vs metagenomes at the time of sequencing. Other forms of variation observed include genome presence/absence, genome quality, and encoded protein content between viromes and metagenomes, but the magnitude of these differences varied by environment. ConclusionsOverall, our results show that the choice of method can lead to differing interpretations of viral community ecology. We suggest that the choice of whether to target a metagenome or virome to study viral communities should be dependent on the environmental context and ecological questions being asked. However, our overall recommendation to researchers investigating viral ecology and evolution is to pair both approaches to maximize their respective benefits. 

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5. The Global Virome in One Network (VIRION): an Atlas of Vertebrate-Virus Associations

   https://doi.org/10.1128/mbio.02985-21  

   Carlson, Colin J.; Gibb, Rory J.; Albery, Gregory F.; Brierley, Liam; Connor, Ryan P.; Dallas, Tad A.; Eskew, Evan A.; Fagre, Anna C.; Farrell, Maxwell J.; Frank, Hannah K.; et al (April 2022, mBio)

   Pickett, Brett E.; Jurado, Kellie (Ed.)

   ABSTRACT Data that catalogue viral diversity on Earth have been fragmented across sources, disciplines, formats, and various degrees of open sharing, posing challenges for research on macroecology, evolution, and public health. Here, we solve this problem by establishing a dynamically maintained database of vertebrate-virus associations, called The Global Virome in One Network (VIRION). The VIRION database has been assembled through both reconciliation of static data sets and integration of dynamically updated databases. These data sources are all harmonized against one taxonomic backbone, including metadata on host and virus taxonomic validity and higher classification; additional metadata on sampling methodology and evidence strength are also available in a harmonized format. In total, the VIRION database is the largest open-source, open-access database of its kind, with roughly half a million unique records that include 9,521 resolved virus “species” (of which 1,661 are ICTV ratified), 3,692 resolved vertebrate host species, and 23,147 unique interactions between taxonomically valid organisms. Together, these data cover roughly a quarter of mammal diversity, a 10th of bird diversity, and ∼6% of the estimated total diversity of vertebrates, and a much larger proportion of their virome than any previous database. We show how these data can be used to test hypotheses about microbiology, ecology, and evolution and make suggestions for best practices that address the unique mix of evidence that coexists in these data. IMPORTANCE Animals and their viruses are connected by a sprawling, tangled network of species interactions. Data on the host-virus network are available from several sources, which use different naming conventions and often report metadata in different levels of detail. VIRION is a new database that combines several of these existing data sources, reconciles taxonomy to a single consistent backbone, and reports metadata in a format designed by and for virologists. Researchers can use VIRION to easily answer questions like “Can any fish viruses infect humans?” or “Which bats host coronaviruses?” or to build more advanced predictive models, making it an unprecedented step toward a full inventory of the global virome. 

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