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1. Virioplankton, the carbon cycle, and our future ocean

   Locke, H.; K.D. Bidle; K. Thamatrakoln; C. Johns; J.A. Bonachela; B.D. Ferrell; K.E. Wommack. (January 2022, Advances in virus research)

   Marilyn J. Roossinck (Ed.)

   Interactions between marine viruses and microbes are a critical part of the oceanic carbon cycle. The impacts of virus–host interactions range from short-term disruptions in the mobility of microbial biomass carbon to higher trophic levels through cell lysis (i.e., the viral shunt) to long-term reallocation of microbial biomass carbon to the deep sea through accelerating the biological pump (i.e., the viral shuttle). The biogeochemical backdrop of the ocean—the physical, chemical, and biological landscape—influences the likelihood of both virus–host interactions and particle formation, and the fate and flow of carbon. As climate change reshapes the oceanic landscape through large-scale shifts in temperature, circulation, stratification, and acidification, virus-mediated carbon flux is likely to shift in response. Dynamics in the directionality and magnitude of changes in how, where, and when viruses mediate the recycling or storage of microbial biomass carbon is largely unknown. Integrating viral infection dynamics data obtained from experimental models and field systems, with particle motion microphysics and global observations of oceanic biogeochemistry, into improved ecosystem models will enable viral oceanographers to better predict the role of viruses in marine carbon cycling in the future ocean. 

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2. Virioplankton, the carbon cycle, and our future ocean.

   Locke, H; Bidle, KD; Thamatrakoln, K; Johns, C; Bonachela, JA; Ferrell, BD; Wommack, KE (October 2022, Advances in virus research)

   Interactions between marine viruses and microbes are a critical part of the oceanic carbon cycle. The impacts of virus–host interactions range from short-term disruptions in the mobility of microbial biomass carbon to higher trophic levels through cell lysis (i.e., the viral shunt) to long-term reallocation of microbial biomass carbon to the deep sea through accelerating the biological pump (i.e., the viral shuttle). The biogeochemical backdrop of the ocean—the physical, chemical, and biological landscape—influences the likelihood of both virus–host interactions and particle formation, and the fate and flow of carbon. As climate change reshapes the oceanic landscape through large-scale shifts in temperature, circulation, stratification, and acidification, virus-mediated carbon flux is likely to shift in response. Dynamics in the directionality and magnitude of changes in how, where, and when viruses mediate the recycling or storage of microbial biomass carbon is largely unknown. Integrating viral infection dynamics data obtained from experimental models and field systems, with particle motion microphysics and global observations of oceanic biogeochemistry, into improved ecosystem models will enable viral oceanographers to better predict the role of viruses in marine carbon cycling in the future ocean. 

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3. High Transcriptional Activity and Diverse Functional Repertoires of Hundreds of Giant Viruses in a Coastal Marine System

   https://doi.org/10.1128/mSystems.00293-21  

   Ha, Anh D.; Moniruzzaman, Mohammad; Aylward, Frank O.; Etten, James Van (January 2021, mSystems)

   Bordenstein, Seth (Ed.)

   ABSTRACT Viruses belonging to the Nucleocytoviricota phylum are globally distributed and include members with notably large genomes and complex functional repertoires. Recent studies have shown that these viruses are particularly diverse and abundant in marine systems, but the magnitude of actively replicating Nucleocytoviricota present in ocean habitats remains unclear. In this study, we compiled a curated database of 2,431 Nucleocytoviricota genomes and used it to examine the gene expression of these viruses in a 2.5-day metatranscriptomic time-series from surface waters of the California Current. We identified 145 viral genomes with high levels of gene expression, including 90 Imitervirales and 49 Algavirales viruses. In addition to recovering high expression of core genes involved in information processing that are commonly expressed during viral infection, we also identified transcripts of diverse viral metabolic genes from pathways such as glycolysis, the TCA cycle, and the pentose phosphate pathway, suggesting that virus-mediated reprogramming of central carbon metabolism is common in oceanic surface waters. Surprisingly, we also identified viral transcripts with homology to actin, myosin, and kinesin domains, suggesting that viruses may use these gene products to manipulate host cytoskeletal dynamics during infection. We performed phylogenetic analysis on the virus-encoded myosin and kinesin proteins, which demonstrated that most belong to deep-branching viral clades, but that others appear to have been acquired from eukaryotes more recently. Our results highlight a remarkable diversity of active Nucleocytoviricota in a coastal marine system and underscore the complex functional repertoires expressed by these viruses during infection. IMPORTANCE The discovery of giant viruses has transformed our understanding of viral complexity. Although viruses have traditionally been viewed as filterable infectious agents that lack metabolism, giant viruses can reach sizes rivalling cellular lineages and possess genomes encoding central metabolic processes. Recent studies have shown that giant viruses are widespread in aquatic systems, but the activity of these viruses and the extent to which they reprogram host physiology in situ remains unclear. Here, we show that numerous giant viruses consistently express central metabolic enzymes in a coastal marine system, including components of glycolysis, the TCA cycle, and other pathways involved in nutrient homeostasis. Moreover, we found expression of several viral-encoded actin, myosin, and kinesin genes, indicating viral manipulation of the host cytoskeleton during infection. Our study reveals a high activity of giant viruses in a coastal marine system and indicates they are a diverse and underappreciated component of microbial diversity in the ocean. 

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4. Matryoshka Dolls of Virus Evolution: The Internal Forces That Shape Viral Fate

   https://doi.org/10.1093/icb/icaf063  

   Yin, John (May 2025, Integrative And Comparative Biology)

   Synopsis Viral evolution unfolds across nested layers of adaptation, much like a set of Matryoshka dolls. The outermost, well-studied layer involves interactions between viruses and their hosts—where immune evasion, cross-species transmission, and long-term coevolution drive viral diversification. Yet, hidden within this framework is an often-overlooked inner layer: the coevolution of viruses with their own molecular parasites, defective interfering (DI) particles, and defective viral genomes (DVGs). These molecular parasites exploit viral replication machinery, reshaping infection dynamics and imposing selective pressures that influence viral fitness, transmission, and persistence. This perspective synthesizes evidence from experimental evolution, mathematical modeling, and molecular virology to propose a more integrated view of viral evolution. By framing host–virus interactions and virus-DI particle dynamics within a unified evolutionary framework, we highlight the underappreciated role of DI particles as evolutionary players, not just aberrant byproducts. Recognizing these internal layers of viral evolution may inform the development of antiviral strategies and broader questions in host–pathogen coevolution. 

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5. Active virus-host interactions at sub-freezing temperatures in Arctic peat soil

   https://doi.org/10.1186/s40168-021-01154-2  

   Trubl, Gareth; Kimbrel, Jeffrey A.; Liquet-Gonzalez, Jose; Nuccio, Erin E.; Weber, Peter K.; Pett-Ridge, Jennifer; Jansson, Janet K.; Waldrop, Mark P.; Blazewicz, Steven J. (October 2021, Microbiome)

   Abstract BackgroundWinter carbon loss in northern ecosystems is estimated to be greater than the average growing season carbon uptake and is primarily driven by microbial decomposers. Viruses modulate microbial carbon cycling via induced mortality and metabolic controls, but it is unknown whether viruses are active under winter conditions (anoxic and sub-freezing temperatures). ResultsWe used stable isotope probing (SIP) targeted metagenomics to reveal the genomic potential of active soil microbial populations under simulated winter conditions, with an emphasis on viruses and virus-host dynamics. Arctic peat soils from the Bonanza Creek Long-Term Ecological Research site in Alaska were incubated under sub-freezing anoxic conditions with H₂¹⁸O or natural abundance water for 184 and 370 days. We sequenced 23 SIP-metagenomes and measured carbon dioxide (CO₂) efflux throughout the experiment. We identified 46 bacterial populations (spanning 9 phyla) and 243 viral populations that actively took up¹⁸O in soil and respired CO₂throughout the incubation. Active bacterial populations represented only a small portion of the detected microbial community and were capable of fermentation and organic matter degradation. In contrast, active viral populations represented a large portion of the detected viral community and one third were linked to active bacterial populations. We identified 86 auxiliary metabolic genes and other environmentally relevant genes. The majority of these genes were carried by active viral populations and had diverse functions such as carbon utilization and scavenging that could provide their host with a fitness advantage for utilizing much-needed carbon sources or acquiring essential nutrients. ConclusionsOverall, there was a stark difference in the identity and function of the active bacterial and viral community compared to the unlabeled community that would have been overlooked with a non-targeted standard metagenomic analysis. Our results illustrate that substantial active virus-host interactions occur in sub-freezing anoxic conditions and highlight viruses as a major community-structuring agent that likely modulates carbon loss in peat soils during winter, which may be pivotal for understanding the future fate of arctic soils' vast carbon stocks. 

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