Viruses are the most abundant, diverse, and widespread known biological entities in aquatic systems. Viruses infect a diverse range of organisms, from bacteria to whales, and their impacts on aquatic ecosystems extend beyond causing mortality and disease. Viral infections play a crucial role in shaping biogeochemical cycles, facilitating gene transfer, and altering metabolic processes of host cells. Ecologically, viruses have different lifestyles that exist on a continuum between horizontal and vertical transmission (e.g., spanning lysis to lysogeny) – and they also differ in host specificity – leading to questions of how coexistence is mediated and what conditions favor particular virus life-history strategies. Additionally, ongoing research is needed to better understand the factors regulating virus-host interactions and how these interactions vary across different spatial and temporal scales. Biogeochemically, in marine systems viral-induced lysis is hypothesized: (a) to enhance microbial mediated respiration and nutrient recycling in the microbial loop via the release of labile nutrients retained in surface waters – the viral shunt; and also (b) to increase particle aggregation and export to the deep oceans – the viral shuttle. The large-scale biogeochemical impacts of small, yet abundant viruses in aquatic systems remains open to investigation. While new technologies have advanced the roles of viruses in aquatic ecology and biogeochemistry over the last three decades, identifying and quantifying the importance of virus-mediated processes and how they scale up across differing aquatic ecosystems remains challenging. We invite submissions focusing on the analysis of field sampling, experimental systems, theory, modeling, and/or bioinformatics approaches. We encourage interdisciplinary submissions that integrate multiple lines of evidence and those which seek to quantify rates and processes. Topics of interest include the regulation of virus-host interactions, biophysical interactions, mortality rates and population dynamics, the influence on aquatic food web functioning and biogeochemical cycling, novel host-virus systems, and other studies that advance our understanding of the vast roles that viruses play in aquatic ecosystems.
Lead Organizer: Stephen Beckett, University of Maryland (beckett@umd.edu)
Co-organizers:
Elaine Luo, University of North Carolina at Charlotte (elaine.luo@charlotte.edu)
Kristina Mojica, University of Southern Mississippi (Kristina.Mojica@usm.edu)
Presentations
02:30 PM
Metagenomics combined with stable isotope probing link novel viral genomic diversity to biogeochemical cycling (8710)
Primary Presenter: Elaine Luo, University of North Carolina at Charlotte (elaine.luo@charlotte.edu)
Viruses play a major role in carbon cycling in aquatic ecosystems via host cell lysis. Although metagenomic studies have revealed unprecedented microbial diversity in the ocean, linking novel viruses to their biogeochemical impacts remains challenging, particularly in under-sampled aquatic environments that lack reference databases for effective taxonomic and functional annotation. Microbial communities in the dark are under-studied relative to photic habitats, and identifying the key primary producers and their viruses that regulate dark carbon cycling remains challenging. Metagenomics combined with stable isotope probing (DNA-SIP) has potential to provide critical links between novel genomic diversity and biogeochemical cycling. Here, we present results from DNA-SIP experiments on microbial communities sampled from a meromictic, sulfidic coastal pond and deep-sea hydrothermal vents. 13C-dissolved inorganic carbon SIP incubations were combined with metagenomics to link novel viruses to their hosts and to quantify their carbon cycling activity. Our experiments yielded successful density-fractionation of both cell-enriched and virus-enriched samples for metagenomic sequencing along density gradients to enable quantitative DNA-SIP analyses. For each recovered cellular contig, metagenome-assembled genome, and viral population genome, we calculated their 13C enrichment to quantify carbon cycling activity and identify virus-host links. We demonstrate that SIP combined with metagenomics can be a powerful reference-independent approach to link novel viruses to their cellular hosts, identify key microbial players in biogeochemical processes, and contribute to modeling microbial carbon cycling in dark aquatic habitats.
02:45 PM
Mechanisms of coexistence between photosynthetic marine microbes and their viral and micrograzer predators (9214)
Primary Presenter: Paul Fremont, University of Maryland (pfremont@umd.edu)
Photosynthetic marine microbes, both bacterial and eukaryotic, play a crucial role in ocean biogeochemistry and ecology through primary productivity. These microbes are preyed upon by heterotrophic nanoflagellates, zooplankton, and viruses, which coexist despite their competition for the same microbial prey. Here, we develop population dynamics models to investigate mechanisms facilitating the coexistence of a virus and a grazer preying upon a photosynthetic algae, either bacterial or eukaryotic: (i) the inclusion of an infected class of the algae, potentially subject to intraguild predation, where grazers feed on virally infected microbes; (ii) heterogeneity in susceptibility to infection, where microbes vary in their resistance to the virus either intracellularly or extracellularly; and (iii) the inclusion of quadratic mortality terms for the predators. Our results show that each of these mechanisms can facilitate virus and zooplankton coexistence within a specific range of the virulence spectrum of the virus, shifting toward more virulent strategies for larger microbes. Additionally, we observe strong sensitivity of the models, including shifts in infected cell percentages and the balance between virally and zooplankton-induced mortality. Finally, we identify parameter combinations in models that yield realistic ecological properties across various simplified marine environments such as oligotrophic, mesotrophic, and upwelling regions. In doing so, the study represents an enabling step toward integration of models of lytic viruses in large ecosystem models.
03:00 PM
EVALUATING THE INTERACTIONS BETWEEN SMALL AND GIANT DNA VIRUSES THROUGH THE INVESTIGATION OF ENDOGENOUS VIRAL ELEMENTS WITHIN THE GENOMES OF SINGLE-CELLED EUKARYOTES (9713)
Primary Presenter: Danae Stephens, University of Miamii (dcs186@miami.edu)
Single-Celled Eukaryotes (otherwise characterized as Protists) compose roughly 50% of all oceanic biomass and thus play a pivotal role in nutrient cycling throughout our oceans. Recent studies have shown that diverse viruses exert top-down control over these protist populations, influencing their dynamics and biogeochemical fate. Giant viruses (GVs) within the phylum Nucleocytoviricota are among the key viral "predators” of protists. Recently it has been shown that smaller DNA viruses from the phylum Preplasmiviricota, namely virophages (VPs) and polinton-like viruses (PLVs) compete with GVs for resources during infection; leading to lower replication success of GVs. However, due in part to difficulties culturing both protists and their associated viruses, the true extent of interactions between the VP-PLV group and GVs is currently unknown. Both GVs and VP-PLVs are known to integrate their complete or partial genomes into the genomes of their protist hosts. We have developed and leveraged bioinformatic approaches to identify the GV and VP-PLV signatures in over 650 sequenced protist genomes. By examining both full virus genomes (VP and PLVs) and genome fragments (GVs) integrated within these protist genomes, we identified possible virus-protist interactions and interactions between GV and VP-PLV members. These results will be key for deciphering some of the complexity within the interactions of giant viruses with both their protist hosts and viral competitors in nature.
03:15 PM
Integrated ‘omics uncovers phage-host dynamics in the ETNP Oxygen Minimum Zone (9278)
Primary Presenter: Julia Brown, Bigelow Laboratory for Ocean Sciences (julia@bigelow.org)
Viruses are the most abundant biological entities in seawater, yet their complex relationship with hosts, ecosystems and biogeochemistry make them one of the least understood components of the marine realm. Marine oxygen minimum zones (OMZs) are naturally occurring oxygen-depleted areas of the ocean. Increasing ocean temperatures due to global climate change are leading to a net loss of oceanic dissolved oxygen and intensifying stratification, consequently expanding their size and severity. Microbial processes carried out within OMZs contribute to global cycling of nitrogen, sulfur and carbon. Previous work suggests that viruses impact microbe-driven cycling of nutrients within OMZs, but the extent of this impact is unknown. Additionally, links between OMZ phages and their hosts remain unexplored. Using several interaction-based approaches for pairing phages and hosts, namely metaHi-C, single cell genomics and CRISPR spacer matching, we identify novel phage-host pairs from the oxic-anoxic transition zone, and the anoxic core of the Eastern North Tropical Pacific OMZ. With these pairs in hand, we layer additional ‘omics data to better understand the intracellular activity and abundance of phages relative to hosts across OMZ biogeochemical gradients. These profiles reveal differences in putative phage infection strategy across phage-host pairs, shining light on the impacts of phage infection in these globally important systems.
03:30 PM
PROKARYOTIC-VIRUS-ENCODED AUXILIARY METABOLIC GENES THROUGHOUT THE GLOBAL OCEANS (9033)
Primary Presenter: James Wainaina, Woods Hole Oceanographic Institution (jwmbora@gmail.com)
Viruses impact biogeochemical cycles, through lysis, horizontal gene transfer, and encoding and expressing genes that contribute to metabolic reprogramming of prokaryotic cells. While this impact is difficult to quantify in nature, we hypothesized that it can be examined qualitatively by surveying virus-encoded auxiliary metabolic genes (AMGs) and assessing their ecological context. We systematically developed a global ocean AMG catalog by integrating previously described and newly identified AMGs, and then placed this catalog into ecological and metabolic contexts. From 7.6 terabases of Tara Oceans paired prokaryote- and virus-enriched metagenomic sequence data, we increased known ocean virus populations to 579,904 (up 16%). From these virus populations, we then conservatively identified 86,913 AMGs that grouped into 22,779 sequence-based gene clusters, 7,248 (~32%) of which were not previously reported. Using our catalog and modeled data from mock communities, we estimate that ~19% of ocean virus populations carry at least one AMG. To understand AMGs in their metabolic context, we identified 340 metabolic pathways encoded by ocean microbes, and showed that AMGs map to 128 of them. Furthermore, we identified metabolic ‘hot spots’ targeted by virus AMGs, including nine pathways where most steps (≥0.75) were AMG-targeted. Together, this systematically curated, global ocean AMG catalog and analyses provides a valuable resource and foundational observations to understand the role of viruses in modulating global ocean metabolisms and their biogeochemical implications.
03:45 PM
Distinct viral influences on particle-associated vs. free-living bacterial communities and particulate vs. dissolved elemental pools (9325)
Primary Presenter: John Paul Balmonte, Lehigh University (jp.balmonte@gmail.com)
Viruses tightly regulate microbial community metabolism and activities, but does viral control differ for particle-associated (PA) vs free-living (FL) bacteria and the partitioning of elements between the particulate and dissolved pools? Resolving viral influences across size fractions is relevant in aquatic systems as PA vs FL bacteria play varying roles in carbon remineralization and may have distinct susceptibility to viruses. We performed a virus enrichment experiment and coupled metagenomics, metabolomic, geochemical analyses and enzyme assays to study viral control of freshwater PA and FL bacteria and biogeochemical cycles in an oligotrophic lake and a peat bog lake. We found the environmental dependence of virus-host dynamics: a nearly 10-fold enrichment in virus:bacteria ratio increased cell lysis but only in the peat bog lake. We also found that: 1) viral regulation was strongest for PA bacteria; 2) viral infection of PA bacteria promoted enzyme production to scavenge for carbon and phosphorus; 3) increased lysis, which releases sticky exopolymeric substances, likely promoted the flocculation of high O:C, but low H:C dissolved compounds into particulate organic matter; 4) over 100 dissolved organic matter (DOM) ‘peaks’ from the metabolomic data were only detectable with increased lysis, indicating a viral impact on the DOM pool; and 5) viral auxiliary metabolic genes related to carbon and phosphorus cycling were abundant in metagenomes. These findings highlight distinct viral influences on PA vs FL bacterial communities and biogeochemical cycling.
SS17 - Viral interactions and ecological dynamics
Description
Time: 2:30 PM
Date: 27/3/2025
Room: W206B