Project: Ecology and biogeochemical impacts of DNA and RNA viruses throughout the global oceans

NSF abstract:
In the oceans, microbial life sits at the base of the food chain, but microbes also control the flow of nutrients and energy. While our knowledge of microbial impacts on the oceans is rapidly advancing, we remain far behind in studying the impact of viruses. Decades of experiments and global surveys that have focused on common ocean viruses (double-stranded DNA viruses) suggest that they kill many cells, change the genes that cells encode in their genomes, and reprogram how cells function during infection. This project seeks to create a metabolic map of the global oceans and quantify which of these microbial processes common viruses manipulate. Further, this project will expand to other types of viruses (RNA viruses) that are less well studied, as well as advance our knowledge of both DNA and RNA viruses with respect to global patterns and distributions to assess viral activity. Such analyses are critical to better understand how viruses of all types alter microbial processes and thereby drive nutrient cycling in the oceans. Beyond the science, this project will train two postdocs, a graduate student and five undergraduate students, as well as conduct outreach through Columbus-area seminars and lecture series and provide a training workshop for researchers in each years 1 and 3.

Microbial metabolisms alter nutrients and energy flow in ways that impact global ocean biogeochemistry, but associated viruses modulate these metabolic impacts through mortality, horizontal gene transfer and metabolic reprogramming. The latter impact is particularly understudied due to being a largely manual process, though early data hints that it likely impacts photosynthesis, central carbon metabolism, and nitrogen and sulfur cycling. Further, though eukaryotes are likely most commonly infected by RNA viruses and RNA viruses are thought to represent about half of viral particles in seawater, very little information on RNA virus diversity or ecology exists. Finally, particles are not the 'active' form of viruses, which begs for the development of new approaches to assess activity using the newly-available reference genomes against expression (e.g., metatranscriptomic) datasets. This project seeks to leverage extensive organismal, physical, and chemical datasets from the global Tara Oceans expedition to (i) advance from surveying dsDNA viral biodiversity towards inferring their metabolic impacts and active infection ecology, and (ii) build a parallel RNA virus biodiversity inventory from which to establish foundational ecological understanding of drivers and community structure. Scientifically, these efforts will evaluate more than a dozen hypotheses and establish countless more hypotheses about viral roles in marine microbial ecology and biogeochemistry. The project will train two postdocs, a graduate student and five undergraduate students, some through engagement with international Tara Oceans Consortium meetings, as well as provide public outreach through classroom and seminar visits at a Columbus area school (~240 students), a local chapter of the MIT Alumni club, an OSU Center for RNA Biology 'Science Sundays' lecture series, and seminars and interactive activities with Canada's indigenous people. A viromics training workshop will be held in each years 1 and 3 to maximize research community involvement and engagement.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

Affiliated program:
Tara Oceans: https://oceans.taraexpeditions.org/en/m/about-tara/les-expeditions/tara-oceans/
Youtube playlist link for the TARA odyssey: https://www.youtube.com/playlist?list=PL0cA6oCJaXodaj3225MArm6Uc5mXZa436

This project was funded to analyze GOV2.0 viral population data available at the following links:
* bitbucket: https://bitbucket.org/MAVERICLab/gov2/downloads/
* iVirus: http://datacommons.cyverse.org/browse/iplant/home/shared/iVirus/GOV2.0
* Raw read availability can be found in Supplemental Table 3 of of Gregory et al. 2019. https://doi.org/10.1016/j.cell.2019.03.040

Reference: 
Gregory, A. C., Zayed, A. A., Conceição-Neto, N., Temperton, B., Bolduc, B., Alberti, A., … Cruaud, C. (2019). Marine DNA Viral Macro- and Microdiversity from Pole to Pole. Cell, 177(5), 1109–1123.e14. doi:10.1016/j.cell.2019.03.040

Data Availability:
eFam database (HMM profile database of viral protein families): doi.org/10.25739/9vze-4143 and the paper citation: "Zayed, A.A., Lücking, D., Mohssen, M., Cronin, D., Bolduc, B., Gregory, A.C., Hargreaves, K.R., Piehowski, P.D., White, R.A., Huang, E.L. and Adkins, J.N., 2021. efam: an expanded, metaproteome-supported HMM profile database of viral protein families. Bioinformatics.".

Bioinformatics tools and protocols:
Annotation and AMG detection in microbes and viruses: DRAM (https://doi.org/10.1093/nar/gkaa621).
Viromics best practices and benchmarks paper: "Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation" (https://peerj.com/articles/11447/).
Latest virus identifier tool, VirSorter2 (https://doi.org/10.1186/s40168-020-00990-y) and step-by-step usage on protocol.io (https://www.protocols.io/view/viral-sequence-identification-sop-with-virsorter2-btv8nn9w).

Assemblies, contigs, HMMs and more: https://datacommons.cyverse.org/browse/iplant/home/shared/iVirus/ZayedWainainaDominguez-Huerta_RNAevolution_Dec2021
Phylogenetic analysis: https://datadryad.org/stash/share/iedoz2eM4ex3bW_PNHthskIgWLTs1WpcHB0QKk5SoGo.
Scripts repository for RNA virus discovery pipeline via RdRp HMMs: https://zenodo.org/record/5731488#.Y35tpbLMK7

For a full list of publications generated by this project, see the NSF award page: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1829831