Metagenomics combined with stable isotope probing link novel viral genomic diversity to biogeochemical cycling

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.

Presentation Preference: Oral

Primary Presenter: Elaine Luo, University of North Carolina at Charlotte (elaine.luo@charlotte.edu)

Authors:

Elaine Luo, University of North Carolina at Charlotte  (elaine.luo@charlotte.edu)

Bayleigh Benner, Woods Hole Oceanographic Institution  (bbenner@whoi.edu)

Sabrina Elkassas, Woods Hole Oceanographic Institution  (selkassas@whoi.edu)

Gary Trubl, Lawrence Livermore National Laboratory  (trubl1@llnl.gov)

Julie Huber, Woods Hole Oceanographic Institution  (jhuber@whoi.edu)