Project: Dimensions: The Role of Viruses in Structuring Biodiversity in Methanotrophic Marine Ecosystems

Marine methanotrophic ecosystems are responsible for consuming around 75 Tg of methane annually, preventing this potent greenhouse gas from entering the atmosphere. These microbial ecosystems thus play a vital role in the global climate system. The nature of these communities depends on the presence or absence of oxygen: methanotrophy is a bacterial lifestyle in aerobic shallow sediments, but in deeper anaerobic sediments it is the exclusive province of archaea, in syntrophy with sulfate-reducing bacteria. It is known which phyla are most commonly found in methanotrophic environments. However, because of these environments' physical inaccessibility and because nearly all microbes from these systems have resisted cultivation, understanding of these communities lags far behind their importance. The cultivation-resistance of microbial hosts from these systems has additionally prevented the use of classical methods to study the viral community. Thus, to date science is largely unable to fill in the broad outlines of marine methanotrophic biodiversity, to fully describe the microbial communities or determine what shapes them.

This project seeks to define the importance of viruses in structuring functional, genetic, and taxonomic diversity in methanotrophic marine ecosystems. The underlying assertion is that viruses structure the diversity of archaeal and bacterial communities in these ecosystems by causing both mortality and horizontal gene transfer. To establish viral contributions to biodiversity of aerobic and anaerobic marine methanotrophic ecosystems, this project combines biogeochemical, genomic, and metagenomic approaches, in both field and laboratory settings.

The project first seeks to assess viral activity in situ by extending established stable isotope probing techniques to quantify rates of viral production at sea floor methane seeps. The same techniques will be used to track the flow of carbon from methane to microbes to viruses and to isolate genetic material from just those organisms that actively cycle methane-derived carbon, enabling the production of microbial and viral metagenomes that are anchored in ecosystem function. Comparisons among these metagenomes will reveal any functional sequences in transit between organisms, providing the basis for an evaluation of the relationships between functional and genetic diversity. At the same time, single-cell whole-genome amplification will pinpoint individual cells for comparison with the microbial and viral assemblages, permitting assessment of the relationships between taxonomic and genetic diversity. Last, the comparison of genomic and metagenomic data both within and across distinctive marine methanotrophic ecosystems will enable analysis of the relationship between functional and taxonomic diversity.