AbstractThanks to C-DEBI’s generous travel support, I traveled to the Joint Genome Institute (JGI) to attend a Microbial Dark Matter (MDM) Meeting and a workshop entitled, “New Lineages of Life” (NeLLi) in April 2017. Both events were focused on JGI’s initiative to characterize yet-to-be-cultivated organisms using single-cell and metagenomic sequencing techniques. Currently, I am working to describe the functional potential of an uncultured archaeal lineage sampled from the Juan de Fuca ridge flank (a project that relates to C-DEBI research theme 2: Activities, Communities, and Ecosystems), and thus most of the content presented throughout the week was applicable to my work. Attending these events allowed me to see how other investigators were approaching the characterization of other new lineages. I was introduced to new open source software and databases (for example, the Genome Taxonomy Database, [http://gtdb.ecogenomic.org, unpublished], GREMLIN, a protein modeling program [http://gremlin.bakerlab.org/index.php] and Data2, a new amplicon pipeline, [https://github.com/benjjneb/dada2]). Being at the NeLLi workshop also gave me the opportunity to meet with my JFR collaborators and share my recent progress. Together we developed a plan for future work and manuscript submission. Additionally, these events provided me with a great networking opportunity, allowing me to meet other scientists with similar interests.
To understand the biogeochemical roles of microorganisms in the environment, it is important to determine when and under which conditions they are metabolically active. Bioorthogonal noncanonical amino acid tagging (BONCAT) can reveal active cells by tracking the incorporation of synthetic amino acids into newly synthesized proteins. The phylogenetic identity of translationally active cells can be determined by combining BONCAT with rRNA-targeted fluorescence in situ hybridization (BONCAT-FISH). In theory, BONCAT-labeled cells could be isolated with fluorescence-activated cell sorting (BONCAT-FACS) for subsequent genetic analyses. Here, in the first application, to our knowledge, of BONCAT-FISH and BONCAT-FACS within an environmental context, we probe the translational activity of microbial consortia catalyzing the anaerobic oxidation of methane (AOM), a dominant sink of methane in the ocean. These consortia, which typically are composed of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria, have been difficult to study due to their slow in situ growth rates, and fundamental questions remain about their ecology and diversity of interactions occurring between ANME and associated partners. Our activity-correlated analyses of >16,400 microbial aggregates provide the first evidence, to our knowledge, that AOM consortia affiliated with all five major ANME clades are concurrently active under controlled conditions. Surprisingly, sorting of individual BONCAT-labeled consortia followed by whole-genome amplification and 16S rRNA gene sequencing revealed previously unrecognized interactions of ANME with members of the poorly understood phylum Verrucomicrobia. This finding, together with our observation that ANME-associated Verrucomicrobia are found in a variety of geographically distinct methane seep environments, suggests a broader range of symbiotic relationships within AOM consortia than previously thought.