Dissertation Research: Intra-population genomic and metabolic diversity among understudied archaea in methane-cycling wetlands

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Archaea are microorganisms that are known to play critical roles in carbon and nitrogen cycling, but little is known about the diversity and evolution of the group. Woesearchaeota, is a poorly known group of Archaea that is commonly found in freshwater wetlands but can also be found in diverse ecosystems globally. As with most members of Archaea, there are no cultured representatives to study in the laboratory, and few available genomes sequences to help infer function. This research will employ environmental DNA sequencing methods and associated computational approaches to generate multiple novel Woesearchaeota genomes from a freshwater wetland. Analysis of these genomes will advance knowledge of the functional potential of this group globally. This work will provide new insights into the role of Archaea in regulating biogeochemical processes. One graduate student will be trained in molecular systematics and undergraduates will receive hands-on research experience on the fundamentals of scientific computing and bioinformatics. This research will produce novel whole-genome sequences and inferences about the metabolic potential for the recently described archaeal group, Woesearchaeota. To-date only a handful of Woesearchaeota genomes and partial genomes have been reconstructed. A high-resolution census of Archaea in a freshwater wetland has revealed that Woesearchaeota at this site are phylogenetically diverse, and comprise two ecologically differentiated ecotypes with niches defined by site geochemistry. The hypothesis that observed niche preferences can be explained by genomic variation will be tested by targeted reconstruction of multiple Woesearchaeota genomes. Researchers will also test the hypotheses that local evolutionary diversifications have resulted in a small core genome, and that the high phylogenetic diversity observed within this phylum is mirrored by high levels of inferred functional diversity.