Singled Out: Genomic analysis of uncultured microbes in marine sediments

The vast majority of abundant taxa in marine sediment environments have not yielded to culture, leaving questions about their relationship to other taxa and their functional potential unanswered. However, in the absence of active cultures, careful application of various omics methods can be used to help us make useful inferences about their evolutionary history and how they have continued to survive in environments of extreme energy deprivation. For this dissertation, I have applied comparative genomics methods to members of two uncultured groups, the recently proposed Altiarchaeales order and a cosmopolitan taxon associated with the Actinobacteria phylum. Additionally, I combined transcript recruitment and metabolomic profiles to investigate metabolisms inferred from the single-cell amplified genomes extracted from members of a taxa that thrive in Baltic Sea sediment microbial communities. In Chapter II, I establish a phylogenetic relationship across distantly related members of the order Altiarchaeales and discuss environment-specific adaptations. In Chapter III, transcript recruitment and metabolite profiles support a community-wide focus on microbial persistence with active members of the uncultured Atribacteria phylum playing an important ecological role. In Chapter IV, my analysis leads to the proposal of the new class within the Actinobacteria. Osirisbacteria is a class of Actinobacteria that is specialized for life in anoxic environments. Overall, this work offers new insights into deeply-branching microbial taxa, improved understanding of recently considered branches of the evolutionary tree, and new perspective on metabolisms important for survival in low-energy marine sediment environments.