Buried Alive: Analysis of Uncultured Microbes in Marine Sediments

The vast majority of microbes in marine sediments have yet to be isolated in pure culture, this leaves many questions as to their ecological relevance and relationship with other taxa and their environment. We applied next generation sequencing techniques to high resolution depth profiles of marine sediments and geochemical analyses to investigate microbial population abundance and composition with depth in Chapter 2. This revealed a putative methanotroph, ANME-1, to be the sole microbe capable of producing methane in the methane producing zone and the area suspected of methane oxidation. This suggests that these OTU’s of ANME-1 are capable of both methane production and oxidation, the mechanism used dependent upon geochemical conditions. In Chapter 3, RNA transcript abundance was combined with 16SrRNA gene composition analysis and long-term incubations of marine sediments to investigate microbial population succession in concert with the depletion of sulfate as a temporal analog for depth. This separated methane production from sulfate reduction, revealing an increase in abundance of ANME-3, a methanotroph, simultaneous to an increase in methane concentrations, indicating that this methanotroph is also capable of methane production. Additionally, methanotrophic archaea could not be stimulated to increase in abundance by the addition of methane to the sulfate reduction zone; again, ANME-3 only increased after sulfate was depleted and was observed alongside an increase in methane production, further supporting its role as a putative methane producer. Lastly, in Chapter 4 metabolomic profiles were combined with single cell amplified genomes to explore microbial life in serpentinization sourced mud volcanoes associated with the Mariana Forearc. These constitute the first single cell genomes isolated from marine sediments of this type and alkalinity. Overall, this work offers new insights into methanogenic metabolism flexibility, as well as an improved understanding of microbes associated with sediments influenced by serpentinization sourced fluids.