Active populations and preserved signals: molecular- and cultivation-based geobiological analyses from microbialites to the marine deep biosphere

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University of Delaware
The application of DNA- and RNA-based molecular tools to lithological environments has allowed characterization of endemic microbial members and their biogeochemical roles at unprecedented scale, particularly in the marine deep biosphere. However, the preservation potential of nucleic acids within many of these environments is not well established. Here, microbial community composition and function are investigated across several geological environments, ranging from growing microbialite structures in a temperate Canadian lake to deep marine sediments, using molecular techniques and cultivations. Results show that DNA and RNA can be preserved on geological timescales in marine sediments, but show an exponential decay in amplification and sequencing viability with sediment age. Comparing molecular data to these patterns can identify putative active members of this environment. In Chapter 2, high-throughput tagged sequencing analyses show that the microbial communities of Pavilion Lake microbialites are diverse compared to non-lithifying microbial mats also found in the lake. Phototrophs were shown as the most influential contributors to community differences above and below 25 meters, and corresponding shifts in heterotrophic populations were observed at this interface as well. Microbial community composition did not correlate with changing microbialite morphology with depth, suggesting something other than community changes may be key to observed variations in microbialite structure. In Chapter 3 and 4, signals from preserved DNA and RNA were seen in samples from the Iberian Margin, up to 123 meters below seafloor (mbsf), in 1.2 million year old sediment. Comparisons of down-core molecular data to geochemistry identified members of the candidate phyla Atribacteria and Aerophobetes as ecologically relevant and distinct from the preservation signal. Binned metagenomic data indicate the importance of fermentative metabolisms in these candidate phyla, which are most abundant at the SMTZ. In Chapter 5, several enrichment strategies were initiated for aerobic and anaerobic metabolisms on sediment and underlying basalt samples from North Pond, a sediment basin ringed by basalt outcrops underlying an oligotrophic water-column west of the Mid-Atlantic Ridge at 22°N. Microbes isolated from these enrichments include an Arthrobacter species from 4 mbsf and Pseudomonas and Paracoccus species from 68 mbsf. Reported here are phylogeny and growth rate characteristics of isolates and taxonomic descriptions of overall microbial assemblage at their respective depths. This work extends the preservation timescale of nucleic acids, both DNA and RNA, in deep marine sediments by orders of magnitude over what has previously been seen. This is an important result, as it serves as a caution against over-interpretation of rRNA transcripts as a proxy for activity in geological settings, as well as extending the possible range of use for ancient DNA and ancient RNA in paleobiology studies. This work includes the sixth metagenomic or metatranscriptomic dataset from deep marine sediments (> 1 mbsf), and the only such dataset from the Atlantic Ocean seafloor to date.