Text

theses

Despite being ubiquitous, shallow-water marine geothermal environments are under-studied compared to their deep-sea counterparts. In this study, I investigated the geochemistry and the composition, physiology and function of microbial communities at Tor Caldara, a shallow-water gas vent in the Tyrrhenian Sea. The four microbial habitats sampled included: crusts originated from compacted sediments, venting sandy sediments, control sediments and substrate-attached filamentous bacteria (young as well as established). At Tor Caldara, the venting gases are mainly composed of CO2 and H2S, with trace amounts of CH4, and a thermal anomaly could not be detected. The crust community is very unique, comprising phylotypes associated with sulfate reducing bacteria belonging to Deltaproteobacteria that are usually found in syntrophic association with anaerobic methane oxidizers at hydrocarbon seeps. The venting sediment community is dominated by sulfur-oxidizing chemoautotrophic and heterotrophic bacterial groups belonging to Alpha-, Gamma-, and Epsilonproteobacteria, while that of the non-venting sediment is dominated by phototrophic members belonging to Cyanobacteria. The established and young microbial filaments are dominated by chemoautotrophic, sulfur-oxidizing members of Gammaproteobacteria and Epsilonproteobacteria, respectively. Integrating geochemical measurements, microbial diversity surveys and physiological characterization of laboratory strains, I demonstrated that there is a temporal succession between the two filamentous microbial communities in response to age and possibly sulfide concentrations. Metagenomic and metaproteomic results showed presence of genes and proteins involved in nitrate reduction, denitrification, nitrogen fixation, sulfur oxidation/reduction, oxygen respiration, heavy metal detoxification and two carbon fixation pathways. Temporal succession between the young and established filamentous communities at a functional level was confirmed by differential abundance of key proteins involved in the carbon, sulfur and nitrogen cycles. Three metagenome-assembled genome (MAGs) representative of the filament community were also recovered. Based on taxonomic and functional diversity, chemoautotrophic, sulfur-oxidizing members of Epsilonproteobacteria dominated the young microbial filaments while the established microbial filaments are dominated by Gammaproteobacteria, demonstrating a shift in community over time. In addition to diversity and functional surveys, I isolated several bacterial strains and characterized a novel alphaproteobacterial genus with high metabolic versatility and sequenced its genome. Broadly, this study shows that Tor Caldara hosts very diverse and niche-specific microbial communities consisting of numerous previously uncharacterized bacterial and archaeal groups.

ETD_9131

Ph.D.

Includes bibliographical references

by Sushmita S. Patwardhan

doi:10.7282/t3-ggna-cz18

ETD doctoral

The author owns the copyright to this work.