Open Access
Jones, Daniel Seth
Graduate Program:
Doctor of Philosophy
Document Type:
Date of Defense:
September 09, 2011
Committee Members:
  • Jennifer Macalady, Dissertation Advisor
  • Jennifer Macalady, Committee Chair
  • Matthew Scott Fantle, Committee Chair
  • Mark E Patzkowsky, Committee Member
  • Christopher Howard House, Committee Member
  • Brian Dempsey, Committee Member
  • biogeography
  • sulfide oxidation
  • acidophile
  • karst
  • Hydrogen sulfide
  • Acidithiobacillus
Sulfidic caves form in carbonate bedrock where H2S-rich groundwaters interact with oxygenated surface waters and cave air. H2S oxidation in sulfidic caves causes rapid carbonate dissolution and aggressive speleogenesis, and provides chemical energy for diverse communities of chemolithoautotrophic sulfur-oxidizing microorganisms. At the cave watertable, the fate of dissolved sulfide is controlled by three processes that independently influence cave formation: degassing of H2S(g) to the cave atmosphere, biological oxidation in sulfur-oxidizing stream biofilms, and abiotic sulfide oxidation. In contrast to previous research, we found that H2S(g) degassing accounts for the majority of sulfide disappearance from Frasassi streams and that little to no acid is produced in the microaerophilic stream communities. On the cave walls and ceilings, extremely acidic (pH 0-1.5) biofilms known as ‘snottites’ form where gypsum corrosion residues isolate microbial sulfide oxidizers from limestone buffering. We used a combination of metagenomics and other culture-independent methods and found that Frasassi snottites are dominated by Acidithiobacillus thiooxidans, with smaller populations of an archaeon in the uncultivated ‘G-plasma’ clade of Thermoplasmatales, a bacterium in the Acidimicrobiaceae family, and several rare taxa. The Acidithiobacillus population is autotrophic and oxidize sulfur by the sulfide-quinone reductase (SQR) and sox pathways, while the archaeal and Acidimicrobiaceae populations are likely heterotrophic. We sampled sulfidic cave snottites at spatial scales ranging from meters to 1000s of kilometers to test whether geographical barriers affect microbial biogeography. Given the extreme geochemistry and subsurface location of the biofilms, we hypothesized that snottites from different locations could contain genetically isolated populations and distinct community structures. By (i) sequencing 16S rRNA genes, (ii) sequencing 16S-23S intergenic transcribed spacer (ITS) regions, and (iii) multi-locus sequencing typing (MLST), we found that the dominant Acidithiobacillus populations are genetically divergent, but also identified recent long distance dispersal. We then used a combination of 16S rDNA cloning and fluorescence in situ hybridization (FISH) to investigate snottite community structure, and found that at a global scale, communities from different caves are significantly different and the major axes of variance in the dataset are related to cave location.