The epsilon-proteobacteria have recently been recognized as globally ubiquitous in modern marine and terrestrial ecosystems, and have had a significant role in biogeochemical and geological processes throughout Earth's history. To place this newly expanded group, which consists mainly of uncultured representatives, in an evolutionary context, we present an overview of the taxonomic classification for the class, review ecological and metabolic data in key sulphidic habitats and consider the ecological and geological potential of the epsilon-proteobacteria in modern and ancient systems. These integrated perspectives provide a framework for future culture- and genomic-based studies.

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Among vertebrate gastrointestinal microbiome studies, complete representation of taxa is limited, particularly among reptiles. Here, we provide evidence for previously unrecognized host-microbiome associations along the gastrointestinal tract from the American alligator, a crown archosaur with shared ancestry to extinct taxa, including dinosaurs. Microbiome compositional variations reveal that the digestive system consists of multiple, longitudinally heterogeneous microbiomes that strongly correlate to specific gastrointestinal tract organs, regardless of rearing histories or feeding status. A core alligator gut microbiome comprised of Fusobacteria, but depleted in Bacteroidetes and Proteobacteria common to mammalians, is compositionally unique from other vertebrate gut microbiomes, including other reptiles, fish, and herbivorous and carnivorous mammals. As such, modern alligator gut microbiomes advance our understanding of archosaur gut microbiome evolution, particularly if conserved host ecology has retained archosaur-specific symbioses over geologic time.

Filamentous microbial mats from three aphotic sulfidic springs in Lower Kane Cave, Wyoming, were assessed with regard to bacterial diversity, community structure, and ecosystem function using a 16S rDNA-based phylogenetic approach combined with elemental content and stable carbon isotope ratio analyses. The most prevalent mat morphotype consisted of white filament bundles, with low C:N ratios (3.5-5.4) and high sulfur content (16.1-51.2%). White filament bundles and two other mat morphotypes had organic carbon isotope values (mean delta13C=-34.7 per thousand, 1sigma=3.6) consistent with chemolithoautotrophic carbon fixation from a dissolved inorganic carbon reservoir (cave water, mean delta13C=-7.4 per thousand for two springs, n=8). Bacterial diversity was low overall in the clone libraries, and the most abundant taxonomic group was affiliated with the "Epsilonproteobacteria" (68%), with other bacterial sequences affiliated with Gammaproteobacteria (12.2%), Betaproteobacteria (11.7%), Deltaproteobacteria (0.8%), and the Acidobacterium (5.6%) and Bacteriodetes/Chlorobi (1.7%) divisions. Six distinct epsilonproteobacterial taxonomic groups were identified from the microbial mats. Epsilonproteobacterial and bacterial group abundances and community structure shifted from the spring orifices downstream, corresponding to changes in dissolved sulfide and oxygen concentrations and metabolic requirements of certain bacterial groups. Most of the clone sequences for epsilonproteobacterial groups were retrieved from areas with high sulfide and low oxygen concentrations, whereas Thiothrix spp. and Thiobacillus spp. had higher retrieved clone abundances where conditions of low sulfide and high oxygen concentrations were measured. Genetic and metabolic diversity among the "Epsilonproteobacteria" maximizes overall cave ecosystem function, and these organisms play a significant role in providing chemolithoautotrophic energy to the otherwise nutrient-poor cave habitat. Our results demonstrate that sulfur cycling supports subsurface ecosystems through chemolithoautotrophy and expand the evolutionary and ecological views of "Epsilonproteobacteria" in terrestrial habitats.

The sulfuric acid speleogenesis (SAS) model was introduced in the early 1970s from observations of Lower Kane Cave, Wyoming, and was proposed as a cave-enlargement process due to primarily H 2 S autoxidation to sulfuric acid and subaerial replacement of carbonate by gypsum. Here we present a reexamination of the SAS type locality in which we make use of uniquely applied geochemical and microbiological methods. Little H 2 S escapes to the cave atmosphere, or is lost by abiotic autoxidation, and instead the primary H 2 S loss mechanism is by subaqueous sulfur-oxidizing bacterial communities that consume H 2 S. Filamentous ''Epsilonproteobacteria'' and Gammaproteobacteria, characterized by fluorescence in situ hybridization, colonize carbonate surfaces and generate sulfuric acid as a metabolic byproduct. The bacteria focus carbonate dissolution by locally depressing pH, compared to bulk cave waters near equilibrium or slightly supersaturated with calcite. These findings show that SAS occurs in subaqueous environments and potentially at much greater phreatic depths in carbonate aquifers, thereby offering new insights into the microbial roles in subsurface karstification.Keywords: cave, hydrogen sulfide, geomicrobiology, sulfur-oxidizing bacteria, fluorescence in situ hybridization, carbonate dissolution. Figure 1. Site location map and plan-view cave map showing main spring sites and stream channel in Lower Kane Cave, Wyoming (modified from Egemeier, 1981). Photograph shows white filamentous microbial mats downstream from Upper Spring orifice (flow is left to right).