Phylogenetic diversity and functional gene patterns of sulfur-oxidizing subseafloor Epsilonproteobacteria in diffuse hydrothermal vent fluids

Abstract

Microorganisms throughout the dark ocean use reduced sulfur compounds for chemolithoautotrophy. In many deep-sea hydrothermal vents, sulfide oxidation is quantitatively the most important chemical energy source for microbial metabolism both at and beneath the seafloor. In this study, the presence and activity of vent endemic Epsilonproteobacteria was examined in six low-temperature diffuse vents over a range of geochemical gradients from Axial Seamount, a deep-sea volcano in the Northeast Pacific. PCR primers were developed and applied to target the sulfur oxidation soxB gene of Epsilonproteobacteria. soxB genes belonging to the genera Sulfurimonas and Sulfurovum are both present and expressed at most diffuse vent sites, but not in background seawater. Although Sulfurovum-like soxB genes were detected in all fluid samples, the RNA profiles were nearly identical among the vents and suggest that Sulfurimonas-like species are the primary Epsilonproteobacteria responsible for actively oxidizing sulfur via the Sox pathway at each vent. Community patterns of subseafloor Epsilonproteobacteria 16S rRNA genes were best matched to methane concentrations in vent fluids, as well as individual vent locations, indicating that both geochemistry and geographical isolation play a role in structuring subseafloor microbial populations. The data show that in the subseafloor at Axial Seamount, Epsilonproteobacteria are expressing the soxB gene and that microbial patterns in community distribution are linked to both vent location and chemistry.

Keywords: 16S rRNA; Epsilonproteobacteria; functional genes; hydrothermal vent microbiology; subseafloor; sulfur oxidation.

Figure 1

Maximum likelihood phylogenetic tree showing the relationships of the 15% soxB gene OTUs found in this study (indicated in boldface) with number of sequences belonging to each OTU indicated in parentheses. The maximum likelihood tree was calculated based on ~234 amino acid residues and bootstrap values above 50 are shown.

Figure 2

Relative abundance with taxonomic affiliation of the 15% soxB gene OTUs in the DNA and RNA fractions of different vents classified according to the phylogenetic tree in Figure 1.

Figure 3

Taxonomic breakdown and relative abundance at the phylum (and class for Proteobacteria) level for the 96% 16S rRNA gene OTUs in all samples. Only those taxa that occurred more than 3% in any individual dataset are included. Taxa that occurred less than 3% are placed into “Other.”

Figure 4

Taxonomic breakdown and relative abundance of dominant Epsilonproteobacteria at the genus level for the 96% 16S rRNA gene OTUs in each vent fluid sample. All other Epsilonproteobacterial sequences are placed into “Other.”

Figure 5

Principal coordinates analysis of all 96% 16S rRNA gene OTUs.

Figure 6

Principal coordinates analysis of all 96% Epsilonproteobacterial 16S rRNA gene OTUs with CH₄/Heat ratios shown in bubbles surrounding symbols.

Figure 7

Taxonomic breakdown and relative abundance of dominant Gammaproteobacteria at the genus level for 96% 16S rRNA gene OTUs in each sample. All other Gammaproteobacteria sequences are lumped into “Other.”