Takacs-Vesbach, Cristina3; Inskeep, William P10; Jay, Zackary J10; Herrgard, Markus1; Rusch, Douglas B5; Tringe, Susannah G5; Kozubal, Mark A10; Hamamura, Natsuko11; Macur, Richard E10; Fouke, Bruce W7; Reysenbach, Anna-Louise12; McDermott, Timothy R10; Jennings, Ryan deM10; Hengartner, Nicolas W13; Xie, Gary13
1 Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark2 CFB - Core Flow, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark3 University of New Mexico4 Montana State University5 Joint Genome Institute6 Ehime University7 University of Illinois8 Portland State University9 Los Alamos National Laboratory10 Montana State University11 Ehime University12 Portland State University13 Los Alamos National Laboratory
The Aquificales are thermophilic microorganisms that inhabit hydrothermal systems worldwide and are considered one of the earliest lineages of the domain Bacteria. We analyzed metagenome sequence obtained from six thermal "filamentous streamer" communities (∼40 Mbp per site), which targeted three different groups of Aquificales found in Yellowstone National Park (YNP). Unassembled metagenome sequence and PCR-amplified 16S rRNA gene libraries revealed that acidic, sulfidic sites were dominated by Hydrogenobaculum (Aquificaceae) populations, whereas the circum-neutral pH (6.5-7.8) sites containing dissolved sulfide were dominated by Sulfurihydrogenibium spp. (Hydrogenothermaceae). Thermocrinis (Aquificaceae) populations were found primarily in the circum-neutral sites with undetectable sulfide, and to a lesser extent in one sulfidic system at pH 8. Phylogenetic analysis of assembled sequence containing 16S rRNA genes as well as conserved protein-encoding genes revealed that the composition and function of these communities varied across geochemical conditions. Each Aquificales lineage contained genes for CO2 fixation by the reverse-TCA cycle, but only the Sulfurihydrogenibium populations perform citrate cleavage using ATP citrate lyase (Acl). The Aquificaceae populations use an alternative pathway catalyzed by two separate enzymes, citryl-CoA synthetase (Ccs), and citryl-CoA lyase (Ccl). All three Aquificales lineages contained evidence of aerobic respiration, albeit due to completely different types of heme Cu oxidases (subunit I) involved in oxygen reduction. The distribution of Aquificales populations and differences among functional genes involved in energy generation and electron transport is consistent with the hypothesis that geochemical parameters (e.g., pH, sulfide, H2, O2) have resulted in niche specialization among members of the Aquificales.