Abstract
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.
Highlights
The order Aquificales represents a group of thermophilic microorganisms that inhabit marine and terrestrial hydrothermal systems worldwide (Ferrera et al, 2007)
We provide a phylogenetic and functional analysis of metagenome sequence obtained from six Aquificales “streamer” communities, representing two replicate communities of each of the three major Aquificales lineages found in high-velocity outflow channels of Yellowstone National Park (YNP)
The sites were chosen to obtain a range in pH (3–8) and other geochemical attributes such as dissolved oxygen, dissolved sulfide, and/or predominant solid-phases associated with each microbial community (Figure 1; Table 1)
Summary
The order Aquificales represents a group of thermophilic microorganisms that inhabit marine and terrestrial hydrothermal systems worldwide (Ferrera et al, 2007). This lineage is of significant interest because its members are believed to comprise the deepest lineage of the domain Bacteria (Coenye and Vandamme, 2004; Barion et al, 2007), alternative evolutionary histories have been suggested (Griffiths and Gupta, 2004; Boussau et al, 2008; Zhaxybayeva et al, 2009). The Aquificales include two predominant families, the Hydrogenothermaceae and Aquificaceae, and both are well-represented in different geothermal features of Yellowstone National Park (YNP) (Reysenbach et al, 2005).
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