Predominant Acidilobus-Like Populations from Geothermal Environments in Yellowstone National Park Exhibit Similar Metabolic Potential in Different Hypoxic Microbial Communities

Abstract

c High-temperature (>70°C) ecosystems in Yellowstone National Park (YNP) provide an unparalleled opportunity to study chemotrophic archaea and their role in microbial community structure and function under highly constrained geochemical conditions. Acidilobus spp. (order Desulfurococcales) comprise one of the dominant phylotypes in hypoxic geothermal sulfur sediment and Fe(III)-oxide environments along with members of the Thermoproteales and Sulfolobales. Consequently, the primary goals of the current study were to analyze and compare replicate de novo sequence assemblies of Acidilobus-like populations from four different mildly acidic (pH 3.3 to 6.1) high-temperature (72°C to 82°C) environments and to identify metabolic pathways and/or protein-encoding genes that provide a detailed foundation of the potential functional role of these populations in situ. De novo assemblies of the highly similar Acidilobus-like populations (>99% 16S rRNA gene identity) represent near-complete consensus genomes based on an inventory of single-copy genes, deduced metabolic potential, and assembly statistics generated across sites. Functional analysis of coding sequences and confirmation of gene transcription by Acidilobus-like populations provide evidence that they are primarily chemoorganoheterotrophs, generating acetyl coenzyme A (acetyl-CoA) via the degradation of carbohydrates, lipids, and proteins, and auxotrophic with respect to several external vitamins, cofactors, and metabolites. No obvious pathways or protein-encoding genes responsible for the dissimilatory reduction of sulfur were identified. The presence of a formate dehydrogenase (Fdh) and other protein-encoding genes involved in mixed-acid fermentation supports the hypothesis that Acidilobus spp. function as degraders of complex organic constituents in high-temperature, mildly acidic, hypoxic geothermal systems. Microbial communities in high-temperature geothermal environments provide unique opportunities for determining the physiology of specific populations and for studying geobiological interactions central to a comprehensive functional and evolutionary understanding of thermophilic microorganisms. Acidic, hyperthermal (Ͼ70°C) systems from Yellowstone National Park (YNP) contain significant concentrations of reduced constituents such as H 2 , H 2 S, elemental sulfur, As(III) (e.g., H 3 AsO 3 ), Fe(II), and organic carbon (1, 2), which are often used as electron donors for different chemotrophic microorganisms (3). The oxidation of reduced compounds is coupled with the reduction of terminal electron acceptors, including O 2 , Fe(III), and different sulfur species, generating energy for cellular processes (3, 4). Thermophilic organisms catalyze reactions of geochemical significance (e.g., oxidation-reduction, biomineralization, acidification, and mineral dissolution) that are often orders of magnitude faster than the corresponding abiotic mechanisms (4-7).High-temperature acidic geothermal systems contain several predominant archaeal populations within the phylum Cr...

Carbon Dioxide Fixation by Metallosphaera yellowstonensis and Acidothermophilic Iron-Oxidizing Microbial Communities from Yellowstone National Park

“…Other archaea present in these communities include members of two novel archaeal groups, the Thaumarchaeota and the Euryarchaeota (Thermoplasmatales-like), as well as other crenarchaea within the orders Thermoproteales and Desulfurococcales (19,24,25). However, sequence assemblies corresponding to these populations do not contain evidence of marker genes for known CO 2 fixation pathways and appear to be primarily heterotrophic (18,19,24,25,37,41). Despite the diversity of archaea in these Fe(II)-oxidizing communities, the only known CO 2 fixation pathways found in metagenome sequence analyses included the 3-HP/4-HB pathway (contributed by M. yellowstonensis-like and other Sulfolobales populations) and the r-TCA cycle (contributed by Hydrogenobaculum-like populations).…”

Hydrogen Peroxide Cycling in High-Temperature Acidic Geothermal Springs and Potential Implications for Oxidative Stress Response

“…Ferric iron concentrations were then calculated as the difference between total soluble iron and ferrous iron. Total dissolved sulfide (TS) was assessed using the amine sulfuric acid method (APHA, 1998;Macur et al, 2013;Jay et al, 2014) with 7.5 mL of unfiltered samples [to avoid rapid degassing of H 2 S(aq) upon filtration].…”

Viral assemblage composition in Yellowstone acidic hot springs assessed by network analysis

“…High temperatures (480C), low pH (pHo3) conditions generally favor Archaea-dominated communities (Bolduc et al, 2012). Bacteria and eukaryotes are few or in many cases, absent (Reysenbach et al, 1994;Blank et al, 2002;Kozubal et al, 2012;Macur et al, 2012;Jay et al, 2013). These extreme environmental conditions favor not only the Archaea but also result in a relatively simplified microbial community structure.…”