Anaerobic biodegradation of the isoprenoid biomarkers pristane and phytane

Isoprenoids, a diverse class of compounds synthesized by all three domains of life, comprise many of the biomarker compounds used in paleoenvironmental and paleoecological reconstruction of Earth history. These biomarkers include hopanoids, sterols and archaeal membrane lipids. While changes in hydrocarbon profiles in anoxic sediments and oilfields indicate that anaerobic microbial metabolism is involved in the disappearance or alteration of isoprenoids, direct links between specific compounds and their microbial degraders are lacking. Here we describe pristane (Pr) and phytane (Ph) degradation associated with NO^-_3 reduction. We confirmed isoprenoid conversion to CO_2 using ^(13)C-labeled Ph. After 120 days, dissolved inorganic carbon (DIC) produced in incubations grown with ^(13)C-labeled Ph had a δ^(13)C value of +76.7 ± 11.9‰, significantly higher than values for incubations with unlabeled Ph (−35.7 ± 2.0‰) and those without an added carbon substrate (−30.0 ± 2.1‰). Additional incubations, displayed NO^-_3 reduction after amendment with archaeal diphytanyl glycerol diether (DGD) core lipids, but not in those amended with glycerol diphytanyl glycerol tetraether (GDGT) core lipids. Both 16S rRNA clone libraries and whole cell rRNA-targeted fluorescent in situ hybridization (FISH) indicated that the likely Pr and Ph degrading Bacteria were Gamma proteobacteria, with > 99% similarity to Pseudomonas stutzeri

Metagenomic Evidence for Sulfide Oxidation in Extremely Acidic Cave Biofilms

<div><p>Snottites are extremely acidic (pH 0–2) biofilms that form on the walls and ceilings of hydrogen sulfide-rich caves. Recent work suggests that microbial communities including snottites and related cave wall biofilms accelerate cave formation by oxidizing sulfide to sulfuric acid. Therefore, we used full-cycle rRNA methods and metagenomics to explore the community composition and sulfur metabolism of snottites from the sulfidic Frasassi and Acquasanta cave systems, Italy. Acquasanta snottites were dominated by strains of <i>Acidithiobacillus thiooxidans</i>, with a smaller population of <i>Ferroplasma</i> sp. Frasassi snottites were also dominated by <i>At. thiooxidans</i> but with a more diverse community including relatives of ‘G-plasma’ (Thermoplasmatales), <i>Acidimicrobium</i>, and rare taxa. We identified diverse homologues of sulfide:quinone oxidoreductase (SQR) in the metagenomic datasets. Based on phylogenetic analysis, the numerically dominant <i>At. thiooxidans</i> populations have four different types of SQR, while <i>Ferroplasma</i> has two and <i>Acidimicrobium</i> and G-plasma each have one. No other genetic evidence for sulfur oxidation was detected for either <i>Acidimicrobium</i> or G-plasma, suggesting that they do not generate sulfuric acid. Our results confirm earlier findings that <i>At. thiooxidans</i> is the dominant primary producer and sulfide oxidizer in sulfidic cave snottites.</p> </div

Niche differentiation among sulfur-oxidizing bacterial populations in cave waters

The sulfidic Frasassi cave system affords a unique opportunity to investigate niche relationships among sulfur-oxidizing bacteria, including epsilonproteobacterial clades with no cultivated representatives. Oxygen and sulfide concentrations in the cave waters range over more than two orders of magnitude as a result of seasonally and spatially variable dilution of the sulfidic groundwater. A full-cycle rRNA approach was used to quantify dominant populations in biofilms collected in both diluted and undiluted zones. Sulfide concentration profiles within biofilms were obtained in situ using microelectrode voltammetry. Populations in rock-attached streamers depended on the sulfide/oxygen supply ratio of bulk water (r=0.97; P\u3c0.0001). Filamentous epsilonproteobacteria dominated at high sulfide to oxygen ratios (\u3e150), whereas Thiothrix dominated at low ratios (\u3c75). In contrast, Beggiatoa was the dominant group in biofilms at the sediment–water interface regardless of sulfide and oxygen concentrations or supply ratio. Our results highlight the versatility and ecological success of Beggiatoa in diffusion-controlled niches, and demonstrate that high sulfide/oxygen ratios in turbulent water are important for the growth of filamentous epsilonproteobacteria

Community genomic analysis of an extremely acidophilic sulfur-oxidizing biofilm

Highly acidic (pH 0–1) biofilms, known as ‘snottites’, form on the walls and ceilings of hydrogen sulfide-rich caves. We investigated the population structure, physiology and biogeochemistry of these biofilms using metagenomics, rRNA methods and lipid geochemistry. Snottites from the Frasassi cave system (Italy) are dominated (\u3e70% of cells) by Acidithiobacillus thiooxidans, with smaller populations including an archaeon in the uncultivated ‘G-plasma’ clade of Thermoplasmatales (\u3e15%) and a bacterium in the Acidimicrobiaceae family (\u3e5%). Based on metagenomic evidence, the Acidithiobacillus population is autotrophic (ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), carboxysomes) and oxidizes sulfur by the sulfide–quinone reductase and sox pathways. No reads matching nitrogen fixation genes were detected in the metagenome, whereas multiple matches to nitrogen assimilation functions are present, consistent with geochemical evidence, that fixed nitrogen is available in the snottite environment to support autotrophic growth. Evidence for adaptations to extreme acidity include Acidithiobacillus sequences for cation transporters and hopanoid synthesis, and direct measurements of hopanoid membrane lipids. Based on combined metagenomic, molecular and geochemical evidence, we suggest that Acidithiobacillus is the snottite architect and main primary producer, and that snottite morphology and distributions in the cave environment are directly related to the supply of C, N and energy substrates from the cave atmosphere

Methane-Producing Microbial Community in a Coal Bed of the Illinois Basin▿

A series of molecular and geochemical studies were performed to study microbial, coal bed methane formation in the eastern Illinois Basin. Results suggest that organic matter is biodegraded to simple molecules, such as H2 and CO2, which fuel methanogenesis and the generation of large coal bed methane reserves. Small-subunit rRNA analysis of both the in situ microbial community and highly purified, methanogenic enrichments indicated that Methanocorpusculum is the dominant genus. Additionally, we characterized this methanogenic microorganism using scanning electron microscopy and distribution of intact polar cell membrane lipids. Phylogenetic studies of coal water samples helped us develop a model of methanogenic biodegradation of macromolecular coal and coal-derived oil by a complex microbial community. Based on enrichments, phylogenetic analyses, and calculated free energies at in situ subsurface conditions for relevant metabolisms (H2-utilizing methanogenesis, acetoclastic methanogenesis, and homoacetogenesis), H2-utilizing methanogenesis appears to be the dominant terminal process of biodegradation of coal organic matter at this location