RS24 snottite metagenome
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 (>70% of cells) by Acidithiobacillus thiooxidans, with smaller populations including an archaeon in the uncultivated ‘G-plasma’ clade of Thermoplasmatales (>15%) and a bacterium in the Acidimicrobiaceae family (>5%). Based on metagenomic evidence, the Acidithiobacillus population is autotrophic (RuBisCO, carboxysomes) and oxidize sulfur by the sulfide-quinone reductase (SQR) 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.
Metagenomic analysis of highly acidic (pH 0-1) biofilms known as ‘snottites’ that form on the walls and ceilings of hydrogen sulfide-rich caves. The metagenome was generated using first generation 454 pyrosequencing technology (GS 20 platform).