Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla

Bacterial PERegrinations Many branches of the bacterial domain of life are only known from sequences that turn up in metagenomic analyses and are still only named by acronym—for example, the phylum-level groups BD1-5, OP11, OD1, and the PERs. The parent organisms are probably widespread, but they have not been cultured, and very little is known about their metabolisms or their contributions and functions in the natural environment. Wrighton et al. (p. 1661) pumped acetate into an aquifer in Colorado to prompt the naturally occurring bacteria into action and then, from the runoff, filtered out the smaller microbial cells for further analysis. Mass-spectrometry–based proteomics was used to test for functional activity, and 49 distinct genomes were recovered, many with surprising functional attributes. All of the recovered organisms appeared to be strict anaerobes with a full glycolytic pathway that were capable of augmenting energy production by coupling proton-pumping activity to adenosine triphosphate synthase. Several hydrogenases were found that seemed to be able to switch between hydrogen production and polysulfide reduction, depending on the substrate available. Notably, carbon dioxide assimilation was a common feature, with many genes having similarity to those of archaea. Near-complete reconstruction of the genomes of 21 widespread uncultured environmental bacteria reveals metabolic novelties. BD1-5, OP11, and OD1 bacteria have been widely detected in anaerobic environments, but their metabolisms remain unclear owing to lack of cultivated representatives and minimal genomic sampling. We uncovered metabolic characteristics for members of these phyla, and a new lineage, PER, via cultivation-independent recovery of 49 partial to near-complete genomes from an acetate-amended aquifer. All organisms were nonrespiring anaerobes predicted to ferment. Three augment fermentation with archaeal-like hybrid type II/III ribulose-1,5-bisphosphate carboxylase-oxygenase (RuBisCO) that couples adenosine monophosphate salvage with CO2 fixation, a pathway not previously described in Bacteria. Members of OD1 reduce sulfur and may pump protons using archaeal-type hydrogenases. For six organisms, the UGA stop codon is translated as tryptophan. All bacteria studied here may play previously unrecognized roles in hydrogen production, sulfur cycling, and fermentation of refractory sedimentary carbon.