Abstract
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.
