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

TLDR

Many bacterial lineages are known only from metagenomic sequences and remain uncultured, leaving their metabolic roles largely unknown. Acetate was injected into a Colorado aquifer to stimulate native bacteria, after which microbial cells were isolated and proteomic analysis recovered 49 distinct genomes. The recovered organisms were strict anaerobes with glycolysis and proton‑pumping ATP synthase, possessed versatile hydrogenases for hydrogen production or polysulfide reduction, and frequently encoded CO₂‑assimilation genes resembling archaeal sequences. Wrighton et al.

Abstract

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.