Journal Article

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

Castelle, Cindy J., Sharon, Itai, VerBerkmoes, Nathan C., Long, Philip E., Miller, Christopher S., Thomas, Brian C., Hettich, Robert L., Banfield, Jillian F., Wrighton, Kelly C., Lipton, Mary S., Williams, Kenneth H., Wilkins, Michael J.

2012

Overview

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 ll/lll ribulose-l, 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.

• Publisher: American Association for the Advancement of Science,The American Association for the Advancement of Science
• Subject: Acetates / Adenosine triphosphate / Amino Acid Sequence / anaerobes / Animal, plant and microbial ecology / Aquifers / Archaea / Archaeal Proteins - chemistry / Archaeal Proteins - genetics / Archaeal Proteins - metabolism / ATP / Bacteria / Bacteria, Anaerobic - classification / Bacteria, Anaerobic - enzymology / Bacteria, Anaerobic - genetics / Biological and medical sciences / Biological evolution / carbon dioxide / Carbon dioxide fixation / Codon, Terminator - genetics / Colorado / Cultivars / DNA, Bacterial / energy / Fermentation / Fundamental and applied biological sciences. Psychology / genes / Genetics of eukaryotes. Biological and molecular evolution / Genome, Bacterial / Genomes / Genomics / glycolysis / Hydrogen / Hydrogen - metabolism / Hydrogen production / Hydrogenase - chemistry / Hydrogenase - genetics / Hydrogenase - metabolism / Metabolism / metagenomics / Microbial ecology / Molecular Sequence Data / Natural environment / Organisms / Oxidation-Reduction / Phylogenetics / Phylogeny / Proteomics / Reduction / Ribulose-Bisphosphate Carboxylase - chemistry / Ribulose-Bisphosphate Carboxylase - genetics / Ribulose-Bisphosphate Carboxylase - metabolism / runoff / Similarity / Spectrometry / Sulfur / Sulfur - metabolism / Tryptophan - genetics / Various environments (extraatmospheric space, air, water)