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

  title={Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla},
  author={Kelly C. Wrighton and Brian C. Thomas and Itai Sharon and Christopher S. Miller and Cindy J. Castelle and Nathan Verberkmoes and Michael J. Wilkins and Robert L. Hettich and Mary S. Lipton and Kenneth Hurst Williams and Philip E. Long and Jillian F. Banfield},
  pages={1661 - 1665}
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… 

The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle

Pan-genome analysis indicates a broad genotypic diversity and perhaps a highly fluid gene complement, indicating historical adaptation to a wide range of growth environments and a high degree of specialization.

Unusual respiratory capacity and nitrogen metabolism in a Parcubacterium (OD1) of the Candidate Phyla Radiation

A curated draft genome for ‘Candidatus Parcunitrobacter nitroensis’ a member of the Parcubacteria (OD1) superphylum of the CPR is reported, which substantially expand the known metabolic potential of CPR bacteria, although sequence comparisons indicate that these capacities are very rare in members of this radiation.

Unusual Metabolism and Hypervariation in the Genome of a Gracilibacterium (BD1-5) from an Oil-Degrading Community

The first closed, curated genome of agracilibacterium from an enrichment experiment inoculated from the Gulf of Mexico and designed to investigate hydrocarbon degradation is reported, predicting that this gracilibacteria completely lacks glycolysis, the pentose phosphate and Entner-Doudoroff pathways.

Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations

The metabolic potential of CPR and DPANN radiation is explored, focusing in particular on metabolic gaps and unexpected biological features that are unusual outside of these groups.

Single-cell genomics reveals metabolic strategies for microbial growth and survival in an oligotrophic aquifer.

Analysis of four Pedobacter single amplified genomes from Hanford Site sediments revealed a chemoheterotrophic lifestyle, with the potential to exist under both aerobic and microaerophilic conditions, and demonstrated the potential mechanisms utilized for persistence by heterotrophic micro-organisms in a carbon-limited aquifer.

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Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer

Fermentation-based metabolism is an important ecosystem function often associated with environments rich in organic carbon, such as wetlands, sewage sludge and the mammalian gut. The diversity of

Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria

It is predicted that sediment-associated Margulisbacteria have a fermentation-based metabolism featuring a variety of hydrogenases, a streamlined nitrogenase, and electron bifurcating complexes involved in cycling of reducing equivalents, and inferring their metabolic potential and supporting that their common ancestor was an anaerobe capable of fermentation and H2 metabolism.

Genomic characterization of three novel Desulfobacterota classes expand the metabolic and phylogenetic diversity of the Phylum

The results expand the high-rank diversity within the bacterial tree of life by describing three novel classes within the phylum Desulfobacterota, document the utilization of multiple metabolic processes, e.g. iron-oxidation, aromatic hydrocarbon degradation, reduction of sulfur-cycling intermediates, and features, e-g. coenzyme M biosynthesis, and pigmentation, as salient characteristics in these novel Desulf Obacterota classes.

Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla

Deep sequenced microbial communities from acetate-stimulated aquifer sediment are deeply sequenced to recover the complete and essentially complete genomes of single representatives of the candidate phyla SR1, WWE3, TM7, and OD1, revealing metabolic capabilities on the basis of gene content.



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Maturation of the [NiFe] hydrogenases.

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The microfluidic isolation, multiple-displacement-amplification, pyrosequencing, and genomic analysis of a single cell belonging to candidate division OP11 provide the first glimpse into the lifestyle of a member of a ubiquitous, yet poorly understood bacterial candidate division.

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Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota

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The uncultured microbial majority.

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Distinct Physiological Roles of the Three [NiFe]-Hydrogenase Orthologs in the Hyperthermophilic Archaeon Thermococcus kodakarensis

Important genetic evidence is provided for understanding the physiological roles of hydrogenase orthologs in the Thermococcales and the copresence of Hyh and Mbh raised the possibility of intraspecies H₂ transfer in this archaeon.

Phylogenomic evidence for the presence of a flagellum and cbb(3) oxidase in the free-living mitochondrial ancestor.

Results indicate that the FMA played a more active and potentially parasitic role in eukaryogenesis than currently appreciated and provide an explanation for how the symbiosis could have evolved under low levels of oxygen.

Archaeal Type III RuBisCOs Function in a Pathway for AMP Metabolism

The type III ribulose-1,5-bisphosphate carboxylase-oxygenase (RuBisCO) present in the archaeon Thermococcus kodakaraensis was found to participate in adenosine 5′-monophosphate (AMP) metabolism, a

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