Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
Donovan H. Parks,Christian Rinke,Maria Chuvochina,Pierre-Alain Chaumeil,Ben J. Woodcroft,Paul N. Evans,Philip Hugenholtz,Gene W. Tyson +7 more
TLDR
The recovery of 7,903 bacterial and archaeal metagenome-assembled genomes increases the phylogenetic diversity represented by public genome repositories and provides the first representatives from 20 candidate phyla.Abstract:
Challenges in cultivating microorganisms have limited the phylogenetic diversity of currently available microbial genomes. This is being addressed by advances in sequencing throughput and computational techniques that allow for the cultivation-independent recovery of genomes from metagenomes. Here, we report the reconstruction of 7,903 bacterial and archaeal genomes from >1,500 public metagenomes. All genomes are estimated to be ≥50% complete and nearly half are ≥90% complete with ≤5% contamination. These genomes increase the phylogenetic diversity of bacterial and archaeal genome trees by >30% and provide the first representatives of 17 bacterial and three archaeal candidate phyla. We also recovered 245 genomes from the Patescibacteria superphylum (also known as the Candidate Phyla Radiation) and find that the relative diversity of this group varies substantially with different protein marker sets. The scale and quality of this data set demonstrate that recovering genomes from metagenomes provides an expedient path forward to exploring microbial dark matter.read more
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A genomic perspective on genome size distribution across Earth's microbiomes reveals a tendency to gene loss
Alejandro Rodríguez-Gijón,Julia K. Nuy,Maliheh Mehrshad,Moritz Buck,Frederik Schulz,Tanja Woyke,Sarahi L. Garcia +6 more
TL;DR: It is suggested that the known phylogenetic diversity of environmental microorganisms possess significantly smaller genomes than the collection of laboratory isolated microorganisms, and the variation in genome sizes across different types of environments reflects the different ecological and evolutionary strategies used by microorganisms to thrive in their native environment.
Journal ArticleDOI
Vulcanimicrobium alpinus gen. nov. sp. nov., the first cultivated representative of the candidate phylum “Eremiobacterota”, is a metabolically versatile aerobic anoxygenic phototroph
TL;DR: Vulcanimicrobium alpinus gen. nov. as discussed by the authors is the first successful isolation of a Ca Eremiobacterota strain from a fumarolic ice cave on Mt. Erebus volcano (Antarctica).
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Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments
Xiyang Dong,Chris Greening,Jayne E. Rattray,Anirban Chakraborty,Maria Chuvochina,Daisuke Mayumi,Daisuke Mayumi,Jan Dolfing,Carmen Li,James M. Brooks,Bernie B. Bernard,Ryan A. Groves,Ian A. Lewis,Casey R. J. Hubert +13 more
TL;DR: It is inferred that deep-sea sediments experiencing thermogenic hydrocarbon inputs harbor phylogenetically and functionally diverse communities potentially sustained through anaerobic hydrocarbon, acetate and hydrogen metabolism.
Journal ArticleDOI
Microbial communities of stratified aquatic ecosystems of Kandalaksha Bay (White Sea) shed light on the evolutionary history of green and brown morphotypes of Chlorobiota.
Denis S. Grouzdev,Vasil A. Gaisin,O. N. Lunina,Maria S. Krutkina,Elena D. Krasnova,D. A. Voronov,R. V. Baslerov,Pavel Sigalevich,Alexander S Savvichev,Vladimir M. Gorlenko +9 more
TL;DR: The results support the suggestion that the last common ancestor of Chlorobiaceae belonged to the brown form, i.e. it was adapted to the conditions of low illumination, and the genes responsible for synthesizing the pigments of the Brown form are subject to active horizontal transfer.
Journal ArticleDOI
Molecular hydrogen in seawater supports growth of diverse marine bacteria
Rachael Lappan,Guy Shelley,Zahra F. Islam,Pok Man Leung,Scott Lockwood,Philipp A. Nauer,Thanavit Jirapanjawat,Gaofeng Ni,Ya-Jou Chen,Adam J. Kessler,Timothy J. Williams,Ricardo Cavicchioli,Federico Baltar,Perran L. M. Cook,Sergio E. Morales,Chris Greening +15 more
TL;DR: In this article , the authors used a suite of approaches to show that marine bacteria consume hydrogen to support growth and showed that H2 is a notable energy source for marine bacteria and may influence oceanic ecology and biogeochemistry.
References
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