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 taxonomic note on the genus Prevotella: Description of four novel genera and emended description of the genera Hallella and Xylanibacter.
Thomas C. A. Hitch,Kevin Bisdorf,Afrizal Afrizal,Thomas Riedel,Jörg Overmann,Till Strowig,Thomas Clavel +6 more
TL;DR: This paper used a range of comparative genome approaches to identify large differences between the 53 species for which genomes are available, as well as two effectively published yet not validly named species and four novel species.
Journal ArticleDOI
Salvaging high-quality genomes of microbial species from a meromictic lake using a hybrid sequencing approach.
Yu-Hsiang Chen,Yu-Hsiang Chen,Pei-Wen Chiang,Denis Yu. Rogozin,Denis Yu. Rogozin,Andrey G. Degermendzhy,Hsiu-Hui Chiu,Sen-Lin Tang +7 more
TL;DR: Chen et al. as mentioned in this paper combined Illumina and Nanopore data to develop a new workflow to reconstruct 233 MAGs from Lake Shunet, a secluded meromictic lake in Siberia.
Journal ArticleDOI
Catabolic protein degradation in marine sediments confined to distinct archaea
Xiuran Yin,Guowei Zhou,Mingwei Cai,Qing Zhu,Tim Richter-Heitmann,David A. Aromokeye,Yang Liu,Rolf Nimzyk,Qingfei Zheng,Xiaoyu Tang,Marcus Elvert,Meng Li,Michael W. Friedrich +12 more
TL;DR: In this article , RNA-and lipid-stable isotope probing was used to identify catabolism in three archaeal phyla (uncultivated Thermoplasmata, SG8-5; Bathyarchaeota subgroup 15; Lokiarchaeotas subgroup 2c) by RNA and lipid stable isotope probes in incubations with different marine sediments.
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Deep-branching acetogens in serpentinized subsurface fluids of Oman
Daniel R. Colman,E. A. Kraus,Patrick Thieringer,K. R. Rempfert,Alexis S. Templeton,John R. Spear,Eric S. Boyd +6 more
TL;DR: The discovery of dominant and early-branching acetogens in subsurface waters of the largest near-surface serpentinite formation provides insight into the physiological traits that likely facilitated rock-supported life to flourish on a primitive Earth and possibly on other rocky planets undergoing serpentinization.
Journal ArticleDOI
Niche Differentiation among Three Closely Related Competibacteraceae Clades at a Full-Scale Activated Sludge Wastewater Treatment Plant and Putative Linkages to Process Performance.
TL;DR: Evidence is found for niche differentiation among the three clades with temporal variability in clade dominance that correlates with operational changes at the treatment plant and for episodic dominance of a likely motile clade during periods of elevated effluent turbidity.
References
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