DiTing: A Pipeline to Infer and Compare Biogeochemical Pathways From Metagenomic and Metatranscriptomic Data DOI Creative Commons

Chun‐Xu Xue,

Heyu Lin, Xiaoyu Zhu

et al.

Frontiers in Microbiology, Journal Year: 2021, Volume and Issue: 12

Published: Aug. 2, 2021

Metagenomics and metatranscriptomics are powerful methods to uncover key micro-organisms processes driving biogeochemical cycling in natural ecosystems. Databases dedicated depicting pathways (for example, metabolism of dimethylsulfoniopropionate (DMSP), which is an abundant organosulfur compound) from metagenomic/metatranscriptomic data rarely seen. Additionally, a recognized normalization model estimate the relative abundance environmental importance metagenomic metatranscriptomic has not been organized date. These limitations impact ability accurately relate microbial-driven differences conditions. Thus, easy-to-use, specialized tool that infers visually compares potential for processes, including DMSP cycling, urgently required. To solve these issues, we developed DiTing, wrapper infer compare among set given or reads one step, based on Kyoto Encyclopedia Genes Genomes (KEGG) manually created gene database. Accurate specific formulae over 100 were calculate their abundance. Output reports detail both text graphical format. DiTing was applied simulated resulted consistent genetic features benchmark genomic data. Subsequently, when hydrothermal vents Tara Ocean project, functional profiles predicted by correlated with condition changes. can now be confidently wider datasets, it available at https://github.com/xuechunxu/DiTing .

Language: Английский

A genomic catalog of Earth’s microbiomes DOI Creative Commons
Stephen Nayfach, Simon Roux, R. Seshadri

et al.

Nature Biotechnology, Journal Year: 2020, Volume and Issue: 39(4), P. 499 - 509

Published: Nov. 9, 2020

Abstract The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology evolution environmental host-associated microbiomes. Here we applied this approach to >10,000 collected diverse habitats covering all Earth’s continents oceans, including human animal hosts, engineered environments, natural agricultural soils, capture extant microbial, metabolic functional potential. This comprehensive catalog includes 52,515 metagenome-assembled representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. expands known phylogenetic diversity bacteria archaea by 44% is broadly available for streamlined comparative analyses, interactive exploration, modeling bulk download. We demonstrate utility collection understanding secondary-metabolite biosynthetic potential resolving thousands new host linkages uncultivated viruses. resource underscores value genome-centric approaches revealing genomic properties microorganisms that affect ecosystem processes.

Language: Английский

Citations

692
Isolation of an archaeon at the prokaryote–eukaryote interface DOI Creative Commons
Hiroyuki Imachi, Masaru K. Nobu, Nozomi Nakahara

et al.

Nature, Journal Year: 2020, Volume and Issue: 577(7791), P. 519 - 525

Published: Jan. 15, 2020

The origin of eukaryotes remains unclear1–4. Current data suggest that may have emerged from an archaeal lineage known as 'Asgard' archaea5,6. Despite the eukaryote-like genomic features are found in these archaea, evolutionary transition archaea to unclear, owing lack cultured representatives and corresponding physiological insights. Here we report decade-long isolation Asgard archaeon related Lokiarchaeota deep marine sediment. archaeon—'Candidatus Prometheoarchaeum syntrophicum' strain MK-D1—is anaerobic, extremely slow-growing, small coccus (around 550 nm diameter) degrades amino acids through syntrophy. Although intracellular complexes been proposed for archaea6, isolate has no visible organelle-like structure. Instead, Ca. P. syntrophicum is morphologically complex unique protrusions long often branching. On basis available obtained cultivation genomics, reasoned interpretations existing literature, propose a hypothetical model eukaryogenesis, termed entangle–engulf–endogenize (also E3) model. Isolation characterization most closely reveals insights into how evolved prokaryotes.

Language: Английский

Citations

541
Diversity, ecology and evolution of Archaea DOI
Brett J. Baker, Valerie De Anda,

Kiley W. Seitz

et al.

Nature Microbiology, Journal Year: 2020, Volume and Issue: 5(7), P. 887 - 900

Published: May 4, 2020

Language: Английский

Citations

406
Microbial diversity in extreme environments DOI

Wensheng Shu,

Li‐Nan Huang

Nature Reviews Microbiology, Journal Year: 2021, Volume and Issue: 20(4), P. 219 - 235

Published: Nov. 9, 2021

Language: Английский

Citations

353
Automated analysis of genomic sequences facilitates high-throughput and comprehensive description of bacteria DOI Creative Commons
Thomas C. A. Hitch, Thomas Riedel, Aharon Oren

et al.

ISME Communications, Journal Year: 2021, Volume and Issue: 1(1)

Published: May 20, 2021

The study of microbial communities is hampered by the large fraction still unknown bacteria. However, many these species have been isolated, yet lack a validly published name or description. validation names for novel bacteria requires that uniqueness those taxa demonstrated and their properties are described. accepted format this protologue, which can be time-consuming to create. Hence, research fields in microbiology biotechnology will greatly benefit from new approaches reduce workload harmonise generation protologues.We developed Protologger, bioinformatic tool automatically generates all necessary readouts writing detailed protologue. By producing multiple taxonomic outputs, functional features ecological analysis using 16S rRNA gene genome sequences single species, time needed gather information describing substantially reduced. usefulness Protologger was three isolate collections describe 34 taxa, encompassing 17 genera, including automatic ecologically functionally relevant names. We also highlight need utilise delineation methods, as while inconsistencies between each method occur, combined approach provides robust placement. open source; scripts datasets available, along with webserver at www.protologger.de.

Language: Английский

Citations

291
The fate of organic carbon in marine sediments - New insights from recent data and analysis DOI
Douglas E. LaRowe, Sandra Arndt, James A. Bradley

et al.

Earth-Science Reviews, Journal Year: 2020, Volume and Issue: 204, P. 103146 - 103146

Published: Feb. 29, 2020

Language: Английский

Citations

223
Asgard archaea capable of anaerobic hydrocarbon cycling DOI Creative Commons

Kiley W. Seitz,

Nina Dombrowski, Laura Eme

et al.

Nature Communications, Journal Year: 2019, Volume and Issue: 10(1)

Published: April 23, 2019

Abstract Large reservoirs of natural gas in the oceanic subsurface sustain complex communities anaerobic microbes, including archaeal lineages with potential to mediate oxidation hydrocarbons such as methane and butane. Here we describe a previously unknown phylum, Helarchaeota, belonging Asgard superphylum for hydrocarbon oxidation. We reconstruct Helarchaeota genomes from metagenomic data derived hydrothermal deep-sea sediments hydrocarbon-rich Guaymas Basin. The encode methyl-CoM reductase-like enzymes that are similar those found butane-oxidizing archaea, well several potentially involved alkyl-CoA Wood-Ljungdahl pathway. suggest members have activate subsequently anaerobically oxidize hydrothermally generated short-chain hydrocarbons.

Language: Английский

Citations

208
Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments DOI Creative Commons
Xiyang Dong, Chris Greening, Jayne E. Rattray

et al.

Nature Communications, Journal Year: 2019, Volume and Issue: 10(1)

Published: April 18, 2019

Abstract The lack of microbial genomes and isolates from the deep seabed means that very little is known about ecology this vast habitat. Here, we investigate energy carbon acquisition strategies communities three petroleum seeps (3 km water depth) in Eastern Gulf Mexico. Shotgun metagenomic analysis reveals each sediment harbors diverse chemoheterotrophs chemolithotrophs. We recovered 82 metagenome-assembled affiliated with 21 different archaeal bacterial phyla. Multiple encode enzymes for anaerobic oxidation aliphatic aromatic compounds, including those candidate phyla Aerophobetes, Aminicenantes, TA06 Bathyarchaeota. Microbial interactions are predicted to be driven by acetate molecular hydrogen. These findings supported geochemistry, metabolomics, thermodynamic modelling. Overall, infer deep-sea sediments experiencing thermogenic hydrocarbon inputs harbor phylogenetically functionally potentially sustained through hydrocarbon, hydrogen metabolism.

Language: Английский

Citations

154
Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes DOI Creative Commons
Laura Eme, Daniel Tamarit, Eva Caceres

et al.

Nature, Journal Year: 2023, Volume and Issue: 618(7967), P. 992 - 999

Published: June 14, 2023

Abstract In the ongoing debates about eukaryogenesis—the series of evolutionary events leading to emergence eukaryotic cell from prokaryotic ancestors—members Asgard archaea play a key part as closest archaeal relatives eukaryotes 1 . However, nature and phylogenetic identity last common ancestor remain unresolved 2–4 Here we analyse distinct marker datasets an expanded genomic sampling evaluate competing scenarios using state-of-the-art phylogenomic approaches. We find that are placed, with high confidence, well-nested clade within sister lineage Hodarchaeales, newly proposed order Heimdallarchaeia. Using sophisticated gene tree species reconciliation approaches, show analogous evolution genomes, genome in involved significantly more duplication fewer loss compared other archaea. Finally, infer was probably thermophilic chemolithotroph which evolved adapted mesophilic conditions acquired genetic potential support heterotrophic lifestyle. Our work provides insights into prokaryote-to-eukaryote transition platform for better understanding cellular complexity cells.

Language: Английский

Citations

128
Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups DOI Open Access
Marguerite V. Langwig, Valerie De Anda, Nina Dombrowski

et al.

The ISME Journal, Journal Year: 2021, Volume and Issue: 16(1), P. 307 - 320

Published: July 30, 2021

Language: Английский

Citations

114