4.6 Article

Evidence for non-methanogenic metabolisms in globally distributed archaeal clades basal to the Methanomassiliicoccales

Related references

Note: Only part of the references are listed.
Article Biochemical Research Methods

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

Pierre-Alain Chaumeil et al.

BIOINFORMATICS (2020)

Article Biotechnology & Applied Microbiology

A complete domain-to-species taxonomy for Bacteria and Archaea

Donovan H. Parks et al.

NATURE BIOTECHNOLOGY (2020)

Article Biotechnology & Applied Microbiology

The importance of designating type material for uncultured taxa

Maria Chuvochina et al.

SYSTEMATIC AND APPLIED MICROBIOLOGY (2019)

Article Multidisciplinary Sciences

Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens

Bojk A. Berghuis et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Microbiology

Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea

Guillaume Borrel et al.

NATURE MICROBIOLOGY (2019)

Article Multidisciplinary Sciences

Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea

Zheng-Shuang Hua et al.

NATURE COMMUNICATIONS (2019)

Review Microbiology

An evolving view of methane metabolism in the Archaea

Paul N. Evans et al.

NATURE REVIEWS MICROBIOLOGY (2019)

Article Ecology

Methanotrophy across a natural permafrost thaw environment

Caitlin M. Singleton et al.

ISME JOURNAL (2018)

Article Multidisciplinary Sciences

Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis

Alexander Crits-Christoph et al.

NATURE (2018)

Article Ecology

Horizontal gene transfer constrains the timing of methanogen evolution

Joanna M. Wolfe et al.

NATURE ECOLOGY & EVOLUTION (2018)

Article Multidisciplinary Sciences

Genome-centric view of carbon processing in thawing permafrost

Ben J. Woodcroft et al.

NATURE (2018)

Article Biotechnology & Applied Microbiology

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

Donovan H. Parks et al.

NATURE BIOTECHNOLOGY (2018)

Letter Ecology

Reply to 'Molecular clocks provide little information to date methanogenic Archaea'

Joanna M. Wolfe et al.

NATURE ECOLOGY & EVOLUTION (2018)

Letter Ecology

Molecular clocks provide little information to date methanogenic Archaea

Andrew J. Roger et al.

NATURE ECOLOGY & EVOLUTION (2018)

Article Ecology

Uncultivated microbes in need of their own taxonomy

Konstantinos T. Konstantinidis et al.

ISME JOURNAL (2017)

Article Biotechnology & Applied Microbiology

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Robert M. Bowers et al.

NATURE BIOTECHNOLOGY (2017)

Article Astronomy & Astrophysics

Methane: Fuel or Exhaust at the Emergence of Life?

Michael J. Russell et al.

ASTROBIOLOGY (2017)

Article Evolutionary Biology

Methanogenesis and the Wood-Ljungdahl Pathway: An Ancient, Versatile, and Fragile Association

Guillaume Borrel et al.

GENOME BIOLOGY AND EVOLUTION (2016)

Review Biochemistry & Molecular Biology

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

Minoru Kanehisa et al.

JOURNAL OF MOLECULAR BIOLOGY (2016)

Article Multidisciplinary Sciences

Thermophilic archaea activate butane via alkyl-coenzyme M formation

Rafael Laso-Perez et al.

NATURE (2016)

Article Biochemistry & Molecular Biology

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

Ivica Letunic et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Multidisciplinary Sciences

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

Karthik Anantharaman et al.

NATURE COMMUNICATIONS (2016)

Article Microbiology

Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota

Inka Vanwonterghem et al.

NATURE MICROBIOLOGY (2016)

Article Microbiology

A new view of the tree of life

Laura A. Hug et al.

NATURE MICROBIOLOGY (2016)

Article Biochemistry & Molecular Biology

Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling

Cindy J. Castelle et al.

CURRENT BIOLOGY (2015)

Article Biochemistry & Molecular Biology

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

Donovan H. Parks et al.

GENOME RESEARCH (2015)

Article Multidisciplinary Sciences

Unusual biology across a group comprising more than 15% of domain Bacteria

Christopher T. Brown et al.

NATURE (2015)

Review Multidisciplinary Sciences

Microbiomes in light of traits: A phylogenetic perspective

Jennifer B. H. Martiny et al.

SCIENCE (2015)

Article Biotechnology & Applied Microbiology

New Mode of Energy Metabolism in the Seventh Order of Methanogens as Revealed by Comparative Genome Analysis of Candidatus Methanoplasma termitum

Kristina Lang et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2015)

Article Biochemical Research Methods

Prokka: rapid prokaryotic genome annotation

Torsten Seemann

BIOINFORMATICS (2014)

Article Biochemical Research Methods

InterProScan 5: genome-scale protein function classification

Philip Jones et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

Alexandros Stamatakis

BIOINFORMATICS (2014)

Article Biochemistry & Molecular Biology

The SILVA and All-species Living Tree Project (LTP) taxonomic frameworks

Pelin Yilmaz et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Multidisciplinary Sciences

A nonpyrrolysine member of the widely distributed trimethylamine methyltransferase family is a glycine betaine methyltransferase

Tomislav Ticak et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Multidisciplinary Sciences

Discovery of a novel methanogen prevalent in thawing permafrost

Rhiannon Mondav et al.

NATURE COMMUNICATIONS (2014)

Article Biochemistry & Molecular Biology

Characterization of the Type III sulfide:quinone oxidoreductase from Caldivirga maquilingensis and its membrane binding

Andrea M. Lencina et al.

BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS (2013)

Article Energy & Fuels

Investigation of coal-associated bacterial and archaeal populations from a diffusive microbial sampler (DMS)

Elliott P. Barnhart et al.

INTERNATIONAL JOURNAL OF COAL GEOLOGY (2013)

Article Multidisciplinary Sciences

Predominant archaea in marine sediments degrade detrital proteins

Karen G. Lloyd et al.

NATURE (2013)

Article Biochemistry & Molecular Biology

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

Christian Quast et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Multidisciplinary Sciences

Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment

Cindy J. Castelle et al.

NATURE COMMUNICATIONS (2013)

Article Biochemical Research Methods

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

Elmar Pruesse et al.

BIOINFORMATICS (2012)

Article Biology

ggplot2: Elegant Graphics for Data Analysis by WICKHAM, H.

Leland Wilkinson

BIOMETRICS (2011)

Article Biochemical Research Methods

Accelerated Profile HMM Searches

Sean R. Eddy

PLOS COMPUTATIONAL BIOLOGY (2011)

Article Microbiology

A comparative genomic analysis of energy metabolism in sulfate reducing bacteria and archaea

Ines A. Cardoso Pereira et al.

FRONTIERS IN MICROBIOLOGY (2011)

Article Biochemical Research Methods

Prodigal: prokaryotic gene recognition and translation initiation site identification

Doug Hyatt et al.

BMC BIOINFORMATICS (2010)

Article Multidisciplinary Sciences

FastTree 2-Approximately Maximum-Likelihood Trees for Large Alignments

Morgan N. Price et al.

PLOS ONE (2010)

Review Microbiology

Selenocysteine, Pyrrolysine, and the Unique Energy Metabolism of Methanogenic Archaea

Michael Rother et al.

ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL (2010)

Article Biochemistry & Molecular Biology

Structural and Functional Insights into Sulfide:Quinone Oxidoreductase

Jose A. Brito et al.

BIOCHEMISTRY (2009)

Article Biochemical Research Methods

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

Salvador Capella-Gutierrez et al.

BIOINFORMATICS (2009)

Article Biochemistry & Molecular Biology

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

Morgan N. Price et al.

MOLECULAR BIOLOGY AND EVOLUTION (2009)

Article Biochemistry & Molecular Biology

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

J. R. Cole et al.

NUCLEIC ACIDS RESEARCH (2009)

Review Biochemistry & Molecular Biology

Acetogenesis and the Wood-Ljungdahl pathway of CO2 fixation

Stephen W. Ragsdale et al.

BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS (2008)

Article Biochemistry & Molecular Biology

SILVA:: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB

Elmar Pruesse et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Biotechnology & Applied Microbiology

Molecular analysis of the diversity of sulfate-reducing and sulfur-oxidizing prokaryotes in the environment, using aprA as functional marker gene

Birte Meyer et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2007)

Article Biotechnology & Applied Microbiology

Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy

Qiong Wang et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2007)

Article Biochemistry & Molecular Biology

Haloarcula marismortui cytochrome b-561 is encoded by the narC gene in the dissimilatory nitrate reductase operon

Katsuhiko Yoshimatsu et al.

EXTREMOPHILES (2007)

Article Multidisciplinary Sciences

Loss of the mtr operon in Methanosarcina blocks growth on methanol, but not methanogenesis, and reveals an unknown methanogenic pathway

PV Welander et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Biochemistry & Molecular Biology

Two distinct heterodisulfide reductase-like enzymes in the sulfate-reducing archaeon Archaeoglobus profundus

GJ Mander et al.

EUROPEAN JOURNAL OF BIOCHEMISTRY (2004)

Article Biochemical Research Methods

MUSCLE: a multiple sequence alignment method with reduced time and space complexity

RC Edgar

BMC BIOINFORMATICS (2004)

Article Multidisciplinary Sciences

A simple energy-conserving system: Proton reduction coupled to proton translocation

R Sapra et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)