Phylogenomics suggests oxygen availability as a driving force in Thaumarchaeota evolution

Patterns of thaumarchaeal gene expression in culture and diverse marine environments

(2018) Paul Carini et al.   ENVIRONMENTAL MICROBIOLOGY

Metabolic potential and in situ transcriptomic profiles of previously uncharacterized key microbial groups involved in coupled carbon, nitrogen and sulfur cycling in anoxic marine zones

(2018) Alvaro M. Plominsky et al.   ENVIRONMENTAL MICROBIOLOGY

Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes

(2018) Ricardo J. Eloy Alves et al.   Nature Communications

Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota

(2018) Zheng-Shuang Hua et al.   Nature Communications

Candidatus Nitrosocaldus cavascurensis, an Ammonia Oxidizing, Extremely Thermophilic Archaeon with a Highly Mobile Genome

(2018) Sophie S. Abby et al.   Frontiers in Microbiology

Cultivation and Genomic Analysis of “Candidatus Nitrosocaldus islandicus,” an Obligately Thermophilic, Ammonia-Oxidizing Thaumarchaeon from a Hot Spring Biofilm in Graendalur Valley, Iceland

(2018) Anne Daebeler et al.   Frontiers in Microbiology

Role of the Extremolytes Ectoine and Hydroxyectoine as Stress Protectants and Nutrients: Genetics, Phylogenomics, Biochemistry, and Structural Analysis

(2018) Laura Czech et al.   Genes

Horizontal gene transfer constrains the timing of methanogen evolution

(2018) Joanna M. Wolfe et al.   Nature Ecology & Evolution

The Thaumarchaeon N. gargensis carries functional bioABD genes and has a promiscuous E. coli ΔbioH-complementing esterase EstN1

(2018) Jennifer Chow et al.   Scientific Reports

Integrated genomic and fossil evidence illuminates life’s early evolution and eukaryote origin

(2018) Holly C. Betts et al.   Nature Ecology & Evolution

Genome and epigenome of a novel marine Thaumarchaeota strain suggest viral infection, phosphorothioation DNA modification and multiple restriction systems

(2017) Nathan A. Ahlgren et al.   ENVIRONMENTAL MICROBIOLOGY

Nitrosopumilus maritimus gen. nov., sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., four marine ammonia-oxidizing archaea of the phylum Thaumarchaeota

(2017) Wei Qin et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

The growing tree of Archaea: new perspectives on their diversity, evolution and ecology

(2017) Panagiotis S Adam et al.   ISME Journal

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

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

Integrative modeling of gene and genome evolution roots the archaeal tree of life

(2017) Tom A. Williams et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Influence of oxygen availability on the activities of ammonia-oxidizing archaea

(2017) Wei Qin et al.   Environmental Microbiology Reports

Strangers in the archaeal world: osmostress-responsive biosynthesis of ectoine and hydroxyectoine by the marine thaumarchaeonNitrosopumilus maritimus

(2016) Nils Widderich et al.   ENVIRONMENTAL MICROBIOLOGY

Genomic evidence for distinct carbon substrate preferences and ecological niches of Bathyarchaeota in estuarine sediments

(2016) Cassandre Sara Lazar et al.   ENVIRONMENTAL MICROBIOLOGY

Oceanic oxygenation events in the anoxic Ediacaran ocean

(2016) S. K. Sahoo et al.   Geobiology

Consequences of Secondary Calibrations on Divergence Time Estimates

(2016) John J. Schenk   PLoS One

Two distinct pools of B12analogs reveal community interdependencies in the ocean

(2016) Katherine R. Heal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A hydrophobic ammonia-oxidizing archaeon of theNitrosocosmicusclade isolated from coal tar-contaminated sediment

(2016) Man-Young Jung et al.   Environmental Microbiology Reports

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

(2016) Karthik Anantharaman et al.   Nature Communications

A catalogue of 136 microbial draft genomes from Red Sea metagenomes

(2016) Mohamed F. Haroon et al.   Scientific Data

Genomic and enzymatic evidence for acetogenesis among multiple lineages of the archaeal phylum Bathyarchaeota widespread in marine sediments

(2016) Y. He et al.   Nature Microbiology

Rapid oxygenation of Earths atmosphere 2.33 billion years ago

(2016) G. Luo et al.   Science Advances

Metabolic potential of fatty acid oxidation and anaerobic respiration by abundant members of Thaumarchaeota and Thermoplasmata in deep anoxic peat

(2015) Xueju Lin et al.   ISME Journal

Physiological and genomic characterization of two novel marine thaumarchaeal strains indicates niche differentiation

(2015) Barbara Bayer et al.   ISME Journal

Ecophysiology of an uncultivated lineage of Aigarchaeota from an oxic, hot spring filamentous ‘streamer’ community

(2015) Jacob P Beam et al.   ISME Journal

Bacterial gene import and mesophilic adaptation in archaea

(2015) Purificación López-García et al.   NATURE REVIEWS MICROBIOLOGY

Genomic and proteomic characterization of “CandidatusNitrosopelagicus brevis”: An ammonia-oxidizing archaeon from the open ocean

(2015) Alyson E. Santoro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The two-domain tree of life is linked to a new root for the Archaea

(2015) Kasie Raymann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics

(2015) P. N. Evans et al.   SCIENCE

NADPH-generating systems in bacteria and archaea

(2015) Sebastiaan K. Spaans et al.   Frontiers in Microbiology

Pangenome Evidence for Extensive Interdomain Horizontal Transfer Affecting Lineage Core and Shell Genes in Uncultured Planktonic Thaumarchaeota and Euryarchaeota

(2014) Philippe Deschamps et al.   Genome Biology and Evolution

Rooting the Domain Archaea by Phylogenomic Analysis Supports the Foundation of the New Kingdom Proteoarchaeota

(2014) Céline Petitjean et al.   Genome Biology and Evolution

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic and Metabolic Diversity of Marine Group I Thaumarchaeota in the Mesopelagic of Two Subtropical Gyres

(2014) Brandon K. Swan et al.   PLoS One

Genome Sequence of Candidatus Nitrososphaera evergladensis from Group I.1b Enriched from Everglades Soil Reveals Novel Genomic Features of the Ammonia-Oxidizing Archaea

(2014) Kateryna V. Zhalnina et al.   PLoS One

Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO2 fixation

(2014) M. Konneke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Low Mid-Proterozoic atmospheric oxygen levels and the delayed rise of animals

(2014) N. J. Planavsky et al.   SCIENCE

Single-cell genomics shedding light on marine Thaumarchaeota diversification

(2013) Haiwei Luo et al.   ISME Journal

Niche specialization of novel Thaumarchaeota to oxic and hypoxic acidic geothermal springs of Yellowstone National Park

(2013) Jacob P Beam et al.   ISME Journal

DNA Protection by the Bacterial Ferritin Dps via DNA Charge Transport

(2013) Anna R. Arnold et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Predominant archaea in marine sediments degrade detrital proteins

(2013) Karen G. Lloyd et al.   NATURE

Hydroxylamine as an intermediate in ammonia oxidation by globally abundant marine archaea

(2013) N. Vajrala et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Physiology and Diversity of Ammonia-Oxidizing Archaea

(2012) David A. Stahl et al.   Annual Review of Microbiology

Dps biomineralizing proteins: multifunctional architects of nature

(2012) Kornelius Zeth   BIOCHEMICAL JOURNAL

Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer

(2012) Yuri I Wolf et al.   Biology Direct

Horizontal gene transfer of a chloroplast DnaJ-Fer protein to Thaumarchaeota and the evolutionary history of the DnaK chaperone system in Archaea

(2012) Céline Petitjean et al.   BMC EVOLUTIONARY BIOLOGY

The genome of the ammonia-oxidizingCandidatusNitrososphaera gargensis: insights into metabolic versatility and environmental adaptations

(2012) Anja Spang et al.   ENVIRONMENTAL MICROBIOLOGY

Spotlight on the Thaumarchaeota

(2011) C Brochier-Armanet et al.   ISME Journal

Complete-fosmid and fosmid-end sequences reveal frequent horizontal gene transfers in marine uncultured planktonic archaea

(2011) Céline Brochier-Armanet et al.   ISME Journal

An Expansion of Age Constraints for Microbial Clades that Lack a Conventional Fossil Record Using Phylogenomic Dating

(2011) Carrine E. Blank   JOURNAL OF MOLECULAR EVOLUTION

Adaptation to Environmental Temperature Is a Major Determinant of Molecular Evolutionary Rates in Archaea

(2011) M. Groussin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil

(2011) M. Tourna et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Best Practices for Justifying Fossil Calibrations

(2011) James F. Parham et al.   SYSTEMATIC BIOLOGY

Depth distributions of alkaline phosphatase and phosphonate utilization genes in the North Pacific Subtropical Gyre

(2010) H Luo et al.   AQUATIC MICROBIAL ECOLOGY

Mechanisms of the Hsp70 chaperone systemThis paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal's usual peer review process.

(2010) Jason C. Young   Biochemistry and Cell Biology

Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea

(2010) C. B. Walker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenomic Dating—A Method of Constraining the Age of Microbial Taxa That Lack a Conventional Fossil Record

(2009) Carrine E. Blank   ASTROBIOLOGY

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

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Extending the models for iron and sulfur oxidation in the extreme Acidophile Acidithiobacillus ferrooxidans

(2009) Raquel Quatrini et al.   BMC GENOMICS

Not so old Archaea - the antiquity of biogeochemical processes in the archaeal domain of life

(2009) CARRINE E. BLANK   Geobiology

Structural and functional diversity of ferredoxin-NADP+ reductases

(2008) Alessandro Aliverti et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring

(2008) R. Hatzenpichler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The crystal structure of the protein YhaK fromEscherichia colireveals a new subclass of redox sensitive enterobacterial bicupins

(2008) Daniel Gurmu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS