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

Novel Families of Archaeo-Eukaryotic Primases Associated with Mobile Genetic Elements of Bacteria and Archaea

(2018) Darius Kazlauskas et al.   JOURNAL OF MOLECULAR BIOLOGY

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

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

(2017) Panagiotis S Adam et al.   ISME Journal

The enigmatic archaeal virosphere

(2017) David Prangishvili et al.   NATURE REVIEWS MICROBIOLOGY

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

Nitric oxide is an obligate bacterial nitrification intermediate produced by hydroxylamine oxidoreductase

(2017) Jonathan D. Caranto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification and characterization of a heterotrimeric archaeal DNA polymerase holoenzyme

(2017) Jiangyu Yan et al.   Nature Communications

Nitrogen and Oxygen Isotope Effects of Ammonia Oxidation by Thermophilic Thaumarchaeota from a Geothermal Water Stream

(2016) Manabu Nishizawa et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Pathways and key intermediates required for obligate aerobic ammonia-dependent chemolithotrophy in bacteria and Thaumarchaeota

(2016) Jessica A Kozlowski et al.   ISME Journal

MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes

(2016) David Vallenet et al.   NUCLEIC ACIDS RESEARCH

Proteomics and comparative genomics ofNitrososphaera viennensisreveal the core genome and adaptations of archaeal ammonia oxidizers

(2016) Melina Kerou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hydrogen peroxide detoxification is a key mechanism for growth of ammonia-oxidizing archaea

(2016) Jong-Geol Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparison of Nitrogen Oxide Metabolism among Diverse Ammonia-Oxidizing Bacteria

(2016) Jessica A. Kozlowski et al.   Frontiers in Microbiology

Diversity and Evolution of Type IV pili Systems in Archaea

(2016) Kira S. Makarova et al.   Frontiers in Microbiology

HydDB: A web tool for hydrogenase classification and analysis

(2016) Dan Søndergaard et al.   Scientific Reports

Integrative and Conjugative Elements (ICEs): What They Do and How They Work

(2015) Christopher M. Johnson et al.   Annual Review of Genetics

[FeFe]- and [NiFe]-hydrogenase diversity, mechanism, and maturation

(2015) John W. Peters et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

DNA repair in hyperthermophilic and hyperradioresistant microorganisms

(2015) Yoshizumi Ishino et al.   CURRENT OPINION IN MICROBIOLOGY

The production of nitric oxide by marine ammonia-oxidizing archaea and inhibition of archaeal ammonia oxidation by a nitric oxide scavenger

(2015) Willm Martens-Habbena et al.   ENVIRONMENTAL MICROBIOLOGY

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

Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival

(2015) Chris Greening et al.   ISME Journal

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

The impact of temperature on microbial diversity and AOA activity in the Tengchong Geothermal Field, China

(2015) Haizhou Li et al.   Scientific Reports

Understanding DNA Repair in Hyperthermophilic Archaea: Persistent Gaps and Other Reasons to Focus on the Fork

(2015) Dennis W. Grogan   ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL

Malonic Semialdehyde Reductase from the Archaeon Nitrosopumilus maritimus Is Involved in the Autotrophic 3-Hydroxypropionate/4-Hydroxybutyrate Cycle

(2014) Julia Otte et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Base excision repair in Archaea: Back to the future in DNA repair

(2014) Stefano Grasso et al.   DNA REPAIR

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

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

Nitrososphaera viennensis gen. nov., sp. nov., an aerobic and mesophilic, ammonia-oxidizing archaeon from soil and a member of the archaeal phylum Thaumarchaeota

(2014) M. Stieglmeier et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

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

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

MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems

(2014) Sophie S. Abby 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

Marine ammonia-oxidizing archaeal isolates display obligate mixotrophy and wide ecotypic variation

(2014) W. Qin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pervasive domestication of defective prophages by bacteria

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

Variability of the transporter gene complement in ammonia-oxidizing archaea

(2014) Pierre Offre et al.   TRENDS IN MICROBIOLOGY

Evolution of replicative DNA polymerases in archaea and their contributions to the eukaryotic replication machinery

(2014) Kira S. Makarova et al.   Frontiers in Microbiology

Ori-Finder 2, an integrated tool to predict replication origins in the archaeal genomes

(2014) Hao Luo et al.   Frontiers in Microbiology

Archaea in Biogeochemical Cycles

(2013) Pierre Offre et al.   Annual Review of Microbiology

How hyperthermophiles adapt to change their lives: DNA exchange in extreme conditions

(2013) Marleen van Wolferen et al.   EXTREMOPHILES

Responses of the terrestrial ammonia-oxidizing archaeonCa. Nitrososphaera viennensis and the ammonia-oxidizing bacteriumNitrosospira multiformisto nitrification inhibitors

(2013) Tianlin Shen et al.   FEMS MICROBIOLOGY LETTERS

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

(2013) Jacob P Beam et al.   ISME Journal

Nitrification rates in Arctic soils are associated with functionally distinct populations of ammonia-oxidizing archaea

(2013) Ricardo J Eloy Alves et al.   ISME Journal

Archaeal DNA Polymerase D but Not DNA Polymerase B Is Required for Genome Replication in Thermococcus kodakarensis

(2013) L. Cubonova et al.   JOURNAL OF BACTERIOLOGY

Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products

(2013) Sergey Nurk et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

The Transporter Classification Database

(2013) Milton H. Saier et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

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

Metagenomics of Kamchatkan hot spring filaments reveal two new major (hyper)thermophilic lineages related to Thaumarchaeota

(2013) Laura Eme et al.   RESEARCH IN MICROBIOLOGY

TheNitrosopumilus maritimusCdvB, but Not FtsZ, Assembles into Polymers

(2013) Kian-Hong Ng et al.   ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL

Physiology and Diversity of Ammonia-Oxidizing Archaea

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

Diversity, Physiology, and Niche Differentiation of Ammonia-Oxidizing Archaea

(2012) Roland Hatzenpichler   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Diversity and evolution of bioenergetic systems involved in microbial nitrogen compound transformations

(2012) Jörg Simon et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

High-quality sequence clustering guided by network topology and multiple alignment likelihood

(2012) Vincent Miele et al.   BIOINFORMATICS

Unipro UGENE: a unified bioinformatics toolkit

(2012) Konstantin Okonechnikov et al.   BIOINFORMATICS

Structure and function of the adhesive type IV pilus ofSulfolobus acidocaldarius

(2012) Anna-Lena Henche et al.   ENVIRONMENTAL MICROBIOLOGY

Mimicking the oxygen minimum zones: stimulating interaction of aerobic archaeal and anaerobic bacterial ammonia oxidizers in a laboratory-scale model system

(2012) Jia Yan et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2012) Anja Spang et al.   ENVIRONMENTAL MICROBIOLOGY

Sediment microbial communities in Great Boiling Spring are controlled by temperature and distinct from water communities

(2012) Jessica K Cole et al.   ISME Journal

Draft Genome Sequence of an Ammonia-Oxidizing Archaeon, "Candidatus Nitrosopumilus sediminis" AR2, from Svalbard in the Arctic Circle

(2012) S.-J. Park et al.   JOURNAL OF BACTERIOLOGY

A thaumarchaeal provirus testifies for an ancient association of tailed viruses with archaea

(2011) Mart Krupovic et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Ultra-fast sequence clustering from similarity networks with SiLiX

(2011) Vincent Miele et al.   BMC BIOINFORMATICS

The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology

(2011) Michael Pester et al.   CURRENT OPINION IN MICROBIOLOGY

Ammonia oxidation, denitrification and dissimilatory nitrate reduction to ammonium in two US Great Basin hot springs with abundant ammonia-oxidizing archaea

(2011) Jeremy A. Dodsworth et al.   ENVIRONMENTAL MICROBIOLOGY

Spotlight on the Thaumarchaeota

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

Distinct Physiological Roles of the Three [NiFe]-Hydrogenase Orthologs in the Hyperthermophilic Archaeon Thermococcus kodakarensis

(2011) T. Kanai et al.   JOURNAL OF BACTERIOLOGY

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

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

Molecular and Structural Basis of ESCRT-III Recruitment to Membranes during Archaeal Cell Division

(2011) Rachel Y. Samson et al.   MOLECULAR CELL

Cdv-based cell division and cell cycle organization in the thaumarchaeon Nitrosopumilus maritimus

(2011) Erik A. Pelve et al.   MOLECULAR MICROBIOLOGY

Thaumarchaeotes abundant in refinery nitrifying sludges express amoA but are not obligate autotrophic ammonia oxidizers

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

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

Synthesis, Production, and Biotechnological Applications of Exopolysaccharides and Polyhydroxyalkanoates by Archaea

(2011) Annarita Poli et al.   ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

RNA-Based Investigation of Ammonia-Oxidizing Archaea in Hot Springs of Yunnan Province, China

(2010) H. Jiang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

ScripTree: scripting phylogenetic graphics

(2010) François Chevenet et al.   BIOINFORMATICS

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

(2010) Alexis Criscuolo et al.   BMC EVOLUTIONARY BIOLOGY

Homologues of nitrite reductases in ammonia-oxidizing archaea: diversity and genomic context

(2010) Rita Bartossek et al.   ENVIRONMENTAL MICROBIOLOGY

Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean

(2010) Yanmei Shi et al.   ISME Journal

Haloferax volcanii Flagella Are Required for Motility but Are Not Involved in PibD-Dependent Surface Adhesion

(2010) M. Tripepi et al.   JOURNAL OF BACTERIOLOGY

Identification of Missing Genes and Enzymes for Autotrophic Carbon Fixation in Crenarchaeota

(2010) W. H. Ramos-Vera et al.   JOURNAL OF BACTERIOLOGY

Comparative Analysis of the Mosaic Genomes of Tailed Archaeal Viruses and Proviruses Suggests Common Themes for Virion Architecture and Assembly with Tailed Viruses of Bacteria

(2010) Mart Krupovič et al.   JOURNAL OF MOLECULAR BIOLOGY

UV-inducible cellular aggregation of the hyperthermophilic archaeon Sulfolobus solfataricus is mediated by pili formation

(2010) Sabrina Fröls et al.   MOLECULAR MICROBIOLOGY

Evolution of diverse cell division and vesicle formation systems in Archaea

(2010) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group

(2010) Takuro Nunoura et al.   NUCLEIC ACIDS RESEARCH

The evolution and mechanisms of nucleotide excision repair proteins

(2010) Christophe Rouillon et al.   RESEARCH IN MICROBIOLOGY

Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota

(2010) Anja Spang et al.   TRENDS IN MICROBIOLOGY

Malonic Semialdehyde Reductase, Succinic Semialdehyde Reductase, and Succinyl-Coenzyme A Reductase from Metallosphaera sedula: Enzymes of the Autotrophic 3-Hydroxypropionate/4-Hydroxybutyrate Cycle in Sulfolobales

(2009) D. Kockelkorn et al.   JOURNAL OF BACTERIOLOGY

MicroScope: a platform for microbial genome annotation and comparative genomics

(2009) D. Vallenet et al.   Database-The Journal of Biological Databases and Curation

Global Occurrence of Archaeal amoA Genes in Terrestrial Hot Springs

(2008) C. L. Zhang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria

(2008) Graeme W. Nicol et al.   ENVIRONMENTAL MICROBIOLOGY

Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol

(2008) José R. de la Torre et al.   ENVIRONMENTAL MICROBIOLOGY

Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment

(2008) James I. Prosser et al.   ENVIRONMENTAL MICROBIOLOGY

Nitrification in terrestrial hot springs of Iceland and Kamchatka

(2008) Laila J. Reigstad et al.   FEMS MICROBIOLOGY ECOLOGY

Crenarchaeal Arginine Decarboxylase Evolved from anS-Adenosylmethionine Decarboxylase Enzyme

(2008) Teresa N. Giles et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota

(2008) Céline Brochier-Armanet et al.   NATURE REVIEWS MICROBIOLOGY