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

Ammonia-oxidising archaea living at low pH: Insights from comparative genomics

(2017) Craig W. Herbold et al.   ENVIRONMENTAL MICROBIOLOGY

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

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

Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system

(2017) Laura A Sauder et al.   ISME Journal

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

Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life

(2017) Anja Spang et al.   SCIENCE

Elevational characteristics of the archaeal community in full-scale activated sludge wastewater treatment plants at a 3,660-meter elevational scale

(2017) Lihua Niu et al.   WATER SCIENCE AND TECHNOLOGY

Identification and characterization of a heterotrimeric archaeal DNA polymerase holoenzyme

(2017) Jiangyu Yan et al.   Nature Communications

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

AmoA-Targeted Polymerase Chain Reaction Primers for the Specific Detection and Quantification of Comammox Nitrospira in the Environment

(2017) Petra Pjevac et al.   Frontiers in Microbiology

Identifying Potential Mechanisms Enabling Acidophily in the Ammonia-Oxidizing Archaeon “Candidatus Nitrosotalea devanaterra”

(2016) Laura E. Lehtovirta-Morley et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences

(2016) Heng Li   BIOINFORMATICS

Biochemical characterization of translesion synthesis by Sulfolobus acidocaldarius DNA polymerases

(2016) Li Peng et al.   CHEMICAL RESEARCH IN CHINESE UNIVERSITIES

A structural phylogeny for understanding 2-oxoacid oxidoreductase function

(2016) Marcus I Gibson et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

(2016) Jessica A Kozlowski et al.   ISME Journal

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

IMNGS: A comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies

(2016) Ilias Lagkouvardos et al.   Scientific Reports

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

High Concentrations of the Antibiotic Spiramycin in Wastewater Lead to High Abundance of Ammonia-Oxidizing Archaea in Nitrifying Populations

(2015) Yu Zhang et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

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

(2015) Donovan H. Parks et al.   GENOME RESEARCH

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

The [NiFe]-Hydrogenase of Pyrococcus furiosus Exhibits a New Type of Oxygen Tolerance

(2015) Patrick Kwan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Cyanate as an energy source for nitrifiers

(2015) Marton Palatinszky et al.   NATURE

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

Bacterial gene import and mesophilic adaptation in archaea

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

Microbial species delineation using whole genome sequences

(2015) Neha J. Varghese et al.   NUCLEIC ACIDS RESEARCH

Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes

(2015) Jimmy H. Saw et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genusNitrospira

(2015) Hanna Koch 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

Chemoautotrophic growth of ammonia-oxidizing Thaumarchaeota enriched from a pelagic redox gradient in the Baltic Sea

(2015) Carlo Berg et al.   Frontiers in Microbiology

A Mesophilic, Autotrophic, Ammonia-Oxidizing Archaeon of Thaumarchaeal Group I.1a Cultivated from a Deep Oligotrophic Soil Horizon

(2014) Man-Young Jung et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

A Proposed Genus Boundary for the Prokaryotes Based on Genomic Insights

(2014) Q.-L. Qin et al.   JOURNAL OF BACTERIOLOGY

Genomes of Two New Ammonia-Oxidizing Archaea Enriched from Deep Marine Sediments

(2014) Soo-Je Park et al.   PLoS One

An obligately aerobic soil bacterium activates fermentative hydrogen production to survive reductive stress during hypoxia

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

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

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

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

Transferable Denitrification Capability of Thermus thermophilus

(2013) Laura Alvarez et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Linking isoprenoidal GDGT membrane lipid distributions with gene abundances of ammonia-oxidizingThaumarchaeotaand uncultured crenarchaeotal groups in the water column of a tropical lake (Lake Challa, East Africa)

(2013) Laura K. Buckles et al.   ENVIRONMENTAL MICROBIOLOGY

Elucidating the microbial resuscitation cascade in biological soil crusts following a simulated rain event

(2013) Roey Angel et al.   ENVIRONMENTAL MICROBIOLOGY

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

Nitrification-driven forms of nitrogen metabolism in microbial mat communities thriving along an ammonium-enriched subsurface geothermal stream

(2013) Manabu Nishizawa et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

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

(2013) Jacob P Beam 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

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Enrichment and Genome Sequence of the Group I.1a Ammonia-Oxidizing Archaeon “Ca. Nitrosotenuis uzonensis” Representing a Clade Globally Distributed in Thermal Habitats

(2013) Elena V. Lebedeva et al.   PLoS One

Physiology and Diversity of Ammonia-Oxidizing Archaea

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

Energy conservation via electron bifurcating ferredoxin reduction and proton/Na+ translocating ferredoxin oxidation

(2012) Wolfgang Buckel et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

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

(2012) Anja Spang et al.   ENVIRONMENTAL MICROBIOLOGY

Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi

(2012) Dimitry Y Sorokin et al.   ISME Journal

Genome Sequence of "Candidatus Nitrosoarchaeum limnia" BG20, a Low-Salinity Ammonia-Oxidizing Archaeon from the San Francisco Bay Estuary

(2012) A. C. Mosier et al.   JOURNAL OF BACTERIOLOGY

Indolepyruvate ferredoxin oxidoreductase: An oxygen-sensitive iron–sulfur enzyme from the hyperthermophilic archaeon Thermococcus profundus

(2012) Yukiko Ozawa et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data

(2012) David Vallenet et al.   NUCLEIC ACIDS RESEARCH

Archaeal and bacterial ammonia-oxidisers in soil: the quest for niche specialisation and differentiation

(2012) James I. Prosser et al.   TRENDS IN MICROBIOLOGY

Archaeal dominated ammonia-oxidizing communities in Icelandic grassland soils are moderately affected by long-term N fertilization and geothermal heating

(2012) Anne Daebeler et al.   Frontiers in Microbiology

Environmental factors determining ammonia-oxidizing organism distribution and diversity in marine environments

(2011) Nicholas J. Bouskill et al.   ENVIRONMENTAL 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

Ammonia-oxidizing Archaea in Kamchatka Hot Springs

(2011) Weidong Zhao et al.   GEOMICROBIOLOGY JOURNAL

Spotlight on the Thaumarchaeota

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

Heat Treatment Effects on the Antimicrobial Activity of Macrolide and Lincosamide Antibiotics in Milk

(2011) M. A. Zorraquino et al.   JOURNAL OF FOOD PROTECTION

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

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

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

The archaeal ‘TACK’ superphylum and the origin of eukaryotes

(2011) Lionel Guy et al.   TRENDS IN MICROBIOLOGY

Bacterial and archaeal amoA gene distribution covaries with soil nitrification properties across a range of land uses

(2011) Lydia H. Zeglin et al.   Environmental Microbiology Reports

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

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

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

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

(2010) Rita Bartossek et al.   ENVIRONMENTAL MICROBIOLOGY

High diversity of ammonia-oxidizing archaea in permanent and seasonal oxygen-deficient waters of the eastern South Pacific

(2010) Verónica Molina et al.   ENVIRONMENTAL MICROBIOLOGY

Structural and functional characterisation of the chlorite dismutase from the nitrite-oxidizing bacterium “Candidatus Nitrospira defluvii”: Identification of a catalytically important amino acid residue

(2010) Julius Kostan et al.   JOURNAL OF STRUCTURAL BIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

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

Diversity and Abundance of Ammonia-Oxidizing Archaea in Hydrothermal Vent Chimneys of the Juan de Fuca Ridge

(2009) S. Wang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

Archaeal ammonia oxidizers and nirS-type denitrifiers dominate sediment nitrifying and denitrifying populations in a subtropical macrotidal estuary

(2009) Guy C J Abell et al.   ISME Journal

The linkage between reverse gyrase and hyperthermophiles: A review of their invariable association

(2009) Michelle Heine et al.   JOURNAL OF MICROBIOLOGY

Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria

(2009) Willm Martens-Habbena et al.   NATURE

Global Occurrence of Archaeal amoA Genes in Terrestrial Hot Springs

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

Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol

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

Environmental genomics reveals a functional chlorite dismutase in the nitrite-oxidizing bacterium ‘CandidatusNitrospira defluvii’

(2008) Frank Maixner et al.   ENVIRONMENTAL MICROBIOLOGY

Growth, activity and temperature responses of ammonia-oxidizing archaea and bacteria in soil microcosms

(2008) Maria Tourna et al.   ENVIRONMENTAL MICROBIOLOGY

Nitrification in terrestrial hot springs of Iceland and Kamchatka

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

Physiological and phylogenetic characterization of a novel lithoautotrophic nitrite-oxidizing bacterium, 'Candidatus Nitrospira bockiana'

(2008) E. V. Lebedeva et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Evidence that Ammonia-Oxidizing Archaea are More Abundant than Ammonia-Oxidizing Bacteria in Semiarid Soils of Northern Arizona, USA

(2008) Karen L. Adair et al.   MICROBIAL ECOLOGY

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

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

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

Nitrile degradation by free and immobilized cells of the thermophile Bacillus sp. UG-5B, isolated from polluted industrial waters

(2008) Ludmila Kabaivanova et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY