Genome-resolved metagenomics analysis provides insights into the ecological role of Thaumarchaeota in the Amazon River and its plume

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

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

Nitrosarchaeum koreense gen. nov., sp. nov., an aerobic and mesophilic, ammonia-oxidizing archaeon member of the phylum Thaumarchaeota isolated from agricultural soil

(2018) Man-Young Jung et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Insights into the physiology of ammonia-oxidizing microorganisms

(2018) Lisa Y Stein   CURRENT OPINION IN CHEMICAL BIOLOGY

Research trends and hotspots related to ammonia oxidation based on bibliometric analysis

(2017) Maosheng Zheng et al.   ENVIRONMENTAL SCIENCE AND POLLUTION 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

Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2concentrations

(2016) Alexander J. Probst et al.   ENVIRONMENTAL MICROBIOLOGY

Contribution of ammonia oxidation to chemoautotrophy in Antarctic coastal waters

(2016) Bradley B Tolar et al.   ISME Journal

IMG/M: integrated genome and metagenome comparative data analysis system

(2016) I-Min A. Chen 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

An extensive reef system at the Amazon River mouth

(2016) R. L. Moura et al.   Science Advances

Mixing and Transport in Coastal River Plumes

(2015) Alexander R. Horner-Devine et al.   Annual Review of Fluid Mechanics

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

Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota

(2015) Eduard Vico Oton et al.   ISME Journal

Microbial species delineation using whole genome sequences

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

The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

(2015) Marcel Huntemann et al.   Standards in Genomic Sciences

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

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

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

Aquatic metagenomes implicate Thaumarchaeota in global cobalamin production

(2014) Andrew C Doxey et al.   ISME Journal

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

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

Microspatial gene expression patterns in the Amazon River Plume

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

Areas of the global major river plumes

(2013) Yan Kang et al.   ACTA OCEANOLOGICA SINICA

Targeting spatiotemporal dynamics of planktonic SAGMGC-1 and segregation of ammonia-oxidizing thaumarchaeota ecotypes by newly designed primers and quantitative polymerase chain reaction

(2013) Claudia X. Restrepo-Ortiz et al.   ENVIRONMENTAL MICROBIOLOGY

Single-cell genomics shedding light on marine Thaumarchaeota diversification

(2013) Haiwei Luo et al.   ISME Journal

A review of allochthonous organic matter dynamics and metabolism in streams

(2013) Jennifer L. Tank et al.   JOURNAL OF THE NORTH AMERICAN BENTHOLOGICAL SOCIETY

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

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

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

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

Correction: Nuclear Survivin and Its Relationship to DNA Damage Repair Genes in Non-Small Cell Lung Cancer Investigated Using Tissue Array

(2013) Songliu Hu et al.   PLoS One

An Analysis of Thaumarchaeota Populations from the Northern Gulf of Mexico

(2013) Bradley B. Tolar et al.   Frontiers in Microbiology

Physiology and Diversity of Ammonia-Oxidizing Archaea

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

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Molecular analysis of methanogenic archaea in the forestomach of the alpaca (Vicugna pacos)

(2012) Benoit St-Pierre et al.   BMC MICROBIOLOGY

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

(2012) Anja Spang et al.   ENVIRONMENTAL MICROBIOLOGY

ArchaealamoA gene diversity points to distinct biogeography of ammonia-oxidizingCrenarchaeotain the ocean

(2012) Eva Sintes et al.   ENVIRONMENTAL MICROBIOLOGY

Seasonal and vertical distribution of putative ammonia-oxidizing thaumarchaeotal communities in an oligotrophic lake

(2012) Elisabeth W. Vissers et al.   FEMS MICROBIOLOGY ECOLOGY

Abrolhos Bank Reef Health Evaluated by Means of Water Quality, Microbial Diversity, Benthic Cover, and Fish Biomass Data

(2012) Thiago Bruce et al.   PLoS One

Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla

(2012) K. C. Wrighton et al.   SCIENCE

Spotlight on the Thaumarchaeota

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

Enrichment and characterization of ammonia-oxidizing archaea from the open ocean: phylogeny, physiology and stable isotope fractionation

(2011) Alyson E Santoro et al.   ISME Journal

Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil

(2011) L. E. Lehtovirta-Morley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Niche specialization of terrestrial archaeal ammonia oxidizers

(2011) C. Gubry-Rangin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diversity, abundance and distribution of amoA-encoding archaea in deep-sea methane seep sediments of the Okhotsk Sea

(2010) Hongyue Dang et al.   FEMS MICROBIOLOGY ECOLOGY

Archaea rather than bacteria control nitrification in two agricultural acidic soils

(2010) Cécile Gubry-Rangin et al.   FEMS MICROBIOLOGY ECOLOGY

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

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

(2010) Anja Spang et al.   TRENDS IN MICROBIOLOGY

Bacteriarather thanArchaeadominate microbial ammonia oxidation in an agricultural soil

(2009) Zhongjun Jia et al.   ENVIRONMENTAL MICROBIOLOGY

Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria

(2009) Willm Martens-Habbena et al.   NATURE

Laboratory procedures to generate viral metagenomes

(2009) Rebecca V Thurber et al.   Nature Protocols

The radiocarbon signature of microorganisms in the mesopelagic ocean

(2009) R. L. Hansman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conversion of NO2 to NO by reduced coenzyme F420 protects mycobacteria from nitrosative damage

(2009) E. Purwantini et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Shifting the genomic gold standard for the prokaryotic species definition

(2009) Michael Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Relative abundance and diversity of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary

(2008) Annika C. Mosier et al.   ENVIRONMENTAL MICROBIOLOGY

Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol

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

Abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea communities of an alkaline sandy loam

(2008) Ju-pei Shen et al.   ENVIRONMENTAL MICROBIOLOGY

Nitrification in terrestrial hot springs of Iceland and Kamchatka

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

Molecular and biogeochemical evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of California

(2008) J Michael Beman et al.   ISME Journal

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

Major gradients in putatively nitrifying and non-nitrifying Archaea in the deep North Atlantic

(2008) Hélène Agogué et al.   NATURE

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

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