Genomic Insights of “Candidatus Nitrosocaldaceae” Based on Nine New Metagenome-Assembled Genomes, Including “Candidatus Nitrosothermus” Gen Nov. and Two New Species of “Candidatus Nitrosocaldus”

Genome wide transcriptomic analysis of the soil ammonia oxidizing archaeon Nitrososphaera viennensis upon exposure to copper limitation

(2020) Carolina Reyes et al.   ISME Journal

Phylogenomics suggests oxygen availability as a driving force in Thaumarchaeota evolution

(2019) Minglei Ren et al.   ISME Journal

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Accumulation of NO2 -cobalamin in nutrient-stressed ammonia-oxidizing archaea and in the oxygen deficient zone of the Eastern Tropical North Pacific

(2018) Katherine R. Heal et al.   Environmental Microbiology Reports

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

(2018) Ricardo J. Eloy Alves 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

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

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

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

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

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

Uncultivated microbes in need of their own taxonomy

(2017) Konstantinos T Konstantinidis et al.   ISME Journal

Thioredoxin A Is Essential for Motility and Contributes to Host Infection of Listeria monocytogenes via Redox Interactions

(2017) Changyong Cheng et al.   Frontiers in Cellular and Infection Microbiology

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens

(2016) Leighton Pritchard et al.   Analytical Methods

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

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

A single electrochemical biosensor for detecting the activity and inhibition of both protein kinase and alkaline phosphatase based on phosphate ions induced deposition of redox precipitates

(2016) Congcong Shen et al.   BIOSENSORS & BIOELECTRONICS

Highly diverse nirK genes comprise two major clades that harbour ammonium-producing denitrifiers

(2016) Decleyre Helen et al.   BMC GENOMICS

Cyanobacteria and Eukaryotic Algae Use Different Chemical Variants of Vitamin B12

(2016) Katherine Emma Helliwell et al.   CURRENT BIOLOGY

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

(2016) Jessica A Kozlowski et al.   ISME Journal

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa 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

Novel viral genomes identified from six metagenomes reveal wide distribution of archaeal viruses and high viral diversity in terrestrial hot springs

(2015) Sóley Ruth Gudbergsdóttir et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

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

Characterization of thel-alanine exporter AlaE ofEscherichia coliand its potential role in protecting cells from a toxic-level accumulation ofl-alanine and its derivatives

(2015) Seryoung Kim et al.   MicrobiologyOpen

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers

(2014) Qiyun Zhu et al.   BMC GENOMICS

Characterisation of terrestrial acidophilic archaeal ammonia oxidisers and their inhibition and stimulation by organic compounds

(2014) Laura E. Lehtovirta-Morley et al.   FEMS MICROBIOLOGY ECOLOGY

Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics

(2014) Zheng-Shuang Hua et al.   ISME Journal

Aquatic metagenomes implicate Thaumarchaeota in global cobalamin production

(2014) Andrew C Doxey et al.   ISME Journal

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

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

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

The Wonderful World of Archaeal Viruses

(2013) David Prangishvili   Annual Review of Microbiology

Competition for Ammonia Influences the Structure of Chemotrophic Communities in Geothermal Springs

(2013) Trinity L. Hamilton et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Emerging concepts in the flavinylation of succinate dehydrogenase

(2013) Hyung J. Kim et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

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

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

A Comprehensive Census of Microbial Diversity in Hot Springs of Tengchong, Yunnan Province China Using 16S rRNA Gene Pyrosequencing

(2013) Weiguo Hou et al.   PLoS One

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

(2013) Nicola Segata et al.   Nature Communications

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

(2012) Anja Spang et al.   ENVIRONMENTAL MICROBIOLOGY

Calculation of total free energy yield as an alternative approach for predicting the importance of potential chemolithotrophic reactions in geothermal springs

(2012) Jeremy A. Dodsworth et al.   FEMS MICROBIOLOGY ECOLOGY

Vitamin B12 Synthesis and Salvage Pathways Were Acquired by Horizontal Gene Transfer to the Thermotogales

(2012) Kristen S. Swithers et al.   Genome Biology and Evolution

The Divergent AmoC3 Subunit of Ammonia Monooxygenase Functions as Part of a Stress Response System in Nitrosomonas europaea

(2012) P. M. Berube et al.   JOURNAL OF BACTERIOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Differences in lateral gene transfer in hypersaline versus thermal environments

(2011) Matthew E Rhodes et al.   BMC EVOLUTIONARY BIOLOGY

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

Ammonium in thermal waters of Yellowstone National Park: Processes affecting speciation and isotope fractionation

(2011) JoAnn M. Holloway et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Genome of a Low-Salinity Ammonia-Oxidizing Archaeon Determined by Single-Cell and Metagenomic Analysis

(2011) Paul C. Blainey et al.   PLoS One

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

A review of the microbiology of the Rehai geothermal field in Tengchong, Yunnan Province, China

(2011) Brian P. Hedlund et al.   Geoscience Frontiers

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

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

(2010) Anja Spang et al.   TRENDS IN MICROBIOLOGY

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

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

Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization

(2009) Yan Zhang et al.   BMC GENOMICS

Polyamine Accumulation in Transgenic Tomato Enhances the Tolerance to High Temperature Stress

(2009) Lin Cheng et al.   Journal of Integrative Plant Biology

Global Occurrence of Archaeal amoA Genes in Terrestrial Hot Springs

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

Transport pathways for arsenic and selenium: A minireview

(2008) Barry P. Rosen et al.   ENVIRONMENT INTERNATIONAL

Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol

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

Nitrification in terrestrial hot springs of Iceland and Kamchatka

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