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

A Multicopper Oxidase Is Required for Copper Resistance in Mycobacterium tuberculosis

(2013) J. L. Rowland et al.   JOURNAL OF BACTERIOLOGY

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

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

Ca. Nitrososphaera and Bradyrhizobium are inversely correlated and related to agricultural practices in long-term field experiments

(2013) Kateryna Zhalnina et al.   Frontiers in Microbiology

Physiology and Diversity of Ammonia-Oxidizing Archaea

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

Intact Polar and Core Glycerol Dibiphytanyl Glycerol Tetraether Lipids of Group I.1a and I.1b Thaumarchaeota in Soil

(2012) Jaap S. Sinninghe Damsté et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2012) Y. Peng et al.   BIOINFORMATICS

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

Cultivation of a highly enriched ammonia-oxidizing archaeon of thaumarchaeotal group I.1b from an agricultural soil

(2012) Jong-Geol Kim 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

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

Genome Sequence of "Candidatus Nitrosopumilus salaria" BD31, an Ammonia-Oxidizing Archaeon from the San Francisco Bay Estuary

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

Draft Genome Sequence of an Ammonia-Oxidizing Archaeon, "Candidatus Nitrosopumilus koreensis" AR1, from Marine Sediment

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

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

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

Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli

(2012) L. Fried et al.   JOURNAL OF BACTERIOLOGY

TIGRFAMs and Genome Properties in 2013

(2012) Daniel H. Haft et al.   NUCLEIC ACIDS RESEARCH

GenBank

(2012) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

The CopRS Two-Component System Is Responsible for Resistance to Copper in the Cyanobacterium Synechocystis sp. PCC 6803

(2012) J. Giner-Lamia et al.   PLANT PHYSIOLOGY

Marine archaea take a short cut in the nitrogen cycle

(2012) D. L. Kirchman   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Role for urea in nitrification by polar marine Archaea

(2012) L. Alonso-Saez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

F420-dependent enzymes – potential for applications in biotechnology

(2012) Matthew Taylor et al.   TRENDS IN BIOTECHNOLOGY

Drivers of archaeal ammonia-oxidizing communities in soil

(2012) Kateryna Zhalnina et al.   Frontiers in Microbiology

Enrichment and Characterization of an Autotrophic Ammonia-Oxidizing Archaeon of Mesophilic Crenarchaeal Group I.1a from an Agricultural Soil

(2011) Man-Young Jung et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Phylogeny and evolution of the Archaea: one hundred genomes later

(2011) Celine Brochier-Armanet et al.   CURRENT OPINION IN MICROBIOLOGY

amoA-based consensus phylogeny of ammonia-oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions

(2011) Michael Pester et al.   ENVIRONMENTAL MICROBIOLOGY

Ammonia-oxidizing archaea as main drivers of nitrification in cold-water sponges

(2011) Regina Radax et al.   ENVIRONMENTAL MICROBIOLOGY

Characterization of the Induction and Cellular Role of the BaeSR Two-Component Envelope Stress Response of Escherichia coli

(2011) S. K. D. Leblanc et al.   JOURNAL OF BACTERIOLOGY

morePhyML: Improving the phylogenetic tree space exploration with PhyML 3

(2011) Alexis Criscuolo   MOLECULAR PHYLOGENETICS AND EVOLUTION

A plastidial sodium-dependent pyruvate transporter

(2011) Tsuyoshi Furumoto et al.   NATURE

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

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

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

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

The dynamic roles of intracellular lipid droplets: from archaea to mammals

(2011) Denis J. Murphy   PROTOPLASMA

Isotopic Signature of N2O Produced by Marine Ammonia-Oxidizing Archaea

(2011) A. E. Santoro et al.   SCIENCE

Cultivation of Autotrophic Ammonia-Oxidizing Archaea from Marine Sediments in Coculture with Sulfur-Oxidizing Bacteria

(2010) B.-J. Park et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Use of Cellular CRISPR (Clusters of Regularly Interspaced Short Palindromic Repeats) Spacer-Based Microarrays for Detection of Viruses in Environmental Samples

(2010) J. C. Snyder et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Both Forward and Reverse TCA Cycles Operate in Green Sulfur Bacteria

(2010) Kuo-Hsiang Tang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea

(2010) Luciano A. Marraffini et al.   NATURE REVIEWS GENETICS

Autotrophic carbon fixation in archaea

(2010) Ivan A. Berg et al.   NATURE REVIEWS MICROBIOLOGY

CDD: a Conserved Domain Database for the functional annotation of proteins

(2010) A. Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Structural basis for mRNA surveillance by archaeal Pelota and GTP-bound EF1α complex

(2010) Kan Kobayashi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Autotrophic ammonia oxidation by soil thaumarchaea

(2010) L.-M. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic arrangement of bacterial operons is constrained by biological pathways encoded in the genome

(2010) Y. Yin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

CRISPR/Cas, the Immune System of Bacteria and Archaea

(2010) P. Horvath et al.   SCIENCE

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

(2010) Anja Spang et al.   TRENDS IN MICROBIOLOGY

Synthesis and production of polyhydroxyalkanoates by halophiles: current potential and future prospects

(2009) Jorge Quillaguamán et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Role of multiprotein bridging factor 1 in archaea: bridging the domains?

(2009) Bart de Koning et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

IMG ER: a system for microbial genome annotation expert review and curation

(2009) Victor M. Markowitz et al.   BIOINFORMATICS

Crenarchaeol dominates the membrane lipids of Candidatus Nitrososphaera gargensis, a thermophilic Group I.1b Archaeon

(2009) Angela Pitcher et al.   ISME Journal

Global ecological patterns in uncultured Archaea

(2009) Jean-Christophe Auguet et al.   ISME Journal

Phosphate-Dependent Behavior of the Archaeon Halobacterium salinarum Strain R1

(2009) A. Wende et al.   JOURNAL OF BACTERIOLOGY

Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria

(2009) Willm Martens-Habbena et al.   NATURE

Do ammonia-oxidizing archaea respond to soil Cu contamination similarly asammonia-oxidizing bacteria?

(2009) Xiaofang Li et al.   PLANT AND SOIL

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

Evolution of Complex RNA Polymerases: The Complete Archaeal RNA Polymerase Structure

(2009) Yakov Korkhin et al.   PLOS BIOLOGY

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol

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

DNA Microarray Analysis of Central Carbohydrate Metabolism: Glycolytic/Gluconeogenic Carbon Switch in the Hyperthermophilic Crenarchaeum Thermoproteus tenax

(2008) M. Zaparty et al.   JOURNAL OF BACTERIOLOGY

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH

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

Nitrifier genomics and evolution of the nitrogen cycle

(2007) Martin G. Klotz et al.   FEMS MICROBIOLOGY LETTERS