Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the tropical sponge Ianthella basta

Low yield and abiotic origin of N2O formed by the complete nitrifier Nitrospira inopinata

(2019) K. Dimitri Kits et al.   Nature Communications

TIR Domain Proteins Are an Ancient Family of NAD + -Consuming Enzymes

(2018) Kow Essuman et al.   CURRENT BIOLOGY

Patterns of thaumarchaeal gene expression in culture and diverse marine environments

(2018) Paul Carini et al.   ENVIRONMENTAL MICROBIOLOGY

Nutrient transport suggests an evolutionary basis for charged archaeal surface layer proteins

(2018) Po-Nan Li et al.   ISME Journal

Occurrence, evolution, and functions of DNA phosphorothioate epigenetics in bacteria

(2018) Tong Tong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

“Candidatus Nitrosotenuis aquarius,” an Ammonia-Oxidizing Archaeon from a Freshwater Aquarium Biofilter

(2018) Laura A. Sauder et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Cyanate and urea are substrates for nitrification by Thaumarchaeota in the marine environment

(2018) Katharina Kitzinger et al.   Nature Microbiology

Evaluating the core microbiota in complex communities: A systematic investigation

(2017) Carmen Astudillo-García 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

Temperature Decouples Ammonium and Nitrite Oxidation in Coastal Waters

(2017) Sylvia C. Schaefer et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

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

Integrated metabolism in sponge–microbe symbiosis revealed by genome-centered metatranscriptomics

(2017) Lucas Moitinho-Silva et al.   ISME Journal

Uncultivated microbes in need of their own taxonomy

(2017) Konstantinos T Konstantinidis et al.   ISME Journal

Expression of eukaryotic-like protein in the microbiome of sponges

(2017) C. Díez-Vives et al.   MOLECULAR ECOLOGY

Metagenomic discovery of polybrominated diphenyl ether biosynthesis by marine sponges

(2017) Vinayak Agarwal et al.   Nature Chemical Biology

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

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

Influence of oxygen availability on the activities of ammonia-oxidizing archaea

(2017) Wei Qin et al.   Environmental Microbiology Reports

The sponge microbiome project

(2017) Lucas Moitinho-Silva et al.   GigaScience

Genome Reconstruction from Metagenomic Data Sets Reveals Novel Microbes in the Brackish Waters of the Caspian Sea

(2016) Maliheh Mehrshad et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Polytheonamide biosynthesis showcasing the metabolic potential of sponge-associated uncultivated ‘Entotheonella’ bacteria

(2016) Michael F Freeman et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

The deep-sea glass sponge L ophophysema eversa harbours potential symbionts responsible for the nutrient conversions of carbon, nitrogen and sulfur

(2016) Ren-Mao Tian et al.   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

A Purple Cupredoxin from Nitrosopumilus maritimus Containing a Mononuclear Type 1 Copper Center with an Open Binding Site

(2016) Parisa Hosseinzadeh et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Evolution and function of eukaryotic-like proteins from sponge symbionts

(2016) David Reynolds et al.   MOLECULAR ECOLOGY

Novel genomic island modifies DNA with 7-deazaguanine derivatives

(2016) Jennifer J. Thiaville et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

The Sponge Hologenome

(2016) Nicole S. Webster et al.   mBio

Diversity, structure and convergent evolution of the global sponge microbiome

(2016) Torsten Thomas et al.   Nature Communications

An ancient role for nitric oxide in regulating the animal pelagobenthic life cycle: evidence from a marine sponge

(2016) Nobuo Ueda et al.   Scientific Reports

An Enrichment of CRISPR and Other Defense-Related Features in Marine Sponge-Associated Microbial Metagenomes

(2016) Hannes Horn et al.   Frontiers in Microbiology

A novel ammonia-oxidizing archaeon from wastewater treatment plant: Its enrichment, physiological and genomic characteristics

(2016) Yuyang Li et al.   Scientific Reports

Molecular insights into proton coupled peptide transport in the PTR family of oligopeptide transporters

(2015) Simon Newstead   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

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

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

Cyanate as an energy source for nitrifiers

(2015) Marton Palatinszky et al.   NATURE

Complete nitrification by Nitrospira bacteria

(2015) Holger Daims et al.   NATURE

Microbial species delineation using whole genome sequences

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

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

Genomic and transcriptomic evidence for scavenging of diverse organic compounds by widespread deep-sea archaea

(2015) Meng Li et al.   Nature Communications

Transcriptional activity of the giant barrel sponge, Xestospongia muta Holobiont: molecular evidence for metabolic interchange

(2015) Cara L. Fiore et al.   Frontiers in Microbiology

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

(2015) Dongwan D. Kang et al.   PeerJ

New mini- zincin structures provide a minimal scaffold for members of this metallopeptidase superfamily

(2014) Christine B Trame et al.   BMC BIOINFORMATICS

Host-specificity among abundant and rare taxa in the sponge microbiome

(2014) Julie Reveillaud et al.   ISME Journal

Mep72, a Metzincin Protease That Is Preferentially Secreted by Biofilms of Pseudomonas aeruginosa

(2014) Ian J. Passmore et al.   JOURNAL OF BACTERIOLOGY

Compositional Biases among Synonymous Substitutions Cause Conflict between Gene and Protein Trees for Plastid Origins

(2014) Blaise Li et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Analysis of Eight Transcriptomes from All Poriferan Classes Reveals Surprising Genetic Complexity in Sponges

(2014) Ana Riesgo et al.   MOLECULAR BIOLOGY AND EVOLUTION

An environmental bacterial taxon with a large and distinct metabolic repertoire

(2014) Micheal C. Wilson et al.   NATURE

MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences

(2014) Chengwei Luo et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Soo-Je Park et al.   PLoS One

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

(2014) Kateryna V. Zhalnina et al.   PLoS One

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

Growth of nitrite-oxidizing bacteria by aerobic hydrogen oxidation

(2014) H. Koch et al.   SCIENCE

Variability of the transporter gene complement in ammonia-oxidizing archaea

(2014) Pierre Offre et al.   TRENDS IN MICROBIOLOGY

Two TIR-like domain containing proteins in a newly emerging zoonotic Staphylococcus aureus strain sequence type 398 are potential virulence factors by impacting on the host innate immune response

(2014) Nicholas J. Patterson et al.   Frontiers in Microbiology

Transcriptional Response of the Archaeal Ammonia Oxidizer Nitrosopumilus maritimus to Low and Environmentally Relevant Ammonia Concentrations

(2013) Tatsunori Nakagawa et al.   APPLIED AND 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

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

(2013) Jacob P Beam et al.   ISME Journal

Neuroglobins, Pivotal Proteins Associated with Emerging Neural Systems and Precursors of Metazoan Globin Diversity

(2013) Christophe Lechauve et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Predominant archaea in marine sediments degrade detrital proteins

(2013) Karen G. Lloyd et al.   NATURE

Pfam: the protein families database

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

Surviving in a Marine Desert: The Sponge Loop Retains Resources Within Coral Reefs

(2013) Jasper M. de Goeij et al.   SCIENCE

Tyrosine kinase signaling and the emergence of multicellularity

(2012) W. Todd Miller   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

Transcriptome profiling of the demosponge Amphimedon queenslandica reveals genome-wide events that accompany major life cycle transitions

(2012) Cecilia Conaco et al.   BMC GENOMICS

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

Metatranscriptomics of the marine sponge Geodia barretti: tackling phylogeny and function of its microbial community

(2012) Regina Radax 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

Metaproteogenomic analysis of a community of sponge symbionts

(2012) Michael Liu et al.   ISME Journal

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

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

Genomic insights into the marine sponge microbiome

(2012) Ute Hentschel et al.   NATURE REVIEWS MICROBIOLOGY

Thermal and Sedimentation Stress Are Unlikely Causes of Brown Spot Syndrome in the Coral Reef Sponge, Ianthella basta

(2012) Heidi M. Luter et al.   PLoS One

Functional equivalence and evolutionary convergence in complex communities of microbial sponge symbionts

(2012) L. Fan et al.   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

Host–microbe interactions that facilitate gut colonization by commensal bifidobacteria

(2012) Marco Ventura et al.   TRENDS IN MICROBIOLOGY

The Genome of the Obligate Intracellular Parasite Trachipleistophora hominis: New Insights into Microsporidian Genome Dynamics and Reductive Evolution

(2012) Eva Heinz et al.   PLoS Pathogens

Diversity of Archaeosine Synthesis in Crenarchaeota

(2011) Gabriela Phillips et al.   ACS Chemical Biology

The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology

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

Sponge-specific clusters revisited: a comprehensive phylogeny of sponge-associated microorganisms

(2011) Rachel L. Simister et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2011) Regina Radax et al.   ENVIRONMENTAL MICROBIOLOGY

Qualitative variation in colour morphotypes of Ianthella basta (Porifera: Verongida)

(2011) Marnie L. Freckelton et al.   HYDROBIOLOGIA

Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges

(2011) Susanne Schmitt et al.   ISME Journal

Anti-protease and Immunomodulatory Activities of Bacteria Associated with Caribbean Sponges

(2011) Paula Tabares et al.   MARINE BIOTECHNOLOGY

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

The archaeal ‘TACK’ superphylum and the origin of eukaryotes

(2011) Lionel Guy et al.   TRENDS IN MICROBIOLOGY

Enrichment and Physiological Characterization of a Novel Nitrospira-Like Bacterium Obtained from a Marine Sponge

(2010) S. Off et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Exploring the Role of Microorganisms in the Disease-Like Syndrome Affecting the Sponge Ianthella basta

(2010) H. M. Luter et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

The origins of eukaryotic-like proteins in Legionella pneumophila

(2010) Mor N. Lurie-Weinberger et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Determination of gross rates of amino acid production and immobilization in decomposing leaf litter by a novel 15N isotope pool dilution technique

(2010) Wolfgang Wanek et al.   SOIL BIOLOGY & BIOCHEMISTRY

Systems-wide temporal proteomic profiling in glucose-starved Bacillus subtilis

(2010) Andreas Otto et al.   Nature Communications

Double Labeling of Oligonucleotide Probes for Fluorescence In Situ Hybridization (DOPE-FISH) Improves Signal Intensity and Increases rRNA Accessibility

(2009) K. Stoecker et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Complex nitrogen cycling in the spongeGeodia barretti

(2009) Friederike Hoffmann et al.   ENVIRONMENTAL MICROBIOLOGY

Diversity of aerobic and anaerobic ammonia-oxidizing bacteria in marine sponges

(2009) Naglaa M Mohamed et al.   ISME Journal

Evidence of nitrification and denitrification in high and low microbial abundance sponges

(2009) Marie-Lise Schläppy et al.   MARINE BIOLOGY

Fossil steroids record the appearance of Demospongiae during the Cryogenian period

(2009) Gordon D. Love et al.   NATURE

Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria

(2009) Willm Martens-Habbena et al.   NATURE

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models

(2009) Arthur Brady et al.   NATURE METHODS

MicroScope: a platform for microbial genome annotation and comparative genomics

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

Physiology, phylogeny andin situevidence for bacterial and archaeal nitrifiers in the marine spongeAplysina aerophoba

(2008) Kristina Bayer et al.   ENVIRONMENTAL MICROBIOLOGY

Diversity and mode of transmission of ammonia-oxidizing archaea in marine sponges

(2008) Doris Steger et al.   ENVIRONMENTAL MICROBIOLOGY

The functional roles of marine sponges

(2008) James J. Bell   ESTUARINE COASTAL AND SHELF SCIENCE

Shotgun metaproteomics of the human distal gut microbiota

(2008) Nathan C Verberkmoes et al.   ISME Journal

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

Nitrification controls on fluxes and isotopic composition of nitrate from Florida Keys sponges

(2007) Melissa W. Southwell et al.   MARINE CHEMISTRY