Comparative genomics sheds light on niche differentiation and the evolutionary history of comammox Nitrospira

Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle

(2017) K. Dimitri Kits et al.   NATURE

Comammox in drinking water systems

(2017) Yulin Wang et al.   WATER RESEARCH

Freshwater Recirculating Aquaculture System Operations Drive Biofilter Bacterial Community Shifts around a Stable Nitrifying Consortium of Ammonia-Oxidizing Archaea and Comammox Nitrospira

(2017) Ryan P. Bartelme et al.   Frontiers in Microbiology

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

Genome-Enabled Insights into the Ecophysiology of the Comammox Bacterium “ Candidatus Nitrospira nitrosa”

(2017) Pamela Y. Camejo et al.   mSystems

ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony: Table 1.

(2016) Edwin Jacox et al.   BIOINFORMATICS

Metagenomic analysis of rapid gravity sand filter microbial communities suggests novel physiology of Nitrospira spp.

(2016) Alejandro Palomo et al.   ISME Journal

Ecological patterns, diversity and core taxa of microbial communities in groundwater-fed rapid gravity filters

(2016) Arda Gülay et al.   ISME Journal

Different Functions of Phylogenetically Distinct Bacterial Complex I Isozymes

(2016) Melanie A. Spero et al.   JOURNAL OF BACTERIOLOGY

Expressions of alkaline phosphatase genes during phosphate starvation are under positive influences of multiple cell wall hydrolase genes in Bacillus subtilis

(2016) Yueh-Chi Shen et al.   JOURNAL OF GENERAL AND APPLIED MICROBIOLOGY

A New Perspective on Microbes Formerly Known as Nitrite-Oxidizing Bacteria

(2016) Holger Daims et al.   TRENDS IN MICROBIOLOGY

Copper deficiency can limit nitrification in biological rapid sand filters for drinking water production

(2016) Florian B. Wagner et al.   WATER RESEARCH

Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system

(2016) Daan R. Speth et al.   Nature Communications

MeDuSa: a multi-draft based scaffolder

(2015) Emanuele Bosi et al.   BIOINFORMATICS

SylvX: a viewer for phylogenetic tree reconciliations

(2015) François Chevenet et al.   BIOINFORMATICS

Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages

(2015) Laura A. Hug 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

Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival

(2015) Chris Greening et al.   ISME Journal

Cyanate as an energy source for nitrifiers

(2015) Marton Palatinszky et al.   NATURE

Complete nitrification by a single microorganism

(2015) Maartje A. H. J. van Kessel et al.   NATURE

Complete nitrification by Nitrospira bacteria

(2015) Holger Daims et al.   NATURE

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

Phylogenomic Analysis and Predicted Physiological Role of the Proton-Translocating NADH:Quinone Oxidoreductase (Complex I) Across Bacteria

(2015) Melanie A. Spero et al.   mBio

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

Cytochrome bd oxidase and bacterial tolerance to oxidative and nitrosative stress

(2014) Alessandro Giuffrè et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Functionally relevant diversity of closely related Nitrospira in activated sludge

(2014) Christiane Gruber-Dorninger et al.   ISME Journal

A Biochemical Approach to Study the Role of the Terminal Oxidases in Aerobic Respiration in Shewanella oneidensis MR-1

(2014) Sébastien Le Laz et al.   PLoS One

Growth of nitrite-oxidizing bacteria by aerobic hydrogen oxidation

(2014) H. Koch et al.   SCIENCE

A Bayesian Method for Analyzing Lateral Gene Transfer

(2014) J. Sjostrand et al.   SYSTEMATIC BIOLOGY

Variability of the transporter gene complement in ammonia-oxidizing archaea

(2014) Pierre Offre et al.   TRENDS IN MICROBIOLOGY

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Methionine salvage andS-adenosylmethionine: essential links between sulfur, ethylene and polyamine biosynthesis

(2013) Margret Sauter et al.   BIOCHEMICAL JOURNAL

NxrBencoding the beta subunit of nitrite oxidoreductase as functional and phylogenetic marker for nitrite-oxidizingNitrospira

(2013) Michael Pester et al.   ENVIRONMENTAL MICROBIOLOGY

Copper requirements of the ammonia-oxidizing archaeonNitrosopumilus maritimusSCM1 and implications for nitrification in the marine environment

(2013) Shady A. Amin et al.   LIMNOLOGY AND OCEANOGRAPHY

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

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

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

Editorial: NAR Surveys the Past, Present and Future of Restriction Endonucleases

(2013) W. Dynan et al.   NUCLEIC ACIDS RESEARCH

The Genome of Nitrospina gracilis Illuminates the Metabolism and Evolution of the Major Marine Nitrite Oxidizer

(2013) Sebastian Lücker et al.   Frontiers in Microbiology

Toward almost closed genomes with GapFiller

(2012) Marten Boetzer et al.   GENOME BIOLOGY

An Alkaline Phosphatase/Phosphodiesterase, PhoD, Induced by Salt Stress and Secreted Out of the Cells of Aphanothece halophytica, a Halotolerant Cyanobacterium

(2011) Hakuto Kageyama et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The cytochrome bd respiratory oxygen reductases

(2011) Vitaliy B. Borisov et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

The Evolution of Respiratory Chain Complex I from a Smaller Last Common Ancestor Consisting of 11 Protein Subunits

(2011) Vamsi K. Moparthi et al.   JOURNAL OF MOLECULAR EVOLUTION

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Phosphorus limitation in nitrifying groundwater filters

(2011) W.W.J.M. de Vet et al.   WATER RESEARCH

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

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

The stressosome: molecular architecture of a signalling hub

(2010) Jon Marles-Wright et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria

(2010) S. Lucker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metabolic characteristics and importance of the universal methionine salvage pathway recycling methionine from 5′-methylthioadenosine

(2009) Eva Albers   IUBMB LIFE

Peroxidase-like activity of Thermobifida fusca hemoglobin: The oxidation of dibenzylbutanolide

(2009) Roberta Torge et al.   JOURNAL OF MOLECULAR CATALYSIS B-ENZYMATIC

Phosphorus and nitrogen profile measurements to locate phosphorus limitation in a fixed bed filter

(2009) S. M. Scherrenberg et al.   WATER SCIENCE AND TECHNOLOGY

Dissection of Ammonium Uptake Systems in Corynebacterium glutamicum: Mechanism of Action and Energetics of AmtA and AmtB

(2008) B. Walter et al.   JOURNAL OF BACTERIOLOGY