Activity and Metabolic Versatility of Complete Ammonia Oxidizers in Full-Scale Wastewater Treatment Systems

Metagenomic recovery of two distinct comammox Nitrospira from the terrestrial subsurface

(2019) Lianna Poghosyan et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Expansion of Thaumarchaeota habitat range is correlated with horizontal transfer of ATPase operons

(2019) Baozhan Wang et al.   ISME Journal

Complex microbial nitrogen-cycling networks in three distinct anammox-inoculated wastewater treatment systems

(2019) Yuchun Yang et al.   WATER RESEARCH

Comammox Nitrospira are abundant ammonia oxidizers in diverse groundwater-fed rapid sand filter communities

(2018) Susan Jane Fowler et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2018) Alejandro Palomo et al.   ISME Journal

Single cell genomic and transcriptomic evidence for the use of alternative nitrogen substrates by anammox bacteria

(2018) Sangita Ganesh et al.   ISME Journal

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

Comammox Functionality Identified in Diverse Engineered Biological Wastewater Treatment Systems

(2018) Medini K. Annavajhala et al.   Environmental Science & Technology Letters

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

(2018) Katharina Kitzinger et al.   Nature Microbiology

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Erratum to: Novel nitrifiers and comammox in a full-scale hybrid biofilm and activated sludge reactor revealed by metagenomic approach

(2016) Yuanqing Chao et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Application of the MAFFT sequence alignment program to large data—reexamination of the usefulness of chained guide trees

(2016) Kazunori D. Yamada et al.   BIOINFORMATICS

Detection of comammox bacteria in full-scale wastewater treatment bioreactors using tag-454-pyrosequencing

(2016) Alejandro Gonzalez-Martinez et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

OrthoANI: An improved algorithm and software for calculating average nucleotide identity

(2016) Imchang Lee et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

Bacterial polyhydroxyalkanoates: Still fabulous?

(2016) Justyna Możejko-Ciesielska et al.   MICROBIOLOGICAL RESEARCH

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

(2016) Karthik Anantharaman et al.   Nature Communications

HydDB: A web tool for hydrogenase classification and analysis

(2016) Dan Søndergaard et al.   Scientific Reports

Substrate, product, and cofactor: The extraordinarily flexible relationship between the CDE superfamily and heme

(2015) Arianna I. Celis et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

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

Metagenomic Evidence for the Presence of Comammox Nitrospira -Like Bacteria in a Drinking Water System

(2015) Ameet J. Pinto et al.   mSphere

Engineering the diversity of polyesters

(2014) De-Chuan Meng et al.   CURRENT OPINION IN BIOTECHNOLOGY

Functionally relevant diversity of closely related Nitrospira in activated sludge

(2014) Christiane Gruber-Dorninger 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

An obligately aerobic soil bacterium activates fermentative hydrogen production to survive reductive stress during hypoxia

(2014) M. Berney 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

MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm

(2014) Yu-Wei Wu et al.   Microbiome

Isolation of Nitrospira belonging to Sublineage II from a Wastewater Treatment Plant

(2013) Norisuke Ushiki et al.   MICROBES AND ENVIRONMENTS

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

(2012) Y. Peng et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Identification and removal of ribosomal RNA sequences from metatranscriptomes

(2011) Robert Schmieder et al.   BIOINFORMATICS

Unexpected Diversity of Chlorite Dismutases: a Catalytically Efficient Dimeric Enzyme from Nitrobacter winogradskyi

(2011) G. Mlynek et al.   JOURNAL OF BACTERIOLOGY

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

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

PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes

(2010) Nancy Y. Yu et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

The influence of nitrogen limitation on mcl-PHA synthesis by two newly isolated strains of Pseudomonas sp.

(2010) Slawomir Ciesielski et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Structural and functional characterisation of the chlorite dismutase from the nitrite-oxidizing bacterium “Candidatus Nitrospira defluvii”: Identification of a catalytically important amino acid residue

(2010) Julius Kostan et al.   JOURNAL OF STRUCTURAL BIOLOGY

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

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

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

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The PHA Depolymerase Engineering Database: A systematic analysis tool for the diverse family of polyhydroxyalkanoate (PHA) depolymerases

(2009) Michael Knoll et al.   BMC BIOINFORMATICS

High-performance signal peptide prediction based on sequence alignment techniques

(2008) K. Frank et al.   BIOINFORMATICS

Environmental genomics reveals a functional chlorite dismutase in the nitrite-oxidizing bacterium ‘CandidatusNitrospira defluvii’

(2008) Frank Maixner et al.   ENVIRONMENTAL MICROBIOLOGY