Efficient conversion of organic nitrogenous wastewater to nitrate solution driven by comammox Nitrospira

Transition of microbial community structures after development of membrane fouling in membrane bioreactors (MBRs)

(2020) Yuya Sato et al.   AMB Express

High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant

(2020) Emilie Spasov et al.   ISME Journal

Comammox Nitrospira are the dominant ammonia oxidizers in a mainstream low dissolved oxygen nitrification reactor

(2019) Paul Roots et al.   WATER RESEARCH

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

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

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

DNA- and RNA-SIP Reveal Nitrospira spp. as Key Drivers of Nitrification in Groundwater-Fed Biofilters

(2019) Arda Gülay et al.   mBio

Complete ammonia oxidation: an important control on nitrification in engineered ecosystems?

(2018) Christopher E Lawson et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

The microbial nitrogen-cycling network

(2018) Marcel M. M. Kuypers et al.   NATURE REVIEWS MICROBIOLOGY

Complete nitrification: insights into the ecophysiology of comammox Nitrospira

(2018) Hanna Koch et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle

(2017) K. Dimitri Kits et al.   NATURE

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

Culture-Independent Analyses Reveal Novel Anaerolineaceae as Abundant Primary Fermenters in Anaerobic Digesters Treating Waste Activated Sludge

(2017) Simon J. McIlroy 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

Functional maintenance and structural flexibility of microbial communities perturbed by simulated intense rainfall in a pilot-scale membrane bioreactor

(2016) Yuya Sato et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

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

Fine-scale monitoring of shifts in microbial community composition after high organic loading in a pilot-scale membrane bioreactor

(2016) Yuya Sato et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

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

Ultra-high-sensitivity stable-isotope probing of rRNA by high-throughput sequencing of isopycnic centrifugation gradients

(2015) Tomo Aoyagi et al.   Environmental Microbiology Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Disturbance and temporal partitioning of the activated sludge metacommunity

(2014) David C Vuono et al.   ISME Journal

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Identification and removal of ribosomal RNA sequences from metatranscriptomes

(2011) Robert Schmieder et al.   BIOINFORMATICS

Using network analysis to explore co-occurrence patterns in soil microbial communities

(2011) Albert Barberán et al.   ISME Journal

Comparison among amoA Primers Suited for Quantification and Diversity Analyses of Ammonia-Oxidizing Bacteria in Soil

(2011) Yumi Shimomura et al.   MICROBES AND ENVIRONMENTS

Microbial mineralization of organic nitrogen into nitrate to allow the use of organic fertilizer in hydroponics

(2011) Makoto Shinohara et al.   SOIL SCIENCE AND PLANT NUTRITION

UniFrac: an effective distance metric for microbial community comparison

(2010) Catherine Lozupone et al.   ISME Journal

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

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

Phylogenomics and protein signatures elucidating the evolutionary relationships among the Gammaproteobacteria

(2009) B. Gao et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

An Earth-system perspective of the global nitrogen cycle

(2008) Nicolas Gruber et al.   NATURE