Microbial Nitrogen Metabolism in Chloraminated Drinking Water Reservoirs

Extracellular DNA in Monochloraminated Drinking Water and Its Influence on DNA-Based Profiling of a Microbial Community

(2019) Bairoliya Sakcham et al.   Environmental Science & Technology Letters

The microbial nitrogen-cycling network

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

Nitrospira

(2018) Holger Daims et al.   TRENDS IN MICROBIOLOGY

Long-term spatial and temporal microbial community dynamics in a large-scale drinking water distribution system with multiple disinfectant regimes

(2018) Sarah Potgieter et al.   WATER RESEARCH

Characterization of the First “Candidatus Nitrotoga” Isolate Reveals Metabolic Versatility and Separate Evolution of Widespread Nitrite-Oxidizing Bacteria

(2018) Katharina Kitzinger et al.   mBio

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

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Nitrite oxidation kinetics of two Nitrospira strains: The quest for competition and ecological niche differentiation

(2017) Norisuke Ushiki et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

Comammox in drinking water systems

(2017) Yulin Wang et al.   WATER RESEARCH

An experimental study on the influence of water stagnation and temperature change on water quality in a full-scale domestic drinking water system

(2017) Lj. Zlatanović et al.   WATER RESEARCH

Small-scale variation of ammonia oxidisers within intertidal sediments dominated by ammonia-oxidising bacteria Nitrosomonas sp. amoA genes and transcripts

(2017) Aoife M. Duff et al.   Scientific Reports

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

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

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

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

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

Long-Term Bacterial Dynamics in a Full-Scale Drinking Water Distribution System

(2016) E. I. Prest et al.   PLoS One

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

(2016) Holger Daims et al.   TRENDS IN MICROBIOLOGY

Emerging investigators series: microbial communities in full-scale drinking water distribution systems – a meta-analysis

(2016) Quyen M. Bautista-de los Santos et al.   Environmental Science-Water Research & Technology

Using Amplicon Sequencing To Characterize and Monitor Bacterial Diversity in Drinking Water Distribution Systems

(2015) Jennifer L. A. Shaw et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Nitric Oxide Regulation of Bacterial Biofilms

(2015) Dhruv P. Arora et al.   BIOCHEMISTRY

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Unusual biology across a group comprising more than 15% of domain Bacteria

(2015) Christopher T. Brown 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

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

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

Diversity and functions of bacterial community in drinking water biofilms revealed by high-throughput sequencing

(2015) Yuanqing Chao et al.   Scientific Reports

Seasonal variation in denitrification and dissimilatory nitrate reduction to ammonia process rates and corresponding key functional genes along an estuarine nitrate gradient

(2015) Cindy J. Smith et al.   Frontiers in Microbiology

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

(2015) A. Murat Eren et al.   PeerJ

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

(2015) Ameet J. Pinto et al.   mSphere

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Comparing Spatial and Temporal Diversity of Bacteria in a Chlorinated Drinking Water Distribution System

(2014) Stacia T. McCoy et al.   ENVIRONMENTAL ENGINEERING SCIENCE

Microbial Community Response to Chlorine Conversion in a Chloraminated Drinking Water Distribution System

(2014) Hong Wang et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

The environmental controls that govern the end product of bacterial nitrate respiration

(2014) B. Kraft et al.   SCIENCE

Spatial-Temporal Survey and Occupancy-Abundance Modeling To Predict Bacterial Community Dynamics in the Drinking Water Microbiome

(2014) A. J. Pinto et al.   mBio

Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets

(2013) Luis M. Rodriguez-R et al.   BIOINFORMATICS

Microbial community changes with decaying chloramine residuals in a lab-scale system

(2013) K.C. Bal Krishna et al.   WATER RESEARCH

Metagenomic Analyses of Drinking Water Receiving Different Disinfection Treatments

(2012) Vicente Gomez-Alvarez et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Bacterial Community Structure in the Drinking Water Microbiome Is Governed by Filtration Processes

(2012) Ameet J. Pinto et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Nitrifying and denitrifying pathways of methanotrophic bacteria

(2011) Lisa Y. Stein et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology

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

High Abundance of Ammonia-Oxidizing Archaea in Coastal Waters, Determined Using a Modified DNA Extraction Method

(2010) H. Urakawa et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Biofilm Formation on Reverse Osmosis Membranes Is Initiated and Dominated by Sphingomonas spp.

(2010) L. A. Bereschenko et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

Nitrification in Drinking Water Systems

(2009) Yan Zhang et al.   CRITICAL REVIEWS IN ENVIRONMENTAL SCIENCE AND TECHNOLOGY

Nitrate attenuation in groundwater: A review of biogeochemical controlling processes

(2008) Michael O. Rivett et al.   WATER RESEARCH

Flow-cytometric total bacterial cell counts as a descriptive microbiological parameter for drinking water treatment processes

(2007) Frederik Hammes et al.   WATER RESEARCH