Selective enrichment of comammox from activated sludge using antibiotics

Biotransformation of lincomycin and fluoroquinolone antibiotics by the ammonia oxidizers AOA, AOB and comammox: A comparison of removal, pathways, and mechanisms

(2021) Li-Jun Zhou et al.   WATER RESEARCH

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

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

(2020) Yuchun Yang et al.   mBio

Enrichment of Comammox and Nitrite-Oxidizing Nitrospira From Acidic Soils

(2020) Yu Takahashi et al.   Frontiers in Microbiology

Ammonium concentration determines differential growth of comammox and canonical ammonia-oxidizing prokaryotes in soil microcosms

(2020) Shishi He et al.   APPLIED SOIL ECOLOGY

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

(2019) Paul Roots et al.   WATER RESEARCH

Metagenomic recovery of two distinct comammox Nitrospira from the terrestrial subsurface

(2019) Lianna Poghosyan et al.   ENVIRONMENTAL MICROBIOLOGY

Abundance and community composition of comammox bacteria in different ecosystems by a universal primer set

(2019) Zhirong Zhao et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Long solids retention times and attached growth phase favor prevalence of comammox bacteria in nitrogen removal systems

(2019) Irmarie Cotto et al.   WATER RESEARCH

ARGs-OAP v2.0 with an expanded SARG database and Hidden Markov Models for enhancement characterization and quantification of antibiotic resistance genes in environmental metagenomes

(2018) Xiaole Yin et al.   BIOINFORMATICS

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

The microbial nitrogen-cycling network

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

Genomic Analysis of Two Phylogenetically Distinct Nitrospira Species Reveals Their Genomic Plasticity and Functional Diversity

(2018) Norisuke Ushiki 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

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

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Ubiquity and Diversity of Complete Ammonia Oxidizers (Comammox)

(2018) Fei Xia et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

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

(2018) Katharina Kitzinger et al.   Nature Microbiology

Deciphering of microbial community and antibiotic resistance genes in activated sludge reactors under high selective pressure of different antibiotics

(2018) Renxin Zhao et al.   WATER RESEARCH

Effects of antibiotic residuals in dewatered sludge on the behavior of ammonia oxidizers during vermicomposting maturation process

(2018) Hui Xia et al.   CHEMOSPHERE

Comammox—a newly discovered nitrification process in the terrestrial nitrogen cycle

(2017) Hang-Wei Hu et al.   JOURNAL OF SOILS AND SEDIMENTS

Relative impacts of light, temperature, and reactive oxygen on thaumarchaeal ammonia oxidation in the North Pacific Ocean

(2017) Rachel E. A. Horak et al.   LIMNOLOGY AND OCEANOGRAPHY

Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle

(2017) K. Dimitri Kits et al.   NATURE

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

Comammox in drinking water systems

(2017) Yulin Wang et al.   WATER RESEARCH

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

The nitrogen cycle

(2016) Lisa Y. Stein et al.   CURRENT BIOLOGY

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

(2016) Alejandro Palomo 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

The microbiome in early life: implications for health outcomes

(2016) Sabrina Tamburini et al.   NATURE MEDICINE

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability

(2016) Moran Yassour et al.   Science Translational Medicine

Antibiotics, birth mode, and diet shape microbiome maturation during early life

(2016) Nicholas A. Bokulich et al.   Science Translational Medicine

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

(2016) Holger Daims et al.   TRENDS IN MICROBIOLOGY

High Concentrations of the Antibiotic Spiramycin in Wastewater Lead to High Abundance of Ammonia-Oxidizing Archaea in Nitrifying Populations

(2015) Yu Zhang et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

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

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

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

MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences

(2014) Chengwei Luo et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

Enrichment and Genome Sequence of the Group I.1a Ammonia-Oxidizing Archaeon “Ca. Nitrosotenuis uzonensis” Representing a Clade Globally Distributed in Thermal Habitats

(2013) Elena V. Lebedeva et al.   PLoS One

Microbial community functional structure in response to antibiotics in pharmaceutical wastewater treatment systems

(2013) Yu Zhang et al.   WATER RESEARCH

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

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

IMG ER: a system for microbial genome annotation expert review and curation

(2009) Victor M. Markowitz et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Dynamics and functional relevance of ammonia-oxidizing archaea in two agricultural soils

(2009) Kristina Schauss et al.   ENVIRONMENTAL MICROBIOLOGY

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Antibiotics and antibiotic resistance in water environments

(2008) Fernando Baquero et al.   CURRENT OPINION IN BIOTECHNOLOGY