Comammox Nitrospira within the Yangtze River continuum: community, biogeography, and ecological drivers

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Solving the mystery of vanishing rivers in China

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Anammox response to natural and anthropogenic impacts over the Yangtze River

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Field Investigation on River Hydrochemical Characteristics and Larval and Juvenile Fish in the Source Region of the Yangtze River

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Patterns of bacterial and archaeal communities in sediments in response to dam construction and sewage discharge in Lhasa River

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

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Molecular biogeography of planktonic and benthic diatoms in the Yangtze River

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

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What drives the vegetation restoration in Yangtze River basin, China: Climate change or anthropogenic factors?

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

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

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The microbial nitrogen-cycling network

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Seasonal distribution of nitrifiers and denitrifiers in urban river sediments affected by agricultural activities

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Integrated biogeography of planktonic and sedimentary bacterial communities in the Yangtze River

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Niche separation of comammox Nitrospira and canonical ammonia oxidizers in an acidic subtropical forest soil under long-term nitrogen deposition

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The Genomic Potentials of NOB and Comammox Nitrospira in River Sediment Are Impacted by Native Freshwater Mussels

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Habitat-specific patterns and drivers of bacterial β-diversity in China’s drylands

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

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Stochastic Community Assembly: Does It Matter in Microbial Ecology?

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Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle

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Shotgun metagenomics, from sampling to analysis

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Comammox in drinking water systems

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

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AmoA-Targeted Polymerase Chain Reaction Primers for the Specific Detection and Quantification of Comammox Nitrospira in the Environment

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

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Metagenomic Analysis Revealing Antibiotic Resistance Genes (ARGs) and Their Genetic Compartments in the Tibetan Environment

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

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

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Importance and controls of anaerobic ammonium oxidation influenced by riverbed geology

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The ecology and biogeochemistry of stream biofilms

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

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Relative importance of advective flow versus environmental gradient in shaping aquatic ammonium oxidizers near the Three Gorges Dam of the Yangtze River, China

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MeDuSa: a multi-draft based scaffolder

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A novel psychrophilic alkaline phosphatase from the metagenome of tidal flat sediments

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Experimental Design and Bioinformatics Analysis for the Application of Metagenomics in Environmental Sciences and Biotechnology

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Metagenomic Assembly Reveals Hosts of Antibiotic Resistance Genes and the Shared Resistome in Pig, Chicken, and Human Feces

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

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Complete nitrification by a single microorganism

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Complete nitrification by Nitrospira bacteria

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MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

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

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Spatial biodiversity of bacteria along the largest Arctic river determined by next-generation sequencing

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Binning metagenomic contigs by coverage and composition

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Evaluation of a Hybrid Approach Using UBLAST and BLASTX for Metagenomic Sequences Annotation of Specific Functional Genes

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PhyloSift: phylogenetic analysis of genomes and metagenomes

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Archaeal Biofilms: The Great Unexplored

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

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Physiology and Diversity of Ammonia-Oxidizing Archaea

(2012) David A. Stahl et al.   Annual Review of Microbiology

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

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NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

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Toward almost closed genomes with GapFiller

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BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

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Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw

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Prodigal: prokaryotic gene recognition and translation initiation site identification

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Experimental tests of the bacterial distance–decay relationship

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QIIME allows analysis of high-throughput community sequencing data

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Conceptual Synthesis in Community Ecology

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Shifting the genomic gold standard for the prokaryotic species definition

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Sediment transport from the Yangtze River, China, into the sea over the Post-Three Gorge Dam Period: A discussion

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