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

The Bacterial Communities of Full-Scale Biologically Active, Granular Activated Carbon Filters Are Stable and Diverse and Potentially Contain Novel Ammonia-Oxidizing Microorganisms

(2015) Timothy M. LaPara et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Effective start-up biofiltration method for Fe, Mn, and ammonia removal and bacterial community analysis

(2015) Yan’an Cai et al.   BIORESOURCE TECHNOLOGY

Microbial community composition of a household sand filter used for arsenic, iron, and manganese removal from groundwater in Vietnam

(2015) Katja Sonja Nitzsche et al.   CHEMOSPHERE

Groundwater Chemistry Determines the Prokaryotic Community Structure of Waterworks Sand Filters

(2015) Christian N. Albers et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor

(2015) Masaru K Nobu et al.   ISME Journal

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

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

A novel pathway producing dimethylsulphide in bacteria is widespread in soil environments

(2015) O. Carrión et al.   Nature Communications

Characterization of MtoD from Sideroxydans lithotrophicus: a cytochrome c electron shuttle used in lithoautotrophic growth

(2015) Christopher R. Beckwith et al.   Frontiers in Microbiology

VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data

(2015) Cedric C Laczny et al.   Microbiome

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

(2015) Ameet J. Pinto et al.   mSphere

Internal Porosity of Mineral Coating Supports Microbial Activity in Rapid Sand Filters for Groundwater Treatment

(2014) Arda Gülay et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

MS2 Bacteriophage Reduction and Microbial Communities in Biosand Filters

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

Estimating coverage in metagenomic data sets and why it matters

(2014) Luis M Rodriguez-R et al.   ISME Journal

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

Large-scale analysis of tandem repeat variability in the human genome

(2014) Jorge Duitama et al.   NUCLEIC ACIDS RESEARCH

Abundance and composition of indigenous bacterial communities in a multi-step biofiltration-based drinking water treatment plant

(2014) Karin Lautenschlager et al.   WATER RESEARCH

Effects of dynamic operating conditions on nitrification in biological rapid sand filters for drinking water treatment

(2014) Carson O. Lee et al.   WATER RESEARCH

PhyloSift: phylogenetic analysis of genomes and metagenomes

(2014) Aaron E. Darling et al.   PeerJ

Molecular characterization of microbial populations in full-scale biofilters treating iron, manganese and ammonia containing groundwater in Harbin, China

(2013) Xiang-kun Li et al.   BIORESOURCE TECHNOLOGY

Making a living while starving in the dark: metagenomic insights into the energy dynamics of a carbonate cave

(2013) Marianyoly Ortiz et al.   ISME Journal

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

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

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

Where the genes flow

(2013) Frank J. Stewart   Nature Geoscience

MEROPS: the database of proteolytic enzymes, their substrates and inhibitors

(2013) Neil D. Rawlings et al.   NUCLEIC ACIDS RESEARCH

Integrated Metagenomic and Physiochemical Analyses to Evaluate the Potential Role of Microbes in the Sand Filter of a Drinking Water Treatment System

(2013) Yaohui Bai et al.   PLoS One

A novel bench-scale column assay to investigate site-specific nitrification biokinetics in biological rapid sand filters

(2013) K. Tatari et al.   WATER RESEARCH

Microbial Survey of a Full-Scale, Biologically Active Filter for Treatment of Drinking Water

(2012) Colin P. White et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2012) Y. Peng et al.   BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

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

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

The interconnection between biofilm formation and horizontal gene transfer

(2012) Jonas Stenløkke Madsen et al.   FEMS IMMUNOLOGY AND MEDICAL MICROBIOLOGY

Ammonium removal pathways and microbial community in GAC-sand dual media filter in drinking water treatment

(2012) Shuo Feng et al.   JOURNAL OF ENVIRONMENTAL SCIENCES

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

Gallionella spp. in trickling filtration of subsurface aerated and natural groundwater

(2011) W.W.J.M. de Vet et al.   BIOTECHNOLOGY AND BIOENGINEERING

WebMGA: a customizable web server for fast metagenomic sequence analysis

(2011) Sitao Wu et al.   BMC GENOMICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Nitrite-driven anaerobic methane oxidation by oxygenic bacteria

(2010) Katharina F. Ettwig et al.   NATURE

Transposases are the most abundant, most ubiquitous genes in nature

(2010) Ramy K. Aziz et al.   NUCLEIC ACIDS RESEARCH

Manganese-oxidizing and -reducing microorganisms isolated from biofilms in chlorinated drinking water systems

(2010) José M. Cerrato et al.   WATER RESEARCH

Ammonia-Oxidizing Bacteria and Archaea in Groundwater Treatment and Drinking Water Distribution Systems

(2009) P. W. J. J. van der Wielen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The genomic basis of trophic strategy in marine bacteria

(2009) F. M. Lauro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial co-habitation and lateral gene transfer: what transposases can tell us

(2009) Sean D Hooper et al.   GENOME BIOLOGY

Genomic Insights into Mn(II) Oxidation by the Marine Alphaproteobacterium Aurantimonas sp. Strain SI85-9A1

(2008) G. J. Dick et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

Multiple Rubisco forms in proteobacteria: their functional significance in relation to CO2 acquisition by the CBB cycle

(2008) Murray Ronald Badger et al.   JOURNAL OF EXPERIMENTAL BOTANY