SAR11 bacteria linked to ocean anoxia and nitrogen loss

Metagenomic analysis of nitrogen and methane cycling in the Arabian Sea oxygen minimum zone

(2016) Claudia Lüke et al.   PeerJ

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

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

Size-fraction partitioning of community gene transcription and nitrogen metabolism in a marine oxygen minimum zone

(2015) Sangita Ganesh et al.   ISME Journal

Meta-omic signatures of microbial metal and nitrogen cycling in marine oxygen minimum zones

(2015) Jennifer B. Glass et al.   Frontiers in Microbiology

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

Seasonal dynamics of active SAR11 ecotypes in the oligotrophic Northwest Mediterranean Sea

(2014) Ian Salter et al.   ISME Journal

Evolutionary origin of a streamlined marine bacterioplankton lineage

(2014) Haiwei Luo   ISME Journal

Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype

(2014) J Cameron Thrash et al.   ISME Journal

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification

(2014) T.B.K. Reddy et al.   NUCLEIC ACIDS RESEARCH

MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences

(2014) Chengwei Luo et al.   NUCLEIC ACIDS RESEARCH

A New Highly Sensitive Method to Assess Respiration Rates and Kinetics of Natural Planktonic Communities by Use of the Switchable Trace Oxygen Sensor and Reduced Oxygen Concentrations

(2014) Laura Tiano et al.   PLoS One

Oxygen at Nanomolar Levels Reversibly Suppresses Process Rates and Gene Expression in Anammox and Denitrification in the Oxygen Minimum Zone off Northern Chile

(2014) Tage Dalsgaard et al.   mBio

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

High-resolution SAR11 ecotype dynamics at the Bermuda Atlantic Time-series Study site by phylogenetic placement of pyrosequences

(2013) Kevin L Vergin et al.   ISME Journal

Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone

(2013) Sangita Ganesh et al.   ISME Journal

The unique metabolism of SAR11 aquatic bacteria

(2013) H. James Tripp   JOURNAL OF MICROBIOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Nitrogen cycling driven by organic matter export in the South Pacific oxygen minimum zone

(2013) Tim Kalvelage et al.   Nature Geoscience

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Comparative and Phylogenomic Evidence That the Alphaproteobacterium HIMB59 Is Not a Member of the Oceanic SAR11 Clade

(2013) Johan Viklund et al.   PLoS One

Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment

(2013) Cindy J. Castelle et al.   Nature Communications

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

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

(2012) Y. Peng et al.   BIOINFORMATICS

Fate and effect of benzalkonium chlorides in a continuous-flow biological nitrogen removal system treating poultry processing wastewater

(2012) Malek G. Hajaya et al.   BIORESOURCE TECHNOLOGY

Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi

(2012) Dimitry Y Sorokin et al.   ISME Journal

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A Deeply Branching Thermophilic Bacterium with an Ancient Acetyl-CoA Pathway Dominates a Subsurface Ecosystem

(2012) Hideto Takami et al.   PLoS One

The SAR11 Group of Alpha-Proteobacteria Is Not Related to the Origin of Mitochondria

(2012) Naiara Rodríguez-Ezpeleta et al.   PLoS One

Microbial oceanography of anoxic oxygen minimum zones

(2012) O. Ulloa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Streamlining and Core Genome Conservation among Highly Divergent Members of the SAR11 Clade

(2012) J. Grote et al.   mBio

Microbial metatranscriptomics in a permanent marine oxygen minimum zone

(2011) Frank J. Stewart et al.   ENVIRONMENTAL MICROBIOLOGY

Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage

(2011) Chris L Dupont et al.   ISME Journal

Determination of ultra-low oxygen concentrations in oxygen minimum zones by the STOX sensor

(2011) Niels Peter Revsbech et al.   LIMNOLOGY AND OCEANOGRAPHY-METHODS

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Oxygen Sensitivity of Anammox and Coupled N-Cycle Processes in Oxygen Minimum Zones

(2011) Tim Kalvelage et al.   PLoS One

Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean

(2011) B. K. Swan et al.   SCIENCE

Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood

(2011) Simon A. Berger et al.   SYSTEMATIC BIOLOGY

Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade

(2011) J. Cameron Thrash et al.   Scientific Reports

Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities

(2011) Frank J Stewart et al.   GENOME BIOLOGY

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

(2010) Murray P Cox et al.   BMC BIOINFORMATICS

Ab initio gene identification in metagenomic sequences

(2010) Wenhan Zhu et al.   NUCLEIC ACIDS RESEARCH

FragGeneScan: predicting genes in short and error-prone reads

(2010) Mina Rho et al.   NUCLEIC ACIDS RESEARCH

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

Comparative Metagenomic Analysis of a Microbial Community Residing at a Depth of 4,000 Meters at Station ALOHA in the North Pacific Subtropical Gyre

(2009) K. T. Konstantinidis et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Dynamics of the SAR11 bacterioplankton lineage in relation to environmental conditions in the oligotrophic North Pacific subtropical gyre

(2009) Alexander Eiler et al.   ENVIRONMENTAL MICROBIOLOGY

Genomic patterns of recombination, clonal divergence and environment in marine microbial populations

(2008) Konstantinos T Konstantinidis et al.   ISME Journal

Seasonal dynamics of SAR11 populations in the euphotic and mesopelagic zones of the northwestern Sargasso Sea

(2008) Craig A Carlson et al.   ISME Journal

Oxygen minimum zones (OMZs) in the modern ocean

(2008) A. Paulmier et al.   PROGRESS IN OCEANOGRAPHY

The prokaryotic complex iron–sulfur molybdoenzyme family

(2007) Richard A. Rothery et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES