Metabolic potential and in situ transcriptomic profiles of previously uncharacterized key microbial groups involved in coupled carbon, nitrogen and sulfur cycling in anoxic marine zones

Metabolic potential and in situ activity of marine Marinimicrobia bacteria in an anoxic water column

(2017) Anthony D. Bertagnolli et al.   ENVIRONMENTAL MICROBIOLOGY

Upper ocean O2 trends: 1958-2015

(2017) Takamitsu Ito et al.   GEOPHYSICAL RESEARCH LETTERS

Decline in global oceanic oxygen content during the past five decades

(2017) Sunke Schmidtko et al.   NATURE

Diverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients

(2017) Alyse K. Hawley et al.   Nature Communications

Cultivation of a chemoautotroph from the SUP05 clade of marine bacteria that produces nitrite and consumes ammonium

(2016) Vega Shah et al.   ISME Journal

NC10 bacteria in marine oxygen minimum zones

(2016) Cory C Padilla et al.   ISME Journal

In situ quantification of ultra-low O2 concentrations in oxygen minimum zones: Application of novel optodes

(2016) Morten Larsen et al.   LIMNOLOGY AND OCEANOGRAPHY-METHODS

SAR11 bacteria linked to ocean anoxia and nitrogen loss

(2016) Despina Tsementzi et al.   NATURE

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

Ammonium and nitrite oxidation at nanomolar oxygen concentrations in oxygen minimum zone waters

(2016) Laura A. Bristow et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrating biogeochemistry with multiomic sequence information in a model oxygen minimum zone

(2016) Stilianos Louca et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

metaxa2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data

(2015) Johan Bengtsson-Palme et al.   Molecular Ecology Resources

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

(2015) Christopher T. Brown et al.   NATURE

Microbial species delineation using whole genome sequences

(2015) Neha J. Varghese et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2015) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Diversity of methanogens and sulfate-reducing bacteria in the interfaces of five deep-sea anoxic brines of the Red Sea

(2015) Yue Guan et al.   RESEARCH IN MICROBIOLOGY

Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics

(2015) P. N. Evans et al.   SCIENCE

Methane oxidation in the eastern tropical North Pacific Ocean water column

(2015) Mary A. Pack et al.   Journal of Geophysical Research-Biogeosciences

Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes

(2014) M. Kim et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Gene-centric approach to integrating environmental genomics and biogeochemical models

(2014) Daniel C. Reed et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Niche specialization of novel Thaumarchaeota to oxic and hypoxic acidic geothermal springs of Yellowstone National Park

(2013) Jacob P Beam et al.   ISME Journal

Genomic properties of Marine Group A bacteria indicate a role in the marine sulfur cycle

(2013) Jody J Wright 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

Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage

(2013) Mohamed F. Haroon et al.   NATURE

Accurate and universal delineation of prokaryotic species

(2013) Daniel R Mende et al.   NATURE METHODS

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu 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

Widespread functional anoxia in the oxygen minimum zone of the Eastern South Pacific

(2012) Bo Thamdrup et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Lutibacter flavus sp. nov., a marine bacterium isolated from a tidal flat sediment

(2012) A. Choi et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Diversity and population structure of Marine Group A bacteria in the Northeast subarctic Pacific Ocean

(2012) Elke Allers et al.   ISME Journal

Anammox and denitrification in the oxygen minimum zone of the eastern South Pacific

(2012) Tage Dalsgaard et al.   LIMNOLOGY AND OCEANOGRAPHY

Microbial ecology of expanding oxygen minimum zones

(2012) Jody J. Wright et al.   NATURE REVIEWS MICROBIOLOGY

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

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes

(2011) Beifang Niu et al.   BIOINFORMATICS

Microbial metatranscriptomics in a permanent marine oxygen minimum zone

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

Abundance and phylogenetic identity of archaeoplankton in the permanent oxygen minimum zone of the eastern tropical South Pacific

(2011) Lucy Belmar et al.   FEMS MICROBIOLOGY ECOLOGY

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

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

Temporal variability and phylogenetic characterization of planktonic anammox bacteria in the coastal upwelling ecosystem off central Chile

(2011) Alexander Galán et al.   PROGRESS IN OCEANOGRAPHY

Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean

(2011) B. K. Swan et al.   SCIENCE

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

(2011) Frank J Stewart et al.   GENOME BIOLOGY

Microbial Nitrogen Cycling Processes in Oxygen Minimum Zones

(2010) Phyllis Lam et al.   Annual Review of Marine Science

Nitrite-driven anaerobic methane oxidation by oxygenic bacteria

(2010) Katharina F. Ettwig et al.   NATURE

Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea

(2010) C. B. Walker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Cryptic Sulfur Cycle in Oxygen-Minimum-Zone Waters off the Chilean Coast

(2010) D. E. Canfield et al.   SCIENCE

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

(2009) Victor M. Markowitz et al.   BIOINFORMATICS

Denitrification as the dominant nitrogen loss process in the Arabian Sea

(2009) B. B. Ward et al.   NATURE

Metagenome of a Versatile Chemolithoautotroph from Expanding Oceanic Dead Zones

(2009) D. A. Walsh et al.   SCIENCE

Bacterial diversity in the oxygen minimum zone of the eastern tropical South Pacific

(2008) Heike Stevens et al.   ENVIRONMENTAL MICROBIOLOGY

Expanding Oxygen-Minimum Zones in the Tropical Oceans

(2008) L. Stramma et al.   SCIENCE