Transcriptomic evidences for microbial carbon and nitrogen cycles in the deoxygenated seawaters of Bohai Sea

Opportunistic bacteria with reduced genomes are effective competitors for organic nitrogen compounds in coastal dinoflagellate blooms

(2021) Yu Han et al.   Microbiome

Dark biological superoxide production as a significant flux and sink of marine dissolved oxygen

(2020) Kevin M. Sutherland et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coordinated photodegradation and biodegradation of organic matter from macrophyte litter in shallow lake water: Dual role of solar irradiation

(2020) Na Song et al.   WATER RESEARCH

Diverse nitrogen cycling pathways across a marine oxygen gradient indicate nitrogen loss coupled to chemoautotrophic activity

(2020) Elizabeth A. Suter et al.   ENVIRONMENTAL MICROBIOLOGY

Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea

(2020) Wei Qin et al.   ISME Journal

Tight Regulation of Extracellular Superoxide Points to Its Vital Role in the Physiology of the Globally Relevant Roseobacter Clade

(2019) Colleen M. Hansel et al.   mBio

Extracellular superoxide production by key microbes in the global ocean

(2019) Kevin M. Sutherland et al.   LIMNOLOGY AND OCEANOGRAPHY

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Proteomic Response of Three Marine Ammonia-Oxidizing Archaea to Hydrogen Peroxide and Their Metabolic Interactions with a Heterotrophic Alphaproteobacterium

(2019) Barbara Bayer et al.   mSystems

Emergence of Summertime Hypoxia and Concurrent Carbonate Mineral Suppression in the Central Bohai Sea, China

(2019) Wei‐dong Zhai et al.   Journal of Geophysical Research-Biogeosciences

High-throughput absolute quantification sequencing reveals the effect of different fertilizer applications on bacterial community in a tomato cultivated coastal saline soil

(2019) Si-Qi Jiang et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Microbial Processing of Sediment‐Derived Dissolved Organic Matter: Implications for Its Subsequent Biogeochemical Cycling in Overlying Seawater

(2019) Ruanhong Cai et al.   Journal of Geophysical Research-Biogeosciences

Biogeochemical Controls on Coastal Hypoxia

(2018) Katja Fennel et al.   Annual Review of Marine Science

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

(2018) Alvaro M. Plominsky et al.   ENVIRONMENTAL MICROBIOLOGY

Current status of emerging hypoxia in a eutrophic estuary: The lower reach of the Pearl River Estuary, China

(2018) Wei Qian et al.   ESTUARINE COASTAL AND SHELF SCIENCE

Drivers and mechanisms of ocean deoxygenation

(2018) Andreas Oschlies et al.   Nature Geoscience

Declining oxygen in the global ocean and coastal waters

(2018) Denise Breitburg et al.   SCIENCE

Cross-protection from hydrogen peroxide by helper microbes: the impacts on the cyanobacterium Prochlorococcus and other beneficiaries in marine communities

(2018) Erik R. Zinser   Environmental Microbiology Reports

The microbial contribution to reactive oxygen species dynamics in marine ecosystems

(2018) Erik R. Zinser   Environmental Microbiology Reports

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

(2018) Nicholas A. Bokulich et al.   Microbiome

Absolute quantitation of microbiota abundance in environmental samples

(2018) Andrzej Tkacz et al.   Microbiome

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

(2018) Katharina Kitzinger et al.   Nature Microbiology

Nitrosopumilus maritimus gen. nov., sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., four marine ammonia-oxidizing archaea of the phylum Thaumarchaeota

(2017) Wei Qin et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Degradation of hydrogen peroxide at the ocean’s surface: the influence of the microbial community on the realized thermal niche of Prochlorococcus

(2017) Lanying Ma et al.   ISME Journal

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

(2017) Benjamin J Callahan et al.   ISME Journal

Decline in global oceanic oxygen content during the past five decades

(2017) Sunke Schmidtko et al.   NATURE

Characterization of Potential Polysaccharide Utilization Systems in the Marine Bacteroidetes Gramella Flava JLT2011 Using a Multi-Omics Approach

(2017) Kai Tang et al.   Frontiers in Microbiology

Hypoxia causes preservation of labile organic matter and changes seafloor microbial community composition (Black Sea)

(2017) Gerdhard L. Jessen et al.   Science Advances

Pathways and key intermediates required for obligate aerobic ammonia-dependent chemolithotrophy in bacteria and Thaumarchaeota

(2016) Jessica A Kozlowski et al.   ISME Journal

Proteomics and comparative genomics ofNitrososphaera viennensisreveal the core genome and adaptations of archaeal ammonia oxidizers

(2016) Melina Kerou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial diversity in the surface sediments of the hypoxic zone near the Changjiang Estuary and in the East China Sea

(2016) Qi Ye et al.   MicrobiologyOpen

Archaeal enrichment in the hypoxic zone in the northern Gulf of Mexico

(2015) Lauren E. Gillies et al.   ENVIRONMENTAL MICROBIOLOGY

Illumina MiSeq investigations on the changes of microbial community in the Fusarium oxysporum f.sp. cubense infected soil during and after reductive soil disinfestation

(2015) Xinqi Huang et al.   MICROBIOLOGICAL RESEARCH

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

A Dissolved Oxygen Threshold for Shifts in Bacterial Community Structure in a Seasonally Hypoxic Estuary

(2015) Rachel L. Spietz et al.   PLoS One

Aerobic Microbial Respiration In Oceanic Oxygen Minimum Zones

(2015) Tim Kalvelage et al.   PLoS One

Environmental Variables Shaping the Ecological Niche of Thaumarchaeota in Soil: Direct and Indirect Causal Effects

(2015) Jin-Kyung Hong et al.   PLoS One

Molecular evidence for rapid dissolved organic matter turnover in Arctic fjords

(2014) Helena Osterholz et al.   MARINE CHEMISTRY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO2 fixation

(2014) M. Konneke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Marine ammonia-oxidizing archaeal isolates display obligate mixotrophy and wide ecotypic variation

(2014) W. Qin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Variability of the transporter gene complement in ammonia-oxidizing archaea

(2014) Pierre Offre et al.   TRENDS IN MICROBIOLOGY

Metatranscriptomic Analyses of Plankton Communities Inhabiting Surface and Subpycnocline Waters of the Chesapeake Bay during Oxic-Anoxic-Oxic Transitions

(2013) Ian Hewson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Spatial patterns of bacterial and archaeal communities along the Romanche Fracture Zone (tropical Atlantic)

(2013) Itziar Lekunberri et al.   FEMS MICROBIOLOGY ECOLOGY

Responses of the terrestrial ammonia-oxidizing archaeonCa. Nitrososphaera viennensis and the ammonia-oxidizing bacteriumNitrosospira multiformisto nitrification inhibitors

(2013) Tianlin Shen et al.   FEMS MICROBIOLOGY LETTERS

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

Widespread Production of Extracellular Superoxide by Heterotrophic Bacteria

(2013) J. M. Diaz et al.   SCIENCE

Why do bacteria use so many enzymes to scavenge hydrogen peroxide?

(2012) Surabhi Mishra et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

Isotope constraints on particulate nitrogen source and dynamics in the upper water column of the oligotrophic South China Sea

(2012) Shuh-Ji Kao et al.   GLOBAL BIOGEOCHEMICAL CYCLES

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

Substrate-Controlled Succession of Marine Bacterioplankton Populations Induced by a Phytoplankton Bloom

(2012) H. Teeling et al.   SCIENCE

Microbial metatranscriptomics in a permanent marine oxygen minimum zone

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

Beyond the Calvin Cycle: Autotrophic Carbon Fixation in the Ocean

(2010) Michael Hügler et al.   Annual Review of Marine Science

High diversity of ammonia-oxidizing archaea in permanent and seasonal oxygen-deficient waters of the eastern South Pacific

(2010) Verónica Molina et al.   ENVIRONMENTAL MICROBIOLOGY

CAZymes Analysis Toolkit (CAT): Web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database

(2010) Byung H Park et al.   GLYCOBIOLOGY

Autotrophic carbon fixation in archaea

(2010) Ivan A. Berg et al.   NATURE REVIEWS MICROBIOLOGY

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

Ocean Deoxygenation in a Warming World

(2009) Ralph F. Keeling et al.   Annual Review of Marine Science

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Superoxide Decay Kinetics in the Southern Ocean

(2009) Maija I. Heller et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

The Transporter Classification Database: recent advances

(2008) M. H. Saier et al.   NUCLEIC ACIDS RESEARCH

Thresholds of hypoxia for marine biodiversity

(2008) R. Vaquer-Sunyer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA