Quantifying the effects of hydrogen on carbon assimilation in a seafloor microbial community associated with ultramafic rocks

Abiotic Sources of Molecular Hydrogen on Earth

(2020) Frieder Klein et al.   Elements

Substrate-dependent CO2 fixation in heterotrophic bacteria revealed by stable isotope labelling

(2020) Marina Spona-Friedl et al.   FEMS MICROBIOLOGY ECOLOGY

Anaerobic metabolism of Foraminifera thriving below the seafloor

(2020) William D. Orsi et al.   ISME Journal

A widely distributed hydrogenase oxidises atmospheric H2 during bacterial growth

(2020) Zahra F. Islam et al.   ISME Journal

Measurement Error and Resolution in Quantitative Stable Isotope Probing: Implications for Experimental Design

(2020) Ella T. Sieradzki et al.   mSystems

Atribacteria Reproducing over Millions of Years in the Atlantic Abyssal Subseafloor

(2020) Aurèle Vuillemin et al.   mBio

Diversification of methanogens into hyperalkaline serpentinizing environments through adaptations to minimize oxidant limitation

(2020) Elizabeth M. Fones et al.   ISME Journal

Isolation of a member of the candidate phylum ‘Atribacteria’ reveals a unique cell membrane structure

(2020) Taiki Katayama et al.   Nature Communications

Physiological adaptations to serpentinization in the Samail Ophiolite, Oman

(2019) Elizabeth M. Fones et al.   ISME Journal

Quantifying population-specific growth in benthic bacterial communities under low oxygen using H218O

(2019) Ömer K. Coskun et al.   ISME Journal

Atmospheric carbon monoxide oxidation is a widespread mechanism supporting microbial survival

(2019) Paul R. F. Cordero et al.   ISME Journal

Archaea dominate oxic subseafloor communities over multimillion-year time scales

(2019) Aurèle Vuillemin et al.   Science Advances

HTSSIP: An R package for analysis of high throughput sequencing data from nucleic acid stable isotope probing (SIP) experiments

(2018) Nicholas D. Youngblut et al.   PLoS One

Primary productivity below the seafloor at deep-sea hot springs

(2018) Jesse McNichol et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments

(2018) Nicholas D. Youngblut et al.   Frontiers in Microbiology

Cultivation and Genomic Analysis of “Candidatus Nitrosocaldus islandicus,” an Obligately Thermophilic, Ammonia-Oxidizing Thaumarchaeon from a Hot Spring Biofilm in Graendalur Valley, Iceland

(2018) Anne Daebeler et al.   Frontiers in Microbiology

A 16S rRNA gene sequencing and analysis protocol for the Illumina MiniSeq platform

(2018) Monica Pichler et al.   MicrobiologyOpen

Linking Uncultivated Microbial Populations and Benthic Carbon Turnover by Using Quantitative Stable Isotope Probing

(2018) Ömer K. Coskun et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Effects of organic matter and low oxygen on the mycobenthos in a coastal lagoon

(2018) Ana‐Sofia Ortega‐Arbulú et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial metal-sulfide oxidation in inactive hydrothermal vent chimneys suggested by metagenomic and metaproteomic analyses

(2018) Dimitri V. Meier et al.   ENVIRONMENTAL MICROBIOLOGY

Atmospheric trace gases support primary production in Antarctic desert surface soil

(2017) Mukan Ji et al.   NATURE

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Geological and Geochemical Controls on Subsurface Microbial Life in the Samail Ophiolite, Oman

(2017) Kaitlin R. Rempfert et al.   Frontiers in Microbiology

Energetics and Application of Heterotrophy in Acetogenic Bacteria

(2016) Kai Schuchmann et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Subseafloor microbial communities in hydrogen-rich vent fluids from hydrothermal systems along the Mid-Cayman Rise

(2016) Julie Reveillaud et al.   ENVIRONMENTAL MICROBIOLOGY

Phylogenetic organization of bacterial activity

(2016) Ember M Morrissey et al.   ISME Journal

Diverse, uncultivated bacteria and archaea underlying the cycling of dissolved protein in the ocean

(2016) William D Orsi et al.   ISME Journal

Coupled RNA-SIP and metatranscriptomics of active chemolithoautotrophic communities at a deep-sea hydrothermal vent

(2016) Caroline S Fortunato et al.   ISME Journal

Extreme mantle uplift and exhumation along a transpressive transform fault

(2016) Marcia Maia et al.   Nature Geoscience

W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis

(2016) Jana Trifinopoulos et al.   NUCLEIC ACIDS RESEARCH

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

phylosignal: an R package to measure, test, and explore the phylogenetic signal

(2016) François Keck et al.   Ecology and Evolution

Quantitative Microbial Ecology through Stable Isotope Probing

(2015) Bruce A. Hungate et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples

(2015) Alma E. Parada et al.   ENVIRONMENTAL MICROBIOLOGY

Phylogeny and physiology of candidate phylum ‘Atribacteria’ (OP9/JS1) inferred from cultivation-independent genomics

(2015) Masaru K Nobu et al.   ISME Journal

Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival

(2015) Chris Greening et al.   ISME Journal

The [NiFe]-Hydrogenase of Pyrococcus furiosus Exhibits a New Type of Oxygen Tolerance

(2015) Patrick Kwan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Abundant Atribacteria in deep marine sediment from the Adélie Basin, Antarctica

(2015) Stephanie A. Carr et al.   Frontiers in Microbiology

Stable isotope labeling confirms mixotrophic nature of streamer biofilm communities at alkaline hot springs

(2015) Florence Schubotz et al.   Frontiers in Microbiology

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

Structure, Function, and Mechanism of the Nickel Metalloenzymes, CO Dehydrogenase, and Acetyl-CoA Synthase

(2014) Mehmet Can et al.   CHEMICAL REVIEWS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

An obligately aerobic soil bacterium activates fermentative hydrogen production to survive reductive stress during hypoxia

(2014) M. Berney 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

Bacterial formate hydrogenlyase complex

(2014) J. S. McDowall et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Growth of nitrite-oxidizing bacteria by aerobic hydrogen oxidation

(2014) H. Koch et al.   SCIENCE

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing

(2014) Patrick J. Keeling et al.   PLOS BIOLOGY

Investigations of potential microbial methanogenic and carbon monoxide utilization pathways in ultra-basic reducing springs associated with present-day continental serpentinization: the Tablelands, NL, CAN

(2014) Penny L. Morrill et al.   Frontiers in Microbiology

Linking geology, fluid chemistry, and microbial activity of basalt- and ultramafic-hosted deep-sea hydrothermal vent environments

(2013) M. Perner et al.   Geobiology

Magnetite in seafloor serpentinite--Some like it hot

(2013) F. Klein et al.   GEOLOGY

Bacterial genome replication at subzero temperatures in permafrost

(2013) Steven J Tuorto et al.   ISME Journal

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Serpentinization, Carbon, and Deep Life

(2013) M. O. Schrenk et al.   Reviews in Mineralogy & Geochemistry

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Reaction of the Molybdenum- and Copper-Containing Carbon Monoxide Dehydrogenase fromOligotropha carboxydovoranswith Quinones

(2011) Jarett Wilcoxen et al.   BIOCHEMISTRY

Catabolic and anabolic energy for chemolithoautotrophs in deep-sea hydrothermal systems hosted in different rock types

(2011) Jan P. Amend et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Influence of subsurface biosphere on geochemical fluxes from diffuse hydrothermal fluids

(2011) Scott D. Wankel et al.   Nature Geoscience

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Serpentinization as a source of energy at the origin of life

(2010) M. J. RUSSELL et al.   Geobiology

Temperature-controlled organic carbon mineralization in lake sediments

(2010) Cristian Gudasz et al.   NATURE

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

FragGeneScan: predicting genes in short and error-prone reads

(2010) Mina Rho et al.   NUCLEIC ACIDS RESEARCH

Elevated concentrations of formate, acetate and dissolved organic carbon found at the Lost City hydrothermal field

(2009) Susan Q. Lang et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

(2009) M. Gouy et al.   MOLECULAR BIOLOGY AND EVOLUTION

Prokaryotic diversity, distribution and insights into their role in biogeochemical cycling in marine basalts

(2008) Olivia U Mason et al.   ISME Journal

Abundance and diversity of microbial life in ocean crust

(2008) Cara M. Santelli et al.   NATURE

Hydrothermal vents and the origin of life

(2008) William Martin et al.   NATURE REVIEWS MICROBIOLOGY