Carbon Assimilation Strategies in Ultrabasic Groundwater: Clues from the Integrated Study of a Serpentinization-Influenced Aquifer

Physiological adaptations to serpentinization in the Samail Ophiolite, Oman

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

Reinforcing carbon fixation: CO 2 reduction replacing and supporting carboxylation

(2018) Charles AR Cotton et al.   CURRENT OPINION IN BIOTECHNOLOGY

Geophysical Characterization of Serpentinite Hosted Hydrogeology at the McLaughlin Natural Reserve, Coast Range Ophiolite

(2018) Estefania Ortiz et al.   GEOCHEMISTRY GEOPHYSICS GEOSYSTEMS

Guidelines and considerations for the use of system suitability and quality control samples in mass spectrometry assays applied in untargeted clinical metabolomic studies

(2018) David Broadhurst et al.   Metabolomics

KBase: The United States Department of Energy Systems Biology Knowledgebase

(2018) Adam P Arkin et al.   NATURE BIOTECHNOLOGY

Deeply-sourced formate fuels sulfate reducers but not methanogens at Lost City hydrothermal field

(2018) Susan Q. Lang et al.   Scientific Reports

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Abiotic formation of condensed carbonaceous matter in the hydrating oceanic crust

(2018) Marie Catherine Sforna et al.   Nature Communications

Unusual metabolic diversity of hyperalkaliphilic microbial communities associated with subterranean serpentinization at The Cedars

(2017) Shino Suzuki et al.   ISME Journal

Extraction efficiency and quantification of dissolved metabolites in targeted marine metabolomics

(2017) Winifred M. Johnson et al.   LIMNOLOGY AND OCEANOGRAPHY-METHODS

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH

(2017) Katrina I. Twing et al.   Frontiers in Microbiology

Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy

(2017) William J. Brazelton et al.   PeerJ

BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation

(2017) Elaina D. Graham et al.   PeerJ

Formate Assimilation: The Metabolic Architecture of Natural and Synthetic Pathways

(2016) Arren Bar-Even   BIOCHEMISTRY

Formaldehyde as a carbon and electron shuttle between autotroph and heterotroph populations in acidic hydrothermal vents of Norris Geyser Basin, Yellowstone National Park

(2016) James J. Moran et al.   EXTREMOPHILES

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes

(2016) Ivan Gregor et al.   PeerJ

Exploring the metabolic potential of microbial communities in ultra-basic, reducing springs at The Cedars, CA, USA: Experimental evidence of microbial methanogenesis and heterotrophic acetogenesis

(2016) Lukas Kohl et al.   Journal of Geophysical Research-Biogeosciences

Release of ecologically relevant metabolites by the cyanobacteriumSynechococcus elongatus CCMP 1631

(2015) Cara L. Fiore et al.   ENVIRONMENTAL MICROBIOLOGY

Environmental metabolomics: Analytical strategies

(2015) Melissa C. Kido Soule et al.   MARINE CHEMISTRY

Defining the Metabolome: Size, Flux, and Regulation

(2015) Nicola Zamboni et al.   MOLECULAR CELL

Nonequilibrium clumped isotope signals in microbial methane

(2015) D. T. Wang et al.   SCIENCE

Feasible metabolisms in high pH springs of the Philippines

(2015) Dawn Cardace et al.   Frontiers in Microbiology

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus

(2014) Emmanuel Prestat et al.   NUCLEIC ACIDS RESEARCH

Physiological and genomic features of highly alkaliphilic hydrogen-utilizing Betaproteobacteria from a continental serpentinizing site

(2014) Shino Suzuki et al.   Nature Communications

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

Insights into environmental controls on microbial communities in a continental serpentinite aquifer using a microcosm-based approach

(2014) Melitza Crespo-Medina et al.   Frontiers in Microbiology

Bacterial Communities Associated with Subsurface Geochemical Processes in Continental Serpentinite Springs

(2013) William J. Brazelton et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microbial diversity in The Cedars, an ultrabasic, ultrareducing, and low salinity serpentinizing ecosystem

(2013) S. Suzuki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Serpentinization, Carbon, and Deep Life

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

Laboratory Simulations of Abiotic Hydrocarbon Formation in Earth's Deep Subsurface

(2013) T. M. McCollom   Reviews in Mineralogy & Geochemistry

On the Origins of Deep Hydrocarbons

(2013) M. A. Sephton et al.   Reviews in Mineralogy & Geochemistry

Predicting Network Activity from High Throughput Metabolomics

(2013) Shuzhao Li et al.   PLoS Computational Biology

The role of reporting standards for metabolite annotation and identification in metabolomic studies

(2013) Reza M Salek et al.   GigaScience

Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture

(2012) N. Rohland et al.   GENOME RESEARCH

Microbial utilization of abiogenic carbon and hydrogen in a serpentinite-hosted system

(2012) Susan Q. Lang et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

A cross-platform toolkit for mass spectrometry and proteomics

(2012) Matthew C Chambers et al.   NATURE BIOTECHNOLOGY

Life in the hydrated suboceanic mantle

(2012) Bénédicte Ménez et al.   Nature Geoscience

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Hideto Takami et al.   PLoS One

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

(2012) Sahar Abubucker et al.   PLoS Computational Biology

Metagenomic Evidence for H2 Oxidation and H2 Production by Serpentinite-Hosted Subsurface Microbial Communities

(2012) William J. Brazelton et al.   Frontiers in Microbiology

Ray Meta: scalable de novo metagenome assembly and profiling

(2012) Sébastien Boisvert et al.   GENOME BIOLOGY

CAMERA: An Integrated Strategy for Compound Spectra Extraction and Annotation of Liquid Chromatography/Mass Spectrometry Data Sets

(2011) Carsten Kuhl et al.   ANALYTICAL CHEMISTRY

Ecological Aspects of the Distribution of Different Autotrophic CO2Fixation Pathways

(2011) Ivan A. Berg   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

A simple and efficient method for the solid-phase extraction of dissolved organic matter (SPE-DOM) from seawater

(2011) Thorsten Dittmar et al.   LIMNOLOGY AND OCEANOGRAPHY-METHODS

Physiological Differentiation within a Single-Species Biofilm Fueled by Serpentinization

(2011) W. J. Brazelton et al.   mBio

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Multiple origins of methane at the Lost City Hydrothermal Field

(2010) Alexander S. Bradley et al.   EARTH AND PLANETARY SCIENCE LETTERS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

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

A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes

(2009) Yuzhen Ye et al.   PLoS Computational Biology

Carbon geochemistry of serpentinites in the Lost City Hydrothermal System (30°N, MAR)

(2008) Adélie Delacour et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Abiogenic Hydrocarbon Production at Lost City Hydrothermal Field

(2008) G. Proskurowski et al.   SCIENCE

Comparative transcriptome analysis of responses of Methanothermobacter thermautotrophicus to different environmental stimuli

(2007) Souichiro Kato et al.   ENVIRONMENTAL MICROBIOLOGY