Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments

Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2concentrations

(2016) Alexander J. Probst et al.   ENVIRONMENTAL MICROBIOLOGY

RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria

(2016) Kelly C Wrighton et al.   ISME Journal

Archaea catalyze iron-dependent anaerobic oxidation of methane

(2016) Katharina F. Ettwig et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

(2016) Karthik Anantharaman et al.   Nature Communications

Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock

(2016) Alexandre Bagnoud et al.   Nature Communications

A new view of the tree of life

(2016) Laura A. Hug et al.   Nature Microbiology

Formation and Geological Sequestration of Uranium Nanoparticles in Deep Granitic Aquifer

(2016) Yohey Suzuki et al.   Scientific Reports

Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations

(2015) Xiaofen Wu et al.   ISME Journal

A metagenomic window into carbon metabolism at 3 km depth in Precambrian continental crust

(2015) Cara Magnabosco 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

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

(2015) Christopher T. Brown et al.   NATURE

Single cell activity reveals direct electron transfer in methanotrophic consortia

(2015) Shawn E. McGlynn et al.   NATURE

Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development

(2015) Tali Raveh-Sadka et al.   eLife

Microbially induced corrosion of carbon steel in deep groundwater environment

(2015) Pauliina Rajala et al.   Frontiers in Microbiology

A review of prokaryotic populations and processes in sub-seafloor sediments, including biosphere:geosphere interactions

(2014) R. John Parkes et al.   MARINE GEOLOGY

Biology of a widespread uncultivated archaeon that contributes to carbon fixation in the subsurface

(2014) Alexander J. Probst et al.   Nature Communications

PhyloSift: phylogenetic analysis of genomes and metagenomes

(2014) Aaron E. Darling et al.   PeerJ

Microbial Reduction of Fe(III) under Alkaline Conditions Relevant to Geological Disposal

(2013) Adam J. Williamson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Weighing the deep continental biosphere

(2013) Sean McMahon et al.   FEMS MICROBIOLOGY ECOLOGY

Evidence and characteristics of a diverse and metabolically active microbial community in deep subsurface clay borehole water

(2013) Katinka Wouters et al.   FEMS MICROBIOLOGY ECOLOGY

RefSeq microbial genomes database: new representation and annotation strategy

(2013) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

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

Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla

(2013) R. S. Kantor et al.   mBio

Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment

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

FunGene: the functional gene pipeline and repository

(2013) Jordan A. Fish et al.   Frontiers in Microbiology

The Deep, Dark Energy Biosphere: Intraterrestrial Life on Earth

(2012) Katrina J. Edwards et al.   Annual Review of Earth and Planetary Sciences

Energy conservation via electron bifurcating ferredoxin reduction and proton/Na+ translocating ferredoxin oxidation

(2012) Wolfgang Buckel et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Gene and translation initiation site prediction in metagenomic sequences

(2012) Doug Hyatt 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

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

(2012) I. Sharon et al.   GENOME RESEARCH

Immobilization of uranium in biofilm microorganisms exposed to groundwater seeps over granitic rock tunnel walls in Olkiluoto, Finland

(2012) Evelyn Krawczyk-Bärsch et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Redox Buffer Capacity in Water-Rock-Microbe Interaction Systems in Subsurface Environments

(2012) Yuki Amano et al.   GEOMICROBIOLOGY JOURNAL

Metabolic activity of subterranean microbial communities in deep granitic groundwater supplemented with methane and H2

(2012) Karsten Pedersen   ISME Journal

Isolation and identification of bacteria able to form biofilms from deep subsurface environments

(2012) Kenta Sakurai et al.   JOURNAL OF NUCLEAR SCIENCE AND TECHNOLOGY

Microbiological influences on fracture surfaces of intact mudstone and the implications for geological disposal of radioactive waste

(2012) H. Harrison et al.   MINERALOGICAL MAGAZINE

Enriched Iron(III)-Reducing Bacterial Communities are Shaped by Carbon Substrate and Iron Oxide Mineralogy

(2012) Christopher J. Lentini et al.   Frontiers in Microbiology

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

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

Evidence for Direct Electron Transfer by a Gram-Positive Bacterium Isolated from a Microbial Fuel Cell

(2011) K. C. Wrighton et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Interpretation of undisturbed hydrogeochemical conditions in Neogene sediments of the Horonobe area, Hokkaido, Japan

(2011) Hiroshi Sasamoto et al.   APPLIED GEOCHEMISTRY

Mechanical strength of the transition zone at the boundary between opal-A and opal-CT zones in siliceous rocks

(2011) Eiichi Ishii et al.   ENGINEERING GEOLOGY

Microbial methane cycling in a terrestrial mud volcano in eastern Taiwan

(2011) Yung-Hsin Chang et al.   ENVIRONMENTAL MICROBIOLOGY

Diffusion and sorption of Cs+, I− and HTO in samples of the argillaceous Wakkanai Formation from the Horonobe URL, Japan: Clay-based modeling approach

(2011) Yukio Tachi et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Acetate Availability and its Influence on Sustainable Bioremediation of Uranium-Contaminated Groundwater

(2011) Kenneth H. Williams et al.   GEOMICROBIOLOGY JOURNAL

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Molecular hydrogen: An abundant energy source for bacterial activity in nuclear waste repositories

(2011) M. Libert et al.   PHYSICS AND CHEMISTRY OF THE EARTH

UniProt Knowledgebase: a hub of integrated protein data

(2011) M. Magrane et al.   Database-The Journal of Biological Databases and Curation

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

The Deep Biosphere in Terrestrial Sediments in the Chesapeake Bay Area, Virginia, USA

(2011) Anja Breuker et al.   Frontiers in Microbiology

Genomic Insights into Syntrophy: The Paradigm for Anaerobic Metabolic Cooperation

(2010) Jessica R. Sieber et al.   Annual Review of Microbiology

Biochemistry, evolution and physiological function of the Rnf complex, a novel ion-motive electron transport complex in prokaryotes

(2010) Eva Biegel et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Effects of Nitrate on the Stability of Uranium in a Bioreduced Region of the Subsurface

(2010) Wei-Min Wu et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Aciditerrimonas ferrireducens gen. nov., sp. nov., an iron-reducing thermoacidophilic actinobacterium isolated from a solfataric field

(2010) T. Itoh et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Biochemical and genomic facets on the dissimilatory reduction of radionuclides by microorganisms – A review

(2010) Bidyut R. Mohapatra et al.   MINERALS ENGINEERING

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

Metabolic analysis of the soil microbe Dechloromonas aromatica str. RCB: indications of a surprisingly complex life-style and cryptic anaerobic pathways for aromatic degradation

(2009) Kennan Salinero et al.   BMC GENOMICS

Metal reduction by spores ofDesulfotomaculum reducens

(2009) Pilar Junier et al.   ENVIRONMENTAL MICROBIOLOGY

The Iron-Hydrogenase of Thermotoga maritima Utilizes Ferredoxin and NADH Synergistically: a New Perspective on Anaerobic Hydrogen Production

(2009) G. J. Schut et al.   JOURNAL OF BACTERIOLOGY

Phylogenetic diversity of dissimilatory ferric iron reducers in paddy soil of Hunan, South China

(2009) Xin-Jun Wang et al.   JOURNAL OF SOILS AND SEDIMENTS

Manganese- and Iron-Dependent Marine Methane Oxidation

(2009) E. J. Beal et al.   SCIENCE

Unique distribution of deep groundwater bacteria constrained by geological setting

(2009) Kenji Kato et al.   Environmental Microbiology Reports

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Kinetic and product distribution analysis of NO· reductase activity in Nitrosomonas europaea hydroxylamine oxidoreductase

(2008) Joshua Kostera et al.   JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY