Related references
Note: Only part of the references are listed.GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
Pierre-Alain Chaumeil et al.
BIOINFORMATICS (2020)
KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold
Takuya Aramaki et al.
BIOINFORMATICS (2020)
Groundwater cable bacteria conserve energy by sulfur disproportionation
Hubert Mueller et al.
ISME JOURNAL (2020)
Two Routes for Extracellular Electron Transfer in Enterococcus faecalis
Lars Hederstedt et al.
JOURNAL OF BACTERIOLOGY (2020)
The Crystal Structure of a Biological Insulated Transmembrane Molecular Wire
Marcus J. Edwards et al.
CELL (2020)
Editorial: Microbial Hydrogen Metabolism
Chris Greening et al.
FRONTIERS IN MICROBIOLOGY (2020)
FeGenie: A Comprehensive Tool for the Identification of Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome Assemblies
Arkadiy I. Garber et al.
FRONTIERS IN MICROBIOLOGY (2020)
Accurate and complete genomes from metagenomes
Lin-Xing Chen et al.
GENOME RESEARCH (2020)
Mineral-hosted biofilm communities in the continental deep subsurface, Deep Mine Microbial Observatory, SD, USA
Caitlin P. Casar et al.
GEOBIOLOGY (2020)
Evidence for a Growth Zone for Deep-Subsurface Microbial Clades in Near-Surface Anoxic Sediments
Karen G. Lloyd et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2020)
Ultradeep Microbial Communities at 4.4 km within Crystalline Bedrock: Implications for Habitability in a Planetary Context
Lotta Purkamo et al.
LIFE-BASEL (2020)
The Potential Role of Halothiobacillus spp. in Sulfur Oxidation and Acid Generation in Circum-Neutral Mine Tailings Reservoirs
Kelly Whaley-Martin et al.
FRONTIERS IN MICROBIOLOGY (2019)
'Follow the Water': Hydrogeochemical Constraints on Microbial Investigations 2.4 km Below Surface at the Kidd Creek Deep Fluid and Deep Life Observatory
Garnet S. Lollar et al.
GEOMICROBIOLOGY JOURNAL (2019)
MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies
Dongwan D. Kang et al.
PEERJ (2019)
On the evolution and physiology of cable bacteria
Kasper U. Kjeldsen et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)
An evolving view of methane metabolism in the Archaea
Paul N. Evans et al.
NATURE REVIEWS MICROBIOLOGY (2019)
Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing
Rebecca A. Daly et al.
NATURE MICROBIOLOGY (2019)
Subsurface Microbial Hydrogen Cycling: Natural Occurrence and Implications for Industry
Simon P. Gregory et al.
MICROORGANISMS (2019)
Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle
Karthik Anantharaman et al.
ISME JOURNAL (2018)
Structural modeling of an outer membrane electron conduit from a metal-reducing bacterium suggests electron transfer via periplasmic redox partners
Marcus J. Edwards et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2018)
Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales
Mikayla A. Borton et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)
The biomass distribution on Earth
Yinon M. Bar-On et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)
Reversibility of citrate synthase allows autotrophic growth of a thermophilic bacterium
Achim Mall et al.
SCIENCE (2018)
Characterization of the First Candidatus Nitrotoga Isolate Reveals Metabolic Versatility and Separate Evolution of Widespread Nitrite-Oxidizing Bacteria
Katharina Kitzinger et al.
MBIO (2018)
Identification and Removal of Contaminant Sequences From Ribosomal Gene Databases: Lessons From the Census of Deep Life
Cody S. Sheik et al.
FRONTIERS IN MICROBIOLOGY (2018)
Genomic profiling of four cultivated Candidatus Nitrotoga spp. predicts broad metabolic potential and environmental distribution
Andrew M. Boddicker et al.
ISME JOURNAL (2018)
A flavin-based extracellular electron transfer mechanism in diverse Gram-positive bacteria
Samuel H. Light et al.
NATURE (2018)
The biomass and biodiversity of the continental subsurface
C. Magnabosco et al.
NATURE GEOSCIENCE (2018)
High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries
Chirag Jain et al.
NATURE COMMUNICATIONS (2018)
metaSPAdes: a new versatile metagenomic assembler
Sergey Nurk et al.
GENOME RESEARCH (2017)
The relative abundances of resolved 12CH2D2 and 13CH3D and mechanisms controlling isotopic bond ordering in abiotic and biotic methane gases
E. D. Young et al.
GEOCHIMICA ET COSMOCHIMICA ACTA (2017)
Energy and carbon metabolisms in a deep terrestrial subsurface fluid microbial community
Lily Momper et al.
ISME JOURNAL (2017)
Genomic potential of Marinobacter salinus Hb8T as sulfur oxidizing and aromatic hydrocarbon degrading bacterium
Sundas Rani et al.
MARINE GENOMICS (2017)
Methyl-compound use and slow growth characterize microbial life in 2-km-deep subseafloor coal and shale beds
Elizabeth Trembath-Reichert et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)
Disguised as a Sulfate Reducer: Growth of the Deltaproteobacterium Desulfurivibrio alkaliphilus by Sulfide Oxidation with Nitrate
Casper Thorup et al.
MBIO (2017)
A RuBisCO-mediated carbon metabolic pathway in methanogenic archaea
Takunari Kono et al.
NATURE COMMUNICATIONS (2017)
Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH
Katrina I. Twing et al.
FRONTIERS IN MICROBIOLOGY (2017)
Geological and Geochemical Controlson Subsurface Microbial Life in the Samail Ophiolite, Oman
Kaitlin R. Rempfert et al.
FRONTIERS IN MICROBIOLOGY (2017)
Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems
Sean P. Jungbluth et al.
PEERJ (2017)
Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif Italy
William J. Brazelton et al.
PEERJ (2017)
OptiClust, an Improved Method for Assigning Amplicon-Based Sequence Data to Operational Taxonomic Units
Sarah L. Westcott et al.
MSPHERE (2017)
The Abiotic Nitrogen Cycle
Timothy A. Doane
ACS EARTH AND SPACE CHEMISTRY (2017)
A metagenomic window into carbon metabolism at 3 km depth in Precambrian continental crust
Cara Magnabosco et al.
ISME JOURNAL (2016)
Variations in microbial carbon sources and cycling in the deep continental subsurface
Danielle N. Simkus et al.
GEOCHIMICA ET COSMOCHIMICA ACTA (2016)
An oligotrophic deep-subsurface community dependent on syntrophy is dominated by sulfur-driven autotrophic denitrifiers
Maggie C. Y. Lau et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)
Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system
Karthik Anantharaman et al.
NATURE COMMUNICATIONS (2016)
Sulfur mass-independent fractionation in subsurface fracture waters indicates a long-standing sulfur cycle in Precambrian rocks
L. Li et al.
NATURE COMMUNICATIONS (2016)
Isolation and Genomic Characterization of 'Desulfuromonas soudanensis WTL', a Metal- and Electrode-Respiring Bacterium from Anoxic Deep Subsurface Brine
Jonathan P. Badalamenti et al.
FRONTIERS IN MICROBIOLOGY (2016)
Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales
Rebecca A. Daly et al.
NATURE MICROBIOLOGY (2016)
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
Donovan H. Parks et al.
GENOME RESEARCH (2015)
Microbial ecology of the cryosphere: sea ice and glacial habitats
Antje Boetius et al.
NATURE REVIEWS MICROBIOLOGY (2015)
Exploring deep microbial life in coal-bearing sediment down to ∼2.5 km below the ocean floor
F. Inagaki et al.
SCIENCE (2015)
Marinobacter subterrani, a genetically tractable neutrophilic Fe(II)-oxidizing strain isolated from the Soudan Iron Mine
Benjamin M. Bonis et al.
FRONTIERS IN MICROBIOLOGY (2015)
Anvi'o: an advanced analysis and visualization platformfor 'omics data
A. Murat Eren et al.
PEERJ (2015)
Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria
Brett J. Baker et al.
MICROBIOME (2015)
Distribution, Diversity, and Activities of Sulfur Dioxygenases in Heterotrophic Bacteria
Honglei Liu et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2014)
Does aspartic acid racemization constrain the depth limit of the subsurface biosphere?
T. C. Onstott et al.
GEOBIOLOGY (2014)
Taxonomically and functionally diverse microbial communities in deep crystalline rocks of the Fennoscandian shield
Mari Nyyssonen et al.
ISME JOURNAL (2014)
The contribution of the Precambrian continental lithosphere to global H2 production
Barbara Sherwood Lollar et al.
NATURE (2014)
Binning metagenomic contigs by coverage and composition
Johannes Alneberg et al.
NATURE METHODS (2014)
A nonpyrrolysine member of the widely distributed trimethylamine methyltransferase family is a glycine betaine methyltransferase
Tomislav Ticak et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
Chemolithotrophy in the continental deep subsurface: Sanford Underground Research Facility (SURF), USA
Magdalena R. Osburn et al.
FRONTIERS IN MICROBIOLOGY (2014)
Trends and future challenges in sampling the deep terrestrial biosphere
Michael J. Wilkins et al.
FRONTIERS IN MICROBIOLOGY (2014)
Microbial communities in the subglacial waters of the Vatnajokull ice cap, Iceland
Viggo Thor Marteinsson et al.
ISME JOURNAL (2013)
Deep fracture fluids isolated in the crust since the Precambrian era
G. Holland et al.
NATURE (2013)
Microbial life under extreme energy limitation
Tori M. Hoehler et al.
NATURE REVIEWS MICROBIOLOGY (2013)
Turnover of microbial lipids in the deep biosphere and growth of benthic archaeal populations
Sitan Xie et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
Nature and Extent of the Deep Biosphere
Frederick S. Colwell et al.
CARBON IN EARTH (2013)
The Deep, Dark Energy Biosphere: Intraterrestrial Life on Earth
Katrina J. Edwards et al.
ANNUAL REVIEW OF EARTH AND PLANETARY SCIENCES, VOL 40 (2012)
Mind the gap: diversity and reactivity relationships among multihaem cytochromes of the MtrA/DmsE family
Kathryn D. Bewley et al.
BIOCHEMICAL SOCIETY TRANSACTIONS (2012)
The origin of NO3- and N2 in deep subsurface fracture water of South Africa
Bianca J. Silver et al.
CHEMICAL GEOLOGY (2012)
Outer-membrane cytochrome-independent reduction of extracellular electron acceptors in Shewanella oneidensis
Clemens Buecking et al.
MICROBIOLOGY-SGM (2012)
Global distribution of microbial abundance and biomass in subseafloor sediment
Jens Kallmeyer et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)
Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla
Kelly C. Wrighton et al.
SCIENCE (2012)
Metagenomic evidence for H2 oxidation and H2 production by serpentinite-hosted subsurface microbial communities
William J. Brazelton et al.
FRONTIERS IN MICROBIOLOGY (2012)
UCHIME improves sensitivity and speed of chimera detection
Robert C. Edgar et al.
BIOINFORMATICS (2011)
Thermodynamic limits to microbial life at high salt concentrations
Aharon Oren
ENVIRONMENTAL MICROBIOLOGY (2011)
Microbial seed banks: the ecological and evolutionary implications of dormancy
Jay T. Lennon et al.
NATURE REVIEWS MICROBIOLOGY (2011)
Microbial Ecology of the Dark Ocean above, at, and below the Seafloor
Beth N. Orcutt et al.
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS (2011)
Potential for nitrogen fixation and nitrification in the granite-hosted subsurface at Henderson Mine, CO
Elizabeth D. Swanner et al.
FRONTIERS IN MICROBIOLOGY (2011)
Microbial Provinces in the Subseafloor
Matthew O. Schrenk et al.
ANNUAL REVIEW OF MARINE SCIENCE (2010)
Purification and Characterization of OmcZ, an Outer-Surface, Octaheme c-Type Cytochrome Essential for Optimal Current Production by Geobacter sulfurreducens
Kengo Inoue et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2010)
The Mtr Respiratory Pathway Is Essential for Reducing Flavins and Electrodes in Shewanella oneidensis
Dan Coursolle et al.
JOURNAL OF BACTERIOLOGY (2010)
Modularity of the Mtr respiratory pathway of Shewanella oneidensis strain MR-1
Dan Coursolle et al.
MOLECULAR MICROBIOLOGY (2010)
Autotrophic carbon fixation in archaea
Ivan A. Berg et al.
NATURE REVIEWS MICROBIOLOGY (2010)
Fast and accurate short read alignment with Burrows-Wheeler transform
Heng Li et al.
BIOINFORMATICS (2009)
Reverse dissimilatory sulfite reductase as phylogenetic marker for a subgroup of sulfur-oxidizing prokaryotes
Alexander Loy et al.
ENVIRONMENTAL MICROBIOLOGY (2009)
Characterization of Facultative Sulfur-oxidizing Marinobacter sp BR13 Isolated from Marine Sediment of Yellow Sea, Korea
Bo-Ram Choi et al.
JOURNAL OF THE KOREAN SOCIETY FOR APPLIED BIOLOGICAL CHEMISTRY (2009)
Anode Biofilm Transcriptomics Reveals Outer Surface Components Essential for High Density Current Production in Geobacter sulfurreducens Fuel Cells
Kelly P. Nevin et al.
PLOS ONE (2009)
Methanogenic archaea: ecologically relevant differences in energy conservation
Rudolf K. Thauer et al.
NATURE REVIEWS MICROBIOLOGY (2008)
Environmental genomics reveals a single-species ecosystem deep within earth
Dylan Chivian et al.
SCIENCE (2008)
Subsurface microbial diversity in deep-granitic-fracture water in Colorado
Jason W. Sahl et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2008)
Characterization of Shewanella oneidensis MtrC:: a cell-surface decaheme cytochrome involved in respiratory electron transport to extracellular electron acceptors
Robert S. Hartshorne et al.
JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY (2007)
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
Qiong Wang et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2007)
Archaeal type IIIRuBisCOs function in a pathway for AMP metabolism
Takaaki Sato et al.
SCIENCE (2007)
Long-term sustainability of a high-energy, low-diversity crustal biome
Li-Hung Lin et al.
SCIENCE (2006)
Extracellular respiration of dimethyl sulfoxide by Shewanella oneidensis strain MR-1
JA Gralnick et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Using pyrosequencing to shed light on deep mine microbial ecology
Robert A. Edwards et al.
BMC GENOMICS (2006)
Unravelling abiogenic and biogenic sources of methane in the Earth's deep subsurface
BS Lollar et al.
CHEMICAL GEOLOGY (2006)
Outer membrane c-type cytochromes required for Fe(III) and Mn(IV) oxide reduction in Geobacter sulfurreducens
T Mehta et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2005)
OmcF, a putative c-type monoheme outer membrane cytochrome required for the expression of other outer membrane cytochromes in Geobacter sulfurreducens
BC Kim et al.
JOURNAL OF BACTERIOLOGY (2005)
Prokaryotic sulfur oxidation
CG Friedrich et al.
CURRENT OPINION IN MICROBIOLOGY (2005)
In situ bioreduction of technetium and uranium in a nitrate-contaminated aquifer
JD Istok et al.
ENVIRONMENTAL SCIENCE & TECHNOLOGY (2004)
Microbial hydrocarbon gases in the Witwatersrand Basin, South Africa: Implications for the deep biosphere
JA Ward et al.
GEOCHIMICA ET COSMOCHIMICA ACTA (2004)
Geochemical and microbiological evidence for a hydrogen-based, hyperthermophilic subsurface lithoautotrophic microbial ecosystem (HyperSLiME) beneath an active deep-sea hydrothermal field
K Takai et al.
EXTREMOPHILES (2004)
Characterization of the Shewanella oneidensis MR-1 decaheme cytochrome MtrA
KE Pitts et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2003)
Related assemblages of sulphate-reducing bacteria associated with ultradeep gold mines of South Africa and deep basalt aquifers of Washington State
BJ Baker et al.
ENVIRONMENTAL MICROBIOLOGY (2003)
Dating ultra-deep mine waters with noble gases and Cl-36, Witwatersrand Basin, South Africa
J Lippmann et al.
GEOCHIMICA ET COSMOCHIMICA ACTA (2003)
MtrB is required for proper incorporation of the cytochromes OmcA and OmcB into the outer membrane of Shewanella putrefaciens MR-1
CR Myers et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2002)
Abiogenic formation of alkanes in the Earth's crust as a minor source for global hydrocarbon reservoirs
BS Lollar et al.
NATURE (2002)