Active anaerobic methane oxidation and sulfur disproportionation in the deep terrestrial subsurface

ANME ‐1 archaea may drive methane accumulation and removal in estuarine sediments

(2021) Richard T. Kevorkian et al.   Environmental Microbiology Reports

Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems

(2021) Christine He et al.   Nature Microbiology

Anthropogenic and Environmental Constraints on the Microbial Methane Cycle in Coastal Sediments

(2021) Anna J. Wallenius et al.   Frontiers in Microbiology

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

(2021) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater

(2021) Maliheh Mehrshad et al.   Nature Communications

Protein Family Content Uncovers Lineage Relationships and Bacterial Pathway Maintenance Mechanisms in DPANN Archaea

(2021) Cindy J. Castelle et al.   Frontiers in Microbiology

Active sulfur cycling in the terrestrial deep subsurface

(2020) Emma Bell et al.   ISME Journal

Anaerobic methane oxidation coupled to manganese reduction by members of the Methanoperedenaceae

(2020) Andy O. Leu et al.   ISME Journal

Disproportionation of inorganic sulfur compounds by a novel autotrophic bacterium belonging to Nitrospirota

(2020) Kazuhiro Umezawa et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Severe Corrosion of Carbon Steel in Oil Field Produced Water Can Be Linked to Methanogenic Archaea Containing a Special Type of [NiFe] Hydrogenase

(2020) Sven Lahme et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Large Scale Mapping of Fractures and Groundwater Pathways in Crystalline Hardrock By AEM

(2019) Subash Chandra et al.   Scientific Reports

Anaerobic oxidation of ethane by archaea from a marine hydrocarbon seep

(2019) Song-Can Chen et al.   NATURE

GToTree: a user-friendly workflow for phylogenomics

(2019) Michael D Lee   BIOINFORMATICS

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

Diversity of Sulfur-Disproportionating Microorganisms

(2019) A. I. Slobodkin et al.   MICROBIOLOGY

Targeted isolation and cultivation of uncultivated bacteria by reverse genomics

(2019) Karissa L. Cross et al.   NATURE BIOTECHNOLOGY

KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold

(2019) Takuya Aramaki et al.   BIOINFORMATICS

Manganese/iron‐supported sulfate‐dependent anaerobic oxidation of methane by archaea in lake sediments

(2019) Guangyi Su et al.   LIMNOLOGY AND OCEANOGRAPHY

CDD/SPARCLE: the conserved domain database in 2020

(2019) Shennan Lu et al.   NUCLEIC ACIDS RESEARCH

Genome‐inferred spatio‐temporal resolution of an uncultivated Roizmanbacterium reveals its ecological preferences in groundwater

(2019) Patricia Geesink et al.   ENVIRONMENTAL MICROBIOLOGY

Gene expression and ultrastructure of meso- and thermophilic methanotrophic consortia

(2018) Viola Krukenberg et al.   ENVIRONMENTAL MICROBIOLOGY

Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle

(2018) Karthik Anantharaman et al.   ISME Journal

A methanotrophic archaeon couples anaerobic oxidation of methane to Fe(III) reduction

(2018) Chen Cai et al.   ISME Journal

Global diffusive fluxes of methane in marine sediments

(2018) Matthias Egger et al.   Nature Geoscience

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

(2018) Christian M. K. Sieber et al.   Nature Microbiology

The biomass and biodiversity of the continental subsurface

(2018) C. Magnabosco et al.   Nature Geoscience

Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations

(2018) Cindy J. Castelle et al.   NATURE REVIEWS MICROBIOLOGY

Biogeochemical Cycling by a Low-Diversity Microbial Community in Deep Groundwater

(2018) Emma Bell et al.   Frontiers in Microbiology

Metatranscriptomes Reveal That All Three Domains of Life Are Active but Are Dominated by Bacteria in the Fennoscandian Crystalline Granitic Continental Deep Biosphere

(2018) Margarita Lopez-Fernandez et al.   mBio

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

Succession in the petroleum reservoir microbiome through an oil field production lifecycle

(2017) Adrien Vigneron et al.   ISME Journal

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

(2017) Alex W Hernsdorf et al.   ISME Journal

Ecological and genomic profiling of anaerobic methane-oxidizing archaea in a deep granitic environment

(2017) Kohei Ino et al.   ISME Journal

Methyl-compound use and slow growth characterize microbial life in 2-km-deep subseafloor coal and shale beds

(2017) Elizabeth Trembath-Reichert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Disguised as a Sulfate Reducer: Growth of the Deltaproteobacterium Desulfurivibrio alkaliphilus by Sulfide Oxidation with Nitrate

(2017) Casper Thorup et al.   mBio

Members of the Candidate Phyla Radiation are functionally differentiated by carbon- and nitrogen-cycling capabilities

(2017) R. E. Danczak et al.   Microbiome

Rates of microbial hydrogen oxidation and sulfate reduction in Opalinus Clay rock

(2016) Alexandre Bagnoud et al.   APPLIED GEOCHEMISTRY

Biogenic processes in crystalline bedrock fractures indicated by carbon isotope signatures of secondary calcite

(2016) Elina Sahlstedt et al.   APPLIED GEOCHEMISTRY

Biogenic methane production from coal: A review on recent research and development on microbially enhanced coalbed methane (MECBM)

(2016) Stephen Y. Park et al.   FUEL

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

(2016) Kelly C Wrighton et al.   ISME Journal

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

An oligotrophic deep-subsurface community dependent on syntrophy is dominated by sulfur-driven autotrophic denitrifiers

(2016) Maggie C. Y. Lau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Deep microbial life in high-quality granitic groundwater from geochemically and geographically distinct underground boreholes

(2016) Kohei Ino et al.   Environmental Microbiology Reports

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

(2016) Alexandre Bagnoud et al.   Nature Communications

Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales

(2016) Rebecca A. Daly et al.   Nature Microbiology

HydDB: A web tool for hydrogenase classification and analysis

(2016) Dan Søndergaard et al.   Scientific Reports

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling

(2015) Cindy J. Castelle et al.   CURRENT BIOLOGY

Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages

(2015) Laura A. Hug et al.   ENVIRONMENTAL MICROBIOLOGY

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Single cell activity reveals direct electron transfer in methanotrophic consortia

(2015) Shawn E. McGlynn et al.   NATURE

How Bacteria Use Type IV Pili Machinery on Surfaces

(2015) Berenike Maier et al.   TRENDS IN MICROBIOLOGY

Diverse uncultivated ultra-small bacterial cells in groundwater

(2015) Birgit Luef et al.   Nature Communications

Extreme 13C depletion of carbonates formed during oxidation of biogenic methane in fractured granite

(2015) Henrik Drake et al.   Nature Communications

Active Microbial Communities Inhabit Sulphate-Methane Interphase in Deep Bedrock Fracture Fluids in Olkiluoto, Finland

(2015) Malin Bomberg et al.   Biomed Research International

The origin, source, and cycling of methane in deep crystalline rock biosphere

(2015) Riikka Kietäväinen   Frontiers in Microbiology

Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer

(2014) Kelly C Wrighton et al.   ISME Journal

Understanding and modelling dissolved gas transport in the bedrock of three Fennoscandian sites

(2014) Paolo Trinchero et al.   JOURNAL OF HYDROLOGY

The contribution of the Precambrian continental lithosphere to global H2 production

(2014) Barbara Sherwood Lollar et al.   NATURE

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle

(2014) Xuesong He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacteriophage endolysin Lyt μ1/6: characterization of the C-terminal binding domain

(2013) Lenka Tišáková et al.   FEMS MICROBIOLOGY LETTERS

Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage

(2013) Mohamed F. Haroon et al.   NATURE

Microbial life under extreme energy limitation

(2013) Tori M. Hoehler et al.   NATURE REVIEWS MICROBIOLOGY

Pfam: the protein families database

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

Environmental proteomics reveals early microbial community responses to biostimulation at a uranium- and nitrate-contaminated site

(2013) Karuna Chourey et al.   PROTEOMICS

Complete genome sequence of Desulfocapsa sulfexigens, a marine deltaproteobacterium specialized in disproportionating inorganic sulfur compounds

(2013) Kai Waldemar Finster et al.   Standards in Genomic Sciences

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

(2012) Karsten Pedersen   ISME Journal

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Zero-valent sulphur is a key intermediate in marine methane oxidation

(2012) Jana Milucka et al.   NATURE

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads

(2012) Haibin Xu et al.   PLoS One

Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla

(2012) K. C. Wrighton et al.   SCIENCE

Biological souring and mitigation in oil reservoirs

(2011) Lisa M. Gieg et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Deep subseafloor microbial cells on physiological standby

(2011) B. B. Jorgensen   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes

(2010) Nancy Y. Yu et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Evolution of electron transfer out of the cell: comparative genomics of six Geobacter genomes

(2010) Jessica E Butler et al.   BMC GENOMICS

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Anaerobic Oxidation of Methane: Progress with an Unknown Process

(2009) Katrin Knittel et al.   Annual Review of Microbiology

IDPicker 2.0: Improved Protein Assembly with High Discrimination Peptide Identification Filtering

(2009) Ze-Qiang Ma et al.   JOURNAL OF PROTEOME RESEARCH

Enzyme phylogenies as markers for the oxidation state of the environment: The case of respiratory arsenate reductase and related enzymes

(2008) Simon Duval et al.   BMC EVOLUTIONARY BIOLOGY

Microbiological disproportionation of inorganic sulfur compounds

(2008) Kai Finster   Journal of Sulfur Chemistry

Molecular mechanism of energy conservation in polysulfide respiration

(2008) Mika Jormakka et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY