Nitrogen Cycling of Active Bacteria within Oligotrophic Sediment of the Mid-Atlantic Ridge Flank

Fossil DNA persistence and decay in marine sediment over hundred-thousand-year to million-year time scales

(2016) John B. Kirkpatrick et al.   GEOLOGY

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

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

Patient-Specific Bacteroides Genome Variants in Pouchitis

(2016) Joseph H. Vineis et al.   mBio

Nutrient enrichment induces dormancy and decreases diversity of active bacteria in salt marsh sediments

(2016) Patrick J. Kearns et al.   Nature Communications

A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge

(2016) Julie L. Meyer et al.   Scientific Reports

Catabolic rates, population sizes and doubling/replacement times of microorganisms in natural settings

(2015) D. E. LaRowe et al.   AMERICAN JOURNAL OF SCIENCE

Novel abiotic reactions increase nitrous oxide production during partial nitrification: Modeling and experiments

(2015) Willie F. Harper et al.   CHEMICAL ENGINEERING JOURNAL

Subsurface hydrothermal processes and the bioenergetics of chemolithoautotrophy at the shallow-sea vents off Panarea Island (Italy)

(2015) Roy E. Price et al.   CHEMICAL GEOLOGY

Origin, dynamics, and implications of extracellular DNA pools in marine sediments

(2015) Andrea Torti et al.   Marine Genomics

Presence of oxygen and aerobic communities from sea floor to basement in deep-sea sediments

(2015) Steven D’Hondt et al.   Nature Geoscience

Exploring deep microbial life in coal-bearing sediment down to  2.5 km below the ocean floor

(2015) F. Inagaki et al.   SCIENCE

A modular method for the extraction of DNA and RNA, and the separation of DNA pools from diverse environmental sample types

(2015) Mark A. Lever et al.   Frontiers in Microbiology

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

VAMPS: a website for visualization and analysis of microbial population structures

(2014) Susan M Huse et al.   BMC BIOINFORMATICS

Achromobacter sediminum sp. nov., isolated from deep subseafloor sediment of South Pacific Gyre

(2014) Z. Zhang et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Biosphere frontiers of subsurface life in the sedimented hydrothermal system of Guaymas Basin

(2014) Andreas Teske et al.   Frontiers in Microbiology

The phenomenon of microbial uncultivability

(2013) SS Epstein   CURRENT OPINION IN MICROBIOLOGY

Devosia submarina sp. nov., isolated from deep-sea surface sediments

(2013) L. A. Romanenko et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses

(2013) Steven J Blazewicz et al.   ISME Journal

Gene expression in the deep biosphere

(2013) William D. Orsi et al.   NATURE

Deep Sequencing of Subseafloor Eukaryotic rRNA Reveals Active Fungi across Marine Subsurface Provinces

(2013) William Orsi et al.   PLoS One

Microbial Scout Hypothesis, Stochastic Exit from Dormancy, and the Nature of Slow Growers

(2012) S. Buerger et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Interstitial fluid chemistry of sediments underlying the North Atlantic gyre and the influence of subsurface fluid flow

(2012) Wiebke Ziebis et al.   EARTH AND PLANETARY SCIENCE LETTERS

Linking Molecular Microbial Ecology to Geochemistry in a Coastal Hypoxic Zone

(2012) Brandi Kiel Reese et al.   GEOMICROBIOLOGY JOURNAL

Brevundimonas abyssalis sp. nov., a dimorphic prosthecate bacterium isolated from deep-subsea floor sediment

(2012) T. Tsubouchi et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Endospore abundance, microbial growth and necromass turnover in deep sub-seafloor sediment

(2012) Bente Aa. Lomstein et al.   NATURE

Global distribution of microbial abundance and biomass in subseafloor sediment

(2012) J. Kallmeyer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Heterotrophic nitrification by Achromobacter xylosoxidans S18 isolated from a small-scale slaughterhouse wastewater

(2011) Pradyut Kundu et al.   BIOPROCESS AND BIOSYSTEMS ENGINEERING

Interactions of Leptospira with Environmental Bacteria from Surface Water

(2011) Veronica A. Barragan et al.   CURRENT MICROBIOLOGY

Microbial Metabolism in Ice and Brine at −5°C

(2011) Corien Bakermans et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial diversity and stratification of South Pacific abyssal marine sediments

(2011) Alan M. Durbin et al.   ENVIRONMENTAL MICROBIOLOGY

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

Degradation of natural organic matter: A thermodynamic analysis

(2011) Douglas E. LaRowe et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Hydrothermally generated aromatic compounds are consumed by bacteria colonizing in Atlantis II Deep of the Red Sea

(2011) Yong Wang et al.   ISME Journal

New cell extraction procedure applied to deep subsurface sediments

(2011) Jens Kallmeyer et al.   LIMNOLOGY AND OCEANOGRAPHY-METHODS

Bayesian community-wide culture-independent microbial source tracking

(2011) Dan Knights et al.   NATURE METHODS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

A Quantitative PCR Assay for Aerobic, Vinyl Chloride- and Ethene-Assimilating Microorganisms in Groundwater

(2010) Yang Oh Jin et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Acetogenesis in Deep Subseafloor Sediments of The Juan de Fuca Ridge Flank: A Synthesis of Geochemical, Thermodynamic, and Gene-based Evidence

(2010) Mark A. Lever et al.   GEOMICROBIOLOGY JOURNAL

Resting stages and ecology of the planktonic diatom Aulacoseira skvortzowii in Lake Baikal

(2010) David H. Jewson et al.   LIMNOLOGY AND OCEANOGRAPHY

Preservation, origin and genetic imprint of extracellular DNA in permanently anoxic deep-sea sediments

(2010) C. CORINALDESI et al.   MOLECULAR ECOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Dormancy contributes to the maintenance of microbial diversity

(2010) S. E. Jones et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Quantitative PCR methods for RNA and DNA in marine sediments: maximizing yield while overcoming inhibition

(2009) Karen G. Lloyd et al.   FEMS MICROBIOLOGY ECOLOGY

Brevundimonas basaltis sp. nov., isolated from black sand

(2009) J.-H. Choi et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

The versatility and adaptation of bacteria from the genus Stenotrophomonas

(2009) Robert P. Ryan et al.   NATURE REVIEWS MICROBIOLOGY

Subseafloor sedimentary life in the South Pacific Gyre

(2009) Steven D'Hondt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal

(2008) Paul Wilmes et al.   ISME Journal

Tolerance of dormant and active cells in Pseudomonas aeruginosa PA01 biofilm to antimicrobial agents

(2008) Jaeeun Kim et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment

(2008) J. F. Biddle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA