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

Variations in microbial carbon sources and cycling in the deep continental subsurface

(2016) Danielle N. Simkus et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Sulfur mass-independent fractionation in subsurface fracture waters indicates a long-standing sulfur cycle in Precambrian rocks

(2016) L. Li et al.   Nature Communications

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

(2015) Cara Magnabosco et al.   ISME Journal

Intercellular wiring enables electron transfer between methanotrophic archaea and bacteria

(2015) Gunter Wegener et al.   NATURE

Single cell activity reveals direct electron transfer in methanotrophic consortia

(2015) Shawn E. McGlynn et al.   NATURE

Eukaryotic opportunists dominate the deep-subsurface biosphere in South Africa

(2015) G. Borgonie et al.   Nature Communications

Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population

(2015) Jessica M. Labonté et al.   Frontiers in Microbiology

Groundwater Isolation Governs Chemistry and Microbial Community Structure along Hydrologic Flowpaths

(2015) Sarah Ben Maamar et al.   Frontiers in Microbiology

Stable Sulfur and Oxygen Isotope Fractionation of Anoxic Sulfide Oxidation by Two Different Enzymatic Pathways

(2014) Alexander Poser et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

A novel hydrogen oxidizer amidst the sulfur-oxidizing Thiomicrospira lineage

(2014) Moritz Hansen et al.   ISME Journal

Proteogenomics: concepts, applications and computational strategies

(2014) Alexey I Nesvizhskii   NATURE METHODS

Phylogeny and phylogeography of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships

(2014) Maggie C. Y. Lau et al.   Frontiers in Microbiology

Chemolithotrophy in the continental deep subsurface: Sanford Underground Research Facility (SURF), USA

(2014) Magdalena R. Osburn et al.   Frontiers in Microbiology

Comparisons of the composition and biogeographic distribution of the bacterial communities occupying South African thermal springs with those inhabiting deep subsurface fracture water

(2014) Cara Magnabosco et al.   Frontiers in Microbiology

tRNADB-CE: tRNA gene database well-timed in the era of big sequence data

(2014) Takashi Abe et al.   Frontiers in Genetics

Microbial characterization of basalt formation waters targeted for geological carbon sequestration

(2013) Heather J. Lavalleur et al.   FEMS MICROBIOLOGY ECOLOGY

Does aspartic acid racemization constrain the depth limit of the subsurface biosphere?

(2013) T. C. Onstott et al.   Geobiology

Taxonomically and functionally diverse microbial communities in deep crystalline rocks of the Fennoscandian shield

(2013) Mari Nyyssönen et al.   ISME Journal

Gene expression in the deep biosphere

(2013) William D. Orsi et al.   NATURE

Nitrogen losses in anoxic marine sediments driven by Thioploca–anammox bacterial consortia

(2013) M. G. Prokopenko et al.   NATURE

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

Evidence for Microbial Carbon and Sulfur Cycling in Deeply Buried Ridge Flank Basalt

(2013) M. A. Lever et al.   SCIENCE

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Sizing up metatranscriptomics

(2012) Mary Ann Moran et al.   ISME Journal

Microbial diversity within basement fluids of the sediment-buried Juan de Fuca Ridge flank

(2012) Sean P Jungbluth et al.   ISME Journal

MODELING FISH BIOMASS STRUCTURE AT NEAR PRISTINE CORAL REEFS AND DEGRADATION BY FISHING

(2012) ABHINAV SINGH et al.   JOURNAL OF BIOLOGICAL SYSTEMS

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

(2012) Jana Milucka et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

A multiple sulfur and organic carbon isotope record from non-conglomeratic sedimentary rocks of the Mesoarchean Witwatersrand Supergroup, South Africa

(2012) B.M. Guy et al.   PRECAMBRIAN RESEARCH

Evidence for hydrogen oxidation and metabolic plasticity in widespread deep-sea sulfur-oxidizing bacteria

(2012) K. Anantharaman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Neon identifies two billion year old fluid component in Kaapvaal Craton

(2011) Johanna Lippmann-Pipke et al.   CHEMICAL GEOLOGY

The origin of NO3− and N2 in deep subsurface fracture water of South Africa

(2011) Bianca J. Silver et al.   CHEMICAL GEOLOGY

Anaerobic, Nitrate-Dependent Oxidation of Pyrite Nanoparticles by Thiobacillus denitrificans

(2011) Julian Bosch et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Nematoda from the terrestrial deep subsurface of South Africa

(2011) G. Borgonie et al.   NATURE

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

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

Sulfuritalea hydrogenivorans gen. nov., sp. nov., a facultative autotroph isolated from a freshwater lake

(2010) H. Kojima et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Sulfuricella denitrificans gen. nov., sp. nov., a sulfur-oxidizing autotroph isolated from a freshwater lake

(2010) H. Kojima et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

De novo assembly and analysis of RNA-seq data

(2010) Gordon Robertson et al.   NATURE METHODS

tRNADB-CE 2011: tRNA gene database curated manually by experts

(2010) T. Abe et al.   NUCLEIC ACIDS RESEARCH

Sulfur Isotope Enrichment during Maintenance Metabolism in the Thermophilic Sulfate-Reducing Bacterium Desulfotomaculum putei

(2009) M. M. Davidson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Modeling inverted biomass pyramids and refuges in ecosystems

(2009) Hao Wang et al.   ECOLOGICAL MODELLING

Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME-1 group

(2009) Anke Meyerdierks et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial Architecture of Environmental Sulfur Processes: A Novel Syntrophic Sulfur-Metabolizing Consortia

(2009) Kelsey L.I. Norlund et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Universal sample preparation method for proteome analysis

(2009) Jacek R Wiśniewski et al.   NATURE METHODS

Removal of nitrite with sulfamic acid for nitrate N and O isotope analysis with the denitrifier method

(2009) Julie Granger et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

A high-resolution chemical and structural study of framboidal pyrite formed within a low-temperature bacterial biofilm

(2008) L. C. W. MACLEAN et al.   Geobiology

Isotopic signatures of CH4 and higher hydrocarbon gases from Precambrian Shield sites: A model for abiogenic polymerization of hydrocarbons

(2008) B. Sherwood Lollar et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth

(2008) D. Chivian et al.   SCIENCE