Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface

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

Periodic changes in effluent chemistry at cold-water geyser: Crystal geyser in Utah

(2017) Weon Shik Han et al.   JOURNAL OF HYDROLOGY

Asgard archaea illuminate the origin of eukaryotic cellular complexity

(2017) Katarzyna Zaremba-Niedzwiedzka et al.   NATURE

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

Measurement of bacterial replication rates in microbial communities

(2016) Christopher T Brown 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

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

Coupling among Microbial Communities, Biogeochemistry and Mineralogy across Biogeochemical Facies

(2016) James C. Stegen et al.   Scientific Reports

Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum

(2016) Karthik Anantharaman et al.   PeerJ

Large Fractions of CO2-Fixing Microorganisms in Pristine Limestone Aquifers Appear To Be Involved in the Oxidation of Reduced Sulfur and Nitrogen Compounds

(2015) Martina Herrmann et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

Metagenomic analysis of a high carbon dioxide subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla

(2015) Joanne B. Emerson et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2015) Cara Magnabosco et al.   ISME Journal

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

(2015) Christopher T. Brown et al.   NATURE

A viability-linked metagenomic analysis of cleanroom environments: eukarya, prokaryotes, and viruses

(2015) Thomas Weinmaier et al.   Microbiome

Eruption dynamics of CO 2 -driven cold-water geysers: Crystal, Tenmile geysers in Utah and Chimayó geyser in New Mexico

(2014) Z.T. Watson et al.   EARTH AND PLANETARY SCIENCE LETTERS

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

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

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

Drilling and sampling a natural CO2 reservoir: Implications for fluid flow and CO2-fluid–rock reactions during CO2 migration through the overburden

(2013) N. Kampman et al.   CHEMICAL GEOLOGY

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

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

Evaluation of headspace equilibration methods for quantifying greenhouse gases in groundwater

(2012) M.M.R. Jahangir et al.   JOURNAL OF ENVIRONMENTAL MANAGEMENT

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

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

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

Vertical stratification of subsurface microbial community composition across geological formations at the Hanford Site

(2011) Xueju Lin et al.   ENVIRONMENTAL MICROBIOLOGY

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

Hidden Markov model speed heuristic and iterative HMM search procedure

(2010) L Steven Johnson et al.   BMC BIOINFORMATICS

Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group

(2010) Takuro Nunoura et al.   NUCLEIC ACIDS RESEARCH

Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth

(2008) D. Chivian et al.   SCIENCE