Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2concentrations

Genome-Resolved Metagenomic Analysis Reveals Roles for Candidate Phyla and Other Microbial Community Members in Biogeochemical Transformations in Oil Reservoirs

(2016) Ping Hu et al.   mBio

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

Single-cell genomics of uncultivated deep-branching magnetotactic bacteria reveals a conserved set of magnetosome genes

(2015) Sebastian Kolinko et al.   ENVIRONMENTAL MICROBIOLOGY

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

The range and level of impurities in CO2 streams from different carbon capture sources

(2015) Richard T.J. Porter et al.   International Journal of Greenhouse Gas Control

Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival

(2015) Chris Greening et al.   ISME Journal

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

(2015) Christopher T. Brown et al.   NATURE

Axenic Culture of a Candidate Division TM7 Bacterium from the Human Oral Cavity and Biofilm Interactions with Other Oral Bacteria

(2014) Valeria Soro et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

(2014) Kelly C Wrighton et al.   ISME Journal

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences

(2014) Pablo Yarza et al.   NATURE REVIEWS MICROBIOLOGY

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

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

Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO2 fixation

(2014) M. Konneke 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

Changes in the deep subsurface microbial biosphere resulting from a field-scale CO2 geosequestration experiment

(2014) Andre Mu et al.   Frontiers in Microbiology

Characteristics of CO2-driven cold-water geyser, Crystal Geyser in Utah: experimental observation and mechanism analyses

(2013) W. S. Han et al.   GEOFLUIDS

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

“Candidatus Sonnebornia yantaiensis”, a member of candidate division OD1, as intracellular bacteria of the ciliated protist Paramecium bursaria (Ciliophora, Oligohymenophorea)

(2013) Jun Gong et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla

(2013) R. S. Kantor et al.   mBio

Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment

(2013) Cindy J. Castelle et al.   Nature Communications

Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling

(2013) Laura A Hug et al.   Microbiome

A missing link between complex I and group 4 membrane-bound [NiFe] hydrogenases

(2012) Bruno C. Marreiros et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

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

(2012) Y. Peng et al.   BIOINFORMATICS

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

Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community

(2012) Kim M Handley et al.   ISME Journal

Genetic Evidence for Bacterial Chemolithoautotrophy Based on the Reductive Tricarboxylic Acid Cycle in Groundwater Systems

(2012) Albin Alfreider et al.   MICROBES AND ENVIRONMENTS

MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data

(2012) David Vallenet et al.   NUCLEIC ACIDS RESEARCH

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

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

Ecological Aspects of the Distribution of Different Autotrophic CO2Fixation Pathways

(2011) Ivan A. Berg   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Single-cell analysis reveals a novel uncultivated magnetotactic bacterium within the candidate division OP3

(2011) Sebastian Kolinko et al.   ENVIRONMENTAL MICROBIOLOGY

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Mariprofundus ferrooxydans PV-1 the First Genome of a Marine Fe(II) Oxidizing Zetaproteobacterium

(2011) Esther Singer et al.   PLoS One

Genomic Insights into Syntrophy: The Paradigm for Anaerobic Metabolic Cooperation

(2010) Jessica R. Sieber et al.   Annual Review of 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

Phylogenetic diversity and metagenomics of candidate division OP3

(2010) Jana Glöckner et al.   ENVIRONMENTAL MICROBIOLOGY

Autotrophic carbon fixation in archaea

(2010) Ivan A. Berg et al.   NATURE REVIEWS MICROBIOLOGY

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

The Iron-Hydrogenase of Thermotoga maritima Utilizes Ferredoxin and NADH Synergistically: a New Perspective on Anaerobic Hydrogen Production

(2009) G. J. Schut et al.   JOURNAL OF BACTERIOLOGY

Geological carbon storage

(2009) Mike J. Bickle   Nature Geoscience

The Universal Protein Resource (UniProt) in 2010

(2009)   NUCLEIC ACIDS RESEARCH

Multiple Rubisco forms in proteobacteria: their functional significance in relation to CO2 acquisition by the CBB cycle

(2008) Murray Ronald Badger et al.   JOURNAL OF EXPERIMENTAL BOTANY