A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer

In-situ incubation of iron-sulfur mineral reveals a diverse chemolithoautotrophic community and a new biogeochemical role for Thiomicrospira

(2017) Roman A. Barco et al.   ENVIRONMENTAL MICROBIOLOGY

Viruses in the Oceanic Basement

(2017) Olivia D. Nigro et al.   mBio

BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation

(2017) Elaina D. Graham et al.   PeerJ

Potential Mechanisms for Microbial Energy Acquisition in Oxic Deep-Sea Sediments

(2016) Benjamin J. Tully et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Subseafloor microbial communities in hydrogen-rich vent fluids from hydrothermal systems along the Mid-Cayman Rise

(2016) Julie Reveillaud et al.   ENVIRONMENTAL MICROBIOLOGY

Novel microbial assemblages inhabiting crustal fluids within mid-ocean ridge flank subsurface basalt

(2016) Sean P Jungbluth et al.   ISME Journal

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

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

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

Some Compositional and Kinetic Controls on the Bioenergetic Landscapes in Oceanic Basement

(2016) Wolfgang Bach   Frontiers in Microbiology

Nanocalorimetric Characterization of Microbial Activity in Deep Subsurface Oceanic Crustal Fluids

(2016) Alberto Robador et al.   Frontiers in Microbiology

A new view of the tree of life

(2016) Laura A. Hug et al.   Nature Microbiology

New Insight into Microbial Iron Oxidation as Revealed by the Proteomic Profile of an Obligate Iron-Oxidizing Chemolithoautotroph

(2015) Roman A. Barco et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Carbon fixation by basalt-hosted microbial communities

(2015) Beth N. Orcutt et al.   Frontiers in Microbiology

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Short-Read Assembly of Full-Length 16S Amplicons Reveals Bacterial Diversity in Subsurface Sediments

(2013) Christopher S. Miller et al.   PLoS One

Oxygen consumption rates in subseafloor basaltic crust derived from a reaction transport model

(2013) Beth N. Orcutt et al.   Nature Communications

Phylogenetic diversity and functional gene patterns of sulfur-oxidizing subseafloor Epsilonproteobacteria in diffuse hydrothermal vent fluids

(2013) Nancy H. Akerman et al.   Frontiers in Microbiology

Gene and translation initiation site prediction in metagenomic sequences

(2012) Doug Hyatt et al.   BIOINFORMATICS

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

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

(2012) Y. Peng et al.   BIOINFORMATICS

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse 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

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

(2012) Sean P Jungbluth et al.   ISME Journal

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

The Deep Subsurface Biosphere in Igneous Ocean Crust: Frontier Habitats for Microbiological Exploration

(2012) Katrina J. Edwards et al.   Frontiers in Microbiology

Advanced instrument system for real-time and time-series microbial geochemical sampling of the deep (basaltic) crustal biosphere

(2011) James P. Cowen et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

HMMER web server: interactive sequence similarity searching

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

Seamounts as Conduits for Massive Fluid, Heat, and Solute Fluxes on Ridge Flanks

(2011) Andrew Fisher et al.   OCEANOGRAPHY

EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data

(2011) Christopher S Miller et al.   GENOME BIOLOGY

Beyond the Calvin Cycle: Autotrophic Carbon Fixation in the Ocean

(2010) Michael Hügler et al.   Annual Review of Marine Science

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Identification of ribosomal RNA genes in metagenomic fragments

(2009) Ying Huang et al.   BIOINFORMATICS

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Characterization of microbial processes in deep aquifers of the Fennoscandian Shield

(2008) Lotta Hallbeck et al.   APPLIED GEOCHEMISTRY

Reverse dissimilatory sulfite reductase as phylogenetic marker for a subgroup of sulfur-oxidizing prokaryotes

(2008) Alexander Loy et al.   ENVIRONMENTAL MICROBIOLOGY

The diversity and abundance of bacteria inhabiting seafloor lavas positively correlate with rock alteration

(2008) Cara M. Santelli et al.   ENVIRONMENTAL MICROBIOLOGY

Prokaryotic diversity, distribution and insights into their role in biogeochemical cycling in marine basalts

(2008) Olivia U Mason et al.   ISME Journal