Single cell genomic study of Dehalococcoidetes species from deep-sea sediments of the Peruvian Margin

Genome sequences of two dehalogenation specialists- Dehalococcoides mccartyistrains BTF08 and DCMB5 enriched from the highly polluted Bitterfeld region

(2013) Marlén Pöritz et al.   FEMS MICROBIOLOGY LETTERS

Genome sequencing of a single cell of the widely distributed marine subsurface Dehalococcoidia, phylum Chloroflexi

(2013) Kenneth Wasmund et al.   ISME Journal

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Distribution of dehalogenation activity in subseafloor sediments of the Nankai Trough subduction zone

(2013) T. Futagami et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

(2013) M. A. Lever et al.   SCIENCE

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

Growth of Dehalococcoides mccartyi strain CBDB1 by reductive dehalogenation of brominated benzenes to benzene

(2012) Anke Wagner et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Dehalococcoides mccartyi gen. nov., sp. nov., obligately organohalide-respiring anaerobic bacteria relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. and family Dehalococcoidaceae fam. nov., within the phylum Chloroflexi

(2012) F. E. Loffler et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi

(2012) Dimitry Y Sorokin et al.   ISME Journal

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Genomic sequencing of uncultured microorganisms from single cells

(2012) Roger S. Lasken   NATURE REVIEWS MICROBIOLOGY

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

Complete genome sequence of Dehalogenimonas lykanthroporepellens type strain (BL-DC-9T) and comparison to “Dehalococcoides” strains

(2012) Shivakumara Siddaramappa et al.   Standards in Genomic Sciences

Natural Niche for Organohalide-Respiring Chloroflexi

(2011) Mark J. Krzmarzick et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Ecological Aspects of the Distribution of Different Autotrophic CO2Fixation Pathways

(2011) Ivan A. Berg   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Site-Specific Mobilization of Vinyl Chloride Respiration Islands by a Mechanism Common in Dehalococcoides

(2011) Paul J McMurdie et al.   BMC GENOMICS

The genome sequence of Desulfatibacillum alkenivorans AK-01: a blueprint for anaerobic alkane oxidation

(2011) A. V. Callaghan et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial diversity and stratification of South Pacific abyssal marine sediments

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

Enrichment and cultivation of prokaryotes associated with the sulphate-methane transition zone of diffusion-controlled sediments of Aarhus Bay, Denmark, under heterotrophic conditions

(2011) Gordon Webster et al.   FEMS MICROBIOLOGY ECOLOGY

Assemblathon 1: A competitive assessment of de novo short read assembly methods

(2011) D. Earl et al.   GENOME RESEARCH

Metagenomics of the subsurface Brazos-Trinity Basin (IODP site 1320): comparison with other sediment and pyrosequenced metagenomes

(2011) Jennifer F Biddle et al.   ISME Journal

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Decontamination of MDA Reagents for Single Cell Whole Genome Amplification

(2011) Tanja Woyke et al.   PLoS One

Coupling of ferredoxin and heterodisulfide reduction via electron bifurcation in hydrogenotrophic methanogenic archaea

(2011) A.-K. Kaster et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean

(2011) B. K. Swan et al.   SCIENCE

Complete genome sequence of Ferroglobus placidus AEDII12DO

(2011) Iain Anderson et al.   Standards in Genomic Sciences

More Than 200 Genes Required for Methane Formation from H2and CO2and Energy Conservation Are Present inMethanothermobacter marburgensisandMethanothermobacter thermautotrophicus

(2011) Anne-Kristin Kaster et al.   ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL

Emerging Topics in Marine Methane Biogeochemistry

(2010) David L. Valentine   Annual Review of Marine Science

High abundance of JS-1- andChloroflexi-relatedBacteriain deeply buried marine sediments revealed by quantitative, real-time PCR

(2010) Anna Blazejak et al.   FEMS MICROBIOLOGY ECOLOGY

Colonization of subsurface microbial observatories deployed in young ocean crust

(2010) Beth N Orcutt et al.   ISME Journal

Isolation and Characterization of "Dehalococcoides" sp. Strain MB, Which Dechlorinates Tetrachloroethene to trans-1,2-Dichloroethene

(2009) D. Cheng et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Dehalogenation Activities and Distribution of Reductive Dehalogenase Homologous Genes in Marine Subsurface Sediments

(2009) T. Futagami et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genome sequence ofDesulfobacterium autotrophicumHRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide

(2009) Axel W. Strittmatter et al.   ENVIRONMENTAL MICROBIOLOGY

Dehalogenimonas lykanthroporepellens gen. nov., sp. nov., a reductively dehalogenating bacterium isolated from chlorinated solvent-contaminated groundwater

(2009) W. M. Moe et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Cultivation of Uncultured Chloroflexi Subphyla: Significance and Ecophysiology of Formerly Uncultured Chloroflexi 'Subphylum I' with Natural and Biotechnological Relevance

(2009) Takeshi Yamada et al.   MICROBES AND ENVIRONMENTS

The integrated microbial genomes system: an expanding comparative analysis resource

(2009) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

The little bacteria that can - diversity, genomics and ecophysiology of ‘Dehalococcoides’ spp. in contaminated environments

(2009) Neslihan Taş et al.   Microbial Biotechnology

Localized Plasticity in the Streamlined Genomes of Vinyl Chloride Respiring Dehalococcoides

(2009) Paul J. McMurdie et al.   PLoS Genetics

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Prokaryotic biodiversity and activity in the deep subseafloor biosphere

(2008) John C. Fry et al.   FEMS MICROBIOLOGY ECOLOGY

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH

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