Single-Cell Genomics Reveals a Diverse Metabolic Potential of Uncultivated Desulfatiglans-Related Deltaproteobacteria Widely Distributed in Marine Sediment

Metagenomes from deep Baltic Sea sediments reveal how past and present environmental conditions determine microbial community composition

(2018) Ian P.G. Marshall et al.   Marine Genomics

Sulfate Transporters in Dissimilatory Sulfate Reducing Microorganisms: A Comparative Genomics Analysis

(2018) Angeliki Marietou et al.   Frontiers in Microbiology

Significant role of organic sulfur in supporting sedimentary sulfate reduction in low-sulfate environments

(2017) Mojtaba Fakhraee et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Control on rate and pathway of anaerobic organic carbon degradation in the seabed

(2017) F. Beulig et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial community assembly and evolution in subseafloor sediment

(2017) Piotr Starnawski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The novel bacterial phylum Calditrichaeota is diverse, widespread and abundant in marine sediments and has the capacity to degrade detrital proteins

(2017) Ian P. G. Marshall et al.   Environmental Microbiology Reports

The life sulfuric: microbial ecology of sulfur cycling in marine sediments

(2017) Kenneth Wasmund et al.   Environmental Microbiology Reports

Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea

(2017) Connor T. Skennerton et al.   mBio

Bioturbation as a key driver behind the dominance of Bacteria over Archaea in near-surface sediment

(2017) Xihan Chen et al.   Scientific Reports

Slow Microbial Life in the Seabed

(2016) Bo Barker Jørgensen et al.   Annual Review of Marine Science

Comparative Single-Cell Genomics of Chloroflexi from the Okinawa Trough Deep-Subsurface Biosphere

(2016) Heather Fullerton et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

MetalPredator: a web server to predict iron–sulfur cluster binding proteomes

(2016) Yana Valasatava et al.   BIOINFORMATICS

Dethiosulfatarculus sandiegensis gen. nov., sp. nov., isolated from a methanogenic paraffin-degrading enrichment culture and emended description of the family Desulfarculaceae

(2016) Irene A. Davidova et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Single-Cell Genome and Group-Specific dsrAB Sequencing Implicate Marine Members of the Class Dehalococcoidia (Phylum Chloroflexi ) in Sulfur Cycling

(2016) Kenneth Wasmund et al.   mBio

Organohalide Respiring Bacteria and Reductive Dehalogenases: Key Tools in Organohalide Bioremediation

(2016) Bat-Erdene Jugder et al.   Frontiers in Microbiology

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Genomic and enzymatic evidence for acetogenesis among multiple lineages of the archaeal phylum Bathyarchaeota widespread in marine sediments

(2016) Y. He et al.   Nature Microbiology

The FlxABCD-HdrABC proteins correspond to a novel NADH dehydrogenase/heterodisulfide reductase widespread in anaerobic bacteria and involved in ethanol metabolism inDesulfovibrio vulgaris Hildenborough

(2015) Ana Raquel Ramos et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

Activity and community structures of sulfate-reducing microorganisms in polar, temperate and tropical marine sediments

(2015) Alberto Robador et al.   ISME Journal

Intercellular wiring enables electron transfer between methanotrophic archaea and bacteria

(2015) Gunter Wegener et al.   NATURE

A protein trisulfide couples dissimilatory sulfate reduction to energy conservation

(2015) A. A. Santos et al.   SCIENCE

Reductive Dehalogenases Come of Age in Biological Destruction of Organohalides

(2015) Bat-Erdene Jugder et al.   TRENDS IN BIOTECHNOLOGY

Microbial Communities and Organic Matter Composition in Surface and Subsurface Sediments of the Helgoland Mud Area, North Sea

(2015) Oluwatobi E. Oni et al.   Frontiers in Microbiology

Reconstructing each cell's genome within complex microbial communities—dream or reality?

(2015) Scott Clingenpeel et al.   Frontiers in Microbiology

The “bacterial heterodisulfide” DsrC is a key protein in dissimilatory sulfur metabolism

(2014) S.S. Venceslau et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Reclassification of Desulfobacterium anilini as Desulfatiglans anilini comb. nov. within Desulfatiglans gen. nov., and description of a 4-chlorophenol-degrading sulfate-reducing bacterium, Desulfatiglans parachlorophenolica sp. nov.

(2014) D. Suzuki et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes

(2014) M. Kim et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

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

(2014) Anne-Kristin Kaster et al.   ISME Journal

The mechanism of coupling between electron transfer and proton translocation in respiratory complex I

(2014) Leonid A. Sazanov   JOURNAL OF BIOENERGETICS AND BIOMEMBRANES

A review of prokaryotic populations and processes in sub-seafloor sediments, including biosphere:geosphere interactions

(2014) R. John Parkes et al.   MARINE GEOLOGY

Reductive dehalogenase structure suggests a mechanism for B12-dependent dehalogenation

(2014) Karl A. P. Payne et al.   NATURE

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

(2014) Pablo Yarza et al.   NATURE REVIEWS MICROBIOLOGY

MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences

(2014) Chengwei Luo et al.   NUCLEIC ACIDS RESEARCH

Structural basis for organohalide respiration

(2014) Martin Bommer et al.   SCIENCE

High frequency of phylogenetically diverse reductive dehalogenase-homologous genes in deep subseafloor sedimentary metagenomes

(2014) Mikihiko Kawai et al.   Frontiers in Microbiology

Functional role of the MrpA- and MrpD-homologous protein subunits in enzyme complexes evolutionary related to respiratory chain complex I

(2013) Vamsi K. Moparthi et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Anaerobic degradation of homocyclic aromatic compounds via arylcarboxyl-coenzyme A esters: organisms, strategies and key enzymes

(2013) Matthias Boll et al.   ENVIRONMENTAL MICROBIOLOGY

Single-cell genomics shedding light on marine Thaumarchaeota diversification

(2013) Haiwei Luo et al.   ISME Journal

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

(2013) Kenneth Wasmund et al.   ISME Journal

Cyclohexanecarboxyl-Coenzyme A (CoA) and Cyclohex-1-ene-1-Carboxyl-CoA Dehydrogenases, Two Enzymes Involved in the Fermentation of Benzoate and Crotonate in Syntrophus aciditrophicus

(2013) J. W. Kung et al.   JOURNAL OF BACTERIOLOGY

Molecular characterization of the enzymes involved in the degradation of a brominated aromatic herbicide

(2013) Kai Chen et al.   MOLECULAR MICROBIOLOGY

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Predominant archaea in marine sediments degrade detrital proteins

(2013) Karen G. Lloyd et al.   NATURE

IMG 4 version of the integrated microbial genomes comparative analysis system

(2013) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Ribosomal Database Project: data and tools for high throughput rRNA analysis

(2013) James R. Cole et al.   NUCLEIC ACIDS RESEARCH

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

(2013) R. S. Kantor et al.   mBio

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

(2012) Elmar Pruesse et al.   BIOINFORMATICS

Endospore abundance and d:l-amino acid modeling of bacterial turnover in holocene marine sediment (Aarhus Bay)

(2012) Alice T. Langerhuus et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

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

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

Endospore abundance, microbial growth and necromass turnover in deep sub-seafloor sediment

(2012) Bente Aa. Lomstein et al.   NATURE

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

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

Acetogenesis in the Energy-Starved Deep Biosphere – A Paradox?

(2012) Mark Alexander Lever   Frontiers in Microbiology

The membrane QmoABC complex interacts directly with the dissimilatory adenosine 5′-phosphosulfate reductase in sulfate reducing bacteria

(2012) Ana Raquel Ramos   Frontiers in Microbiology

Anaerobic Oxidation of Benzene by the Hyperthermophilic Archaeon Ferroglobus placidus

(2011) Dawn E. Holmes et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Sulfatases and a RadicalS-Adenosyl-l-methionine (AdoMet) Enzyme Are Key for Mucosal Foraging and Fitness of the Prominent Human Gut Symbiont,Bacteroides thetaiotaomicron

(2011) Alhosna Benjdia et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Simple Protocol for the Comparative Analysis of the Structure and Occurrence of Biochemical Pathways Across Superkingdoms

(2011) Claudia Andreini et al.   Journal of Chemical Information and Modeling

Microbial Ecology of the Dark Ocean above, at, and below the Seafloor

(2011) B. N. Orcutt et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Microbial degradation of aromatic compounds — from one strategy to four

(2011) Georg Fuchs et al.   NATURE REVIEWS MICROBIOLOGY

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

A Comparative Genomic Analysis of Energy Metabolism in Sulfate Reducing Bacteria and Archaea

(2011) Inês A. Cardoso Pereira et al.   Frontiers in Microbiology

Metabolic Flexibility of Sulfate-Reducing Bacteria

(2011) Caroline M. Plugge et al.   Frontiers in Microbiology

Biochemistry, evolution and physiological function of the Rnf complex, a novel ion-motive electron transport complex in prokaryotes

(2010) Eva Biegel et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Comparative metagenomics of bathypelagic plankton and bottom sediment from the Sea of Marmara

(2010) Achim Quaiser et al.   ISME Journal

Genome Sequence of the Deltaproteobacterial Strain NaphS2 and Analysis of Differential Gene Expression during Anaerobic Growth on Naphthalene

(2010) Raymond J. DiDonato et al.   PLoS One

Degradation of Phenol via Phenylphosphate and Carboxylation to 4-Hydroxybenzoate by a Newly Isolated Strain of the Sulfate-Reducing Bacterium Desulfobacterium anilini

(2009) Y.-B. Ahn et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Sulfate-reducing bacteria in marine sediment (Aarhus Bay, Denmark): abundance and diversity related to geochemical zonation

(2009) Julie Leloup et al.   ENVIRONMENTAL MICROBIOLOGY

Towards a consistent classification scheme for geochemical environments, or, why we wish the term ‘suboxic’ would go away

(2009) D. E. CANFIELD et al.   Geobiology

Decarboxylating and Nondecarboxylating Glutaryl-Coenzyme A Dehydrogenases in the Aromatic Metabolism of Obligately Anaerobic Bacteria

(2009) S. Wischgoll et al.   JOURNAL OF BACTERIOLOGY

Combined Genomic and Proteomic Approaches Identify Gene Clusters Involved in Anaerobic 2-Methylnaphthalene Degradation in the Sulfate-Reducing Enrichment Culture N47

(2009) D. Selesi et al.   JOURNAL OF BACTERIOLOGY

Shifting the genomic gold standard for the prokaryotic species definition

(2009) Michael Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Localized Plasticity in the Streamlined Genomes of Vinyl Chloride Respiring Dehalococcoides

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

Acetogenesis and the Wood–Ljungdahl pathway of CO2 fixation

(2008) Stephen W. Ragsdale et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Anaerobic degradation of naphthalene and 2-methylnaphthalene by strains of marine sulfate-reducing bacteria

(2008) Florin Musat et al.   ENVIRONMENTAL MICROBIOLOGY

Reaction Mechanism and Structural Model of ADP-forming Acetyl-CoA Synthetase from the Hyperthermophilic ArchaeonPyrococcus furiosus

(2008) Christopher Bräsen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The ecology and biotechnology of sulphate-reducing bacteria

(2008) Gerard Muyzer et al.   NATURE REVIEWS MICROBIOLOGY

The Mosaic Genome of Anaeromyxobacter dehalogenans Strain 2CP-C Suggests an Aerobic Common Ancestor to the Delta-Proteobacteria

(2008) Sara H. Thomas et al.   PLoS One