Methanogenic paraffin degradation proceeds via alkane addition to fumarate by ‘Smithella’ spp. mediated by a syntrophic coupling with hydrogenotrophic methanogens

Abyssivirga alkaniphila gen. nov., sp. nov., an alkane-degrading, anaerobic bacterium from a deep-sea hydrothermal vent system, and emended descriptions of Natranaerovirga pectinivora and Natranaerovirga hydrolytica

(2016) Anders Schouw et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Reduction of ferredoxin or oxygen by flavin-based electron bifurcation inMegasphaera elsdenii

(2015) Nilanjan P. Chowdhury et al.   FEBS Journal

Comparative analysis of metagenomes from three methanogenic hydrocarbon-degrading enrichment cultures with 41 environmental samples

(2015) Boonfei Tan et al.   ISME Journal

Networks of energetic and metabolic interactions define dynamics in microbial communities

(2015) Mallory Embree et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Proteomic analysis reveals metabolic and regulatory systems involved in the syntrophic and axenic lifestyle of Syntrophomonas wolfei

(2015) Jessica R. Sieber et al.   Frontiers in Microbiology

Anaerolineaceae and Methanosaeta turned to be the dominant microorganisms in alkanes-dependent methanogenic culture after long-term of incubation

(2015) Bo Liang et al.   AMB Express

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Biodegradation of C7and C8iso-alkanes under methanogenic conditions

(2014) Nidal Abu Laban et al.   ENVIRONMENTAL MICROBIOLOGY

The genome ofSyntrophorhabdus aromaticivoransstrain UI provides new insights for syntrophic aromatic compound metabolism and electron flow

(2014) Masaru K. Nobu et al.   ENVIRONMENTAL MICROBIOLOGY

Re-analysis of omics data indicates Smithella may degrade alkanes by addition to fumarate under methanogenic conditions

(2014) Boonfei Tan et al.   ISME Journal

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

(2014) C. Brasen et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Anaerobic hydrocarbon and fatty acid metabolism by syntrophic bacteria and their impact on carbon steel corrosion

(2014) Christopher N. Lyles et al.   Frontiers in Microbiology

MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm

(2014) Yu-Wei Wu et al.   Microbiome

Metagenomic analysis of an anaerobic alkane-degrading microbial culture: potential hydrocarbon-activating pathways and inferred roles of community members

(2013) Boonfei Tan et al.   GENOME

Evidence that crude oil alkane activation proceeds by different mechanisms under sulfate-reducing and methanogenic conditions

(2013) C.M. Aitken et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community

(2013) Mallory Embree et al.   ISME Journal

Identification and Characterization of Re-Citrate Synthase in Syntrophus aciditrophicus

(2013) M. Kim et al.   JOURNAL OF BACTERIOLOGY

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

A Proteomic View at the Biochemistry of Syntrophic Butyrate Oxidation in Syntrophomonas wolfei

(2013) Alexander Schmidt et al.   PLoS One

Systematic Identification of Gene Families for Use as “Markers” for Phylogenetic and Phylogeny-Driven Ecological Studies of Bacteria and Archaea and Their Major Subgroups

(2013) Dongying Wu et al.   PLoS One

Enzymes involved in the anaerobic oxidation of n-alkanes: from methane to long-chain paraffins

(2013) Amy V. Callaghan   Frontiers in Microbiology

Analysis of alkane-dependent methanogenic community derived from production water of a high-temperature petroleum reservoir

(2012) Serge Maurice Mbadinga et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Gene and translation initiation site prediction in metagenomic sequences

(2012) Doug Hyatt et al.   BIOINFORMATICS

The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools

(2012) Andreas Wilke et al.   BMC BIOINFORMATICS

Microbial Communities Involved in Methane Production from Hydrocarbons in Oil Sands Tailings

(2012) Tariq Siddique et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Enrichment and dynamics of novel syntrophs in a methanogenic hexadecane-degrading culture from a Chinese oilfield

(2012) Lei Cheng et al.   FEMS MICROBIOLOGY ECOLOGY

Methanogenic Microbial Community Composition of Oily Sludge and Its Enrichment Amended with Alkanes Incubated for Over 500 Days

(2012) Li-Ying Wang et al.   GEOMICROBIOLOGY JOURNAL

Microbial community characteristics of petroleum reservoir production water amended with n-alkanes and incubated under nitrate-, sulfate-reducing and methanogenic conditions

(2012) Wei Li et al.   INTERNATIONAL BIODETERIORATION & BIODEGRADATION

Ray Meta: scalable de novo metagenome assembly and profiling

(2012) Sébastien Boisvert et al.   GENOME BIOLOGY

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

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

The quantitative significance of Syntrophaceae and syntrophic partnerships in methanogenic degradation of crude oil alkanes

(2011) N. D. Gray et al.   ENVIRONMENTAL MICROBIOLOGY

Anaerobic Biodegradation of Longer-Chainn-Alkanes Coupled to Methane Production in Oil Sands Tailings

(2011) Tariq Siddique et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Assimilatory nitrate utilization by bacteria on the West Florida Shelf as determined by stable isotope probing and functional microarray analysis

(2011) Boris Wawrik et al.   FEMS MICROBIOLOGY ECOLOGY

Field and laboratory studies on the bioconversion of coal to methane in the San Juan Basin

(2011) Boris Wawrik et al.   FEMS MICROBIOLOGY ECOLOGY

Characterization of an alkane-degrading methanogenic enrichment culture from production water of an oil reservoir after 274 days of incubation

(2011) Li-Ying Wang et al.   INTERNATIONAL BIODETERIORATION & BIODEGRADATION

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

KEGG for integration and interpretation of large-scale molecular data sets

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

KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases

(2011) Chen Xie et al.   NUCLEIC ACIDS RESEARCH

HMMER web server: interactive sequence similarity searching

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

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Mature fine tailings from oil sands processing harbour diverse methanogenic communities

(2010) Tara J. Penner et al.   CANADIAN JOURNAL OF MICROBIOLOGY

Diversity of Benzyl- and Alkylsuccinate Synthase Genes in Hydrocarbon-Impacted Environments and Enrichment Cultures

(2010) Amy V. Callaghan et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies

(2010) Sébastien Boisvert et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

PyNAST: a flexible tool for aligning sequences to a template alignment

(2009) J. G. Caporaso et al.   BIOINFORMATICS

Syntrophy in anaerobic global carbon cycles

(2009) Michael J McInerney et al.   CURRENT OPINION IN BIOTECHNOLOGY

Bioenergy Production via Microbial Conversion of Residual Oil to Natural Gas

(2008) L. M. Gieg et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Methanolinea tarda gen. nov., sp. nov., a methane-producing archaeon isolated from a methanogenic digester sludge

(2008) H. Imachi et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex

(2008) Micah Hamady et al.   NATURE METHODS

Anaerobic alkane-degrading strain AK-01 contains two alkylsuccinate synthase genes

(2007) Amy V. Callaghan et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Genes encoding the candidate enzyme for anaerobic activation of n-alkanes in the denitrifying bacterium, strain HxN1

(2007) Olav Grundmann et al.   ENVIRONMENTAL MICROBIOLOGY