New Frontiers of Anaerobic Hydrocarbon Biodegradation in the Multi-Omics Era

Unfolding microbial community intelligence in aerobic and anaerobic biodegradation processes using metagenomics

(2020) Hitesh Tikariha et al.   ARCHIVES OF MICROBIOLOGY

Anaerobic methane oxidation coupled to manganese reduction by members of the Methanoperedenaceae

(2020) Andy O. Leu et al.   ISME Journal

Metabolic potentials of archaeal lineages resolved from metagenomes of deep Costa Rica sediments

(2020) Ibrahim F. Farag et al.   ISME Journal

Microbial Degradation of Hydrocarbons—Basic Principles for Bioremediation: A Review

(2020) Łukasz Ławniczak et al.   MOLECULES

Assessment of Biodegradation Efficiency of Polychlorinated Biphenyls (PCBs) and Petroleum Hydrocarbons (TPH) in Soil Using Three Individual Bacterial Strains and Their Mixed Culture

(2020) Teresa Steliga et al.   MOLECULES

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0

(2020) Francesco Asnicar et al.   Nature Communications

Benzylsuccinate Synthase is Post-Transcriptionally Regulated in the Toluene-Degrading Denitrifier Magnetospirillum sp. Strain 15-1

(2020) Ingrid Meyer-Cifuentes et al.   Microorganisms

Synthesis and mass spectra of rearrangement bio-signature metabolites of anaerobic alkane degradation via fumarate addition

(2020) Jing Chen et al.   ANALYTICAL BIOCHEMISTRY

Activated carbon stimulates microbial diversity and PAH biodegradation under anaerobic conditions in oil-polluted sediments

(2020) Stefano Bonaglia et al.   CHEMOSPHERE

mRNAs, proteins and the emerging principles of gene expression control

(2020) Christopher Buccitelli et al.   NATURE REVIEWS GENETICS

Adaptation of Carbon Source Utilization Patterns of Geobacter metallireducens During Sessile Growth

(2020) Sviatlana Marozava et al.   Frontiers in Microbiology

Microbial diversity and co-occurrence patterns in deep soils contaminated by polycyclic aromatic hydrocarbons (PAHs)

(2020) Shuying Geng et al.   ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY

An underappreciated DIET for anaerobic petroleum hydrocarbon‐degrading microbial communities

(2020) Federico Aulenta et al.   Microbial Biotechnology

Nitrate-assisted biodegradation of polycyclic aromatic hydrocarbons (PAHs) in the water-level-fluctuation zone of the three Gorges Reservoir, China: Insights from in situ microbial interaction analyses and a microcosmic experiment

(2020) Xinkuan Han et al.   ENVIRONMENTAL POLLUTION

Expanding anaerobic alkane metabolism in the domain of Archaea

(2019) Yinzhao Wang et al.   Nature Microbiology

Co-occurring genomic capacity for anaerobic methane and dissimilatory sulfur metabolisms discovered in the Korarchaeota

(2019) Luke J. McKay et al.   Nature Microbiology

The effect of 16S rRNA region choice on bacterial community metabarcoding results

(2019) Yu. S. Bukin et al.   Scientific Data

More Is Not Always Better: Evaluation of 1D and 2D-LC-MS/MS Methods for Metaproteomics

(2019) Tjorven Hinzke et al.   Frontiers in Microbiology

Gene Editing and Systems Biology Tools for Pesticide Bioremediation: A Review

(2019) Shweta Jaiswal et al.   Frontiers in Microbiology

Anaerobic degradation of hexadecane and phenanthrene coupled to sulfate reduction by enriched consortia from northern Gulf of Mexico seafloor sediment

(2019) Boryoung Shin et al.   Scientific Reports

Aromatoleum gen. nov., a novel genus accommodating the phylogenetic lineage including Azoarcus evansii and related species, and proposal of Aromatoleum aromaticum sp. nov., Aromatoleum petrolei sp. nov., Aromatoleum bremense sp. nov., Aromatoleum toluolicum sp. nov. and Aromatoleum diolicum sp. nov.

(2019) Ralf Rabus et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

New approaches for metagenome assembly with short reads

(2019) Martin Ayling et al.   BRIEFINGS IN BIOINFORMATICS

Hydrocarbon-degrading microbial communities are site-specific and their activity is limited by synergies in temperature and nutrient availability in surface ocean waters

(2019) Xiaoxu Sun et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Advancing biomarkers for anaerobic o-xylene biodegradation via metagenomic analysis of a methanogenic consortium

(2019) Karen Rossmassler et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Characterisation of microbial communities of drill cuttings piles from offshore oil and gas installations

(2019) Lloyd D. Potts et al.   MARINE POLLUTION BULLETIN

Asgard archaea capable of anaerobic hydrocarbon cycling

(2019) Kiley W. Seitz et al.   Nature Communications

Oil Hydrocarbon Degradation by Caspian Sea Microbial Communities

(2019) John I. Miller et al.   Frontiers in Microbiology

Improving anaerobic digestion via direct interspecies electron transfer requires development of suitable characterization methods

(2019) Caroline Van Steendam et al.   CURRENT OPINION IN BIOTECHNOLOGY

Anaerobic hydrocarbon degradation in candidate phylum ‘Atribacteria’ (JS1) inferred from genomics

(2019) Yi-Fan Liu et al.   ISME Journal

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments

(2019) Xiyang Dong et al.   Nature Communications

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

Effect of rhamnolipids on enhanced anaerobic degradation of petroleum hydrocarbons in nitrate and sulfate sediments

(2019) Benru Song et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Anaerobic Degradation of Non-Methane Alkanes by “Candidatus Methanoliparia” in Hydrocarbon Seeps of the Gulf of Mexico

(2019) Rafael Laso-Pérez et al.   mBio

Advances and Challenges in Metatranscriptomic Analysis

(2019) Migun Shakya et al.   Frontiers in Genetics

Insights into Biodegradation Related Metabolism in an Abnormally Low Dissolved Inorganic Carbon (DIC) Petroleum-Contaminated Aquifer by Metagenomics Analysis

(2019) Pingping Cai et al.   Microorganisms

Microaerobic conditions caused the overwhelming dominance of Acinetobacter spp. and the marginalization of Rhodococcus spp. in diesel fuel/crude oil mixture-amended enrichment cultures

(2019) Fruzsina Révész et al.   ARCHIVES OF MICROBIOLOGY

Exploring the genetic potential of a fosmid metagenomic library from an oil-impacted mangrove sediment for metabolism of aromatic compounds

(2019) Sanderson Tarciso Pereira de Sousa et al.   ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY

Hydrochemistry of groundwater contaminated by petroleum hydrocarbons: the impact of biodegradation (Vitanovac, Serbia)

(2019) Nenad Marić et al.   ENVIRONMENTAL GEOCHEMISTRY AND HEALTH

Groundwater cable bacteria conserve energy by sulfur disproportionation

(2019) Hubert Müller et al.   ISME Journal

MGnify: the microbiome analysis resource in 2020

(2019) Alex L Mitchell et al.   NUCLEIC ACIDS RESEARCH

Microbial metatranscriptomic investigations across contaminant gradients of the Detroit River

(2019) N. Falk et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis

(2019) Jethro S. Johnson et al.   Nature Communications

Beyond N and P: The impact of Ni on crude oil biodegradation

(2019) Obioma K. Mejeha et al.   CHEMOSPHERE

Bioelectrochemical remediation of phenanthrene in a microbial fuel cell using an anaerobic consortium enriched from a hydrocarbon-contaminated site

(2019) Mohita Sharma et al.   JOURNAL OF HAZARDOUS MATERIALS

Soil metaproteomics as a tool for monitoring functional microbial communities: promises and challenges

(2019) T. V. Abiraami et al.   REVIEWS IN ENVIRONMENTAL SCIENCE AND BIO-TECHNOLOGY

Quantification of toluene phytoextraction rates and microbial biodegradation functional profiles at a fractured bedrock phytoremediation site

(2019) Michael BenIsrael et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Aerobic bacteria degrading both n-alkanes and aromatic hydrocarbons: an undervalued strategy for metabolic diversity and flexibility

(2018) Joanna Brzeszcz et al.   BIODEGRADATION

Taking the technical microbiome into the next decade

(2018) Jo De Vrieze et al.   ENVIRONMENTAL MICROBIOLOGY

Sphingobium aquiterrae sp. nov., a toluene, meta- and para-xylene-degrading bacterium isolated from petroleum hydrocarbon-contaminated groundwater

(2018) Fruzsina Révész et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Syntrophic growth with direct interspecies electron transfer between pili-free Geobacter species

(2018) Xing Liu et al.   ISME Journal

Hydrocarbon degradation and response of seafloor sediment bacterial community in the northern Gulf of Mexico to light Louisiana sweet crude oil

(2018) Hernando P. Bacosa et al.   ISME Journal

Surfactants selectively reallocated the bacterial distribution in soil bioelectrochemical remediation of petroleum hydrocarbons

(2018) Xiaojing Li et al.   JOURNAL OF HAZARDOUS MATERIALS

Comparative genomic analysis of Geosporobacter ferrireducens and its versatility of anaerobic energy metabolism

(2018) Man-Young Jung et al.   JOURNAL OF MICROBIOLOGY

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

(2018) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Long-distance electron transport in individual, living cable bacteria

(2018) Jesper T. Bjerg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities

(2018) Manuel Kleiner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cable Bacteria Take a New Breath Using Long-Distance Electricity

(2018) Filip J.R. Meysman   TRENDS IN MICROBIOLOGY

Novel insights into freshwater hydrocarbon-rich sediments using metatranscriptomics: Opening the black box

(2018) Thomas Reid et al.   WATER RESEARCH

Microbial community of a gasworks aquifer and identification of nitrate-reducing Azoarcus and Georgfuchsia as key players in BTEX degradation

(2018) Martin Sperfeld et al.   WATER RESEARCH

Selection of validated hypervariable regions is crucial in 16S-based microbiota studies of the female genital tract

(2018) Simon Graspeuntner et al.   Scientific Reports

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

(2018) Christian M. K. Sieber et al.   Nature Microbiology

Bioremediation through microbes: systems biology and metabolic engineering approach

(2018) Arun Kumar Dangi et al.   CRITICAL REVIEWS IN BIOTECHNOLOGY

A benzene-degrading nitrate-reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways

(2018) Siavash Atashgahi et al.   Scientific Reports

Soil Microbial Community Structure and Diversity around the Aging Oil Sludge in Yellow River Delta as Determined by High-Throughput Sequencing

(2018) Shaoping Kuang et al.   ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL

MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis

(2018) Gherman V. Uritskiy et al.   Microbiome

MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs)

(2018) Robert D Stewart et al.   BIOINFORMATICS

Petroleum hydrocarbon rich oil refinery sludge of North-East India harbours anaerobic, fermentative, sulfate-reducing, syntrophic and methanogenic microbial populations

(2018) Ajoy Roy et al.   BMC MICROBIOLOGY

Anaerobic biodegradation of pyrene by Klebsiella sp. LZ6 and its proposed metabolic pathway

(2018) Xiang Li et al.   ENVIRONMENTAL TECHNOLOGY

The Cell Envelope Structure of Cable Bacteria

(2018) Rob Cornelissen et al.   Frontiers in Microbiology

Petroleum Hydrocarbon-Degrading Bacteria for the Remediation of Oil Pollution Under Aerobic Conditions: A Perspective Analysis

(2018) Xingjian Xu et al.   Frontiers in Microbiology

Sequential biodegradation of complex naphtha hydrocarbons under methanogenic conditions in two different oil sands tailings

(2017) Mohd Faidz Mohamad Shahimin et al.   ENVIRONMENTAL POLLUTION

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Metagenomic Analysis of Subtidal Sediments from Polar and Subpolar Coastal Environments Highlights the Relevance of Anaerobic Hydrocarbon Degradation Processes

(2017) Fernando Espínola et al.   MICROBIAL ECOLOGY

Methanogenic biodegradation of paraffinic solvent hydrocarbons in two different oil sands tailings

(2017) Mohd Faidz Mohamad Shahimin et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Metabolomics: A Primer

(2017) Xiaojing Liu et al.   TRENDS IN BIOCHEMICAL SCIENCES

Assessing species biomass contributions in microbial communities via metaproteomics

(2017) Manuel Kleiner et al.   Nature Communications

Cable Bacteria and the Bioelectrochemical Snorkel: The Natural and Engineered Facets Playing a Role in Hydrocarbons Degradation in Marine Sediments

(2017) Bruna Matturro et al.   Frontiers in Microbiology

Metabolomic and Metagenomic Analysis of Two Crude Oil Production Pipelines Experiencing Differential Rates of Corrosion

(2017) Vincent Bonifay et al.   Frontiers in Microbiology

Engineering a bzd cassette for the anaerobic bioconversion of aromatic compounds

(2017) María Teresa Zamarro et al.   Microbial Biotechnology

Conversion of petroleum to methane by the indigenous methanogenic consortia for oil recovery in heavy oil reservoir

(2016) Wenjie Xia et al.   APPLIED ENERGY

ATP-Dependent Electron Activation Module of Benzoyl-Coenzyme A Reductase from the Hyperthermophilic Archaeon Ferroglobus placidus

(2016) Georg Schmid et al.   BIOCHEMISTRY

Insights into the biodegradation of weathered hydrocarbons in contaminated soils by bioaugmentation and nutrient stimulation

(2016) Ying Jiang et al.   CHEMOSPHERE

Protein-SIP in environmental studies

(2016) Nico Jehmlich et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

(2016) Boris Wawrik et al.   ENVIRONMENTAL MICROBIOLOGY

From laboratory to environmental conditions: a new approach for chemical’s biodegradability assessment

(2016) Brillet François et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

Long-distance electron transfer by cable bacteria in aquifer sediments

(2016) Hubert Müller et al.   ISME Journal

Structure and Function of the Unusual Tungsten Enzymes Acetylene Hydratase and Class II Benzoyl-Coenzyme A Reductase

(2016) Matthias Boll et al.   JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY

Anaerobic Microbial Degradation of Hydrocarbons: From Enzymatic Reactions to the Environment

(2016) Ralf Rabus et al.   JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY

Structure and Function of Benzylsuccinate Synthase and Related Fumarate-Adding Glycyl Radical Enzymes

(2016) Johann Heider et al.   JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY

A comprehensive guide of remediation technologies for oil contaminated soil — Present works and future directions

(2016) Mee Wei Lim et al.   MARINE POLLUTION BULLETIN

Thermophilic archaea activate butane via alkyl-coenzyme M formation

(2016) Rafael Laso-Pérez et al.   NATURE

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Preferential methanogenic biodegradation of short-chain n -alkanes by microbial communities from two different oil sands tailings ponds

(2016) Mohd Faidz Mohamad Shahimin et al.   SCIENCE OF THE TOTAL ENVIRONMENT

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

ATP-Dependent C–F Bond Cleavage Allows the Complete Degradation of 4-Fluoroaromatics without Oxygen

(2016) Oliver Tiedt et al.   mBio

Fast and sensitive taxonomic classification for metagenomics with Kaiju

(2016) Peter Menzel et al.   Nature Communications

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

(2016) Daniel H. Huson et al.   PLoS Computational Biology

Species Divergence vs. Functional Convergence Characterizes Crude Oil Microbial Community Assembly

(2016) Yong Nie et al.   Frontiers in Microbiology

Expanding the Diet for DIET: Electron Donors Supporting Direct Interspecies Electron Transfer (DIET) in Defined Co-Cultures

(2016) Li-Ying Wang et al.   Frontiers in Microbiology

High Diversity of Anaerobic Alkane-Degrading Microbial Communities in Marine Seep Sediments Based on (1-methylalkyl)succinate Synthase Genes

(2016) Marion H. Stagars et al.   Frontiers in Microbiology

High Frequency of Thermodesulfovibrio spp. and Anaerolineaceae in Association with Methanoculleus spp. in a Long-Term Incubation of n-Alkanes-Degrading Methanogenic Enrichment Culture

(2016) Bo Liang et al.   Frontiers in Microbiology

Towards an Enhanced Understanding of Plant–Microbiome Interactions to Improve Phytoremediation: Engineering the Metaorganism

(2016) Sofie Thijs et al.   Frontiers in Microbiology

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Recovering complete and draft population genomes from metagenome datasets

(2016) Naseer Sangwan et al.   Microbiome

Patterns of Endemism and Habitat Selection in Coalbed Microbial Communities

(2015) Christopher E. Lawson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Hydrocarbon-Degrading Bacteria Exhibit a Species-Specific Response to Dispersed Oil while Moderating Ecotoxicity

(2015) Will A. Overholt et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metabolic responses of Rhodococcus erythropolis PR4 grown on diesel oil and various hydrocarbons

(2015) Krisztián Laczi et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Metagenomic investigation of the geologically unique Hellenic Volcanic Arc reveals a distinctive ecosystem with unexpected physiology

(2015) Anastasis Oulas et al.   ENVIRONMENTAL MICROBIOLOGY

Biodegradation: Updating the Concepts of Control for Microbial Cleanup in Contaminated Aquifers

(2015) Rainer U. Meckenstock et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Application of nitrate to enhance biodegradation of gasoline components in soil by indigenous microorganisms under anoxic condition

(2015) Su-Cai Yang et al.   ENVIRONMENTAL TECHNOLOGY

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

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

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

(2015) Boonfei Tan et al.   ISME Journal

Modelling extracellular limitations for mediated versus direct interspecies electron transfer

(2015) Tomas Storck et al.   ISME Journal

Cable bacteria generate a firewall against euxinia in seasonally hypoxic basins

(2015) Dorina Seitaj et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metaproteomics and metabolomics analyses of chronically petroleum-polluted sites reveal the importance of general anaerobic processes uncoupled with degradation

(2015) Rafael Bargiela et al.   PROTEOMICS

Whole-genome analysis of Azoarcus sp. strain CIB provides genetic insights to its different lifestyles and predicts novel metabolic features

(2015) Zaira Martín-Moldes et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Harnessing the landscape of microbial culture media to predict new organism–media pairings

(2015) Matthew A. Oberhardt et al.   Nature Communications

Insights into the Anaerobic Biodegradation Pathway of n-Alkanes in Oil Reservoirs by Detection of Signature Metabolites

(2015) Xin-Yu Bian et al.   Scientific Reports

Metagenome and Metatranscriptome Revealed a Highly Active and Intensive Sulfur Cycle in an Oil-Immersed Hydrothermal Chimney in Guaymas Basin

(2015) Ying He et al.   Frontiers in Microbiology

Syntrophic growth via quinone-mediated interspecies electron transfer

(2015) Jessica A. Smith et al.   Frontiers in Microbiology

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

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

Direct Interspecies Electron Transfer between Geobacter metallireducens and Methanosarcina barkeri

(2014) Amelia-Elena Rotaru et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metatranscriptome of an Anaerobic Benzene-Degrading, Nitrate-Reducing Enrichment Culture Reveals Involvement of Carboxylation in Benzene Ring Activation

(2014) Fei Luo et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Towards habitat-oriented systems biology of “Aromatoleum aromaticum” EbN1

(2014) Ralf Rabus et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Uptake and trans-membrane transport of petroleum hydrocarbons by microorganisms

(2014) Fei Hua et al.   BIOTECHNOLOGY & BIOTECHNOLOGICAL EQUIPMENT

Biodegradation of C7and C8iso-alkanes under methanogenic conditions

(2014) Nidal Abu Laban et al.   ENVIRONMENTAL MICROBIOLOGY

Synthesis of Anaerobic Degradation Biomarkers Alkyl-, Aryl- and Cycloalkylsuccinic Acids and Their Mass Spectral Characteristics

(2014) Xin-Yu Bian et al.   EUROPEAN JOURNAL OF MASS SPECTROMETRY

Draft genome sequence of an aromatic compound-degrading bacterium,Desulfobaculasp. TS, belonging to theDeltaproteobacteria

(2014) So-Jeong Kim et al.   FEMS MICROBIOLOGY LETTERS

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

(2014) Boonfei Tan et al.   ISME Journal

Electric coupling between distant nitrate reduction and sulfide oxidation in marine sediment

(2014) Ugo Marzocchi et al.   ISME Journal

Metagenomes from two microbial consortia associated with Santa Barbara seep oil

(2014) Erik R. Hawley et al.   Marine Genomics

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Structures of benzylsuccinate synthase elucidate roles of accessory subunits in glycyl radical enzyme activation and activity

(2014) M. A. Funk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metagenomic analysis of microbial consortium from natural crude oil that seeps into the marine ecosystem offshore Southern California

(2014) Erik R. Hawley et al.   Standards in Genomic Sciences

Microbial transformation of the Deepwater Horizon oil spill—past, present, and future perspectives

(2014) Nikole E. Kimes et al.   Frontiers in Microbiology

Transcriptomic and Genetic Analysis of Direct Interspecies Electron Transfer

(2013) Pravin Malla Shrestha et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Syntrophic biodegradation of hydrocarbon contaminants

(2013) Lisa M Gieg et al.   CURRENT OPINION IN BIOTECHNOLOGY

Gene Capture Coupled to High-Throughput Sequencing as a Strategy for Targeted Metagenome Exploration

(2013) J. Denonfoux et al.   DNA RESEARCH

A new model for electron flow during anaerobic digestion: direct interspecies electron transfer to Methanosaeta for the reduction of carbon dioxide to methane

(2013) Amelia-Elena Rotaru et al.   Energy & Environmental Science

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

(2013) Matthias Boll et al.   ENVIRONMENTAL MICROBIOLOGY

Metagenomics of Hydrocarbon Resource Environments Indicates Aerobic Taxa and Genes to be Unexpectedly Common

(2013) Dongshan An et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Microbial community and potential functional gene diversity involved in anaerobic hydrocarbon degradation and methanogenesis in an oil sands tailings pond

(2013) Dongshan An et al.   GENOME

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

(2013) Mallory Embree et al.   ISME Journal

Analysis of Hydrocarbon-Contaminated Groundwater Metagenomes as Revealed by High-Throughput Sequencing

(2013) Nathlee S. Abbai et al.   MOLECULAR BIOTECHNOLOGY

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Metagenome reveals potential microbial degradation of hydrocarbon coupled with sulfate reduction in an oil-immersed chimney from Guaymas Basin

(2013) Ying He et al.   Frontiers in Microbiology

Enzymes and genes involved in aerobic alkane degradation

(2013) Wanpeng Wang et al.   Frontiers in Microbiology

Substrate and Inhibitor Spectra of Ethylbenzene Dehydrogenase: Perspectives on Application Potential and Catalytic Mechanism

(2012) Daniel Knack et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Enhanced Tolerance to Naphthalene and Enhanced Rhizoremediation Performance for Pseudomonas putida KT2440 via the NAH7 Catabolic Plasmid

(2012) Matilde Fernández et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Enhanced Gene Detection Assays for Fumarate-Adding Enzymes Allow Uncovering of Anaerobic Hydrocarbon Degraders in Terrestrial and Marine Systems

(2012) Frederick von Netzer et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Key players and team play: anaerobic microbial communities in hydrocarbon-contaminated aquifers

(2012) Sabine Kleinsteuber et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

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

(2012) Y. Peng et al.   BIOINFORMATICS

Plant–bacteria interactions in the removal of pollutants

(2012) Ana Segura et al.   CURRENT OPINION IN BIOTECHNOLOGY

Filamentous bacteria transport electrons over centimetre distances

(2012) Christian Pfeffer et al.   NATURE

Microbial interspecies electron transfer via electric currents through conductive minerals

(2012) S. Kato et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Complete genome sequence of Thauera aminoaromatica strain MZ1T

(2012) Ke Jiang et al.   Standards in Genomic Sciences

A metagenomic study of methanotrophic microorganisms in Coal Oil Point seep sediments

(2011) Othilde Håvelsrud et al.   BMC MICROBIOLOGY

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

(2011) A. V. Callaghan 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

Transcriptional profiling of the marine oil-degrading bacterium Alcanivorax borkumensis during growth on n-alkanes

(2011) Julia S. Sabirova et al.   FEMS MICROBIOLOGY LETTERS

Microbial degradation of aromatic compounds — from one strategy to four

(2011) Georg Fuchs et al.   NATURE REVIEWS MICROBIOLOGY

Occurrence, genes and expression of the W/Se-containing class II benzoyl-coenzyme A reductases in anaerobic bacteria

(2010) Claudia Löffler et al.   ENVIRONMENTAL MICROBIOLOGY

Identification of enzymes involved in anaerobic benzene degradation by a strictly anaerobic iron-reducing enrichment culture

(2010) Nidal Abu Laban et al.   ENVIRONMENTAL MICROBIOLOGY

The key nickel enzyme of methanogenesis catalyses the anaerobic oxidation of methane

(2010) Silvan Scheller et al.   NATURE

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

Improving protein extraction and separation methods for investigating the metaproteome of anaerobic benzene communities within sediments

(2009) Dirk Benndorf et al.   BIODEGRADATION

The genome sequence of Geobacter metallireducens: features of metabolism, physiology and regulation common and dissimilar to Geobacter sulfurreducens

(2009) Muktak Aklujkar et al.   BMC MICROBIOLOGY

Anaerobic benzene degradation by Gram-positive sulfate-reducing bacteria

(2009) Nidal Abu Laban et al.   FEMS MICROBIOLOGY ECOLOGY

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

Anaerobic Biodegradation of Aromatic Hydrocarbons: Pathways and Prospects

(2009) Julia Foght   JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY

Anaerobic Catabolism of Aromatic Compounds: a Genetic and Genomic View

(2009) M. Carmona et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Differential Membrane Proteome Analysis Reveals Novel Proteins Involved in the Degradation of Aromatic Compounds inGeobacter metallireducens

(2009) Dimitri Heintz et al.   MOLECULAR & CELLULAR PROTEOMICS

Bioenergy Production via Microbial Conversion of Residual Oil to Natural Gas

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

The Genome of Polaromonas sp. Strain JS666: Insights into the Evolution of a Hydrocarbon- and Xenobiotic-Degrading Bacterium, and Features of Relevance to Biotechnology

(2008) T. E. Mattes et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microbial fuel cell in enhancing anaerobic biodegradation of diesel

(2008) Jeffrey M. Morris et al.   CHEMICAL ENGINEERING JOURNAL

Systems biology approaches to bioremediation

(2008) Víctor de Lorenzo   CURRENT OPINION IN BIOTECHNOLOGY

Identification of intermediates formed during anaerobic benzene degradation by an iron-reducing enrichment culture

(2008) Umakanth Kunapuli et al.   ENVIRONMENTAL MICROBIOLOGY

6-Oxocyclohex-1-ene-1-carbonyl-coenzyme A hydrolases from obligately anaerobic bacteria: characterization and identification of its gene as a functional marker for aromatic compounds degrading anaerobes

(2008) Kevin Kuntze et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2007) Olav Grundmann et al.   ENVIRONMENTAL MICROBIOLOGY