The role of predicted chemotactic and hydrocarbon degrading taxa in natural source zone depletion at a legacy petroleum hydrocarbon site

Bacterial and archaeal diversity in oil fields and reservoirs and their potential role in hydrocarbon recovery and bioprospecting

(2021) Nishi Kumari Singh et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

Unravelling Microbial Communities Associated with Different Light Non-Aqueous Phase Liquid Types Undergoing Natural Source Zone Depletion Processes at a Legacy Petroleum Site

(2021) Melanie C. Bruckberger et al.   Water

Niche partitioning in the Rimicaris exoculata holobiont: the case of the first symbiotic Zetaproteobacteria

(2021) Marie-Anne Cambon-Bonavita et al.   Microbiome

PICRUSt2 for prediction of metagenome functions

(2020) Gavin M. Douglas et al.   NATURE BIOTECHNOLOGY

LNAPL Recovery Endpoints: Lessons Learnt Through Modeling, Experiments, and Field Trials

(2020) Kaveh Sookhak Lari et al.   GROUND WATER MONITORING AND REMEDIATION

Arbuscular Mycorrhizal Fungal Communities of Native Plant Species under High Petroleum Hydrocarbon Contamination Highlights Rhizophagus as a Key Tolerant Genus

(2020) Soon-Jae Lee et al.   Microorganisms

Microbial community responses to different volatile petroleum hydrocarbon class mixtures in an aerobic sandy soil

(2020) George Mangse et al.   ENVIRONMENTAL POLLUTION

Enhanced Anaerobic Biodegradation of Benzoate Under Sulfate-Reducing Conditions With Conductive Iron-Oxides in Sediment of Pearl River Estuary

(2019) Li Zhuang et al.   Frontiers in Microbiology

Biodegradability of legacy crude oil contamination in Gulf War damaged groundwater wells in Northern Kuwait

(2019) Melanie C. Bruckberger et al.   BIODEGRADATION

Chemotaxis Towards Aromatic Compounds: Insights from Comamonas testosteroni

(2019) Yun-Hao Wang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

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

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Natural source zone depletion of LNAPL: A critical review supporting modelling approaches

(2019) Kaveh Sookhak Lari et al.   WATER RESEARCH

Toward understanding the origin and evolution of cellular organisms

(2019) Minoru Kanehisa   PROTEIN SCIENCE

Taxonomic and functional diversity of the microbiome in a jet fuel contaminated site as revealed by combined application of in situ microcosms with metagenomic analysis

(2019) K.J. Hidalgo et al.   SCIENCE OF THE TOTAL ENVIRONMENT

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

Characterization of the microbial community diversity and composition of the coast of Lebanon: Potential for petroleum oil biodegradation

(2019) Hamdan Z. Hamdan et al.   MARINE POLLUTION BULLETIN

Investigation into the microbial communities and associated crude oil-contamination along a Gulf War impacted groundwater system in Kuwait

(2019) Melanie C. Bruckberger et al.   WATER RESEARCH

Deciphering the electric code of Geobacter sulfurreducens in cocultures with Pseudomonas aeruginosa via SWATH-MS proteomics

(2018) Lucie Semenec et al.   BIOELECTROCHEMISTRY

Hydrogen evolution in microbial electrolysis cells treating landfill leachate: Dynamics of anodic biofilm

(2018) Muhammad Hassan et al.   INTERNATIONAL JOURNAL OF HYDROGEN ENERGY

Field-scale multi-phase LNAPL remediation: Validating a new computational framework against sequential field pilot trials

(2018) Kaveh Sookhak Lari et al.   JOURNAL OF HAZARDOUS MATERIALS

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

(2018) Thomas Reid et al.   WATER RESEARCH

Characterization of a Microbial Consortium for the Bioremoval of Polycyclic Aromatic Hydrocarbons (PAHs) in Water

(2018) Esmeralda Blanco-Enríquez et al.   International Journal of Environmental Research and Public Health

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

(2018) Nicholas A. Bokulich et al.   Microbiome

Biodegradability of polar compounds formed from weathered diesel

(2018) Melanie C. Bruckberger et al.   BIODEGRADATION

Linking initial soil bacterial diversity and polycyclic aromatic hydrocarbons (PAHs) degradation potential

(2018) M. Crampon et al.   JOURNAL OF HAZARDOUS MATERIALS

Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes

(2018) Karen G. Lloyd et al.   mSystems

Biohybrid Microtube Swimmers Driven by Single Captured Bacteria

(2017) Morgan M. Stanton et al.   Small

Genome Sequencing Reveals the Potential of Achromobacter sp. HZ01 for Bioremediation

(2017) Yue-Hui Hong et al.   Frontiers in Microbiology

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

Mobilization of Pollutant-Degrading Bacteria by Eukaryotic Zoospores

(2016) Rungroch Sungthong et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples

(2015) Alma E. Parada et al.   ENVIRONMENTAL MICROBIOLOGY

Identification and analysis of polyaromatic hydrocarbons (PAHs)—biodegrading bacterial strains from refinery soil of India

(2015) Priyanka Chaudhary et al.   ENVIRONMENTAL MONITORING AND ASSESSMENT

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

(2015) Boonfei Tan et al.   ISME Journal

Integration of chemotaxis, transport and catabolism inPseudomonas putidaand identification of the aromatic acid chemoreceptor PcaY

(2015) Rita A. Luu et al.   MOLECULAR MICROBIOLOGY

Organic contaminant transport and fate in the subsurface: Evolution of knowledge and understanding

(2015) Hedeff I. Essaid et al.   WATER RESOURCES RESEARCH

Identification of genes specifically required for the anaerobic metabolism of benzene in Geobacter metallireducens

(2014) Tian Zhang et al.   Frontiers in Microbiology

Where is positional uncertainty a problem for species distribution modelling?

(2013) Babak Naimi et al.   ECOGRAPHY

Microbial communities along biogeochemical gradients in a hydrocarbon-contaminated aquifer

(2013) Karolin Tischer et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2013) Mallory Embree et al.   ISME Journal

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

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

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

Three Types of Taxis Used in the Response ofAcidovoraxsp. Strain JS42 to 2-Nitrotoluene

(2012) Christine A. Rabinovitch-Deere et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Bacterial chemotaxis toward a NAPL source within a pore-scale microfluidic chamber

(2012) Xiaopu Wang et al.   BIOTECHNOLOGY AND BIOENGINEERING

High bacterial biodiversity increases degradation performance of hydrocarbons during bioremediation of contaminated harbor marine sediments

(2012) Antonio Dell'Anno et al.   ENVIRONMENTAL POLLUTION

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Bacterial chemotaxis towards aromatic hydrocarbons in Pseudomonas

(2011) Jesús Lacal et al.   ENVIRONMENTAL MICROBIOLOGY

Activation of Methanogenesis in Arid Biological Soil Crusts Despite the Presence of Oxygen

(2011) Roey Angel et al.   PLoS One

Genome Sequence of a Mesophilic Hydrogenotrophic Methanogen Methanocella paludicola, the First Cultivated Representative of the Order Methanocellales

(2011) Sanae Sakai et al.   PLoS One

Whole-cell bacterial bioreporter for actively searching and sensing of alkanes and oil spills

(2011) Dayi Zhang et al.   Microbial Biotechnology

Physical Modeling of Air Flow During Air Sparging Remediation

(2010) Liming Hu et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Methanocella arvoryzae sp. nov., a hydrogenotrophic methanogen isolated from rice field soil

(2010) S. Sakai et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Bioventing remediation and ecotoxicity evaluation of phenanthrene-contaminated soil

(2010) F. Javier García Frutos et al.   JOURNAL OF HAZARDOUS MATERIALS

Polar Compounds from the Dissolution of Weathered Diesel

(2009) Dale A. Lang et al.   GROUND WATER MONITORING AND REMEDIATION

Desulfitobacterium aromaticivorans sp. nov. and Geobacter toluenoxydans sp. nov., iron-reducing bacteria capable of anaerobic degradation of monoaromatic hydrocarbons

(2009) U. Kunapuli et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY