Stable isotope probing and metagenomics highlight the effect of plants on uncultured phenanthrene-degrading bacterial consortium in polluted soil

SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments

(2018) Nicholas D. Youngblut et al.   Frontiers in Microbiology

Low effect of phenanthrene bioaccessibility on its biodegradation in diffusely contaminated soil

(2017) M. Crampon et al.   ENVIRONMENTAL POLLUTION

Bioremediation of PAH-contamined soils: Consequences on formation and degradation of polar-polycyclic aromatic compounds and microbial community abundance

(2017) Coralie Biache et al.   JOURNAL OF HAZARDOUS MATERIALS

Microbial mechanisms controlling the rhizosphere effect of ryegrass on degradation of polycyclic aromatic hydrocarbons in an aged-contaminated agricultural soil

(2017) Meixia Guo et al.   SOIL BIOLOGY & BIOCHEMISTRY

Comparative Genomic Analysis Reveals Habitat-Specific Genes and Regulatory Hubs within the Genus Novosphingobium

(2017) Roshan Kumar et al.   mSystems

Cooperation in carbon source degradation shapes spatial self-organization of microbial consortia on hydrated surfaces

(2017) Robin Tecon et al.   Scientific Reports

Bacteria capable of degrading anthracene, phenanthrene, and fluoranthene as revealed by DNA based stable-isotope probing in a forest soil

(2016) Mengke Song et al.   JOURNAL OF HAZARDOUS MATERIALS

Proteomic Analysis of Polycyclic Aromatic Hydrocarbons (PAHs) Degradation and Detoxification in Sphingobium chungbukense DJ77

(2016) Soo Youn Lee et al.   JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

The Willow Microbiome Is Influenced by Soil Petroleum-Hydrocarbon Concentration with Plant Compartment-Specific Effects

(2016) Stacie Tardif et al.   Frontiers in Microbiology

Reconstructing metabolic pathways of hydrocarbon-degrading bacteria from the Deepwater Horizon oil spill

(2016) Nina Dombrowski et al.   Nature Microbiology

Identification of Benzo[a]pyrene-Metabolizing Bacteria in Forest Soils by Using DNA-Based Stable-Isotope Probing

(2015) Mengke Song et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Quantitative Microbial Ecology through Stable Isotope Probing

(2015) Bruce A. Hungate et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

“Omics” Insights into PAH Degradation toward Improved Green Remediation Biotechnologies

(2015) Abdelhak El Amrani et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Phenanthrene biodegradation by sphingomonads and its application in the contaminated soils and sediments: A review

(2015) Michael Gatheru Waigi et al.   INTERNATIONAL BIODETERIORATION & BIODEGRADATION

Sphingobium barthaii sp. nov., a high molecular weight polycyclic aromatic hydrocarbon-degrading bacterium isolated from cattle pasture soil

(2015) Allyn H. Maeda et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Novel Phenanthrene-Degrading Bacteria Identified by DNA-Stable Isotope Probing

(2015) Longfei Jiang et al.   PLoS One

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Taxonomical and functional microbial community selection in soybean rhizosphere

(2014) Lucas W Mendes et al.   ISME Journal

AromaDeg, a novel database for phylogenomics of aerobic bacterial degradation of aromatics

(2014) Márcia Duarte et al.   Database-The Journal of Biological Databases and Curation

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metabolic versatility of toluene-degrading, iron-reducing bacteria in tidal flat sediment, characterized by stable isotope probing-based metagenomic analysis

(2013) So-Jeong Kim et al.   ENVIRONMENTAL MICROBIOLOGY

Identification of soil bacteria able to degrade phenanthrene bound to a hydrophobic sorbent in situ

(2013) Raïssa Kom Regonne et al.   ENVIRONMENTAL POLLUTION

Microbial expression profiles in the rhizosphere of willows depend on soil contamination

(2013) Etienne Yergeau et al.   ISME Journal

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

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

Functional Assays and Metagenomic Analyses Reveals Differences between the Microbial Communities Inhabiting the Soil Horizons of a Norway Spruce Plantation

(2013) Stéphane Uroz et al.   PLoS One

Rhizosphere priming: a nutrient perspective

(2013) Feike A. Dijkstra et al.   Frontiers in Microbiology

PANDAseq: paired-end assembler for illumina sequences

(2012) Andre P Masella et al.   BMC BIOINFORMATICS

Plant–bacteria partnerships for the remediation of hydrocarbon contaminated soils

(2012) Sumia Khan et al.   CHEMOSPHERE

PAH biotransformation and sorption by Fusarium solani and Arthrobacter oxydans isolated from a polluted soil in axenic cultures and mixed co-cultures

(2012) Cécile Thion et al.   INTERNATIONAL BIODETERIORATION & BIODEGRADATION

Low-temperature biodegradation of petroleum hydrocarbons (n-alkanes, phenol, anthracene, pyrene) by four actinobacterial strains

(2012) Rosa Margesin et al.   INTERNATIONAL BIODETERIORATION & BIODEGRADATION

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

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

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

The PhyloPythiaS Web Server for Taxonomic Assignment of Metagenome Sequences

(2012) Kaustubh Raosaheb Patil et al.   PLoS One

Identification of Bacteria Utilizing Biphenyl, Benzoate, and Naphthalene in Long-Term Contaminated Soil

(2012) Ondrej Uhlik et al.   PLoS One

The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss

(2012) J. J. Morris et al.   mBio

The Origins of Cooperative Bacterial Communities

(2012) J. L. Sachs et al.   mBio

Dynamics of Bacterial Communities in Two Unpolluted Soils after Spiking with Phenanthrene: Soil Type Specific and Common Responders

(2012) Guo-Chun Ding et al.   Frontiers in Microbiology

Plant root exudates impact the hydrocarbon degradation potential of a weathered-hydrocarbon contaminated soil

(2011) Lori A. Phillips et al.   APPLIED SOIL ECOLOGY

Stable isotope probing identifies anthracene degraders under methanogenic conditions

(2011) Shuying Zhang et al.   BIODEGRADATION

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Stable-isotope probing of the polycyclic aromatic hydrocarbon-degrading bacterial guild in a contaminated soil

(2011) Maiysha D. Jones et al.   ENVIRONMENTAL MICROBIOLOGY

Betaproteobacteria dominance and diversity shifts in the bacterial community of a PAH-contaminated soil exposed to phenanthrene

(2011) Florence Martin et al.   ENVIRONMENTAL POLLUTION

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Root exudates modify bacterial diversity of phenanthrene degraders in PAH-polluted soil but not phenanthrene degradation rates

(2010) Aurélie Cébron et al.   ENVIRONMENTAL MICROBIOLOGY

Reversal of visual hemineglect: Differential influences of deactivating either contralateral posterior parietal cortex or the superior colliculus

(2010) E. M. Woller et al.   JOURNAL OF VISION

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Influence of Vegetation on the In Situ Bacterial Community and Polycyclic Aromatic Hydrocarbon (PAH) Degraders in Aged PAH-Contaminated or Thermal-Desorption-Treated Soil

(2009) A. Cebron et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Bacterial Communities from Shoreline Environments (Costa da Morte, Northwestern Spain) Affected by the Prestige Oil Spill

(2009) J. Alonso-Gutierrez et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

DNA-Stable Isotope Probing Integrated with Metagenomics for Retrieval of Biphenyl Dioxygenase Genes from Polychlorinated Biphenyl-Contaminated River Sediment

(2009) W. J. Sul et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere

(2009) Gabriele Berg et al.   FEMS MICROBIOLOGY ECOLOGY

Advances in the field of high-molecular-weight polycyclic aromatic hydrocarbon biodegradation by bacteria

(2009) Robert A. Kanaly et al.   Microbial Biotechnology

Molecular characteristics of xenobiotic-degrading sphingomonads

(2008) Andreas Stolz   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

Effects of thermal desorption on the composition of two coking plant soils: Impact on solvent extractable organic compounds and metal bioavailability

(2008) Coralie Biache et al.   ENVIRONMENTAL POLLUTION

Plant host habitat and root exudates shape soil bacterial community structure

(2008) Feth el Zahar Haichar et al.   ISME Journal

Real-Time PCR quantification of PAH-ring hydroxylating dioxygenase (PAH-RHDα) genes from Gram positive and Gram negative bacteria in soil and sediment samples

(2008) Aurélie Cébron et al.   JOURNAL OF MICROBIOLOGICAL METHODS

The effect of ryegrass (Lolium perenne) on decrease of PAH content in long term contaminated soil

(2007) Jan Rezek et al.   CHEMOSPHERE