Understanding and Designing the Strategies for the Microbe-Mediated Remediation of Environmental Contaminants Using Omics Approaches

Comparative transcriptomic and proteomic analysis of Arthrobacter sp. CGMCC 3584 responding to dissolved oxygen for cAMP production

(2018) Huanqing Niu et al.   Scientific Reports

Production of gellan gum, an exopolysaccharide, from biodiesel-derived waste glycerol by Sphingomonas spp.

(2018) Kerisha Raghunandan et al.   3 Biotech

Production of gellan gum, an exopolysaccharide, from biodiesel-derived waste glycerol by Sphingomonas spp.

(2018) Kerisha Raghunandan et al.   3 Biotech

Functional soil metagenomics: elucidation of polycyclic aromatic hydrocarbon degradation potential following 12 years of in situ bioremediation

(2017) Márcia Duarte et al.   ENVIRONMENTAL MICROBIOLOGY

Contamination of the Arctic reflected in microbial metagenomes from the Greenland ice sheet

(2017) Aviaja L Hauptmann et al.   Environmental Research Letters

Steering Soil Microbiomes to Suppress Aboveground Insect Pests

(2017) Ana Pineda et al.   TRENDS IN PLANT SCIENCE

Bioinformatic Approaches Including Predictive Metagenomic Profiling Reveal Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments

(2017) Arghya Mukherjee et al.   Scientific Reports

Mass Spectrometry in Plant-omics

(2016) Erin Gemperline et al.   ANALYTICAL CHEMISTRY

Reflection on Molecular Approaches Influencing State-of-the-Art Bioremediation Design: Culturing to Microbial Community Fingerprinting to Omics

(2016) Lauren M. Czaplicki et al.   JOURNAL OF ENVIRONMENTAL ENGINEERING

Metagenomic applications in environmental monitoring and bioremediation

(2016) Stephen M. Techtmann et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Comparison of differential gene expression to water stress among bacteria with relevant pollutant-degradation properties

(2016) Silvia K. Moreno-Forero et al.   Environmental Microbiology Reports

Reflection on Molecular Approaches Influencing State-of-the-Art Bioremediation Design: Culturing to Microbial Community Fingerprinting to Omics

(2016) Lauren M. Czaplicki et al.   JOURNAL OF ENVIRONMENTAL ENGINEERING

The Genome of the Toluene-Degrading Pseudomonas veronii Strain 1YdBTEX2 and Its Differential Gene Expression in Contaminated Sand

(2016) Marian Morales et al.   PLoS One

Metagenomic and functional analyses of the consequences of reduction of bacterial diversity on soil functions and bioremediation in diesel-contaminated microcosms

(2016) Jaejoon Jung et al.   Scientific Reports

Microbiological functioning, diversity, and structure of bacterial communities in ultramafic soils from a tropical savanna

(2015) Marco Pessoa-Filho et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

16S rRNA gene high-throughput sequencing data mining of microbial diversity and interactions

(2015) Feng Ju et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Metagenomics for the discovery of pollutant degrading enzymes

(2015) Lisa Ufarté et al.   BIOTECHNOLOGY ADVANCES

Structure and Function of the Bacterial Root Microbiota in Wild and Domesticated Barley

(2015) Davide Bulgarelli et al.   Cell Host & Microbe

Microbial production of phytases for combating environmental phosphate pollution and other diverse applications

(2015) Ashwani Kumar et al.   CRITICAL REVIEWS IN ENVIRONMENTAL SCIENCE AND TECHNOLOGY

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

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

Toxic elements and persistent organic pollutants derived from industrial emissions in agricultural soils of the Northern Czech Republic

(2015) Radim Vácha et al.   JOURNAL OF SOILS AND SEDIMENTS

Comparative genomics, proteomics and transcriptomics give new insight into the exoproteome of the basidiomyceteHebeloma cylindrosporumand its involvement in ectomycorrhizal symbiosis

(2015) Jeanne Doré et al.   NEW PHYTOLOGIST

enviPath – The environmental contaminant biotransformation pathway resource

(2015) Jörg Wicker et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2015) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

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

Current and future resources for functional metagenomics

(2015) Kathy N. Lam et al.   Frontiers in Microbiology

Characterization of Novel Polycyclic Aromatic Hydrocarbon Dioxygenases from the Bacterial Metagenomic DNA of a Contaminated Soil

(2014) Angelina Chemerys et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Bacterial Targets as Potential Indicators of Diesel Fuel Toxicity in Subantarctic Soils

(2014) Josie van Dorst et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Analysis of Culture-Dependent versus Culture-Independent Techniques for Identification of Bacteria in Clinically Obtained Bronchoalveolar Lavage Fluid

(2014) R. P. Dickson et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Metagenomic Approach Reveals Variation of Microbes with Arsenic and Antimony Metabolism Genes from Highly Contaminated Soil

(2014) Jinming Luo et al.   PLoS One

Increasing phytoremediation efficiency and reliability using novel omics approaches

(2014) Terrence H. Bell et al.   TRENDS IN BIOTECHNOLOGY

Maths on microbes: adding microbial ecophysiology to metagenomics

(2014) Wilfred F. M. Röling   Microbial Biotechnology

Identification of 100 fundamental ecological questions

(2013) William J. Sutherland et al.   JOURNAL OF ECOLOGY

An innovative bioremediation strategy using a bacterial consortium entrapped in chitosan beads

(2013) Alysson Lira Angelim et al.   JOURNAL OF ENVIRONMENTAL MANAGEMENT

Biodegradation of glycerol using bacterial isolates from soil under aerobic conditions

(2013) Kerisha Raghunandan et al.   JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH PART A-TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING

Sustainable development goals for people and planet

(2013) David Griggs et al.   NATURE

Bioremediation: a genuine technology to remediate radionuclides from the environment

(2013) Dhan Prakash et al.   Microbial Biotechnology

Functional assignment of metagenomic data: challenges and applications

(2012) T. Prakash et al.   BRIEFINGS IN BIOINFORMATICS

Systems biology approach to bioremediation

(2012) Romy Chakraborty et al.   CURRENT OPINION IN BIOTECHNOLOGY

Bioremediation of mercury and the importance of bacterial mer genes

(2012) Hirak R. Dash et al.   INTERNATIONAL BIODETERIORATION & BIODEGRADATION

Microbial life in the phyllosphere

(2012) Julia A. Vorholt   NATURE REVIEWS MICROBIOLOGY

Engineering microbial consortia to enhance biomining and bioremediation

(2012) Karl D. Brune et al.   Frontiers in Microbiology

Application of meta-transcriptomics and -proteomics to analysis of in situ physiological state

(2012) Allan Konopka et al.   Frontiers in Microbiology

Global Transcriptomic and Proteomic Responses of Dehalococcoides ethenogenes Strain 195 to Fixed Nitrogen Limitation

(2011) Patrick K. H. Lee et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Oil Biodegradation and Bioremediation: A Tale of the Two Worst Spills in U.S. History

(2011) Ronald M. Atlas et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Environmental Applications of Biosurfactants: Recent Advances

(2011) Magdalena Pacwa-Płociniczak et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Use of immunomagnetic separation for the detection of Desulfovibrio vulgaris from environmental samples

(2011) Romy Chakraborty et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Microfluidic fluorescence in situ hybridization and flow cytometry (μFlowFISH)

(2011) Peng Liu et al.   LAB ON A CHIP

How sulphate-reducing microorganisms cope with stress: lessons from systems biology

(2011) Jizhong Zhou et al.   NATURE REVIEWS MICROBIOLOGY

Laboratory research aimed at closing the gaps in microbial bioremediation

(2011) Juan-Luis Ramos et al.   TRENDS IN BIOTECHNOLOGY

Microbiology of ‘Candidatus Accumulibacter’ in activated sludge

(2011) Shaomei He et al.   Microbial Biotechnology

Asthma and Allergic Inflammation

(2010) Richard M. Locksley   CELL

Biodegradation pathway of mesotrione: Complementarities of NMR, LC–NMR and LC–MS for qualitative and quantitative metabolic profiling

(2010) Stéphanie Durand et al.   CHEMOSPHERE

Methods for investigating biosurfactants and bioemulsifiers: a review

(2010) Surekha K. Satpute et al.   CRITICAL REVIEWS IN BIOTECHNOLOGY

Fourier transform infrared spectroscopy as a metabolite fingerprinting tool for monitoring the phenotypic changes in complex bacterial communities capable of degrading phenol

(2010) Emma S. Wharfe et al.   ENVIRONMENTAL MICROBIOLOGY

Past, Present, and Future Controls on Levels of Persistent Organic Pollutants in the Global Environment

(2010) Luca Nizzetto et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Field Evidence for Co-Metabolism of Trichloroethene Stimulated by Addition of Electron Donor to Groundwater

(2010) Mark E. Conrad et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Physiological and Transcriptional Studies of Cr(VI) Reduction under Aerobic and Denitrifying Conditions by an Aquifer-Derived Pseudomonad

(2010) Ruyang Han et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Strategies for culture of ‘unculturable’ bacteria

(2010) Sonia R. Vartoukian et al.   FEMS MICROBIOLOGY LETTERS

Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community

(2010) Christopher L Hemme et al.   ISME Journal

Construction and Preliminary Analysis of a Deep-Sea Sediment Metagenomic Fosmid Library from Qiongdongnan Basin, South China Sea

(2010) Yongfei Hu et al.   MARINE BIOTECHNOLOGY

Similarity of Bacterial Community Structure between Asian Dust and Its Sources Determined by rRNA Gene-Targeted Approaches

(2010) Yoshinori Nishimura et al.   MICROBES AND ENVIRONMENTS

Where microbiology meets microengineering: design and applications of reporter bacteria

(2010) Jan Roelof van der Meer et al.   NATURE REVIEWS MICROBIOLOGY

Exploiting the ecogenomics toolbox for environmental diagnostics of organohalide-respiring bacteria

(2010) Farai Maphosa et al.   TRENDS IN BIOTECHNOLOGY

Proteomic and Transcriptomic Analyses Reveal Genes Upregulated by cis-Dichloroethene in Polaromonas sp. Strain JS666

(2009) L. K. Jennings et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Advances in molecular and “-omics” technologies to gauge microbial communities and bioremediation at xenobiotic/anthropogen contaminated sites

(2009) Chirayu Desai et al.   BIORESOURCE TECHNOLOGY

Recombinant bacteria for environmental release: what went wrong and what we have learnt from it

(2009) V. de Lorenzo   CLINICAL MICROBIOLOGY AND INFECTION

Performance Assessment of Bioremediation and Natural Attenuation

(2009) Walter A. Illman et al.   CRITICAL REVIEWS IN ENVIRONMENTAL SCIENCE AND TECHNOLOGY

Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre

(2009) Rachel S. Poretsky et al.   ENVIRONMENTAL MICROBIOLOGY

Absolute quantification ofDehalococcoidesproteins: enzyme bioindicators of chlorinated ethene dehalorespiration

(2009) Jeffrey J. Werner et al.   ENVIRONMENTAL MICROBIOLOGY

Proposal of biostimulation for hexachlorocyclohexane (HCH)-decontamination and characterization of culturable bacterial community from high-dose point HCH-contaminated soils

(2009) M. Dadhwal et al.   JOURNAL OF APPLIED MICROBIOLOGY

Functional analysis of natural microbial consortia using community proteomics

(2009) Nathan C. VerBerkmoes et al.   NATURE REVIEWS MICROBIOLOGY

The University of Minnesota Biocatalysis/Biodegradation Database: improving public access

(2009) Junfeng Gao et al.   NUCLEIC ACIDS RESEARCH

Microbial Communities in Contaminated Sediments, Associated with Bioremediation of Uranium to Submicromolar Levels

(2008) E. Cardenas et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Comparative metabolomic analysis of Sinorhizobium sp. C4 during the degradation of phenanthrene

(2008) Young Soo Keum et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Metabolic flux analysis ofShewanellaspp. reveals evolutionary robustness in central carbon metabolism

(2008) Yinjie J. Tang et al.   BIOTECHNOLOGY AND BIOENGINEERING

Systems biology approaches to bioremediation

(2008) Víctor de Lorenzo   CURRENT OPINION IN BIOTECHNOLOGY

Transcription dynamics of the functional tfdA gene during MCPA herbicide degradation by Cupriavidus necator AEO106 (pRO101) in agricultural soil

(2008) Mette Haubjerg Nicolaisen et al.   ENVIRONMENTAL MICROBIOLOGY

Geophysical Monitoring of Hydrological and Biogeochemical Transformations Associated with Cr(VI) Bioremediation

(2008) Susan S. Hubbard et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Bacterial metabolism of polycyclic aromatic hydrocarbons: strategies for bioremediation

(2008) Archana Chauhan et al.   INDIAN JOURNAL OF MICROBIOLOGY

Transcriptome of Geobacter uraniireducens growing in uranium-contaminated subsurface sediments

(2008) Dawn E Holmes et al.   ISME Journal

Shotgun metaproteomics of the human distal gut microbiota

(2008) Nathan C Verberkmoes et al.   ISME Journal

Towards environmental systems biology of Shewanella

(2008) James K. Fredrickson et al.   NATURE REVIEWS MICROBIOLOGY

Real-time PCR quantification of Dehalococcoides populations: Methods and applications

(2007) Alison M. Cupples   JOURNAL OF MICROBIOLOGICAL METHODS