Bioremediation through microbes: systems biology and metabolic engineering approach

Biostimulation and bioaugmentation of native microbial community accelerated bioremediation of oil refinery sludge

(2018) Ajoy Roy et al.   BIORESOURCE TECHNOLOGY

Anthracene drives sub-cellular proteome-wide alterations in the degradative system of Penicillium oxalicum

(2018) R. Lucero Camacho-Morales et al.   ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY

Metagenome enrichment approach used for selection of oil-degrading bacteria consortia for drill cutting residue bioremediation

(2018) Alaine B. Guerra et al.   ENVIRONMENTAL POLLUTION

Transcriptomic responses of catalase, peroxidase and laccase encoding genes and enzymatic activities of oil spill inhabiting rhizospheric fungal strains

(2018) Michael Dare Asemoloye et al.   ENVIRONMENTAL POLLUTION

Pyrene biodegradation and proteomic analysis in Achromobacter xylosoxidans , PY4 strain

(2018) Alexis Nzila et al.   INTERNATIONAL BIODETERIORATION & BIODEGRADATION

Contemporary enzyme based technologies for bioremediation: A review

(2018) Babita Sharma et al.   JOURNAL OF ENVIRONMENTAL MANAGEMENT

What makes A. guillouiae SFC 500-1A able to co-metabolize phenol and Cr(VI)? A proteomic approach

(2018) Ornella Mailén Ontañon et al.   JOURNAL OF HAZARDOUS MATERIALS

Cadmium specific proteomic responses of a highly resistant Pseudomonas aeruginosa san ai

(2018) Lidija Izrael-Živković et al.   RSC Advances

Metagenomic profiling for assessing microbial diversity and microbial adaptation to degradation of hydrocarbons in two South African petroleum-contaminated water aquifers

(2018) Leonard Kachienga et al.   Scientific Reports

Complete genome sequence of Pseudomonas alcaliphila JAB1 (=DSM 26533), a versatile degrader of organic pollutants

(2018) Jakub Ridl et al.   Standards in Genomic Sciences

Metagenomic Functional Potential Predicts Degradation Rates of a Model Organophosphorus Xenobiotic in Pesticide Contaminated Soils

(2018) Thomas C. Jeffries et al.   Frontiers in Microbiology

Metagenomic Analysis of a Biphenyl-Degrading Soil Bacterial Consortium Reveals the Metabolic Roles of Specific Populations

(2018) Daniel Garrido-Sanz et al.   Frontiers in Microbiology

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

(2017) Márcia Duarte et al.   ENVIRONMENTAL MICROBIOLOGY

Evaluating the suitability of different environmental samples for tracing atmospheric pollution in industrial areas

(2017) Anna Francová et al.   ENVIRONMENTAL POLLUTION

Strategies to Improve Saccharomyces cerevisiae: Technological Advancements and Evolutionary Engineering

(2017) Arun Kumar Dangi et al.   INDIAN JOURNAL OF MICROBIOLOGY

Effects of organic aerosol loading and fog processing on organic aerosol volatility

(2017) Abhishek Chakraborty et al.   JOURNAL OF AEROSOL SCIENCE

Microaerophilic alkane degradation in Pseudomonas extremaustralis: a transcriptomic and physiological approach

(2017) Paula M. Tribelli et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Biodiversity change behind wide applications of nanomaterials?

(2017) Ming Chen et al.   Nano Today

Assessment of urban stream sediment pollutants entering estuaries using chemical analysis and multiple bioassays to characterise biological activities

(2017) Svenja Boehler et al.   SCIENCE OF THE TOTAL ENVIRONMENT

How Do Enzymes ‘Meet’ Nanoparticles and Nanomaterials?

(2017) Ming Chen et al.   TRENDS IN BIOCHEMICAL SCIENCES

Biodegradation of Carbon Nanotubes, Graphene, and Their Derivatives

(2017) Ming Chen et al.   TRENDS IN BIOTECHNOLOGY

The Ecological Role of Volatile and Soluble Secondary Metabolites Produced by Soil Bacteria

(2017) Olaf Tyc et al.   TRENDS IN MICROBIOLOGY

The complete genome sequence of the cold adapted crude-oil degrader: Pedobacter steynii DX4

(2017) Sijing Chang et al.   Standards in Genomic Sciences

Heterologous expression of LamA gene encoded endo-β-1,3-glucanase and CO2 fixation by bioengineered Synechococcus sp. PCC 7002

(2017) Di Li et al.   Frontiers of Environmental Science & Engineering

Marine-Derived Biocatalysts: Importance, Accessing, and Application in Aromatic Pollutant Bioremediation

(2017) Efstratios Nikolaivits et al.   Frontiers in Microbiology

Metabolomics for Plant Improvement: Status and Prospects

(2017) Rakesh Kumar et al.   Frontiers in Plant Science

Genome-resolved metagenomics of a bioremediation system for degradation of thiocyanate in mine water containing suspended solid tailings

(2017) Sumayah F. Rahman et al.   MicrobiologyOpen

Bioremediation of petroleum wastewater by hyper-phenol tolerant Bacillus cereus: Preliminary studies with laboratory-scale batch process

(2017) Aditi Banerjee et al.   Bioengineered

Aerobic and anaerobic fungal metabolism and Omics insights for increasing polycyclic aromatic hydrocarbons biodegradation

(2017) Sevcan Aydin et al.   Fungal Biology Reviews

Application of spectroscopic techniques for monitoring microbial diversity and bioremediation

(2016) Jaya Chakraborty et al.   APPLIED SPECTROSCOPY REVIEWS

Simultaneous prediction of enzyme orthologs from chemical transformation patterns forde novometabolic pathway reconstruction

(2016) Yasuo Tabei et al.   BIOINFORMATICS

Microalgal bioengineering for sustainable energy development: Recent transgenesis and metabolic engineering strategies

(2016) Chiranjib Banerjee et al.   Biotechnology Journal

Scalable metagenomics alignment research tool (SMART): a scalable, rapid, and complete search heuristic for the classification of metagenomic sequences from complex sequence populations

(2016) Aaron Y. Lee et al.   BMC BIOINFORMATICS

Treatment of pharmaceutical wastewater using interior micro-electrolysis/Fenton oxidation-coagulation and biological degradation

(2016) Xiaoyi Xu et al.   CHEMOSPHERE

Gene editing for cell engineering: trends and applications

(2016) Sanjeev K. Gupta et al.   CRITICAL REVIEWS IN BIOTECHNOLOGY

Directed evolution and synthetic biology applications to microbial systems

(2016) Marcelo C Bassalo et al.   CURRENT OPINION IN BIOTECHNOLOGY

An automated system for evaluation of the potential functionome: MAPLE version 2.1.0

(2016) Hideto Takami et al.   DNA RESEARCH

The spatial correlation and interaction between manufacturing agglomeration and environmental pollution

(2016) Zhonghua Cheng   ECOLOGICAL INDICATORS

Bioremediation potential of diesel-contaminated Libyan soil

(2016) Eman Koshlaf et al.   ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY

The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis

(2016) Eugeni Belda et al.   ENVIRONMENTAL MICROBIOLOGY

Characterization of the phthalate acid catabolic gene cluster in phthalate acid esters transforming bacterium-Gordonia sp. strain HS-NH1

(2016) Dandan Li et al.   INTERNATIONAL BIODETERIORATION & BIODEGRADATION

Environmental Microbial Community Proteomics: Status, Challenges and Perspectives

(2016) Da-Zhi Wang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Complete genome sequence of an aromatic compound degrader Arthrobacter sp. YC-RL1

(2016) Lei Ren et al.   JOURNAL OF BIOTECHNOLOGY

Genomic and molecular mechanisms for efficient biodegradation of aromatic dye

(2016) Su Sun et al.   JOURNAL OF HAZARDOUS MATERIALS

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

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

Metabolic analysis of the response of Pseudomonas putida DOT-T1E strains to toluene using Fourier transform infrared spectroscopy and gas chromatography mass spectrometry

(2016) Ali Sayqal et al.   Metabolomics

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

BRENDA in 2017: new perspectives and new tools in BRENDA

(2016) Sandra Placzek et al.   NUCLEIC ACIDS RESEARCH

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Enhancing metaproteomics-The value of models and defined environmental microbial systems

(2016) Florian-Alexander Herbst et al.   PROTEOMICS

Phenotype microarray analysis may unravel genetic determinants of the stress response by Rhodococcus aetherivorans BCP1 and Rhodococcus opacus R7

(2016) Martina Cappelletti et al.   RESEARCH IN MICROBIOLOGY

Connecting phenome to genome in Pseudomonas stutzeri 5190: an artwork biocleaning bacterium

(2016) Pilar Bosch-Roig et al.   RESEARCH IN MICROBIOLOGY

The Ensembl gene annotation system

(2016) Bronwen L. Aken et al.   Database-The Journal of Biological Databases and Curation

Microalgal bioengineering for sustainable energy development: Recent transgenesis and metabolic engineering strategies

(2016) Chiranjib Banerjee et al.   Biotechnology Journal

Current Technological Improvements in Enzymes toward Their Biotechnological Applications

(2016) Mehak Baweja et al.   Frontiers in Microbiology

Recent Developments in Systems Biology and Metabolic Engineering of Plant–Microbe Interactions

(2016) Vishal Kumar et al.   Frontiers in Plant Science

Synergistic effect of quorum sensing genes in biofilm development and PAHs degradation by a marine bacterium

(2016) Supriya Kumari et al.   Bioengineered

Improving high carbon dioxide tolerance and carbon dioxide fixation capability of Chlorella sp. by adaptive laboratory evolution

(2015) Dengjin Li et al.   BIORESOURCE TECHNOLOGY

Bioremediation of soils contaminated with polycyclic aromatic hydrocarbons, petroleum, pesticides, chlorophenols and heavy metals by composting: Applications, microbes and future research needs

(2015) Ming Chen et al.   BIOTECHNOLOGY ADVANCES

From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems

(2015) Daniel R. Garza et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Engineering quorum sensing signaling of Pseudomonas for enhanced wastewater treatment and electricity harvest: A review

(2015) Yang-Chun Yong et al.   CHEMOSPHERE

Advanced technologies for improved expression of recombinant proteins in bacteria: perspectives and applications

(2015) Sanjeev K. Gupta et al.   CRITICAL REVIEWS IN BIOTECHNOLOGY

Next-generation genome-scale models for metabolic engineering

(2015) Zachary A King et al.   CURRENT OPINION IN BIOTECHNOLOGY

Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways

(2015) Noushin Hadadi et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Comparative proteomic analysis in Miscanthus sinensis exposed to antimony stress

(2015) Liang Xue et al.   ENVIRONMENTAL POLLUTION

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

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

The Bacterial Origins of the CRISPR Genome-Editing Revolution

(2015) Erik J. Sontheimer et al.   HUMAN GENE THERAPY

Engineering and sustainability performance of self-compacting palm oil mill incinerated waste concrete

(2015) Jegathish Kanadasan et al.   JOURNAL OF CLEANER PRODUCTION

Remediation of textile effluents by membrane based treatment techniques: A state of the art review

(2015) Jhilly Dasgupta et al.   JOURNAL OF ENVIRONMENTAL MANAGEMENT

Enzyme Based Biosensors for Detection of Environmental Pollutants-A Review

(2015) Vinod Kumar Nigam et al.   JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY

'Deadman' and 'Passcode' microbial kill switches for bacterial containment

(2015) Clement T Y Chan et al.   Nature Chemical Biology

The MG-RAST metagenomics database and portal in 2015

(2015) Andreas Wilke 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

Harnessing CRISPR–Cas systems for bacterial genome editing

(2015) Kurt Selle et al.   TRENDS IN MICROBIOLOGY

BioSurfDB: knowledge and algorithms to support biosurfactants and biodegradation studies

(2015) Jorge S. Oliveira et al.   Database-The Journal of Biological Databases and Curation

Metabolomics reveals differences of metal toxicity in cultures of Pseudomonas pseudoalcaligenes KF707 grown on different carbon sources

(2015) Sean C. Booth et al.   Frontiers in Microbiology

Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future

(2015) Georgios A. Pavlopoulos et al.   GigaScience

Importance of Rhodococcus strains in a bacterial consortium degrading a mixture of hydrocarbons, gasoline, and diesel oil additives revealed by metatranscriptomic analysis

(2014) Marc D. Auffret et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Physical and physicochemical cleaning of lignite and the effect of cleaning on biodesulfurization

(2014) Derya Oz Aksoy et al.   FUEL

Degradation of polychlorinated biphenyls (PCBs) by four bacterial isolates obtained from the PCB-contaminated soil and PCB-contaminated sediment

(2014) Slavomíra Murínová et al.   INTERNATIONAL BIODETERIORATION & BIODEGRADATION

Biotechnological domestication of pseudomonads using synthetic biology

(2014) Pablo I. Nikel et al.   NATURE REVIEWS MICROBIOLOGY

Updates in Rhea—a manually curated resource of biochemical reactions

(2014) Anne Morgat et al.   NUCLEIC ACIDS RESEARCH

ArrayExpress update—simplifying data submissions

(2014) Nikolay Kolesnikov et al.   NUCLEIC ACIDS RESEARCH

Gene: a gene-centered information resource at NCBI

(2014) Garth R. Brown et al.   NUCLEIC ACIDS RESEARCH

Pollution from drug manufacturing: review and perspectives

(2014) D. G. J. Larsson   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Pseudomonas putida CSV86: A Candidate Genome for Genetic Bioaugmentation

(2014) Vasundhara Paliwal et al.   PLoS One

Network Meta-Analysis Using R: A Review of Currently Available Automated Packages

(2014) Binod Neupane et al.   PLoS One

The new frontier of genome engineering with CRISPR-Cas9

(2014) J. A. Doudna et al.   SCIENCE

Increasing phytoremediation efficiency and reliability using novel omics approaches

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

Ring-Hydroxylating Oxygenase database: a database of bacterial aromatic ring-hydroxylating oxygenases in the management of bioremediation and biocatalysis of aromatic compounds

(2014) Joydeep Chakraborty et al.   Environmental Microbiology Reports

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

MEMOSys 2.0: an update of the bioinformatics database for genome-scale models and genomic data

(2014) Stephan Pabinger et al.   Database-The Journal of Biological Databases and Curation

Diverse alkane hydroxylase genes in microorganisms and environments

(2014) Yong Nie et al.   Scientific Reports

Supervised de novo reconstruction of metabolic pathways from metabolome-scale compound sets

(2013) M. Kotera et al.   BIOINFORMATICS

A poor man's BLASTX--high-throughput metagenomic protein database search using PAUDA

(2013) D. H. Huson et al.   BIOINFORMATICS

In silico and experimental methods revealed highly diverse bacteria with quorum sensing and aromatics biodegradation systems – A potential broad application on bioremediation

(2013) Yili Huang et al.   BIORESOURCE TECHNOLOGY

Regulation of aromatics biodegradation by rhl quorum sensing system through induction of catechol meta-cleavage pathway

(2013) Yang-Chun Yong et al.   BIORESOURCE TECHNOLOGY

BioFNet: biological functional network database for analysis and synthesis of biological systems

(2013) Hiroyuki Kurata et al.   BRIEFINGS IN BIOINFORMATICS

Electrochemistry: as cause and cure in water pollution—an overview

(2013) Subramanyan Vasudevan et al.   Environmental Chemistry Letters

Proteomic approach of adaptive response to arsenic stress in Exiguobacterium sp. S17, an extremophile strain isolated from a high-altitude Andean Lake stromatolite

(2013) Carolina Belfiore et al.   EXTREMOPHILES

The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases

(2013) Sandra Orchard et al.   NUCLEIC ACIDS RESEARCH

Negatome 2.0: a database of non-interacting proteins derived by literature mining, manual annotation and protein structure analysis

(2013) Philipp Blohm et al.   NUCLEIC ACIDS RESEARCH

Metagenomic analysis and metabolite profiling of deep–sea sediments from the Gulf of Mexico following the Deepwater Horizon oil spill

(2013) Nikole E. Kimes et al.   Frontiers in Microbiology

EnrichNet: network-based gene set enrichment analysis

(2012) Enrico Glaab et al.   BIOINFORMATICS

Systems biology approach to bioremediation

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

Analysis of the microbial gene landscape and transcriptome for aromatic pollutants and alkane degradation using a novel internally calibrated microarray system

(2012) Ramiro Vilchez-Vargas et al.   ENVIRONMENTAL MICROBIOLOGY

Genome-scale genetic manipulation methods for exploring bacterial molecular biology

(2012) Alla Gagarinova et al.   Molecular BioSystems

The 1000 Genomes Project: data management and community access

(2012) Laura Clarke et al.   NATURE METHODS

Metagenomic Analysis of the Bioremediation of Diesel-Contaminated Canadian High Arctic Soils

(2012) Etienne Yergeau et al.   PLoS One

Double-Strand Break End Resection and Repair Pathway Choice

(2011) Lorraine S. Symington et al.   Annual Review of Genetics

Oxidative-Reductionist Approaches to Stem and Progenitor Cell Function

(2011) Mark Noble et al.   Cell Stem Cell

Bioremediation approaches for organic pollutants: A critical perspective

(2011) Mallavarapu Megharaj et al.   ENVIRONMENT INTERNATIONAL

Metabolic Engineering of Bacteria

(2011) Ravi R. Kumar et al.   INDIAN JOURNAL OF MICROBIOLOGY

Emerging pollutants in wastewater: A review of the literature

(2011) Tiphanie Deblonde et al.   INTERNATIONAL JOURNAL OF HYGIENE AND ENVIRONMENTAL HEALTH

SABIO-RK--database for biochemical reaction kinetics

(2011) U. Wittig et al.   NUCLEIC ACIDS RESEARCH

The University of Minnesota Pathway Prediction System: multi-level prediction and visualization

(2011) J. Gao et al.   NUCLEIC ACIDS RESEARCH

Metabolic networks, microbial ecology and ‘omics’ technologies: towards understanding in situ biodegradation processes

(2010) Ramiro Vilchez-Vargas et al.   ENVIRONMENTAL MICROBIOLOGY

Environmental risk assessment and stabilization/solidification of zinc extraction residue: II. Stabilization/solidification

(2010) Mehmet Erdem et al.   HYDROMETALLURGY

Biochemistry of Microbial Degradation of Hexachlorocyclohexane and Prospects for Bioremediation

(2010) R. Lal et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Global threats to human water security and river biodiversity

(2010) C. J. Vörösmarty et al.   NATURE

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

PathPred: an enzyme-catalyzed metabolic pathway prediction server

(2010) Y. Moriya et al.   NUCLEIC ACIDS RESEARCH

Tools of bioinformatics in biodegradation

(2010) Pankaj Kumar Arora et al.   REVIEWS IN ENVIRONMENTAL SCIENCE AND BIO-TECHNOLOGY

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

Computational framework for predictive biodegradation

(2009) Stacey D. Finley et al.   BIOTECHNOLOGY AND BIOENGINEERING

Review: In situ and bioremediation of organic pollutants in aquatic sediments

(2009) Louisa Wessels Perelo   JOURNAL OF HAZARDOUS MATERIALS

Integrating multiple 'omics' analysis for microbial biology: application and methodologies

(2009) W. Zhang et al.   MICROBIOLOGY-SGM

Evolution of efficient pathways for degradation of anthropogenic chemicals

(2009) Shelley D Copley   Nature Chemical Biology

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

(2009) Junfeng Gao et al.   NUCLEIC ACIDS RESEARCH

Chemical cleaning of potable water membranes: A review

(2009) Nicandro Porcelli et al.   SEPARATION AND PURIFICATION TECHNOLOGY

Field metabolomics and laboratory assessments of anaerobic intrinsic bioremediation of hydrocarbons at a petroleum-contaminated site

(2009) Victoria A. Parisi et al.   Microbial Biotechnology

Bacterial Degradation of Aromatic Compounds

(2009) Jong-Su Seo et al.   International Journal of Environmental Research and Public Health

Induction of ortho- and meta-cleavage pathways in Pseudomonas in biodegradation of high benzoate concentration: MS identification of catabolic enzymes

(2008) Bin Cao et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

ProteoWizard: open source software for rapid proteomics tools development

(2008) Darren Kessner et al.   BIOINFORMATICS

Bioremediation: environmental clean-up through pathway engineering

(2008) Shailendra Singh et al.   CURRENT OPINION IN BIOTECHNOLOGY

Systems biology approaches to bioremediation

(2008) Víctor de Lorenzo   CURRENT OPINION IN BIOTECHNOLOGY

Fitness drift of an atrazine-degrading population under atrazine selection pressure

(2008) Marion Devers et al.   ENVIRONMENTAL MICROBIOLOGY

A system for the construction of targeted unmarked gene deletions in the genus Burkholderia

(2008) Ronald S. Flannagan et al.   ENVIRONMENTAL MICROBIOLOGY

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Bionemo: molecular information on biodegradation metabolism

(2008) G. Carbajosa et al.   NUCLEIC ACIDS RESEARCH

Insights into environmental bioremediation by microorganisms through functional genomics and proteomics

(2008) Bing Zhao et al.   PROTEOMICS