4.6 Article

Genome Analysis and Physiology of Pseudomonas sp. Strain OVF7 Degrading Naphthalene and n-Dodecane

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR

Robert D. Olson et al.

Summary: This report introduces the Bioinformatics Resource Center program established by the National Institute of Allergy and Infectious Diseases (NIAID) to aid researchers in analyzing genome sequences and other omics-related data. The merger of PATRIC, IRD, and ViPR BRCs has resulted in the formation of BV-BRC, which offers a unified data model, enhanced visualization and analysis tools, bioinformatics services, and a powerful suite of command line tools for the bacterial and viral research communities.

NUCLEIC ACIDS RESEARCH (2023)

Article Biochemical Research Methods

Galaxy Training: A powerful framework for teaching!

Saskia Hiltemann et al.

Summary: There is a skills gap in life science researchers due to the lack of training in basic computational skills, data analysis, and stewardship. To address this gap, the Galaxy Training Network has developed an open access framework for training materials in data analysis using the user-friendly Galaxy platform. It has been successful in supporting researchers and educators in various fields.

PLOS COMPUTATIONAL BIOLOGY (2023)

Review Environmental Sciences

Recent Advances in Bacterial Degradation of Hydrocarbons

Emiliana Pandolfo et al.

Summary: Hydrocarbons in fossil fuels like crude oil are made up of hydrogen and carbon. Refining crude oil creates commercial products with new properties that can make them more complex, toxic, and harder to degrade. Different bacterial species are involved in the degradation of aliphatic and aromatic hydrocarbons. Hydrocarbon contamination usually involves a mixture of these chemicals and requires bacterial consortia for effective removal.

WATER (2023)

Article Microbiology

Low-temperature phenol-degrading microbial agent: construction and mechanism

Yu Yang et al.

Summary: In this study, three cold-tolerant phenol-degrading strains, Pseudomonas veronii Ju-A1 (Ju-A1), Leifsonia naganoensis Ju-A4 (Ju-A4), and Rhodococcus qingshengii Ju-A6 (Ju-A6), were isolated. All three strains can produce cis, cis-muconic acid by ortho-cleavage of catechol at 12 degrees C. Response surface methodology (RSM) was used to optimize the proportional composition of low-temperature phenol-degrading microbiota. The experiments showed that the microbial agent (three strains of low-temperature phenol-degrading bacteria were fermented separately and constructed in the optimal ratio) could completely degrade 200 mg L-1 phenol within 36 h. The above construction method is more advantageous in bio-enhanced treatment of actual wastewater. Through the construction of microbial agents to enhance the degradation effect of phenol, it provides a feasible scheme for the biodegradation of phenol wastewater at low temperature and shows good application potential.

ARCHIVES OF MICROBIOLOGY (2023)

Article Biochemistry & Molecular Biology

Proksee: in-depth characterization and visualization of bacterial genomes

Jason R. Grant et al.

Summary: Proksee is a powerful and user-friendly system for assembling, annotating, analyzing, and visualizing bacterial genomes. It accepts various file formats and provides unique assembly metrics, a high-performance genome browser, embedded analysis tools, and the option to export data for sharing and reproducibility. The system is designed to scale and ensure a robust and responsive web server.

NUCLEIC ACIDS RESEARCH (2023)

Article Biochemistry & Molecular Biology

TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes

Jan P. Meier-Kolthoff et al.

Summary: Microbial systematics is influenced by genome-based methods and faces challenges from the increasing number of taxon names and associated sequences. Accurate and reliable high-throughput platforms like LPSN and TYGS are essential for handling the data efficiently. The updates include new features and expanded database content to provide easy access to the data.

NUCLEIC ACIDS RESEARCH (2022)

Review Biotechnology & Applied Microbiology

Current research on simultaneous oxidation of aliphatic and aromatic hydrocarbons by bacteria of genus Pseudomonas

Anastasiya A. Ivanova et al.

Summary: One of the most frequently used methods for eliminating oil pollution is the use of biological preparations based on oil-degrading microorganisms, particularly bacteria of the genus Pseudomonas. While individual biochemical pathways and genes related to hydrocarbon degradation have been extensively studied, microorganisms capable of simultaneous degradation of different classes of hydrocarbons are poorly understood. Transcriptomics and proteomics are promising approaches for understanding metabolic interactions under different growth conditions. This review summarizes the current knowledge on Pseudomonas bacteria capable of simultaneous oxidation of hydrocarbons and highlights the most important findings obtained from transcriptomic and proteomic analyses.

FOLIA MICROBIOLOGICA (2022)

Article Multidisciplinary Sciences

Pseudomonas veronii strain 7-41 degrading medium-chain n-alkanes and polycyclic aromatic hydrocarbons

S. A. Mullaeva et al.

Summary: Pollution of the environment by crude oil and oil products poses a global problem. The strain Pseudomonas veronii 7-41 can degrade medium-chain n-alkanes and polycyclic aromatic hydrocarbons. A natural plasmid carrying operons for the degradation of two different classes of hydrocarbons was identified. The strain showed different degradation abilities in single-substrate and double-substrate systems.

SCIENTIFIC REPORTS (2022)

Review Environmental Sciences

Bioremediation Treatment of Polyaromatic Hydrocarbons for Environmental Sustainability

Marjan Salari et al.

Summary: This study focuses on bacteria and fungi that degrade oil and hydrocarbons, demonstrating the effectiveness and efficiency of bioremediation in removing petroleum hydrocarbon contaminants. The study highlights the enzymatic catalytic activities of microorganisms in enhancing the degradation process. Microbial biodegradation of pollutants is cost-effective and can be achieved by stimulating indigenous microorganisms or introducing microorganisms into the environment.

WATER (2022)

Review Multidisciplinary Sciences

Biofilm as an adaptation strategy to extreme conditions

Ermenegilda Parrilli et al.

Summary: Biofilm is a complex biological system that can respond to environmental changes and is the most successful and widely distributed life form on earth. Its unique characteristics make it crucial for microbial evolution and adaptation. The ability to establish biofilms is a key trait for microorganisms growing in extreme environments.

RENDICONTI LINCEI-SCIENZE FISICHE E NATURALI (2022)

Article Biochemistry & Molecular Biology

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

Ivica Letunic et al.

Summary: The Interactive Tree Of Life is an online tool for displaying, manipulating, and annotating phylogenetic and other trees. The latest version 5 introduces a new tree display engine and several new features, such as a new dataset type and expanded annotation options. Users can now also manually annotate trees by hand, providing more flexibility and control.

NUCLEIC ACIDS RESEARCH (2021)

Article Microbiology

Pseudomonas fildesensis sp. nov., a psychrotolerant bacterium isolated from Antarctic soil of King George Island, South Shetland Islands

Maria S. Pavlov et al.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2020)

Review Microbiology

Polycyclic Aromatic Hydrocarbons: Sources, Toxicity, and Remediation Approaches

Avani Bharatkumar Patel et al.

FRONTIERS IN MICROBIOLOGY (2020)

Article Biotechnology & Applied Microbiology

Assembly of long, error-prone reads using repeat graphs

Mikhail Kolmogorov et al.

NATURE BIOTECHNOLOGY (2019)

Article Multidisciplinary Sciences

TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy

Jan P. Meier-Kolthoff et al.

NATURE COMMUNICATIONS (2019)

Article Microbiology

Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes

Jongsik Chun et al.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2018)

Article Biotechnology & Applied Microbiology

LaoABCR, a Novel System for Oxidation of Long-Chain Alcohols Derived from SDS and Alkane Degradation in Pseudomonas aeruginosa

Gianna Panasia et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2018)

Article Multidisciplinary Sciences

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

Chirag Jain et al.

NATURE COMMUNICATIONS (2018)

Article Biotechnology & Applied Microbiology

Screening for biosurfactant production by 2,4,6-trinitrotoluene-transforming bacteria

H. Avila-Arias et al.

JOURNAL OF APPLIED MICROBIOLOGY (2017)

Article Biotechnology & Applied Microbiology

Degradation of Benzene by Pseudomonas veronii 1YdBTEX2 and 1YB2 Is Catalyzed by Enzymes Encoded in Distinct Catabolism Gene Clusters

Daiana de Lima-Morales et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2016)

Article Biochemistry & Molecular Biology

A Review on the Genetics of Aliphatic and Aromatic Hydrocarbon Degradation

Firouz Abbasian et al.

APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY (2016)

Article Microbiology

OrthoANI: An improved algorithm and software for calculating average nucleotide identity

Imchang Lee et al.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2016)

Article Biotechnology & Applied Microbiology

Mash: fast genome and metagenome distance estimation using MinHash

Brian D. Ondov et al.

GENOME BIOLOGY (2016)

Article Biochemistry & Molecular Biology

FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program

Vincent Lefort et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

Article Environmental Sciences

Genetic determinants involved in the biodegradation of naphthalene and phenanthrene in Pseudomonas aeruginosa PAO1

Jing Qi et al.

ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH (2015)

Article Biochemical Research Methods

Prokka: rapid prokaryotic genome annotation

Torsten Seemann

BIOINFORMATICS (2014)

Article Microbiology

Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes

Mincheol Kim et al.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2014)

Article Biochemical Research Methods

Genome sequence-based species delimitation with confidence intervals and improved distance functions

Jan P. Meier-Kolthoff et al.

BMC BIOINFORMATICS (2013)

Article Microbiology

The organization of naphthalene degradation genes in Pseudomonas putida strain AK5

Tatyana Yu. Izmalkova et al.

RESEARCH IN MICROBIOLOGY (2013)

Article Biochemical Research Methods

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

Anton Bankevich et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Biotechnology & Applied Microbiology

Characterization of the Poly-β-1,6-N-Acetylglucosamine Polysaccharide Component of Burkholderia Biofilms

Nandadeva Yakandawala et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2011)

Article Genetics & Heredity

Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison

Alexander F. Auch et al.

STANDARDS IN GENOMIC SCIENCES (2010)

Article Biochemical Research Methods

BLAST plus : architecture and applications

Christiam Camacho et al.

BMC BIOINFORMATICS (2009)

Review Microbiology

Degradation of alkanes by bacteria

Fernando Rojo

ENVIRONMENTAL MICROBIOLOGY (2009)

Article Biochemical Research Methods

Community-based degradation of 4-chorosalicylate tracked on the single cell level

Sonja Pawelczyk et al.

JOURNAL OF MICROBIOLOGICAL METHODS (2008)

Article Biotechnology & Applied Microbiology

Microbial community shifts as a response to efficient degradation of chlorobenzene under hypoxic conditions

Baerbel Kiesel et al.

BIODEGRADATION (2008)

Article Biotechnology & Applied Microbiology

Kinetics of chlorobenzene biodegradation under reduced oxygen levels

Gerd Ulrich Balcke et al.

BIODEGRADATION (2008)

Article Biotechnology & Applied Microbiology

Biodegradation of chlorobenzene under hypoxic and mixed hypoxic-denitrifying conditions

Holger Nestler et al.

BIODEGRADATION (2007)

Article Microbiology

Degradation of alkyl methyl ketones by Pseudomonas veronii MEK700

Christina Onaca et al.

JOURNAL OF BACTERIOLOGY (2007)

Article Biochemistry & Molecular Biology

RNAmmer:: consistent and rapid annotation of ribosomal RNA genes

Karin Lagesen et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Environmental Sciences

Microbial degradation of chlorobenzene under oxygen-limited conditions leads to accumulation of 3-chlorocatechol

C Vogt et al.

ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY (2004)

Article Biotechnology & Applied Microbiology

A novel catabolic activity of Pseudomonas veronii in biotransformation of pentachlorophenol

IH Nam et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2003)

Article Microbiology

Functional characterization of genes involved in alkane oxidation by Pseudomonas aeruginosa

THM Smits et al.

ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY (2003)