Complete Genome Sequence of Pseudomonas aeruginosa MTB-1, Isolated from a Microbial Community Enriched by the Technical Formulation of Hexachlorocyclohexane

Ohtsubo, Yoshiyuki; Sato, Takuya; Kishida, Ken; Tabata, Michro; Ogura, Yoshitoshi; Hayashi, Tetsuya; Tsuda, Masashi; Nagata, Yasunobu

doi:10.1128/genomea.01130-13

Cited by 7 publications

(2 citation statements)

References 8 publications

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“…Pseudomonas sp. TKP [ 59 ] and P. aeruginosa MTB1 [ 60 ] were also included owing to their similar ecotype status as strain RL i.e. isolated from HCH contaminated soils from Japan.…”

Section: Methodsmentioning

confidence: 99%

Pan-genome dynamics of Pseudomonas gene complements enriched across hexachlorocyclohexane dumpsite

et al. 2015

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BackgroundPhylogenetic heterogeneity across Pseudomonas genus is complemented by its diverse genome architecture enriched by accessory genetic elements (plasmids, transposons, and integrons) conferring resistance across this genus. Here, we sequenced a stress tolerant genotype i.e. Pseudomonas sp. strain RL isolated from a hexachlorocyclohexane (HCH) contaminated pond (45 mg of total HCH g−1 sediment) and further compared its gene repertoire with 17 reference ecotypes belonging to P. stutzeri, P. mendocina, P. aeruginosa, P. psychrotolerans and P. denitrificans, representing metabolically diverse ecosystems (i.e. marine, clinical, and soil/sludge). Metagenomic data from HCH contaminated pond sediment and similar HCH contaminated sites were further used to analyze the pan-genome dynamics of Pseudomonas genotypes enriched across increasing HCH gradient.ResultsAlthough strain RL demonstrated clear species demarcation (ANI ≤ 80.03%) from the rest of its phylogenetic relatives, it was found to be closest to P. stutzeri clade which was further complemented functionally. Comparative functional analysis elucidated strain specific enrichment of metabolic pathways like α-linoleic acid degradation and carbazole degradation in Pseudomonas sp. strain RL and P. stutzeri XLDN-R, respectively. Composition based methods (%codon bias and %G + C difference) further highlighted the significance of horizontal gene transfer (HGT) in evolution of nitrogen metabolism, two-component system (TCS) and methionine metabolism across the Pseudomonas genomes used in this study. An intact mobile class-I integron (3,552 bp) with a captured gene cassette encoding for dihydrofolate reductase (dhfra1) was detected in strain RL, distinctly demarcated from other integron harboring species (i.e. P. aeruginosa, P. stutzeri, and P. putida). Mobility of this integron was confirmed by its association with Tnp21-like transposon (95% identity) suggesting stress specific mobilization across HCH contaminated sites. Metagenomics data from pond sediment and recently surveyed HCH adulterated soils revealed the in situ enrichment of integron associated transposase gene (TnpA6100) across increasing HCH contamination (0.7 to 450 mg HCH g−1 of soil).ConclusionsUnlocking the potential of comparative genomics supplemented with metagenomics, we have attempted to resolve the environment and strain specific demarcations across 18 Pseudomonas gene complements. Pan-genome analyses of these strains indicate at astoundingly diverse metabolic strategies and provide genetic basis for the cosmopolitan existence of this taxon.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1488-2) contains supplementary material, which is available to authorized users.

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“…Pseudomonas sp. TKP [ 59 ] and P. aeruginosa MTB1 [ 60 ] were also included owing to their similar ecotype status as strain RL i.e. isolated from HCH contaminated soils from Japan.…”

Section: Methodsmentioning

confidence: 99%

Pan-genome dynamics of Pseudomonas gene complements enriched across hexachlorocyclohexane dumpsite

et al. 2015

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“…In this study, several lines of evidence support the conclusion that the carbapenem-resistant phenotype of these clinical isolates was due to the lack of a functional OprD porin. Since the oprD coding sequences of these isolates were all identical, it is very likely that they originated from the same clone, which may be very closely related to strain MTB-1, an environmental isolate (9). The results of a BLAST tree analysis revealed additional clan members other than MTB-1.…”

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confidence: 96%

A Novel Pseudomonas aeruginosa Strain with an oprD Mutation in Relation to a Nosocomial Respiratory Infection Outbreak in an Intensive Care Unit

Yan

Yao

et al. 2014

J Clin Microbiol

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e Seven imipenem-resistant Pseudomonas aeruginosa isolates were recovered from the sputum samples of pneumonia patients in southwestern China. They had identical antibiotic resistance patterns and indistinguishable pulsed-field gel electrophoresis profiles. Nucleotide sequence analysis revealed a 4-bp (AGTC) insertion in the oprD gene, resulting in a frameshift in the cognate open reading frame. These isolates became imipenem susceptible when the chromosomal oprD lesion was complemented, indicating that the 4-bp insertion in the oprD gene resulted in imipenem resistance.

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Pesticide Bioremediation: OMICs Technologies for Understanding the Processes

Rodríguez

Castrejón-Godínez²,

Sánchez-Salinas³

et al. 2022

Pesticides Bioremediation

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Complete Genome Sequence of Pseudomonas aeruginosa MTB-1, Isolated from a Microbial Community Enriched by the Technical Formulation of Hexachlorocyclohexane

Cited by 7 publications

References 8 publications

Pan-genome dynamics of Pseudomonas gene complements enriched across hexachlorocyclohexane dumpsite

Pan-genome dynamics of Pseudomonas gene complements enriched across hexachlorocyclohexane dumpsite

A Novel Pseudomonas aeruginosa Strain with an oprD Mutation in Relation to a Nosocomial Respiratory Infection Outbreak in an Intensive Care Unit

Pesticide Bioremediation: OMICs Technologies for Understanding the Processes

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