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<p>A crude oil–degrading bacterial strain, CSR1, was isolated from oil-contaminated soil collected in Diyarbakır, southeastern Türkiye, for this study. The strain has been identified as <i>Staphylococcus epidermidis</i> using 16&#xa0;S rRNA gene analysis and whole-genome sequencing. The entire genome of strain CSR1 was found to be 2,595,333&#xa0;bp in length, exhibiting a GC content of 32.12% and comprising 2,396 protein-coding sequences, 61 tRNA genes, and 16 rRNA genes. Genome-based taxonomic investigation by digital DNA–DNA hybridization verified that the strain is classified as <i>S. epidermidis</i>. Analysis of the resistome utilizing the CARD and ResFinder databases identified several antimicrobial resistance determinants, including multidrug efflux pump genes (<i>norA</i>, <i>sdrM</i>, <i>norC</i>, <i>mdeA</i>, and <i>sepA</i>) and antibiotic inactivation genes (<i>blaZ</i>, <i>FosBx1</i>, and <i>dfrC</i>). Genome annotation identified a putative <i>alkB</i>-like alkane degradation–related gene, exhibiting significant similarities to an LLM class flavin-dependent oxidoreductase. A phylogenetic study indicated that this enzyme is part of the oxidoreductase family and may be involved in hydrocarbon degradation pathways. Gas chromatography study revealed that strain CSR1 degraded 91.7% of n-alkanes (C6–C29) in crude oil after seven days of incubation. These findings offer genetic and functional insights into the hydrocarbon-degrading capabilities of <i>S. epidermidis</i> CSR1 and underscore its potential significance in the bioremediation of petroleum-contaminated environments. To the best of our knowledge, this is the first genome-based characterization that integrates hydrocarbon degradation genes and antimicrobial resistance profile of a petroleum-degrading <i>S. epidermidis</i> strain that was isolated from oil-contaminated soil in southeast Türkiye.</p>

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Whole genome insights into hydrocarbon degradation and antimicrobial resistance in Staphylococcus epidermidis CSR1 isolated from oil-contaminated soil

  • 期刊论文

  • 发表日期：

    2026年6月22日

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  • Ömer Acer

摘要

A crude oil–degrading bacterial strain, CSR1, was isolated from oil-contaminated soil collected in Diyarbakır, southeastern Türkiye, for this study. The strain has been identified as Staphylococcus epidermidis using 16 S rRNA gene analysis and whole-genome sequencing. The entire genome of strain CSR1 was found to be 2,595,333 bp in length, exhibiting a GC content of 32.12% and comprising 2,396 protein-coding sequences, 61 tRNA genes, and 16 rRNA genes. Genome-based taxonomic investigation by digital DNA–DNA hybridization verified that the strain is classified as S. epidermidis. Analysis of the resistome utilizing the CARD and ResFinder databases identified several antimicrobial resistance determinants, including multidrug efflux pump genes (norA, sdrM, norC, mdeA, and sepA) and antibiotic inactivation genes (blaZ, FosBx1, and dfrC). Genome annotation identified a putative alkB-like alkane degradation–related gene, exhibiting significant similarities to an LLM class flavin-dependent oxidoreductase. A phylogenetic study indicated that this enzyme is part of the oxidoreductase family and may be involved in hydrocarbon degradation pathways. Gas chromatography study revealed that strain CSR1 degraded 91.7% of n-alkanes (C6–C29) in crude oil after seven days of incubation. These findings offer genetic and functional insights into the hydrocarbon-degrading capabilities of S. epidermidis CSR1 and underscore its potential significance in the bioremediation of petroleum-contaminated environments. To the best of our knowledge, this is the first genome-based characterization that integrates hydrocarbon degradation genes and antimicrobial resistance profile of a petroleum-degrading S. epidermidis strain that was isolated from oil-contaminated soil in southeast Türkiye.