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Issue: Vol. 1 No. 2 (2026)
Section: BIOMEDICAL AND PHARMACEUTICAL SCIENCES
DOI: 10.58334/jtse.vol.001.736
Submitted Date: 15/09/2025
Revised Date: 23/11/2025
Accept Date: 08/01/2026
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How to Cite
Bui, T. H., Do, T. T., Tran, T. T. T., Nguyen, V. C., Nguyen, T. K. T., & Ngo, C. C. Genome-supported identification and physiological characterization of Rhodococcus ruber KHA5.2, a hydrocarbon- oxidizing bacterium from Vietnamese coastal sands. Journal of Tropical Science and Engineering, 1(2). https://doi.org/10.58334/jtse.vol.001.736

Genome-supported identification and physiological characterization of Rhodococcus ruber KHA5.2, a hydrocarbon- oxidizing bacterium from Vietnamese coastal sands

Thu Hang Bui1, Thi Tuyen Do2,3,4, Thi Thanh Thuy Tran2, Viet Cuong Nguyen1, Thi Kim Thanh Nguyen2, Cao Cuong Ngo2,
1 Faculty of Biology, VNU University of Science
2 Department of Biotechnology, Joint Vietnam-Russia Tropical Science and Technology Research Center
3 Graduate University of Science and Technology, Vietnam Academy of Science and Technology
4 Institute of Biology, Vietnam Academy of Science and Technology
Corresponding author:
Cao Cuong Ngo
Department of Biotechnology, Joint Vietnam-Russia Tropical Science and Technology Research Center
No. 63 Nguyen Van Huyen Street, Nghia Do Ward, Hanoi
Phone: +84982010336;  Email: ngocaocuong2011@gmail.com

Main Article Content

Abstract

Petroleum pollution often involves mixtures of volatile monoaromatic compounds and recalcitrant PAHs, but the isolation and characterization of native hydrocarbon‑degrading microbes in Vietnam are still underexplored. In this study, we isolated and characterized an autochthonous hydrocarbon‑oxidizing bacterium, Rhodococcus ruber KHA5.2, from oil‑impacted coastal sands in Khanh Hoa Province, Vietnam. Species assignment was supported by full‑length 16S rRNA similarity > 99.8% to Rhodococcus spp. and confirmed by digital DNA–DNA hybridization of 99.08% to R. ruber NBRC 15591. Short‑read de novo assembly yielded a 5.43‑Mb draft genome (GC 70.1%) across 981 contigs with 94.72% completeness, consistent with typical Rhodococcus genomes in terms of size and GC content. Experimentally, KHA5.2 oxidized  crude oil and representative aromatics spanning BTX constituents (benzene, toluene, xylene) and the low‑molecular‑weight PAH naphthalene. The strain was able to grow at NaCl concentrations up to 5% and across pH 3–11 and 20–40°C; however, hydrocarbon-oxidizing activity, as assessed by the DCPIP reduction assay, was only observed optimally at 0–3% NaCl, indicating that the range of salt tolerance for growth is broader than that for effective oxidative activity. In minimal mineral medium supplemented with 1% (v/v) crude oil, optical density increased to its maximum value on day 6 and then declined, consistent with depletion of readily utilizable fractions and/or accumulation of inhibitory intermediates. The diversity of aromatic compounds oxidized by KHA5.2 matched that observed in closely related Rhodococcus species.. However, these results are based on qualitative assays, and further quantitative evaluation of degradation rates and field trials are needed to fully confirm the strain’s bioremediation capabilities. Taken together, genome-based taxonomy, salinity-tolerant physiology, and qualitative evidence of aromatic substrate oxidation suggest that R. ruber KHA5.2 represents a promising candidate for further bioremediation-oriented investigations in brackish and intertidal settings. To translate laboratory indicators into field‑level performance, standardized experimental conditions and quantitative, mass‑balance measurements (GC–FID/GC–MS) across salinity gradients and environmental matrices will be essential.

Keywords

Bioremediation, BTX biodegradation, Crude oil degradation, Hydrocarbon-degrading enzymes, Rhodococcus ruber KHA5.2, Whole-genome sequencing

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