Comparative genomic and functional analyses of Microbacterium paraoxydans BHS25 reveal key metabolic adaptations for survival in arsenic-contaminated soil ecosystems
Abstract Background Microbacterium paraoxydans is known for its potential in bioremediation and biotechnological applications, including promoting plant growth. However, research on this bacterium in Bangladesh has been limited and until now no reported complete genome of M. paraoxydans is available...
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2025-07-01
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| Online Access: | https://doi.org/10.1186/s12864-025-11811-7 |
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| author | Ayman Bin Abdul Mannan Momtaz Zamila Bukharid M. Anwar Hossain Munawar Sultana |
| author_facet | Ayman Bin Abdul Mannan Momtaz Zamila Bukharid M. Anwar Hossain Munawar Sultana |
| author_sort | Ayman Bin Abdul Mannan |
| collection | DOAJ |
| description | Abstract Background Microbacterium paraoxydans is known for its potential in bioremediation and biotechnological applications, including promoting plant growth. However, research on this bacterium in Bangladesh has been limited and until now no reported complete genome of M. paraoxydans is available from this country. In this study, we have reported the complete genome of M. paraoxydans BHS25, the first case in Bangladesh, isolated from arsenic-contaminated soil in Bogura. Results Complete genome analysis revealed that BHS25 was closely related to Microbacterium paraoxydans LTR1 from Russia, which itself showed similarity to a strain found at the International Space Station, reported to be resistant to extreme conditions. BHS25 possessed a genome of 3.49 Mb with a GC content of 70.12%, comprising 3,415 protein-coding genes, 47 tRNA genes, and 5 rRNA genes. It carried various heavy metal resistance genes and gene islands, such as arsC, arsB, and acr3 for arsenic detoxification/transformation, as well as czcD and copB for resistance to cadmium, zinc, cobalt, and copper. The arrangement of the arsenic resistance genes showed similarity to that in other reported Microbacterium strains, although pangenome and ANI analyses indicated considerable genetic diversity within the species. Additionally, the presence of vanY within the vanB cluster suggested potential vancomycin resistance. Metabolic pathway analyses revealed that BHS25 was well adapted, with different carbohydrate and amino acid metabolism, secondary metabolite biosynthesis, and xenobiotic degradation capabilities. The unique notable anabolic pathways were streptomycin biosynthesis with 14 associated genes, novobiocin biosynthesis and tropane, piperidine, and pyridine alkaloid biosynthesis (8 genes each), as well as monobactam biosynthesis, prodigiosin biosynthesis, and penicillin and cephalosporin biosynthesis, suggesting a potential for production of antimicrobials. Furthermore, it showed an auxin biosynthesis pathway for plant growth, further demonstrating its biotechnological potential. Conclusion This research identified Microbacterium paraoxydans BHS25 as a promising candidate for bioremediation and sustainable environmental management, offering insights into microbial adaptation to challenging environments and potential solutions for pollution encounters. |
| format | Article |
| id | doaj-art-370d7fb2e58a4bc6a37265f7c4315e4f |
| institution | DOAJ |
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| language | English |
| publishDate | 2025-07-01 |
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| series | BMC Genomics |
| spelling | doaj-art-370d7fb2e58a4bc6a37265f7c4315e4f2025-08-20T03:04:17ZengBMCBMC Genomics1471-21642025-07-0126111610.1186/s12864-025-11811-7Comparative genomic and functional analyses of Microbacterium paraoxydans BHS25 reveal key metabolic adaptations for survival in arsenic-contaminated soil ecosystemsAyman Bin Abdul Mannan0Momtaz Zamila Bukharid1M. Anwar Hossain2Munawar Sultana3Department of Microbiology, University of DhakaDepartment of Microbiology, University of DhakaDepartment of Microbiology, University of DhakaDepartment of Microbiology, University of DhakaAbstract Background Microbacterium paraoxydans is known for its potential in bioremediation and biotechnological applications, including promoting plant growth. However, research on this bacterium in Bangladesh has been limited and until now no reported complete genome of M. paraoxydans is available from this country. In this study, we have reported the complete genome of M. paraoxydans BHS25, the first case in Bangladesh, isolated from arsenic-contaminated soil in Bogura. Results Complete genome analysis revealed that BHS25 was closely related to Microbacterium paraoxydans LTR1 from Russia, which itself showed similarity to a strain found at the International Space Station, reported to be resistant to extreme conditions. BHS25 possessed a genome of 3.49 Mb with a GC content of 70.12%, comprising 3,415 protein-coding genes, 47 tRNA genes, and 5 rRNA genes. It carried various heavy metal resistance genes and gene islands, such as arsC, arsB, and acr3 for arsenic detoxification/transformation, as well as czcD and copB for resistance to cadmium, zinc, cobalt, and copper. The arrangement of the arsenic resistance genes showed similarity to that in other reported Microbacterium strains, although pangenome and ANI analyses indicated considerable genetic diversity within the species. Additionally, the presence of vanY within the vanB cluster suggested potential vancomycin resistance. Metabolic pathway analyses revealed that BHS25 was well adapted, with different carbohydrate and amino acid metabolism, secondary metabolite biosynthesis, and xenobiotic degradation capabilities. The unique notable anabolic pathways were streptomycin biosynthesis with 14 associated genes, novobiocin biosynthesis and tropane, piperidine, and pyridine alkaloid biosynthesis (8 genes each), as well as monobactam biosynthesis, prodigiosin biosynthesis, and penicillin and cephalosporin biosynthesis, suggesting a potential for production of antimicrobials. Furthermore, it showed an auxin biosynthesis pathway for plant growth, further demonstrating its biotechnological potential. Conclusion This research identified Microbacterium paraoxydans BHS25 as a promising candidate for bioremediation and sustainable environmental management, offering insights into microbial adaptation to challenging environments and potential solutions for pollution encounters.https://doi.org/10.1186/s12864-025-11811-7MicrobacteriumComparative genomicsMetabolic diversityArsenic transformationMetal tolerance |
| spellingShingle | Ayman Bin Abdul Mannan Momtaz Zamila Bukharid M. Anwar Hossain Munawar Sultana Comparative genomic and functional analyses of Microbacterium paraoxydans BHS25 reveal key metabolic adaptations for survival in arsenic-contaminated soil ecosystems BMC Genomics Microbacterium Comparative genomics Metabolic diversity Arsenic transformation Metal tolerance |
| title | Comparative genomic and functional analyses of Microbacterium paraoxydans BHS25 reveal key metabolic adaptations for survival in arsenic-contaminated soil ecosystems |
| title_full | Comparative genomic and functional analyses of Microbacterium paraoxydans BHS25 reveal key metabolic adaptations for survival in arsenic-contaminated soil ecosystems |
| title_fullStr | Comparative genomic and functional analyses of Microbacterium paraoxydans BHS25 reveal key metabolic adaptations for survival in arsenic-contaminated soil ecosystems |
| title_full_unstemmed | Comparative genomic and functional analyses of Microbacterium paraoxydans BHS25 reveal key metabolic adaptations for survival in arsenic-contaminated soil ecosystems |
| title_short | Comparative genomic and functional analyses of Microbacterium paraoxydans BHS25 reveal key metabolic adaptations for survival in arsenic-contaminated soil ecosystems |
| title_sort | comparative genomic and functional analyses of microbacterium paraoxydans bhs25 reveal key metabolic adaptations for survival in arsenic contaminated soil ecosystems |
| topic | Microbacterium Comparative genomics Metabolic diversity Arsenic transformation Metal tolerance |
| url | https://doi.org/10.1186/s12864-025-11811-7 |
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