Genomic Mining of a Gut-Associated Pseudomonas aeruginosa Isolated from Invasive Suckermouth Catfish in Bangladesh Reveal Bioremediation Potential and Biosafety Challenges

Bioremediation is the process of using living microorganisms to clean up polluted environments by converting harmful substances into safer ones. Microorganisms can act as bioremediating agents because of the stringent biodegradability nature, high specificity, low toxicity in nature and high effectiveness activity under extreme conditions. This study aimed to isolate and genomically characterize bioremediating bacteria Pseudomonas aeruginosa BCSIR-JnU-ISO2 from the gut of the invasive suckermouth catfish ( Hypostomus plecostomus ) collected from the heavily polluted Buriganga River, Bangladesh. Out of the three isolates, one specific isolate Pseudomonas aeruginosa BCSIR-JnU-ISO2 was selected and focused due to the highest oil bioremediation potential in specific conditions. This isolate could utilize waste cooking oil (WCO) as a sole carbon source enriched in Bushnell-Haas broth. WCO biodegradation was qualitatively evaluated using the 2,6-dichlorophenolindophenol (DCPIP) assay. Pseudomonas aeruginosa BCSIR-JnU-ISO2 can produce surface-active agents, and it was qualitatively confirmed using drop-collapse, Parafilm M, and oil-spreading assays, and Fourier Transform Infrared Spectroscopy (FTIR). Whole-genome sequencing (WGS) of Pseudomonas aeruginosa BCSIR-JnU-ISO2 was employed to identify the genetic basis for hydrocarbon degradation, predicted heavy metal tolerance, and rhamnolipid biosynthesis. Genomic analysis using PubMLST substantiated this isolate as Pseudomonas aeruginosa . Further analysis revealed a genetic repertoire, including genes associated with hydrocarbon biodegradation and the rhl ABCR operon (surface-active agents’ production). Additionally, genomic annotation possesses genetic determinants predicted to confer multi-metal resistance, including arsenic ( arsBCH ), copper ( copBDR ), and cobalt-zinc-cadmium ( czc ) efflux systems. The isolate also produced presumptive crude surface-active compounds (2.7 g/L) and exhibited WCO degradation under laboratory conditions. According to the genomic findings, Pseudomonas aeruginosa BCSIR-JnU-ISO2 is a candidate for the bioremediation of hydrocarbon- and metal-contaminated environments. However, this study is limited by the absence of phenotypic validation for metal resistance and the potential biosafety risks associated with releasing a WHO priority pathogen into the environment. Future research should also investigate strategies such as enzyme-based bioremediation, immobilized-cell systems, or the exploitation of non-pathogenic hydrocarbon-degrading microorganisms to minimize biosafety risks while maintaining remediation efficiency.