Comparative Genomics of Rhamnolipid Synthesis and Monoaromatic Hydrocarbon Tolerance Genes in Environmental Pseudomonas aeruginosa strains.

Abstract

Background: Bioremediation faces several compounds to recover oil spilled ecosystem. The BTEX (benzene, toluene, ethylbenzene, and xylene) are toxic hydrocarbons requiring efficient microbial degradation for bioremediation. Pseudomonas aeruginosa can degrade hydrocarbons through emulsification ( rhl genes) and tolerance ( mla genes). However, genomic organization of these systems in environmental P. aeruginosa strains remains unclear. This study aimed to investigate the rhl and mla systems in six strains isolated from hydrocarbon-contaminated sites in Peru.

Methods: Six Pseudomonas aeruginosa strains were evaluated in this study. Each strain were able to degrade hydrocarbon and tolerate heavy metals. DNA extraction, sequencing, and quality-controlled assembly, functional genome annotation was performed using BAKTA. Comparative analysis included high-quality Pseudomonas genomes from RefSeq, with ANI metrics. A phylogenetic tree was built from core gene alignment, revealed evolutionary connections and was visualized with iTOL.

Results: The assembled genomes ranged from 5.6 to 6.0 Mbp with ~66% GC content. All the strains were confirmed as P. aeruginosa by ANI; placing them within Clade 1 alongside environmental and clinical strains. Pangenome analysis identified 3,544 core genes and a diverse accessory genome. All strains had rhlABRI genes in a conserved 3'-5' orientation. Most of them contained duplicated rhlB gene, except C1BHIC5 strain. However, rhlG varied in position and orientation, it was often near rhlC, with C1BHIC5 also displaying an exception in rhlG orientation.100% of strains presented mla system, associated with toluene tolerance, with two copies of mlaA, mlaFEDC, and mlaEFD genes arranged with high synteny but variable orientations. In comparison to Pseudomonas putida, where mla genes are positioned between murA and ppcD with an additional toluene tolerance gene ( ttg2D).

Conclusions: In conclusion, the presence of the rhlABC genes and the BTEX tolerance genes in all of the analyzed strains allowed us to understand the great ability of P. aeruginosa to survive in polluted environments.