Alkhatib Sara Awni, Arya Sagar, Islayem Deema, Nyadzayo Runyararo Memory, Mohamed Sharmarke, Yousef Ahmed F, Hernandez Hector H, Pappa Anna-Maria
Department of Biomedical Engineering and Biotechnology, Khalifa University, Abu Dhabi, United Arab Emirates.
Center for Catalysis and Separation (CeCaS), Khalifa University, Abu Dhabi, United Arab Emirates.
PLoS One. 2025 Aug 12;20(8):e0329515. doi: 10.1371/journal.pone.0329515. eCollection 2025.
Microbial biodegradation of recalcitrant aromatic hydrocarbon pollutants represents an environmentally sustainable strategy for remediating contaminated sites. However, elucidating the metabolic capabilities and genetic determinants of biodegrading strains is crucial for optimizing bioremediation strategies. In this study, we comprehensively characterize the aromatic catabolic potential of two indigenous bacterial isolates, A. xylosoxidans C2 (A. x. C2) and A. xylosoxidans KW38 (A. x. KW38), obtained from hydrocarbon-impacted environments in the United Arab Emirates (UAE). Experimental validation through aromatic hydrocarbons supplemented growth studies confirmed the capability of the isolated bacteria to mineralize bisphenol A, 4-hydroxybenzoic acid, 1-naphthalenemethanol, and the high molecular weight polycyclic aromatic hydrocarbon (PAH), pyrene, in the presence of glucose. Their degradation efficiencies were comparable to or greater than those of Pseudomonas paraeruginosa, a well-characterized model organism for aromatic compound degradation. Integrated bioinformatic analyses uncovered fundamental aromatic catabolic pathways conserved across Achromobacter species, along with strain-specific genes that potentially confer specialized degradative capacities, highlighting the genomic basis of the observed metabolic versatility. Further, protein modeling based on the curated sequences revealed unique features of individual catabolic enzymes and their interaction networks. Notably, a dehydrogenase enzyme involved in aromatic ring cleavage was identified exclusively in these UAE isolates. These findings establish A. x. C2 and A. x. KW38 as promising bioremediators of diverse aromatic pollutants. Overall, the study exemplifies a powerful and comprehensive methodological framework that bridges bioinformatic analysis and experimental research to further optimize the effectiveness of experimental design. We achieved a substantial reduction in the number of unknown genetic and metabolic determinants of aromatic hydrocarbon degradation in the strains, reducing uncertainty by 99.3%, thereby enhancing the overall process and outcomes for systematic biodiscovery of pollutant-degrading environmental microbes to address ecological challenges.
难降解芳烃污染物的微生物生物降解是修复污染场地的一种环境可持续策略。然而，阐明生物降解菌株的代谢能力和遗传决定因素对于优化生物修复策略至关重要。在本研究中，我们全面表征了从阿拉伯联合酋长国（UAE）受烃污染环境中分离得到的两株本土细菌，木糖氧化无色杆菌C2（A. x. C2）和木糖氧化无色杆菌KW38（A. x. KW38）的芳香族分解代谢潜力。通过补充芳烃的生长研究进行的实验验证证实，在葡萄糖存在的情况下，分离出的细菌能够将双酚A、4-羟基苯甲酸、1-萘甲醇以及高分子量多环芳烃（PAH）芘矿化。它们的降解效率与铜绿假单胞菌相当或更高，铜绿假单胞菌是一种已得到充分表征的芳香族化合物降解模式生物。综合生物信息学分析揭示了无色杆菌属物种中保守的基本芳香族分解代谢途径，以及可能赋予特殊降解能力的菌株特异性基因，突出了所观察到的代谢多功能性的基因组基础。此外，基于精心策划的序列进行的蛋白质建模揭示了各个分解代谢酶及其相互作用网络的独特特征。值得注意的是，在这些阿联酋分离株中专门鉴定出了一种参与芳香环裂解的脱氢酶。这些发现确立了A. x. C2和A. x. KW38作为多种芳香族污染物的有前途的生物修复剂。总体而言，该研究例证了一个强大而全面的方法框架，该框架将生物信息学分析与实验研究相结合，以进一步优化实验设计的有效性。我们大幅减少了菌株中芳烃降解未知遗传和代谢决定因素的数量，将不确定性降低了99.3%，从而增强了系统生物发现降解污染物的环境微生物以应对生态挑战的整体过程和结果。
