Metabolism of p-chloro-m-xylenol by a newly isolated marine bacterium Rhodococcus ruber SJ-1: Cellular responses and detoxification mechanisms

p -Chloro- m -xylenol (PCMX), a widely used antimicrobial agent, poses potential ecological risks due to its ubiquitous distribution and documented toxicity to aquatic vertebrates. Although microbial degradation represents a key natural attenuation pathway, the molecular mechanisms governing PCMX biodegradation remain elusive. Here, we report the isolation of three novel Rhodococcus strains from marine sediments capable of mineralizing PCMX. Among these, strain R. ruber SJ-1 completely metabolized 30 mg/L PCMX within 72 h and maintained significant degradation capacity under high-salinity stress. Integrated genomic and transcriptomic analyses revealed that PCMX exposure triggered extensive transcriptional reprogramming in strain SJ-1, with 1063 genes upregulated and 533 downregulated. PCMX inhibited core cellular functions, including key genes related to cell stress resistance, energy production, central carbon metabolism, fatty acid metabolism, and protein biosynthesis. Concurrently, aromatic catabolism pathways were markedly induced. A highly upregulated gene cluster ( sj4821 - sj4838 ) was identified as pivotal for PCMX metabolism, encompassing a flavin-dependent monooxygenase (NphA1-sj, sj4831 ; 2145.26-fold) and catechol 2,3-dioxygenase (C23O, sj4838 , 2052.43-fold) genes. Quantitative PCR assays further validated the upregulation patterns. Based on bioinformatics and high-resolution mass spectrometry analyses, we proposed that strain SJ-1 converted PCMX to 4-chloro-3,5-dimethylcatechol via ortho -hydroxylation, followed by meta -cleavage of the aromatic ring. This study presents the first documented evidence of PCMX degradation by a marine Rhodococcus isolate. Our findings reveal the molecular mechanisms driving PCMX detoxification and cellular adaptation, establishing a foundation for bioremediation in saline ecosystems.