Harnessing a marine-derived Rhodococcus strain for cross-habitat bioaugmentation of malodorant skatole: Performance and ecological response.

Abstract

Skatole, primarily generated via the anaerobic metabolism of tryptophan, is a pervasive nitrogenous heterocyclic malodorant. While ubiquitous in various environments, its microbial remediation in saline ecosystems remains poorly documented. In this study, a skatole-degrading microbial consortium was enriched from marine sediments. High-throughput sequencing revealed distinct successional dynamics during domestication, with Pseudomonas becoming predominant (89.23%) and Rhodococcus persisting as a potential functional taxon (1.98%). An efficient isolate, Rhodococcus sp. SJ-2, was successfully obtained from the consortium. SJ-2 could completely remove 100 mg/L of skatole within 24 h in 2216E medium and 60 h in marine mineral culture medium, with optimal activity at 30-35 °C and pH 6.0-9.0. It also maintained skatole-removing activity across a broad salinity range of 0-45‰ NaCl. 3-Methyloxindole was identified as a detectable intermediate, and the enzymes involved in skatole degradation were inducible. Genomic analysis revealed a 5.77 Mb circular chromosome and two plasmids, but no previously reported skaA homologs, suggesting an as-yet-uncharacterized oxidative system. Bioaugmentation experiments in freshwater and marine sediment microcosms demonstrated that SJ-2 inoculation accelerated skatole removal, shortening the complete removal time to 6 h and 12 h, respectively. Amplicon sequencing showed that bioaugmentation was associated with an increased relative abundance of Rhodococcus and with predicted functional shifts related to aromatic compound degradation. These findings identify Rhodococcus sp. SJ-2 as a promising marine-derived candidate for skatole removal in saline odor-control settings and provide a useful foundation for future studies on the molecular basis of skatole catabolism.