Genome-based characterization and pathway elucidation of dibenzothiophene and 4-methyldibenzothiophene desulfurization in a thiophenic compound desulfurizing Rhodococcus sp. SB1D.

In this study, we present a comprehensive characterization of a highly efficient desulfurizing bacterial isolate, SB1D. The isolate exhibited remarkable desulfurization of dibenzothiophene (DBT) and demonstrated the ability to metabolize benzothiophene (BT) and several of their alkylated derivatives. Genome-related index analyses, including 16S rRNA gene similarity (100%), Average Nucleotide Identity (ANI; 98.7%), digital DNA-DNA hybridization (dDDH; 88.7%), and phylogenomics, identified the strain as Rhodococcus qingshengii. Additionally, orthologous gene cluster analysis showed that SB1D shared the highest number of ortholog clusters (60) with R. qingshengii. The GC-MS analysis of the extracted metabolites identified 2-hydroxybiphenyl (2-HBP) and 4-methylhydroxybiphenyl (4-MHBP) as the major end-products of DBT and 4-methyldibenzothiophene (4-MDBT) desulfurization, respectively. The RAST genomic analysis revealed the presence of several organic-sulfur metabolism-related genes in the genome of SB1D. Together, these findings confirm that the isolate employs the sulfur-specific 4S pathway for the desulfurization of DBT and 4-MDBT. To our knowledge, this is the first report providing genome-based characterization and desulfurization pathway analysis of R. qingshengii SB1D, with the proven ability to desulfurize multiple thiophenic compounds found in diesel, and holds promise as a valuable biocatalyst for applications in biodesulfurization.