# Bioremediation of Crude Oil by _Corynebacterium stationis_ CsPe-1: A Preliminary In Vitro Study
## 3 Results and Discussion
### Genomic Characterization of C. stationis CsPe-1  
The sequencing report indicated that 11,013,512 raw reads were generated, with ap-proximately 92.5% exhibiting a Phred-score greater than 30 (Q30), indicating good sequencing depth and quality. Downstream analyses included de novo assembly using Unicycler, resulting in a 2.8 Mb assembled genome comprising 24 contigs greater than 200 bp, with a 54.8% GC content. Genome annotation using PROKKA produced 2566 CDS, two ribosomal operons, and 51 tRNAs across the 24 annotated contigs. These results are consistent with other _C. stationis_ genomes deposited in the NCBI database ([[https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon=1705](https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon=1705)]([https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon=1705](https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon=1705)), accessed on 1 January 2025). Genomic taxonomy analysis using TYGS (Type Genome Server) suggested that, based on the 16S rRNA gene, strain CsPe-1 belongs to _Corynebacterium ammoniagenes_, clustering with _C. ammoniagenes_ DSM 20306. However, whole-genome analysis revealed higher similarity to _C. stationis_, with a dIDDH value of 85.1% (values \(\geq\) 70% indicate the same species), supporting the classification of CsPe-1 as _C. stationis_ (Figure 2).  
In order to understand the oil-degrading capacity of the CsPe-1 strain and the potential to degrade other xenobiotics, the presence of genes associated with the metabolism and degradation of xenobiotics was evaluated according to their functional category from the KEGG (Kyoto Encyclopedia of Genes and Genomes) database. This is an invaluable tool for exploring metabolic pathways and genes involved in various biological processes, including the degradation of compounds such as oil [61]. Although oil is not considered a xenobiotic (due to its natural origin and biodegradability), according to the KEGG database, the potential genes associated with oil degradation fall under the category of metabolism and metabolic pathway xenobiotic biodegradation and metabolism.  
The analyses identified the potential action in oil degradation of two genes associated with the degradation of polycyclic aromatic hydrocarbons: _pcaG_ and _pcaH_. The degradation of aromatic compounds and petroleum in bacteria is a crucial process for the bioremediation of contaminated environments. The _pcaG_ and _pcaH_ genes, which code for the enzyme protocatechuate 3,4-dioxygenase, play an important role in the degradation of aromatic compounds via the \(\beta\)-ketoadipate pathway. The _pcaG_ and _pcaH_ genes were identified in six isolates of the _Roseobacter lineage_, a major taxon of  
Figure 2: Phylogenetic tree of the CsPe-1 strain based on the complete genome. The tree was generated using the TYGS tool (tyss.dsmz.de), using the orthologous sequences of the CsPe-1 genome (assembly) and other reference species strains.  
marine \(\alpha\)-proteobacteria. These genes enable the degradation of aromatic compounds through the \(\beta\)-ketoadipate pathway [62]. On the other hand, in _Agrobacteriumum radiolacter_, two sets of _pcaH_ and _pcaG_ genes were identified that code for two different protocatechuate 3,4-dioxygenases. One of these sets appears to have been acquired by lateral gene transfer, indicating significant genetic diversity and adaptability in the degradation of aromatic compounds [63].