# Complete Genome Report of a Hydrocarbon-Degrading _Sphingobium yanoikuyae_ S72
## 4 Discussion  
The biochemical characteristics and the molecular identification of S72 confirmed that it is a S. _yanoikuyae_ strain. It grew effectively in the tested hydrocarbon concentration until 100 \(\mu\)g/mL, implying that S72 can use the tested hydrocarbon as substrates for growth. S72's growth rate, however, decreased as the hydrocarbon's concentration increased. The reduction in growth as shown in Figure 1 could be due to increased toxicity that is associated with increased hydrocarbon concentration. This toxicity may be due to the reduction in rate of solubility that may occur as hydrocarbon concentration increases. Previous study has shown that as concentration of hydrocarbon increases, the rate of solubility decreases resulting in the reduction in growth for bacteria [39]. Low solubility could make it difficult for bacteria to utilize certain compounds as a nutrient for growth [40]. S72 successfully degraded the tested hydrocarbons during the 25-day degradation study. S72 was able to degrade phenanthrene by 93% at a concentration of 100 \(\mu\)g/mL (Figure 3). This result is similar to a previous report where _Splingobium chlorophenolicum_ C3R degraded phenanthrene by 65% [19]. Hence, S72 can degrade phenanthrene but has a lower efficacy compared to _Splingobium chlorophenolicum_ C3R because of S72 inactivity in phenanthrene at a concentration higher than 100 \(\mu\)g/mL. S72's ability to degrade hydrocarbon is not limited to phenanthrene (PHE), it also degraded biphenyl and naphthalene by 85 and 81%, respectively. This may imply that S72 had learnt to survive in and use different hydrocarbon as substrates for growth. S72 degradation efficiency is slightly weaker than what was reported for _Burkholderia fungorum_ FM-2 which degraded PHE by 65% after 3 days [19] because the effective degradation of phenanthrene by S72 took more than 3 days. However, it has an advantage of surviving in PHE and ensuring its  
Figure 4: Genomic island predicted in S72 with Island viewer 4.  
degradation after 25 days. On the other hand, S72 did not effectively degrade xylene and toluene. The in-depth analysis of the genome of S72 showed that it lacked some genes that are essential for the complete metabolism of toluene. The absence of these genes may be responsible for S72 inability to effectively degrade toluene or xylene. It has only four genes that that are directly associated with the degradation of toluene (aryl-alcohol dehydrogenase [EC:1.1.1.90], oxidoreductases acting on the CH-OH group of donors with NAD+ or NADP+ as acceptor, and muconate cyclooxygenase [EC:5.5.1.1] a lyase which isomerizes 3 methyl _cis_ muconate to 3 methyl muconolactone. The other two genes encode catechol 1, 2 dioxygenase and carboxomethylenebutenolidase [EC:3.1.1.45]. Catechol 1, 2 dioxygenase catalyzes the decyclizing of the aromatic ring of methyl catechol to generate 3-methyl-cis, cis-hexadienedioate, while carboxomethylenebutenolidase [EC:3.1.1.45] is acting as dienelactone hydrolase converting 3-chloro-2-methyldienelactone to 3-Chloro-2-methylmaleylacetate in the breakdown of toluene). This observation is same for the genes required for the degradation of xylene as reported by the KEGG database. The molecular mechanisms responsible for the survival of S72 in and degradation of hydrocarbons was evaluated by the sequencing of its genome. The genomic analysis of the S72 genome show the presence of some genes which are essential for the degradation of hydrocarbons. Genes such as S-(hydroxymethyl) glutathione dehydrogenase/alcohol dehydrogenase (A6768_05785, COG R) which is known to enhance the degradation of hydrocarbon by catalyzing the oxidation of long chain primary alcohol (Uniprot). S-(hydroxymethyl) glutathione dehydrogenase/alcohol dehydrogenase has been previously reported to be associated with the degradation of naphthalene [8; 40]. Thus, the presence of S-(hydroxymethyl) glutathione dehydrogenase/alcohol dehydrogenase in S72 could be associated with its need to degrade naphthalene as a substrate for growth.