# Complete Genome Report of a Hydrocarbon-Degrading _Sphingobium yanoikuyae_ S72
## 3 Results  
S72 is a Gram-negative rod and moves by means of a monotrichous flagellum. It is 1.0-3.5 \(\upmu\)m in length and 0.6-1 \(\upmu\)m in width (Figure S1). S72 effectively use D-glucose, L-arabinose, mannose, N-acetyl glucosamine, maltose, potassium gluconate, malic acid, citrate, galactose, citrate, and esculin for its growth. However, it could not use mannitol, adipic acid, capric acid, phenyl acetic acid as a substrate for its growth (Table 1). The preliminary analyses showed that S72 can grow in the minimal media (BH) supplemented with either monoaromatic (xylene, toluene) or polycyclic aromatic hydrocarbons (PAH) (biphenyl, phenanthrene, and naphthalene). The number of colonies forming units appearing on the plates decreased as the concentration (0, 20, 40, 80 100, and 150 \(\upmu\)g/mL) of the hydrocarbon in the BH medium increased. The preliminary analysis also revealed that S72 has better tolerance for the hydrocarbons at a concentration that is \(\leq\)100 \(\upmu\)g/mL, and their growth began to decline as the concentrations of the hydrocarbons get higher than 100 \(\upmu\)g/mL. S72 did not show any growth when inoculated in BH medium containing 150 \(\upmu\)g/mL toluene or xylene and showed limited growth in plate with naphthalene, phenanthrene, or biphenyl at this concentration. Moreover, the rate at which S72 grew in medium containing toluene and xylene is lower than other hydrocarbons tested at 100 \(\upmu\)g/mL (Figure 1). Based on the reported observations 100 \(\upmu\)g/mL was selected as the study concentration for the experiment. \begin{table}
\begin{tabular}{c c} \hline
**Biochemical Features** & **Characteristics** \\ \hline D-glucose & ++ \\ L-arabinose & ++ \\ Mannose & + \\ Mannitol & - \\ N-acetyl glucosamine & + \\ Maltose & ++ \\ Potassium gluconate & + \\ Capric Acid & - \\ Adipic acid & - \\ Malic acid & ++ \\ Citrate & ++ \\ Phenyl acetic acid & - \\ PNPC-4-Nitrophenyl 1-1D- & \\ Galactopyranoside & ++ \\ -Galactosidase & ++ \\ Citrate Aesculin & ++ \\ \hline \end{tabular} Legend: ++ means can use these compounds for growth, +, means can slightly use the compound for growth -.  
\end{table} 
Table 1: Biochemical characteristics of _Sphingobium yanoikuyae_ S72. S72 degraded all the hydrocarbons tested at 100 \(\mathrm{\SIUnitSymbolMicro\SIUnitSymbolMicro\SIUnitSymbolMicro}\)/mL with varying efficiencies. S72 showed the best activity in phenanthrene, resulting in 93% degradation. The degradation of biphenyl and naphthalene was up to 85 and 81% reduction, respectively (Figure 2). However, a low degradation efficiency was observed in the media containing xylene (19% and 31%). The degradation activity was confirmed by the reduction in the peak for the hydrocarbons as compared to the control from the GC-MS analysis (Figure S2). Genomic analysis has been used often to unravel several details about bacterial behavior. As a result of this, the genome of S72 was sequenced and analyzed to relate its function with its genetic constituent. The sequenced genome of _S. yanoikuyae_ S72 was reduced to 1 contig, consisting of 5,532,633 bp, 5005 CDS, and 4 identical copies of the rRNA gene operon (23S, 16S, and 5S). The overall G + C content of the assembled genome is 64.23%. The genome has 5231 putative genes and 75 RNAs (67 tRNA and 12 rRNA). A total of 1140 genes are in operons, 2515 are parts of the clusters of orthologous gene (COGs) (Table 2). Figure 1: Growth of _S. yanoikuyae_ S72 in tested hydrocarbons. Bacteria’s growths were measured as optical density (600 nm) in liquid Bushnell Haas medium supplemented with each of the five different hydrocarbons (100 \(\mathrm{\SIUnitSymbolMicro\SIUnitSymbolMicro}\)/mL) as sole source carbon for 25 days. Figure 2: Degradation of hydrocarbons by _S. yanoikuyae_ S72. Hydrocarbon abundance (%) of five polycyclic aromatic hydrocarbons (PAHs) in liquid Bushnell Haas medium supplemented with each of the five different hydrocarbons (100 \(\mathrm{\SIUnitSymbolMicro\SIUnitSymbolMicro}\)/mL) as sole source carbon.