Sphingobium yanoikuyae S72 was isolated from the rhizosphere of sorghum plant in Mexico and we evaluated its survival and role in the degradation of some selected monoaromatic hydrocarbons and polycyclic aromatic hydrocarbons (PAHs) using minimal medium (Bushnell Hass medium (BH)) in which each of the hydrocarbons (naphthalene, phenanthrene, xylene, toluene, and biphenyl) served as sole carbon source. Gas column chromatography–mass spectrometry analysis was used to evaluate the effect of S72’s growth in the medium with the hydrocarbons. The genome of the S72 was sequenced to determine the genetic basis for the degradation of the selected hydrocarbon in S72. The genome was assembled de novo with Spades assembler and Velvet assembler and the obtained contigs were reduced to 1 manually using Consed software. Genome annotation was carried out Prokka version 1.12, and gene calling and further annotation was carried out with NCBI PGAAP. Pangenome analysis and COG annotation were done with bacteria pangenome analysis tool (BPGA) and with PATRIC online server, respectively. S72 grew effectively in the culture medium with the hydrocarbon with concentration ranging from 20–100 mg/mL for each hydrocarbon tested. S72 degraded biphenyl by 85%, phenanthrene by 93%, naphthalene by 81%, xylene by 19%, and toluene by 30%. The sequenced S72 genome was reduced to 1 contig and genome analysis revealed the presence of genes essential for the degradation of hydrocarbons in S72. A total of 126 unique genes in S72 are associated with the degradation of hydrocarbons and xenobiotics. S72 grew effectively in the tested hydrocarbon and shows good degradation efficiency. S72 will therefore be a good candidate for bioremediation of hydrocarbon contaminated soil.

Sphingobium yanoikuyae S72 was isolated from the rhizosphere of sorghum plant, Mexico. Its role on the degradation of polycyclic aromatic hydrocarbon (PAH) was evaluated in a minimal medium containing one of biphenyl, naphthalene, phenanthrene, xylene and Toluene as the only carbon source. It grew effectively in each minimal medium (Bushnell Haas, BH). Gas column chromatography–mass spectrometry (GC-MS) analysis on the metabolite recovered after S72’s growth in BH showed that it successfully degraded the PAHs tested resulting in the degradation of biphenyl (85%), phenanthrene (93%), naphthalene (81%), xylene (19%) and toluene (30%). The complete genome of the S72 was sequenced to evaluate the genetic bases of S72`s degradation of PAH. The genome was assembled de novo and reduced to 1 contig and consists of 5,532,623 bp, 5005 protein-coding genes. The analysis of the COG categories in S72 in comparison with other Sphingobium yanoikuyae and other PAH degrading gene, showed that it has in higher abundance in some categories that have been associated with the degradation of PAH (energy production and conversion (COG C, 6.35), carbohydrate transport and metabolism (COG G, 6.20%), lipid transport and metabolism (COG I, 6.99), secondary metabolites biosynthesis (COG Q, 4.52%), general function prediction only in transport and catabolism (COG R, 9.93),) Pan-core genome analysis revealed that about 126 unique genes in S72 are associated with the degradation of xenobiotics and PAHs. Most gene found in S72 are associated with the peripheral degradation pathway for PAH. Based on our observation we proposed a possible benzoate degradation pathway.