Heavy Crude Oil Biodegradation: Catechol Dioxygenase Gene Copy Number Variation Determination by Droplet Digital Polymerase Chain Reaction

Biji Shibulal*, Saif N. Al Bahry, Aliya Al Ansari, Abdulkhader Elshefie, Yahya M. Al Wahaibi, Ali Al Bemani

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


The crude oil reserves in Oman mainly consist of heavy oil. Microbial enhanced heavy oil recovery (MEOR) has been proved to be an efficient technique in the tertiary heavy oil recovery. Five Bacillus species potential for enhanced heavy oil recovery (EHOR) were isolated and the biodegradation ability of these isolates was studied. As heavy crude oil comprises of aromatic hydrocarbons rather than aliphatic ones, the aromatic catabolism gene, catechol 2,3-dioxygenase (C23O) and catechol 1,2-dioxygenase (C12O) were the genes of interest in this study along with the reference gene, 16S rDNA. The copy number variation of these genes was determined using droplet digital PCR (ddPCR). The primers and probes for ddPCR assay were designed targeting these genes. It was observed that the heavy crude oil biodegradation potential of the isolates correlated with the copy number of C23O gene in the microbial genomes. The isolate, Paenibacillus ehimensis BS1 had the highest C23O gene copy number (1.057) followed by Bacillus firmus BG4 (0.895) and Bacillus halodurans BG5 (0.031) as demonstrated by their biodegradation potential. This is one of the few studies deploying ddPCR in the field of heavy crude oil biodegradation by spore forming bacteria.

Original languageEnglish
Pages (from-to)295-306
Number of pages12
JournalGeomicrobiology Journal
Issue number3
Publication statusPublished - 2023
Externally publishedYes


  • Bacillussp
  • biodegradation genes
  • copy number variation
  • ddPCR
  • Heavy crude oil

ASJC Scopus subject areas

  • Microbiology
  • Environmental Chemistry
  • Environmental Science(all)
  • Earth and Planetary Sciences (miscellaneous)

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