3 Biotech

, 10:42 | Cite as

Microbial diversity changes and enrichment of potential petroleum hydrocarbon degraders in crude oil-, diesel-, and gasoline-contaminated soil

  • Marie Thérèse Bidja Abena
  • Guoqing Chen
  • Zeyu Chen
  • Xiucheng Zheng
  • Shanshan Li
  • Tongtong Li
  • Weihong ZhongEmail author
Original Article


This study investigated the impacts of crude oil, diesel, and gasoline on the diversity of indigenous microbial communities as well as culturable microorganisms in the studied soil. Oil contamination led to shifts in the diversity of the soil’s microbial communities, regardless of the contaminant applied. Unpolluted soils were more diverse and evenly distributed than contaminated samples. The domain Bacteria accounted for 65.15% of the whole microbial community. The bacterial phylum Proteobacteria dominated in all samples, followed by Actinobacteria and Acidobacteria. Pseudomonas with 28.15% of reads dominated in Proteobacteria, while Rhodococcus (3.07%) dominated in Actinobacteria, and Blastocatella (2.53%) dominated in Acidobacteria. The dominant fungal phyla across all samples were Ascomycota dominated by Penicillium (50.48% of sequences), and Zygomycota dominated by Mortierella (16.87%). Sequences similar to the archaeal phyla, Euryarchaeota and Thaumarchaeota, were also detected. The number of culturable microorganisms increased following the contamination and was higher in contaminated samples than in clean samples. Oil contamination also resulted in the enrichment of oil-degrading strains. Two bacteria, Serratia marcescens strain PL and Raoultella ornithinolytica PS, which were isolated from crude oil-contaminated soil, exhibited strong crude oil degradation ability. Strain PL was the most efficient strain and degraded 75.10% of crude oil, while strain PL degraded 65.48%, after 20 days of incubation. However, the mixed culture of the two strains was more effective than single strain and could achieve up to 96.83% of crude oil degradation, with a complete abatement of straight-chain hydrocarbons (from C12 to C25), and more than 91% removal of highly branched hydrocarbons, phytane and pristane, which are known to be more recalcitrant to biodegradation. Strains PS and PL are two newly isolated crude oil degraders that are not among the most prominent crude oil-degrading strains referenced in the literature. Therefore, their high degradation capacity makes them perfect candidates for the bioremediation of petroleum hydrocarbon contaminated environments.


Raoultella ornithinolytica Diversity Microbial communities Crude oil Biodegradation 



This research was supported by the College of Biotechnology and Bioengineering at the Zhejiang University of Technology.

Compliance with ethical standards

Conflict of interest

On behalf of all authors, the corresponding author states that there is no conflict of interest.

Supplementary material

13205_2019_2027_MOESM1_ESM.docx (457 kb)
Supplementary file1 (DOCX 456 kb)
13205_2019_2027_MOESM2_ESM.pdf (669 kb)
Supplementary file2 (PDF 668 kb)
13205_2019_2027_MOESM3_ESM.pdf (127 kb)
Supplementary file3 (PDF 126 kb)
13205_2019_2027_MOESM4_ESM.docx (21 kb)
Supplementary file4 (DOCX 20 kb)


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Copyright information

© King Abdulaziz City for Science and Technology 2020

Authors and Affiliations

  1. 1.College of Biotechnology and BioengineeringZhejiang University of TechnologyHangzhouChina
  2. 2.International CollegeZhejiang University of TechnologyHangzhouChina

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