Bacterial community dynamics during bioremediation of alkane- and PAHs-contaminated soil of Siri island, Persian Gulf: a microcosm study

  • Z. Khomarbaghi
  • M. ShavandiEmail author
  • M. A. Amoozegar
  • S. M. M. Dastgheib
Original Paper


Studding the diversity of soil indigenous microorganisms, and monitoring effect of contaminants on microbial population, is very critical for understanding microbial activity during bioremediation and selecting successful remediation strategy. To simulate the natural environment, four microcosms were prepared by artificially contaminating clean soil with defined amounts of petroleum hydrocarbons including alkanes mixture (C13–C20), polyaromatic hydrocarbons (PAHs) mixture (anthracene, phenanthrene, fluoranthene, pyrene and benzo (α) pyrene) and both alkanes and PAHs. Contaminants degradation and heterotrophic bacterial count were measured during a 6-month study. Copy number of alkB and C23DO genes was studied using real-time PCR, and bacterial diversity was monitored by 16S rRNA gene PCR and denaturing gradient gel electrophoresis (DGGE). Results indicated that all types of contaminants (except the five ring benzo (α) pyrene) were totally degraded after 6 months and the increase in hydrocarbon degradation rate coincided with the enhancement of total heterotrophic bacterial count in each microcosm. Real-time PCR results showed a significant increase in the copy number of both alkB and C23DO genes in alkane- and PAHs-contaminated microcosm comparing with the control microcosm, indicating selection for special hydrocarbon degraders in hydrocarbon-amended microcosms. The results of DGGE revealed that the type of contaminant in the same soil has a remarkable influence on soil bacterial community structure. Sequencing of DGGE bands suggested that most of the dominant members of the microbial community of contaminated soil are unculturable bacteria from Proteobacteria and the genus Bacillus.


Bioremediation Biodegradation Polycyclic aromatic hydrocarbons Alkanes Microbial community structure 



The authors are grateful to Mr. Hassan Tirandaz for his contribution in microbial count analysis. The authors would like to thank Mr Vahid Samimi and Hadi Ghanbarnejad for their assistance in GC and HPLC analysis.


This research was funded by National Iranian Offshore Oil Company (IOOC) under contract Number 1-90-4386.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Human participants and animal rights

This article does not contain any studies with human participants or animals performed by any of the authors.


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Copyright information

© Islamic Azad University (IAU) 2019

Authors and Affiliations

  1. 1.Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of ScienceUniversity of TehranTehranIran
  2. 2.Ecology and Environmental Pollution Control Research GroupResearch Institute of Petroleum IndustryTehranIran
  3. 3.Microbiology and Biotechnology GroupResearch Institute of Petroleum IndustryTehranIran

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