Monitoring the environment for oil spills

Monitoring the environment for oil spills

Cleanup after oil spill, NOAA on Wikipedia
Cleanup after oil spill, NOAA on Wikipedia

The modern world is in large parts build on oil. Plastics and motor power originating from crude oil seem to drive our life. The extraction and handling of the oil however carries an immense risk: A single litre of oil will spoil a million litres of clean water. Spills of the liquid petroleum hydrocarbon have devastating effects on the environment as it contains polycyclic aromatic hydrocarbons (PAHs) which are almost impossible to clean up and can last for years in the sediment and marine environment. The have a toxic effect on any multicellular tissue exposed to it. The mutation rate in the genome rises, increasing the risk of cancer. Animals also suffer in other ways, e.g. the plumage of birds becomes less buoyant and less insulating. Burying, combusting, extracting soil vapor, soil washing, and dispersion are common ways to deal with oil spills but are usually incomplete and sometime increase the toxicity.

Relying on bacteria to do the dirty work might be the only solution for us: Some microorganisms can convert the affected chemicals to nontoxic compounds or even entirely degrade the toxic hydrocarbon compounds to CO2 and H2O! The process is termed bioremediation and can be aided through biostimulation (adding chemicals to the affected site that help the “good” bacteria) and bioaugmentation (releasing the “good” bacteria to the site).

Monitoring and understanding the process is the focus of a project described in the journal Ecotoxicology and Environmental Safety by Aiyoub Shahi et al. from the Environmental Engineering Department at the Istanbul Technical University, Maslak, Istanbul (Turkey). The group combined Illumina sequencing to detect the microbial diversity in the soil and quantitative real-time PCR to determine changes in the bacterial community and in the expression of functional genes.

We have to rely on bacteria to do our dirty work.

Soil samples from petroleum polluted coastal areas and from healthy forest areas were collected and mixed in different ratios. A Miseq instrument was used to sequence to around 10,000 fragments per sample using genomic information from the 16S rRNA regions. The Qiime bioinformatics tools were used for data processing. In order to identify the bacteria found, data from the Greengenes project helped to detect sequence similarities and cluster the results into taxonomic units. Some of the outcomes enabled by qPCR and next-generation sequencing were:

  • Gram-negative bacteria and especially different Pseudomonas species seemed to most dominant during the bioremediation process
  • It is important and possible to monitor the bioremediation process by analysing the 16S rRNA genes
    qPCR data, 16S rRNA sequencing and functional gene analysis are powerful tools for monitoring soil petroleum hydrocarbon-degrading bacterial communities
  • The methods described can be used for the assessment of the biostimulation conditions and for the improvements of such a system at the site of an oil spill.


Venn Diagram evaluating the concentration of oil contamination from Fragoso dos Santos et al.
Venn Diagram correlating the concentration of oil contamination in respect to different microbial populations; from Fragoso dos Santos et al.

In a similar way Henrique Fragoso dos Santos and colleagues of the Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Goes, Federal University of Rio de Janeiro, Rio de Janeiro (Brazil) previously presented a sequencing-based method to detect oil spills in the ocean. In 2011 they described in PLoS One how they used pyrosequencing to identify microbial communities before and after a simulated oil spill event in the waters of a mangrove forest. They too used the information of the 16S rRNA genes for determining the taxonomy.

Sequencing-based analysis allow the monitoring of the healthy and the affected environment

  • Specific positive and negative indicator species for oil spills were detected
  • Figure 2 shows that the degree of contamination can be linked to specific communities
  • The overall diversity did not decrease

From these findings the next steps could be test-kits as handheld devices with nano-wells or regular sequencing-based identification protocols with the aim to detect even small spills of oil-based chemicals as well as to monitor the cleanup process after an event.




  • Evaluation of microbial population and functional genes during the bioremediation of petroleum-contaminated soil as an effective monitoring approach, Aiyoub Shahi, et al. Ecotoxicology and Environmental Safety 2016
  • Mangrove Bacterial Diversity and the Impact of Oil Contamination Revealed by Pyrosequencing: Bacterial Proxies for Oil Pollution, Henrique Fragoso dos Santos, et al. PLoS One 2011
  • Oil tanker and oil spill articles on Wikipedia
  • Featured image: User Clkr on Pixabay