An example of how microbes have been recruited to correct human errors and restore ecosystems

Jennifer Bruton

Microbes tend to get a lot of bad press in the media. The saying, “any publicity is good publicity”, does not quite stretch out to these little guys. While it is true that there are many pathogenic microbes that cause devastating diseases in human, animal and plant hosts, one must also remember that not all microbes are as bad as their relatives; some can actually contribute to society and make their families proud! Examples of useful microbes include commensal bacteria in the human gut that live in symbiosis with their host and often prevent pathogenic microbes from invading (an effect known as colonisation resistance); as well as other bacterial species that are used in the biotechnology industry to produce food preservatives and therapeutic proteins such as insulin. The current list of beneficial microbes is a lengthy one, and so I’ve chosen just one group, the “environmentalist bacteria”, as my ‘friendly bugs of choice’ in this blog-post.

Fun germ

Don’t discriminate! (Image Source)

Bioremediation, PAHs and the Deepwater Horizon oil spill

Bioremediation is an environmentally “green” method of using microbes – either naturally-occurring or introduced – to break down pollutants. A variety of bacterial, fungal and algal species are associated with the degradation of smelly hydrocarbons (such as those in car fuels), with 79 known bacterial genera using these organic pollutants as their main source of energy: including Cycloclasticus spp., Alcanivorax spp. and Oleiphilus spp. – among others (Prince, 2005).

Polycyclic aromatic hydrocarbons (PAHs) are organic pollutant molecules that cause critical damage to the environment and global health due to their toxic and mutagenic properties. These chemicals are abundant as contaminants in soil, air and aquatic environments, arising from both natural and anthropogenic sources (Ghosal et al., 2016). The Deepwater Horizon oil spill (DWH) which began in April 2010 is a prime example of the devastating impacts of PAHs on the environment and marine life. In the largest marine oil spill in history, the DWH oil rig leaked toxic PAHs into the Pacific for 87 days, discharging an estimated 4.1 million barrels of oil into the surrounding waters. As if this wasn’t enough of an environmental disruption, an additional 1.8 million gallons of chemical dispersants were deliberately applied to break up the oil into manageable pieces for bioremediation (Lamendella et al., 2014). Counteracting the physical and chemical processes which occur in the aftermath of an oil spill is extremely challenging, and although efforts were made to prevent the oil from washing up on coastlines, by May it had reached the Gulf Coast of Mexico.


A brief summary of the bioremediation process (Image Source)

Optimizing the bioremediation process

Microbial degradation of PAHs depends on a number of environmental factors: such as available nutrients, microbe(s) used, and the nature of the pollutant(s). Oxygen availability is very important for the breakdown of hydrocarbons, as aerobic processes are more efficient at cleaning up spills than their anaerobic counterparts. Incorporation of oxygen into hydrocarbon molecules allows the bugs to funnel carbon (an energy source) into various metabolic pathways. Deliberate introduction of fertilizing nutrients like nitrogen (N) and phosphorus (P) to the spill is also a strategy that greatly increases the metabolic activity of these microbes. This is because N and P are not readily available in the aromatic compounds of the spill but are needed to make DNA in the bacterial cell (Fuentes et al., 2014).

Halophilic bacteria are those that thrive in environments with high salt concentrations. These organisms are used in the treatment of polluted seawater, as most other microbes are unable to cope with the high salt concentrations. It has been found – in most seawater oil spills – that the predominant, naturally-occurring, oil-degrading bacterium is the marine species Marinobacter hydrocarbonoclasticus: a Gram-negative, halophilic bacterium (Ali et al., 2016).

M. hydrocarbonoclasticus was first isolated on the French coast in 1992, in sediment which had been polluted with hydrocarbons from an oil refinery rig. In general, members of the Marinobacter genus inhabit diverse saline environments and can metabolise multiple compounds in the presence or absence of oxygen. A study on the impact of coast microbial communities after the DWH oil spill found that Marinobacter isolates were able to use the oil as their food source by degrading the PAHs and obtaining carbon from them (Hazen et al., 2010).

Through the breakdown of aromatic hydrocarbons, the oil-degrading bacteria produce secondary metabolites like bioemulsifiers (high molecular weight molecules) and biosurfactants (low molecular weight molecules). These compounds overcome the low solubility of hydrocarbons in water by reducing surface tension; thereby dispersing the hydrocarbons into small manageable droplets that the microbe can then process. Biosurfactants are hydrophobic molecules themselves – generally lipids – that increase the hydrophobicity of the bacterium that produces them, allowing better hydrocarbon-microbe interactions (Handley and Lloyd, 2013).


Human errors can have disastrous effects on the environment

“Oils well that ends well”

So, while the media associate bacteria with disease, this is not an accurate representation of the domain as a whole. Bioremediation is just one example of how microbes can benefit the environment and other organisms – in this case, by physically cleaning up after human errors. Other methods of oil spill clean-up, such as burning, applying chemical dispersants and using boomers to scoop up the oil, can cause various environmental stresses. Bioremediation, however, is a highly efficient, environmentally “green” alternative, and the bacteria used are not known to cause damage to the marine habitat in the aftermath.

Despite the wonders of bioremediation, the effects of the DWH oil spill are still evident today. Barrier islands off the coast of Louisiana are continuing to deal with washed up oil that had been buried under the sand offshore. Bird-nesting islands have been lost and dolphins native to the region are dying much more frequently, often due to oil poisoning. That being said, without the use of bioremediation and other techniques to recover the Gulf, the consequences of the DWH oil spill may have been a lot worse than they were – and we can thank the microbes for that.


  1. Prince, R. (2005) The microbiology of marine oil spill bioremediation. In: Ollivier, B., Magot, M. (eds.) Petroleum microbiology. ASM Press, Washington, DC, 317-335.
  2. Ghosal, D., Ghosh, S., Dutta, T.K. and Ahn, Y. (2016) Current state of knowledge in microbial degradation of polycyclic aromatic hydrocarbons (PAHs): a review. Frontiers in Microbiology. 7, 1369.
  3. Lamendella, R., Strutt, S., Borglin, S., Chakraborty, R., Tas, N., Mason, O.U., Hultman, J., Prestat, E., Hazen, T.C. and Jansson, J.K. (2014) Assessment of the Deepwater Horizon oil spill impact on Gulf coast microbial communities. Frontiers in Microbiology. 5, 130.
  4. Fuentes, S., Mendez, V., Aguila, P. and Seeger, M. (2014) Bioremediation of petroleum hydrocarbons: catabolic genes, microbial communities, and applications. Applied Microbiology and Biotechnology. 98, 4781–94.
  5. Ali, N., Dashti, N., Salamah, S., Sorkhoh, N., Al-Awadhi, H. and Radwan, S. (2016) Dynamics of bacterial populations during bench-scale bioremediation of oily seawater and desert soil bioaugmented with coastal microbial mats. Microbial Biotechnology. 9, 157–71.
  6. Hazen, T.C., Dubinsky, E.A., Desantis, T.Z., Andersen, G.L., Piceno, Y.M., Singh, N., Jansson, J. K., Probst, A., Borglin, S.E., Fortney, J.L., Stringfellow, W.T., Bill, M., Conrad, M.E., Tom, L.M., Chavarria, K.L., Alusi, T.R., Lamendella, R., Joyner, D.C., Spier, C., Baelum, J., Auer, M., Zemla, M.L., Chakraborty, R., Sonnenthal, E.L., D’haeseleer, P., Holman, H.Y., Osman, S., Lu, Z., Van Nostrand, J.D., Deng, Y., Zhou, J. and Mason, O.U. (2010) Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science. 330, 204–8.
  7. Handley, K.M. and Lloyd, J.R. (2013) Biogeochemical implications of the ubiquitous colonization of marine habitats and redox gradients by Marinobacter species. Frontiers in Microbiology. 4, 136.

Featured Image: Taken in the aftermath of the infamous Deepwater Horizon oil spill in 2010, by Prof. Andreas Teske from the University of North Carolina Chapel Hill.