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Biological oceanography

Microbes: The original organic cleaning agents



The Paper: Joye, S. B., Kleindienst, S., Gilbert, J. A., Handley, K. M., Weisenhorn, P., Overholt, W. A. et al. (2016). Responses of microbial communities to hydrocarbon exposures. Oceanography, 29(3), 136-149. DOI: 10.5670/oceanog.2016.78

Environmental Disasters

Figure 1: Deep oil and hydrocarbons from the DWH plume (Source: Woods Hole Oceanographic Institution)

Figure 1: Deep oil and hydrocarbons from the DWH plume (Source: Woods Hole Oceanographic Institution)

The Deep Water Horizon (DWH) oil spill, which occurred in the Gulf of Mexico in 2010, released approximately 5 million barrels of oil and 250,000 metric tons of natural gas to the deep ocean. That is 20 times the oil spilled by the Exxon Valdez and enough to fill 12 million automobile gas tanks. Of this, half of the oil and most of the natural gas stayed in a deep water plume and did not reach the surface (Fig. 1). Since a wide variety of microbes (bacteria, archaea, and fungi) are able to consume and break down hydrocarbons, scientists can study the changes in microbial communities when there is such a rapid and extremely large input.

Microbial Detergents

Hydrocarbons are simple organic molecules contained within oil and gas deposits that can be used for energy by microbes. Some of these microbes use oxygen with the hydrocarbons to perform respiration similar to the way humans do, while others are able to get their energy using other compounds when oxygen is not available. In either case, the microbes use special enzymes (molecules capable of kick-starting a chemical process that would not normally occur on its own) to break down the hydrocarbons. Since they carry out these processes on the oil-water interface, having many small drops of oil is much easier to work with than one large oil patch. This break-up, or dispersal, of the oil can either be physically accomplished by the microbes themselves, or with human added chemical dispersants. It is the combination of enzymes, chemical dispersants and microbial action that allows for the entire community to more efficiently break down the hydrocarbons (Fig. 2). Many of these hydrocarbons are toxic and by understanding how the microbial processes work we may be able to use them to mitigate the impacts of pollution.

Figure 2: Breakdown of chemically and microbially dispersed oil (Source: Joye et al., 2016)

Figure 2: Breakdown of chemically and microbially dispersed oil (Source: Joye et al., 2016)

The organisms that are able to break down hydrocarbons exist in very small numbers in nature and multiply rapidly when exposed to a hydrocarbon input. Once an injection, such as the DWH rupture occurs, scientists sample the environment to figure out rates of oil degradation. These degradation rates – how fast a given quantity of oil is broken down – are important for determining the usefulness of microbes as part of a potential cleanup effort. However, these rates are not easy to determine, and cannot be measured directly. Instead, scientists use what is called a proxy measurement. A proxy is something that can be directly measured that has a known relationship to the quality that cannot be measured. For example, while intelligence cannot be directly measured, a combination of GPA and standardized testing can be used as a proxy to evaluate someone’s scholastic abilities. Proxies used for determining degradation rates are things such as microbial cell counts, CO2 production (a byproduct of the breakdown), and oil depletion rates.

In addition to how fast these processes are occurring, knowing the specific species responsible for hydrocarbon degradation is critical for cleanup efforts. In order to specifically determine which microbes are performing these duties, scientists can either grow them in a lab, or analyze the DNA of large environmental samples that have been exposed to hydrocarbons. By growing cultures in the lab, the scientists can feed them the desired hydrocarbons, see who grows, and directly determine the organism and their particular mechanism for hydrocarbon degradation. However, cultivating environmental microbes in the lab is not an easy task. There are many factors that cannot be regulated and, in fact, the vast majority of microbes in the world have never been cultured. Therefore, DNA techniques provide us with the ability to sample the environment where these microbes thrive and look at their genome to determine who they are and what mechanisms they may be using. Both the rate determination and community composition analysis can be used to infer how hydrocarbons are processed in a spill and were, in fact, used to evaluate the environmental impact of the DWH disaster.

Long Term Effects

In addition to environmental effects during a large hydrocarbon influx, researchers also want to understand what happens to the microbial community once the hydrocarbons are gone. A shifted microbial community can have lasting impacts on the environment by influencing how nutrients are circulated and can therefore affect organisms all throughout the food web. Scientists use the above techniques before, during, and after a spill event to characterize which organisms took advantage of the influx and how long it takes the community to get back to normal. They do this by creating phylogenic trees (graphical representation of relationships between organisms, sort of like a family tree) that detail who the microbes are, what processes they use, and how they are related to one another (Fig. 3).

Figure 3: Phylogenetic tree of microbes capable of hydrocarbon degradation (Source: Joye et al., 2016)

Figure 3: Phylogenetic tree of microbes capable of hydrocarbon degradation (Source: Joye et al., 2016)

As the use of petroleum products for energy continues to increase, so does the possibility of large-scale disasters such as the Exxon Valdez and the DWH. Until we are able to transition to cleaner energy, scientists continue to investigate the most efficient and environmentally friendly ways to help clean up a large oil spill. By understanding the microbial communities that thrive before, during, and after such a spill, we will be better able to act during a spill as well as foster long-term restoration of the affected area.

Zak Kerrigan
I am a fourth year doctoral candidate at the Graduate School of Oceanography at the University of Rhode Island. I work in the D’Hondt Lab and I am using genetic techniques to determine the community structure and evolution of deep-sea sediment bacteria. I earned a B.S. in Aerospace Engineering from the University of Miami and spent 12 years in the US Navy driving submarines before coming back to grad school.


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