Metagenomic Analysis of the Bioremediation of Diesel-Contaminated Canadian High Arctic Soils

Soil bacteria, no matter where you might find them, exhibit incredible adaptations, some of which allow for living in the most extreme climates and subsisting on a wide-array of compounds that seem utterly foreign to us in terms of providing nourishment. Cold-adapted bacteria that live in the soil of the Canadian High Arctic are a great example of this. This area is one of particular interest because recent increases in logging and a large-scale oil spill that took place in 2004 have deposited excess hydrocarbons into the soil, disrupting the delicate balance of this vulnerable ecosystem. Yergeau et al. (2012) had two objectives in this study: to identify the expressed genes that code for cold-adapted enzymes that allow these organisms to live in such an extreme climate and to measure the degradation rates of hydrocarbons in the Arctic soil. Genes that are adapted to the cold could be transposed into crops that would benefit from cold resistance, which is a reason these bacterial species are getting so much attention, in addition to their ability to clean up environmental pollutants. The authors of this study identified about four species that are actively involved in biodegradation of diesel hydrocarbons. Using PCR techniques, they pinpointed some the genes involved in this process, while also recording the relative abundance of the four key species at different time intervals. In all tested soil samples, these four species were found in lower densities before soil contamination when less hydrocarbons were present, and increased dramatically when resampled a month later, indicating that these species indeed rely on the hydrocarbons to live.—Edward McLean

Yergeau E, Sanschagrin S, Beaumier D, Greer CW. 2012 Metagenomic Analysis of the Bioremediation of Diesel-Contaminated Canadian High Arctic Soils. PLoS ONE 7(1) 2012.

Bioremediation in the Arctic continues to be an issue of growing concern. Logging in Canada and the Russian Boreal Forest has steadily increased over the last few decades, and the heavy machinery used to get this job done as efficiently as possible contaminate the soil with diesel pollutants, which decreases the soil pH and puts environmental stress on the whole community. In 2004, a spill occurred in Alert, Canada, and this study was conducted as a result: contaminated soil was put into biopiles and monoammonium phosphate was added as fertilizer to stimulate aerobic microorganisms. Yergeau et al. collected samples from these biopiles (and control samples from nearby uncontaminated soil) and their results were strong. One question they had was whether in situ or ex situ bioremediation was more effective. They found that transporting the soil for off-site remediation got the job done faster: the hydrocarbon concentration fell below safe limits much more quickly when they were able to manipulate the soil in the lab. However, removing the soil in this way can be disastrous to the community and upset the biological balance of the area, so they concluded that whenever possible in situ remediation is the preferred path.

The experiment occurred at three time intervals: directly after collection and analysis, one month into the experiment, and one year after the initial collection period. All soil samples that showed signs of excessive hydrocarbons also contained a higher concentration of those bacterial species that digest them when compared to the control soil samples. Their abundance was greatest one month after the contamination; one year later, most of the diesel byproducts had been consumed, so their abundance dropped back down to normal levels. Digesting environmental pollutants at temperatures below 4C is an incredible ability that bears continued study. As we begin to understand what combination of genes allow for cold-resistant enzymes, we will have a better chance of efficiently and harmlessly cleansing contaminated soils from around the world. Bioremediation is still in its youth and there is a lot of testing that needs to be done. But in terms of cheap, safe, and effective methods to remove pollutants from soil or the water, one would be hard-pressed to find a better way than using preexisting biological machinery and natural processes.

Bioremediation of an Experimental Oil Spill in a Coastal Louisiana Salt Marsh

Since the 1970s, large-scale oil contamination of various marine ecosystems has been a source of much concern.  As our dependence on fossil fuels grows, so to has its environmental impact.  In 2010, an oil rig known as the Deepwater Horizon positioned off the coast of Louisiana in the Gulf of Mexico exploded, resulting in the largest oil spill in United States history.  Many scientists and environmentally savvy individuals thought the gulf was doomed; they assumed the resulting trickle-down of toxins through the ocean’s food web would devastate many populations and upset delicate coastal ecosystems.  To the world’s astonishment, though, most species have not suffered significant losses and only 18 months later, the amount of oil in the water has dropped to normal levels. Several studies that have taken place in the last year have shown that marine microorganisms are responsible for this speedy cleanup.  Academics have been aware of certain bacterial species that can digest oil since the first major spill nearly a half century ago, but lately the big question has been how can we stimulate the bacteria into digesting the hydrocarbons that make up crude oil faster than they do naturally?  This study investigated the possibility that microorganisms that live in close association with a marine plant, Spartina alterniflora, would break down oil faster in the presence of excess nitrogen-containing compounds (ammonium nitrate or urea).  By creating a simulated oil-spill and applying different treatments to certain areas of it, the researchers were able to test oil biodegradation rates against the control plots. Tate et al. conclude that saturating the soil with nitrogen does not accelerate biodegradation of crude oil and that oxygen is much more likely the environmental factor that affects the rate of uptake and digestion.—Edward McLean
         Tate T.,  Shin, W., Pardue, J., Jackson W. Bioremediation of an Experimental Oil Spill in a Coastal Louisiana Salt Marsh. Springer Science+Business Media B.V. 2011.

         For a growing number of years, proponents of in situ (at the source) bioremediation have recommended applying nutrients to an oil-contaminated area to accelerate the process of biodegradation.  However, only a limited amount of information exists on successful nutrient treatments that will have the same effect in different ecosystems, due to the uniqueness of each one’s biodiversity, its soil/water composition, and its overall chemistry.  No such information had yet been published with regards to proper nutrient amendment of salt marshes in the Gulf of Mexico, which Tate et al. set out to change.  Through experimental trial and error under laboratory conditions, they found that nitrogen was most likely to accelerate biodegradation; salt marsh soils contain many nitrogen fixing microbes that also naturally digest hydrocarbons, and both of these processes speed up in the presence of excess nitrogen.  For their study, they chose 10 blocks and then cut each block into quadrants.  Each quadrant received a distinct treatment and quadrants were randomized at every block: the control, which had no oil or fertilizer added, the second with oil, but no fertilizer, the third with oil and nitrate, and the fourth with oil and urea.  Tate et al. added 142 l of sweet Louisiana crude oil (SLCO) to their study site, but only after weathering most of the impurities out of the oil by moving air through the drum for 2 hours at a time.  The authors spent considerable time measuring the soil before their study, especially its nutrient and microbiological composition.  Once they had built up a baseline understanding of the properties of their study site, they began testing. 
         After meticulously setting up this experimental oil spill and accounting for a large range of potential variables, the results of this study must have brought about a certain amount of disappointment in Tate and his team.  In terms of changing the soil composition in the slight way they had desired, it was a success: ammonia concentration increased and the soil was generally more nitrogen-saturated.  But in terms of stimulating uptake and digestion of different hydrocarbons, there was no statistical difference in the plots that received fertilizer and those that did not, leading the authors to conclude that nitrogen is not the key environmental factor in accelerating biodegradation of crude oil.  Despite not finding a nutrient amendment that might benefit future environmentalists hoping to clean up a contaminated salt marsh faster, this study still managed to achieve a great deal: S. alternifloraand its symbiotic microbes have an incredible knack for removing hydrocarbons from the soil with their own biological machinery: it took between 100 – 200 days for most of the simulated contamination to be removed completely.  Continued research into this natural process could shed some much needed light on future bioremediation efforts that set out to clean up oil contamination.

ioremediation of Bisphenol A by Glycosylation with Immobilized Marine Microalga Amphidinium crassum.

Bisphenol A is an organic compound used in the production of many plastic products throughout the industrial world. Since 2008, companies and governments have been questioning its safety and it has garnered considerable attention lately for being an environmental pollutant and for having adverse effects on human endocrine systems, resulting in potential birth defects and other health problems. Bisphenol A is not soluble in water, so factories that operate near rivers or lakes tend to deposit a great deal of this toxic material into the water, along with many other pollutants, that cannot be easily removed. The work of Shimoda et al. (2011) is one study in a sea of recent research into bioremediation, a cheap and safe process that essentially uses microorganisms to remove harmful chemicals from a particular medium through biotransformation. The researchers involved in this study used a microalgal species, Amphidinium crassum, and immobilized cells from a plant species, Catharanthus roseus, to biotransform bisphenol A, and recorded promising results. Biotransformation refers to the effect an organism has on any chemical compound and in this case the two plant species broke the bisphenol A down into glucosides, which is a glucose containing compound the plant can store to metabolize for energy later. This is accomplished by glycosylation, a process common to many plants. The results of this study show clearly that each species is capable of removing bisphenol A from aquatic environments, leaving behind a harmless, soluble organic compound and producing energy for itself, giving further evidence to the usefulness of bioremediation.—Edward McLean

Shimoda, K., Yamamoto, R., Hamada H. 2011. Bioremediation of Bisphenol A by Glycosylation with Immobilized Marine Microalga Amphidinium crassum. Advances in Chemical Engineering and Science, 2011, 1, 90-95.

In this short-and-to-the-point study, Shimoda et al. used the natural process of glycosylation to produce their results, but needed an impressive amount of cultured cells to carry out the experiment. For each trial, they used a centrifuge to separate algal or immobilized cells out of the water, in which they had been incubating for two weeks, until 9 g of plant material had been collected. Using lab manufactured sea water (free of organic compounds) as solution, the plant cells were exposed to bisphenol A and incubated for five days at a time, with measurements being taken daily. The solution was analyzed each day using high-performance liquid chromatography (HPLC), a common method used in biochemistry that separates organic compounds and allows researchers to identify and quantify particular chemicals. Many organic compounds can be biotransformed by plants through the process of glycosylation. The chemical that forms as a result of glycosylation is known as a glucoside, and each plant makes its own unique compound. In this experiment, Shimoda et al. measured the amount of bisphenol A that had been biotransformed by recording the amount of the glucoside that the plant cells synthesized each day and how much less bisphenol A remained. Several trials using both species all returned the same positive results, and within just five days of incubation, up to 17% of the bisphenol A that had been added to the solution had been removed, while the lowest yield still showed a promising 4% removal.

Breakthroughs in bioremediation are happening at an astonishing rate, and many companies and environmental agencies are recognizing the wide-ranging applications of bioremediation, especially because these methods are often inexpensive and harmless. The metabolic machinery that has evolved naturally on this planet is elegant and often far better equipped to handle pollutants than our most dazzling inventions. As a result, the safest way to detoxify our water and soil is through the careful, regulated application of beneficial microorganisms to affected areas. The authors conclude their study optimistically, while mentioning companion studies being carried out by colleagues in the field, noting several other species that might be useful in other bioremediation efforts. Let’s hope many more follow in their footsteps as increased funding for such practices becomes available.