The ARPA-E: Renewable Fuel through Genetic Modification, photosynthesis, and the Electro Fuels Program

The technology needed to create renewable fuel and the solutions to problems like global contaminated drinking water and starvation exist in hundreds of labs around the world.  For example, the Slingshot, a small water purification unit developed by Dean Kamen, runs on cow dung, requires no filters, produces potable water, and can simultaneously power 70 energy efficient light bulbs.  Globally, we produce 150% of the amount of food required to feed everyone, yet we cannot manage to transport it and millions die of starvation every year; small changes in world-wide food distribution and transportation, accomplished through improved international communication, would be a strong step towards ending hunger.  And people are coming up with new sources of renewable energy, and more efficient ways to extract that energy, on a daily basis.  Unfortunately the economic incentive for wide-scale use of expensive inventions usually just isn’t there, and without incentive our progress will always be stunted.  Still, in 2007 the U.S. Department of Energy saw fit to commission a new branch of research known as the Advanced Research Project Agency – Energy.  Its goal has been to investigate and fund cutting edge research into energy technologies and began with a budget of $400 million.  Much of the work they fund is kept under wraps, but Richard Blaustein had the opportunity to review a few projects that will be discussed below.  From genetically modifying plants to electro-stimulating specific microorganisms, the scientists working for the ARPA-E are searching for essentially new sources of renewable energy.  And so far, they have enjoyed a great deal of success.—Edward McLean
            Blaustein, Richard. 2012 Can Biology Transform Our Energy Future?: ARPA-E infuses innovative research ventures with fresh funds. Journal of BioScience, Vol. 62, No. 2.

            While much of their funding is spent on improving existing technologies, the ARPA-E has taken special interest in developing biotechnology that utilizes existing biological processes.  Through genetic modification, several projects focus on using target organisms to produce renewable fuel naturally.  This article focused on two different pursuits, but each requires diligent research across many fields.  The first is genetically modifying plants so that they can photosynthesize more efficiently and produce more oil that can be refined from the plant matter, and used as biofuels.  This project is known as Plants Engineered to Replace Oil (PETRO), and from its outset, its mission has been to “get photosynthesis to produce biofuels directly that provide more of what we need and to use the existing energy-capture process to put more energy into fuel” (116).  Many of the plants that produce biofuels do so indirectly; only after distillation or some other secondary process can their products be made into fuels.  Researchers at PETRO are exploring ways to tweak photosynthesis and other metabolic pathways that will take in sunlight and CO2 and yield a directly usable fuel, stored throughout the plant body.  In processes that produce fuel from crops like maize or sugar cane, the usable product only comes from one part of the plant and the rest is discarded.  If target plants were modified so that their stems and leaves could also be used to supply fuel, the entire process would be enormously more efficient.  The environmental impact of creating fuel this way is meniscal next to the imprint left by searching for and burning fossil fuels, and it is renewable so long as sunlight is available.  PETRO has provided a number of promising breakthroughs that demonstrate considerable hope for the future of renewable energy.  This team now faces the daunting task of supplying incentive to policy makers to adopt and fund this research.  If only that was as doable as producing renewable energy by modifying photosynthesis. 
The second project this article discussed at length is the Electro Fuels Project, which involves essentially engineering the genome of a microorganism and implanting that code into a target E. coli cell.  This engineered genome borrows genes from different microbes—sometimes from as many as 16 different organisms—that code for specific enzymes involved in pathways used to fix CO2 into higher carbon compounds.  Through these modified pathways, much like in the aforementioned photosynthesis example, the E. coli cells will take atmospheric CO2 and transform it into a fuel such as butanol, which is “a high energy carbon-compound,” which would be excreted and easily collected.  This process is known as Electro Fuels because the catalyst that begins the carbon fixation process is an electrical shock, administered by a tiny cathode.  A remarkable branch of their research extends into adapted evolution studies; this type of investigation “instigates and processes mutations and changes for the whole organism.”  In other words, these scientists expose the target organism to a new stimulus, and perhaps the genetic material the bacterium will require to adapt, and do so for generation after generation until the organism possesses the biological machinery to coexist with—maybe even utilize—the introduced stimulus.  In this case that would involve mass producing the colonies of bacteria that are able to process carbon using the newly discovered pathways and identifying the genes that code for the enzymes that allow them to make higher energy carbon compounds as a by product of respiration.  The next step would be removing the target gene, along with up 20 others involved in some other piece of the operation, combining them and correctly inserting them into the malleable E. coli.  The whole procedure sounds maddening and meticulous, but with careful research the project shows remarkable promise.
            Another Electro Fuels project was discussed and it too pertains to the fixation of carbon, but on a much larger scale and smaller focus on creating renewable energy.  The group involved in this research has its sights set on carbonic anhydrases, which are naturally occurring enzymes that capture carbon, sometimes at astonishing rates.  The team reports that one carbonic anhydrase molecule can fix one million CO2 molecules every second, adding that they are among the fastest working enzymes in nature.  They have recently been working on another directed-evolution study to make the enzyme more adapted to the “extreme alkaline and thermal conditions found in emission-capture systems.”  The work is less predicable than the researchers might want, but they cannot complain too much, as they have seen a million-fold increase in their carbonic anhydrase’s stability.  If these enzymes were technologically manipulated and available for widespread use in emission-capture systems installed by factories, the CO2 emissions across the country would rapidly decrease. 
The cutting edge research discussed in this brief review pertains directly to bioremediation, but on a much larger scale than the focus of most remediating projects.  The ARPA-E is actively searching for ways to use the excess CO2 our industrial pursuits have generated to create fuel, fundamentally reversing the production of energy and using the largest source of pollution and existing biological systems to make energy.  We are in a noble age of technological advances and have never been better suited to subdue some of the many issues that plague our world.  But we also have never existed in a world with more opposition, with more of a need for an individual to blame, and with more “extreme economics” (from sociobiologist Rebecca Costa), all three of which are biologically engrained in each of us and stand like unconquerable mountains in the way of progress.  We need to overcome a lot more than the energy crisis if we wish to save ourselves, and I guarantee prevailing over our own hardwiring will be unfathomably more difficult compared to making renewable energy, which has already been done.

Systems Biology Approach to Bioremediation

In the last two hundred years or so of scientific inquiry into the biological world research has mainly focused on one subject, one part of a system, at a time, and bit by bit thousands of dedicated individuals have furthered our understanding of the natural world.  Traditionally, biologists have spent their careers either investigating the very large or very small: ecologists tackle ecosystems, communities, populations, and species, while molecular biologists handle cells, proteins, and nucleic acids.  Until recently, advances in biology generally moved in this way: two distinct fields with different research methods that ultimately contribute to the same goal of understanding the processes that govern life on this planet.  Lately, though, there has been a call to combine molecular research with ecology in an emerging field called systems biology, which integrates research from the molecular, cellular, community, and ecosystem levels of any complex system being studied.  This sort of integrated research model allows for a much more complete understanding of the many biological relationships that exist anywhere you care to look.  Systems biology has proved especially important in our understanding of the underlying mechanisms that affect bioremediation.  Although it has been shown again and again to be a suitable, efficient, and inexpensive method to cleanup contaminated sites, bioremediation has long been referred to as a ‘black box’ because we see patterns and relationships but cannot fully explain why it fails or succeeds.  A systems biology research approach to bioremediation will hopefully begin to fill in this gap as new information on the enzymatic, molecular, and other microbiological factors that come into play is revealed.  Through the use of genomics, transcriptomics, proteomics, metabolomies, phenomics, and lipidomics, microbial communities in a variety of environments are being studied.  The paper at hand focused on several studies that involved the bioremediation of radionuclides, metals, hydrocarbons, and chlorinated solvents using the previously listed methods to demystify the molecular interactions that manage to break these harmful pollutants down.Edward McLean
Chakraborty R., Wu C., and Hazen, T. Systems Biology Approach to Bioremediation. Curr Opin Biotechnology (2012)

            What makes bioremediation so fascinating is both its effectiveness and the amount we still need to learn to know what’s really happening.  As a method to clean up the environment, it has been used for more than 50 years, yet the amount we comprehend about the process can sometimes be reduced to ‘amendments are added, and pollutants are degraded.’  Technological advances in molecular biological equipment have been occurring rapidly; we have the ability to determine whole genome sequences, enzymatic activity, distribution of certain genes, the presence of proteins and lipids, and a long list of methods to do so, each catered to a specific environmental need or constraint.  Deep understanding of the processes that stimulate bioremediation at the cellular level and the effects that trickle through the community will provide unprecedented breakthroughs in environmental biotechnology in the future. 
            Chakraborty and his team looked at different studies that used some of the cutting edge techniques mentioned above.  In one study, researchers found that certain species of bacteria were able to reduce radioactive Uranium (VI) by acting as a electron acceptor.  The same thing occurred in a study that showed a nearly complete reduction of Chromium (VI) from 100 ppb to background levels within a year.  Each of these investigations were successful, but the shortcoming of systems biology is often the cost associated with doing a thorough study.  One can imagine how expensive it is to do a truly comprehensive study of all microbiological interactions in a given area and how they relate to the larger function of the system at hand.  Recently, though, an anthropogenic disaster presented system biologists with an unusual opportunity to study  microbial interactions with as much funding as they needed.  The MC252 spill of 2010 dumped more crude oil into the ocean than any other in history, and as anyone might have imagined the public reaction from this “going green” country was tremendous.  Millions of dollars were immediately pumped into the cleanup effort and millions more went to organizations tasked with finding the most effective, economical, and least intrusive solutions.  Because of the available funding, a complete analysis of the mineral and organic composition of the spill was compiled, along with the microbial community that had begun feeding on it.  Invaluable knowledge came from the many studies involving the MC252 spill, and it will be applied to similar situations that might arise in the future. 
            Systems biology is the next step, the logical progression in scientific understanding as our computing power and research methods develop faster than ever before.  The combined research of the world’s intellectual community is no longer stored in volumes that collect dust until someone stumbles upon the right section, but rather it exists as one continuous, interactive text that grows on a daily basis.  This leads us closer and closer to an elegant synthesis of the natural world, however unattainable that might be.

Potential use of cyanobacterial species in bioremediation of industrial effluents

To date, much of the work that has been done in the field of bioremediation has focused on the use of soil dwelling bacteria or complex fungi.  Little attention has been given to the remediating capabilities of organisms like cyanobacteria because many of the mechanisms they employ to produce energy are less efficient or take longer than those used by other kinds of bacteria because most of their energy comes from the sun.  This is not necessarily accurate, though, and in some cases photosynthetic cyanobacteria are more suitable candidates for bioremediation because they need only to be exposed to sunlight to break down certain compounds effectively, and no further nutrient amendment is necessary.  Those species that live in close association with a contamination source usually find a way to reduce the surrounding toxicity to a comfortable level, and researchers have begun noticing their skill at doing this.  A team of scientists, led by Sanjay Kumar Dubey, isolated five species of cyanobacteria in India that were able to remove contaminants from pharmaceutical and textile wastewater.  An experiment was set up to determine how well these species could remove those contaminants at various concentrations over the course of one week.  Dubey and his team reported strong results: all contaminants were removed at both concentrations given enough time, which was generally no longer than a week.Edward McLean
Dubey, S., Dubey, J., Mehra S., Tiwari, P., and Bishwas A. J. 2011 Potential use of cyanobacterial species in bioremediation of industrial effluents.  African Journal of Biotechnology Vol. 10 (7), pp. 1125-1132

         Dubey et al. set out to see how well isolated species of cyanobacteria could remove calcium, ammonia, nitrate, phosphorus, and several other metals and pollutants from textile and pharmaceutical effluents.  They isolated the species and exposed them to different solutions of the effluents, some containing 5 ppm of pollutant and others with 10 ppm.  They thought with some certainty that 10 ppm would be near the upward threshold of tolerance for these species and that some if not all of their metabolic pathways would shut down as a result, but to their surprise, the organisms cleaned up solutions that had 10 ppm more efficiently than those with 5 ppm.  All five species were isolated into their own flasks to measure the effective rate of each one, but flasks containing mixtures of the five were also used in this experiment.  The contaminated solutions that were exposed to multiple species were degraded fastest, leading Dubey et al. to believe that the most successful treatments for future study would use a mixture of cyanobacteria to remove contaminants rapidly.  Measurements of the effluent were taken at 2, 4, and 7 days after the start of the experiment, and by the end of the week all treatments showed between a 97 – 99.7% removal efficiency of pollutants. 
         Dubey and his team’s findings are practically too good to be true.  They demonstrate that the application of any of these five species, or a mixture, to a contamination source will result in extensive bioremediation of that pollution.  Cyanobacteria are found practically anywhere that moisture or water is: from wet rocks to the ocean, these primitive, photosynthetic organisms grow and help recycle nutrients through the food-web, and our job now is determining which ones can be used in bioremediation.  Because they are so wide-reaching and common, invasion or out-competing native species is less of a concern, so both in situ and ex situ management can take place with little worry about residual effects they might have on the surrounding, often unaffected, environment.  The species this paper investigated have been shown to be beneficial in bioremediation projects, and while this type of work is perhaps the cheapest way of cleaning the environment, it can still be economically beneficial.  The production of large quantities of these species will generate money for local industries and lead to growth in small communities.  We’re still in the baby-steps phase of unlocking the potential of bioremediation, but I believe these kinds of bottom-up decontamination projects are the best way to remove pollution from our planet.

Bioremediation of Pharmaceuticals, Pesticides, and Petrochemicals with Gomeya/Cow Dung

Management of the environment is not a recent development in human history.  For thousands of years, human societies have been learning how to manipulate and control the natural processes of this planet, and while full control of nature is not possible, the god-like technology we possess often produces the illusion that we can.  Now we are essentially in the process of picking up the pieces of the environment; and many believe the solution is found exclusively in the innovations of the last half-century.  But Randhawa and his team approach the world’s environmental problems with a different, more traditional mentality.  Using the Vedic literature as their guide, this group of researchers investigated and reviewed the bioremediating capabilities of cow dung, and how it can remove harmful pollutants from various contaminated sites through biodegradation.  A main aim of their study is to provide a framework for future research into this cheap, safe, and accessible remediation method, especially in developing countries that cannot afford expensive waste-management machinery.  Among its many applications, cow manure has the ability to breakdown pharmaceuticals, pesticides, and petroleum products when applied to the soil or water in the proper way.  While this paper did almost none of its own fieldwork, it compiled information from several sources and allows other researchers to carry out similar projects in their region.—Edward McLean
Randhawa, G. and Kullar, J., Bioremediation of Pharmaceuticals, Pesticides, and Petrochemicals with Gomeya/Cow Dung. ISRN Pharmacology, vol. 2011.

         The authors of this study approached their research in a slightly unconventional way: they consulted ancient texts from India known as the Vedic literature, which list all the medical and scientific understanding and knowledge from roughly 1200 years ago.  Among this information is an account of the many applications of cow milk and dung, and how they can be used to rejuvenate or clean up different contaminated sites, like soils with excessive heavy metals or oil.  It would seem that these ancient people were quite aware of the remediating capacity of cow dung.  But interestingly, Randhawa and Kullar read further into the ancient texts and are convinced that the species of cow that produces the manure matters, and the most effective breed is the indigenous Indian cow.  They found that the zinc, copper, phosphorus, and calcium content in the indigenous cow, versus a cross-breed, was markedly higher.  Having established the proper treatments, Randhawa and Kullar catalogued, and in many cases tested, existing research into the environmental applications of cow dung and the methods to properly use it in decontamination projects.
         The authors of this study list at least seven different ways that manure can degrade or help degrade environmental pollutants like compounds in pharmaceutical and biomedical waste, heavy metals from municipal sludge, excess hydrocarbons from oil found in the water and soil, and a variety of other contaminants.  One especially simplistic and effective procedure is the removal of arsenic from potable water sources using just manure, sunlight, and filtration.  This harmful element is separated from the water through several rinses and then put into a small ditch with dung on top.  The microorganisms convert arsenic to gaseous arsine, which is not necessarily environmentally safe, but at least it is not in the drinking water.  Another remarkable quality of cow dung is its ability to degrade harmful hydrocarbons and other compounds found in crude oil quickly and effectively, many of which are carcinogenic and/or non-biodegradable.  Benzene is one of those compounds, yet one species of bacteria, Pseudomonas putida, is able to degrade this hydrocarbon quite successfully and rapidly. 
         One area of research in which they showed a particular interest was the bioremediation of pesticide residue and runoff.  India is one of the largest pesticide producers in the world, generating roughly 90,000 tons a year.  Most of these compounds are harmful carcinogens and as much as 97 – 98% remains in the soil and ground water, slowly accumulating, trickling up through all trophic levels.  Randhawa found that several members of the microbial community of cow manure can work together to degrade several of the more harmful chemicals in the pesticides.  This process is not fully understood and that is perhaps the most promising realization to take away from bioremediation projects.  Bacteria have been evolving mechanisms to digest every manner of energy that they encounter for nearly as long as life has existed on this planet.  They can work separately or in concert to break down so many different anthropogenic compounds.  Instead of creating powerful machines that sometimes might be seen as more destructive to their cause than helpful, we might want to start using what exists naturally.  Maybe then we will start taking baby steps towards the natural equilibrium this planet so desperately craves.

Enzymatic biodegradation of pharmaceutical wastewater

The use of biological agents in the treatment and cleanup of contaminated sites continues to be explored and implemented in innovated ways, and the scientific community is getting a better sense of the microscopic world that controls the cycling of nutrients and compounds found naturally and added anthropogenically in the environment.  Virtually every exploitable habitat owes its success to the microbial community that transform seemingly unusable sources of energy into the necessary compounds other organisms need to survive.  This is true wherever life is found on this planet, and microorganisms have been working tirelessly to digest the new pollutants and macromolecules that we deposit in the soil and water.  One such source of contamination is pharmaceutical wastewater, both on the industrial and residential level.  Only part of the pills we take and chemicals we otherwise consume usually stay in the body.  The rest is flushed out of our bodies and into the environment.  Bacteria have the ability to degrade most compounds into smaller compounds, which usually results in energy for the bacteria and less harmful molecules in the soil.  Lately, researchers across the globe have been successful in culturing microorganisms with the intent of increasing their ability to digest pollutants.  Sometimes that process is not difficult and can be accomplished with just the application of yeast, which is what Uwadiae and his team did in this study.Edward McLean
         Uwadiae S. E, Yerima Y, Azike R. U 2011 Enzymatic biodegradation of pharmaceutical wastewater.  International Journal of Energy and Environment Volume 2, Issue 4, 2011 pp.683-690.

         Bioremediation is often pointed to as a solution for wastewater treatment in developing countries because it is low-cost and universally accessible, rarely requiring excessive, expensive equipment.  If the remediation work can be done in situ, it can cost no more than the microorganisms themselves. Wastewater treatment in Nigeria fits this profile and is a growing concern; potable drinking water is often contaminated by wastewater from the country’s industry.  This experiment set out to provide a framework for future researchers interested in cheap bioremediation that can be accomplished simply by the addition of enzymes to the affected area.  Here, Uwadiae made a solution of wastewater with yeast and amalayse treatments and tested it against a control that contained no added enzymes.  For six weeks, levels of various contaminants, such as antiinflammatories, antibiotics, beta-blockers, blood lipid regulators, and antidepressants, were recorded along with their reduction in the solution.  By the end of the experiment, Uwadiae and his team recorded promising results and found that both the yeast and amalyase had sped up or at least aided in the bioremediation of industrial pharmaceutical wastewater.  They reported that the wastewater could eventually be treated entirely this way, but given the short time period of only six weeks, full degradation did not occur.  They found that yeast is more effective in enhancing the rate of degradation than amalyase, but both are suitable amendments.  Further research should be done into other enzymes that work in concert with a family or genus of bacteria; that way, the microbial community will grow and therefore digest contaminants more quickly.  Despite its safety and low-cost nature, bioremediation projects are often stifled by the time it takes to complete them.  The process can be slow and uncontrollable, but if solutions are found that galvanize microbial activity, bioremediation may begin to gain popularity in both the developing and industrial world.

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.