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.