When talking about the goals of applied microbiology, one of the largest targets is a process known as ‘bioremediation’, defined as the use of living organisms to remove dangerous or toxic products from the environment. Although breakthroughs in genetic engineering and high throughput screening have changed the way we approach this goal, bioremediation in some form or another has been around for a long time. It has been used in the treatment of sewage since the 19th century to remove nutrients and toxic chemicals before returning sewage water to the environment, and the use of bacteria to break down run off from copper mines has been well documented. In fact, bioremediation has been around since at least Roman times with the first documented use of composting.
With such a diverse and widespread process, it can be hard to identify niches we have yet to fill in the field of bioremediation. There have been a lot of exciting discoveries in the field, such as the intensely radioresistant Deinococcus radiodurans and the uranium-sequestering Geobacter uraniireducens which help clean up soils contaminated by nuclear waste or fallout, bacteria such as Ferroplasma spp. and other Geobacter species which can tolerate and remove high concentrations of metal ions, and hydrocarbon degraders such as Alcanivorax borkumensis which played a key part in clearing up the Deepwater Horizon oil spill in 2010. We are slowly discovering more and more species of bacteria which can live in more extreme conditions and process more dangerous chemicals, and it is difficult to get a grasp on how useful these microorganisms actually can be in practice.
Using microorganisms for bioremediation has many advantages and seems like a great hands-off way to deal with environmental issues, but there are several reality checks that need to be done before bringing bioremediation into the mainstream. The fact that bioremediation relies on living organisms is in both parts its primary appeal and its biggest pitfall, as by beginning bioremediation in an area, you are introducing a foreign species. Most people can bring to mind the extremes of an introduction of a foreign species to a region: gardeners have been plagued by Japanese Knotweed, and the introduction of rabbits to Australia causes millions of dollars to crops every year. It is hard to know the consequences of introducing a non-native species – even of something as small as bacteria – to an entirely new ecosystem. Bacteria multiply rapidly and mutate often, meaning that by the time bioremediation has done its job, the bacteria we are dealing with could be vastly different from the species we first introduced.
Even with the risk assessments and ecological surveys, there is also the other fact that many bacteria we find that can process toxins as part of their ‘in house’ metabolism do so in extremes of temperature, pressure, oxygenation, or any other wild variety of conditions. These extremophiles grow poorly outside of their chosen ecological niche, and so introducing them to a new environment will more than likely have a less than adequate effect on whichever toxic product or hazard the microorganism was chosen to clean up.
Of course, the simple answer many microbiologists will think is to take these extremophiles’ genes and put them in an easy to use, well characterised bacterium which grows in the right conditions. This is an exciting area of research with many breakthroughs in recent years but we have to acknowledge that what we’re talking about here is the release of genetically modified organisms into the ecosystem. And whilst, as far as we know, these organisms will not be dangerous or harmful on the face of it, there is still a lot of legislation and regulation relating to the use of these organisms. Several studies have sought to use bioluminescence genes to keep track of these organisms in the environment, but this leads back to the issues above – once they are in the environment, being able to track them may not be enough, we still have to get rid of them if they cause an issue and it would not be unusual for bacteria to evolve out of their bioluminescence genes: if they give no direct benefit to the organism, it isn’t likely to continue to invest energy into keeping it active.
With all this said, personally I’m a big advocate for bioremediation, but as Spielberg fans will note from Jeff Goldblum’s character in ‘Jurassic Park’: “Life finds a way.” – when we’re exploiting nature to take care of our environmental issues, we just need to make sure that nature doesn’t find a way to come back at us unexpectedly, potentially creating new problems from trying to fix our old ones.
Robert G Millar (University of Warwick)
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