Lab Rat

Lab Rat

Exploring the life and times of bacteria

Cleaning up toxic waste: directed evolution vs. designed machines


Some heavy metals are required in trace amounts for the survival of living organisms, however at higher concentrations these metals can be incredibly toxic. In Europe, the elements of highest concern are arsenic, cadmium, cobalt, chromium, copper, mercury, manganese, nickel, lead, tin, and thallium, all of which can be produced as by-products of industrial processes or along roadways. Unlike organic pollutants, metals don't decay or break-down over time, if anything they have a tendency to precipitate into the soil or surrounding environment and accumulate into dangerous quantities via bioaccumulation.

It should come as no surprise by now that while these metals are dangerous for animals, many bacteria and other micro-organisms thrive on them, and are capable of removing toxic metal elements from water or soil. There is therefore a lot of interest in the use of bacteria as a cheap and non-chemical method of cleaning up toxic waste. A few years ago I was involved in a project that looked at designing a biological biosensor for arsenic within a bacteria, so I was particularly intrigued by a new project put forward to produce bacteria capable of cleaning up heavy metals.

The Berkeley Pit, a former copper mine in the USA. The water is highly acidic (pH 2.5!) and filled with toxic metals. Image from NASA source link below.

The project aims to use special strains of bacteria such as Pseudomonas aeruginosa to clean up heavy metal pollution. By growing successive rounds of bacteria exposed to copper, the researchers have already produced strains that show a greater ability to grow in the presence of toxic levels of copper ions. By selecting the bacteria more likely to survive, and allowing them to produce new mutated strains, the researchers harness the power of natural evolutionary processes in order to produce bacteria that do what they want. This process is known as directed evolution.

The picture below shows part of the process used to produce these special strains of bacteria. The streaks across the circular plate are bacteria, while the little white disk in the centre releases copper ions into the plate. Originally, there were large bacteria-free circles (called 'zones of inhibition') around the white disk where bacteria were killed by the copper. After only four generations of directed evolution, the researchers were seeing much smaller zones of inhibition, showing that the bacteria were capable of surviving at higher levels of copper. The next stage in the research involves producing bacteria that can not only survive high levels of pollutants, but also remove them from the environment.

Growth of bacteria on an agar plate, image from David Finkelstein and Jenny Tran.

How does directed evolution compare to the designed genetic machines that I was working on? The directed evolution approach is a lot broader, and has a lot greater scope for surprising results. When designing a genetic system, the researcher needs to know exactly what genes to use, and which order to put them in. For directed evolution, the researcher needs to produce the right conditions for growth, continual nudges in the right direction, and then see what the bacteria comes up with. The genetically designed machine, if it works as expected (which admittedly, is a big if!) can potentially be transferred from bacteria to bacteria as a discrete unit of DNA, while the evolved bacteria are a unit of themselves. They may be able to remove and neutralise copper toxins, but the mechanism by which they do might require numerous pathways within the same bacteria.

Both systems, however, have a huge amount going for them. What I love about directed evolution is that it uses the already impressive evolutionary abilities of bacteria to create potentially whole new systems. Bacteria reproduce very quickly, very numerously, and despite (or perhaps because of) their inability to share genes by sexual reproduction, they are far more forgiving of mutational changes to the DNA. Furthermore, the more stressful a situation the bacteria is in (for example when surrounded by toxins) the more mutations and changes to its DNA it makes, making it more likely that a solution to their current environmental problem will be found. And with directed evolution, the solutions to their environmental problems, are the solutions to our environmental problems.

This project is currently being crowd-funded at microryza, please visit their website to help show your support!

Researcher David Finkelstein, exposing the bacteria to UV light. Image from David Finkelstein and Jenny Tran.


Credit source for image 1

The views expressed are those of the author and are not necessarily those of Scientific American.

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