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Cleaning up toxic waste: directed evolution vs. designed machines


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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

S.E. Gould About the Author: A biochemist with a love of microbiology, the Lab Rat enjoys exploring, reading about and writing about bacteria. Having finally managed to tear herself away from university, she now works for a small company in Cambridge where she turns data into manageable words and awesome graphs. Follow on Twitter @labratting.

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





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  1. 1. theo52 7:55 am 08/18/2013

    Breading bacteria with characteristics desireable to humans is like breading dogs with desireable characateristics. Calling it “directed evolution” is a stretch.
    There is an inference that this somehow supports Darwinian/Macro evolution which I don’t think it does.

    Richard Lenski has tried to emulate Darwinian/Macro evolution in the lab; but after thousands and thousands of bacteria generations; the bacteria remain bacteria – no new body plans.

    Dr John Sanford (Geneticist and inventor of the GeneGun) said :
    “The bottom line is that the primary axiom [of Darwinian/Macro evolution] is categorically false,
    you can’t create information with misspellings, not even if you use natural selection.”

    Link to this
  2. 2. David Cummings 10:58 am 08/18/2013

    S.E., are you related to S.J.?

    Anyway, excellent blog post and I just started following you on twitter.

    Link to this
  3. 3. S.E. Gould in reply to S.E. Gould 4:05 am 08/19/2013

    I’m not going to get into an evolution debate – this is a blog for flagging up interesting and exciting things about bacteria, not disputing basic biological theories. The name of this technique is “directed evolution” – that’s what it’s called – and it can be used for designing and developing enzymes and proteins, as well as bacterial systems.

    (I love the “bacteria remain bacteria” quote though – as bacteria are the most biochemically diverse organisms on the planet – capable of evolving and developing a variety of genetic pathways in responses to environmental changes. They are an entire kingdom of life, not just a strange little species. Dismissing evolution because they can’t grow an arm is just multicellular snobbery. Either that or God showed considerable foresight in creating bacteria that could digest concrete and then kept them hidden until concrete appeared!)

    Link to this
  4. 4. S.E. Gould in reply to S.E. Gould 4:06 am 08/19/2013

    @David Cummings: Thank you, and I’m glad you enjoy the blog! No relationship to the other S. Gould I’m afraid, or at least not that I know of.

    Link to this
  5. 5. notmebug 4:38 am 08/19/2013

    theo52:
    “Richard Lenski has tried to emulate Darwinian/Macro evolution in the lab; but after thousands and thousands of bacteria generations; the bacteria remain bacteria – no new body plans.”

    Funny. You cite a science experiment which conclusively demonstrates the power of evolution to create complex useful new genetic information, a species evolving new valuable capabilities, and you try to claim it discredits evolution because it doesn’t involve a “new body plan”? haha. The majority of evolution doesn’t involve “new body plans”, and talking of “new body plans” is extremely silly in reference to single-cell bacteria.

    But hey, you want evolution of “new body plans”? Sure.
    http://www.pnas.org/content/109/5/1595
    There’s an evolution experiment demonstrating yeast evolving from single cellular to multicellular…. and furthermore it evolved into a basic but authentic example of complex multicellular life. Specifically it is multicellular *with cell specialization* division of labor. Some of the cells specialized for reproductive functions, including apoptosis in service of reproduction of the larger multicellular entity.

    “Dr John Sanford (Geneticist and inventor of the GeneGun) said : ‘The bottom line is that the primary axiom [of Darwinian/Macro evolution] is categorically false,
    you can’t create information with misspellings, not even if you use natural selection.’”

    And my response is:
    Bill Kaysing (former employee of Rocketdyne, manufacturer of the Saturn V moon mission rocket engines) said: “they simply orbited the Earth for eight days and in the interim they showed these fake pictures of the astronauts on the Moon”. He’s also the author of the book “We Never Went to the Moon: America’s Thirty Billion Dollar Swindle”

    In case my point wasn’t clear, you dug up a a crackpot uttering something laughably false. The experiment you cited by Richard Lenski itself demonstrated evolution creating new useful complex information, and I have over a hundred thousand biologists and other life scientists who all agree evolution can and does create new information. Your one crackpot quote to the contrary is just as meaningless as my quoting a Rocketdyne employee who claims the moon landing was impossible.

    Link to this
  6. 6. David Cummings 6:43 am 08/19/2013

    Maybe no kinship but you are certainly related in spirit. You write very well on the subject and you obviously have a love for it, very much like the elder Gould. I look forward to reading more of your posts in the future.

    As for getting into arguments about evolution, I think you are right to avoid them. I was tempted to post something in response to the first comment but then I stopped myself. What’s the point? It doesn’t matter that evolution is much better understood than gravity; some people just don’t want to understand it. There are none so blind as those who refuse to see.

    Link to this
  7. 7. David Cummings 6:45 am 08/19/2013

    notmebug, well said.

    Link to this
  8. 8. Squish 9:51 am 08/19/2013

    Hey theo52: yes, calling something a type of evolution probably infers something about Darwin just as calling something a type of calculus probably infers something about Newton and Liebnitz. Regardless, don’t worry about the human actors so much (science and math get independently recreated by lots of people all the time), you need to try to understand the theory a bit better.

    Try randomly typing letters. Will you never come up with a word? Mathematics says yes.

    By the way, misspellings are indeed information (people who design predictive text software use this information everyday).

    If novel genetic code is useful for an organism, I guess that novelty would be “spellings” in your book then? Sorry, just can’t figure out the non-applicable misspellings metaphor.

    I can’t make a fish into a chicken. So what. Neither strawman metaphor sheds insight into the process of evolution by natural selection.

    Link to this
  9. 9. David Cummings 1:10 pm 08/19/2013

    Strawman arguments
    Fighting for a losing cause
    Metaphors abound

    Link to this
  10. 10. sault 3:55 pm 08/19/2013

    David,

    Arguing with somebody who gets their information from belief instead of scientific facts and observation is indeed pointless. However, many others who do not participate in the debate still read these posts, so scientific ignorance should be opposed just to keep those folks from getting misled.

    Link to this
  11. 11. S.E. Gould in reply to S.E. Gould 7:08 am 08/20/2013

    Thanks for all the supportive comments! I’ve had the evolution debate continuously since I was a student and there really is so many times I’m willing to hash out the same argument. However as Sault points out, it is important that on a visible forum there is a response to incorrect information for all visitors to the site to read. Thanks to both notmebug and Squish for their responses :)

    Link to this
  12. 12. David Cummings 7:21 am 08/20/2013

    sault, I think the best way to address the lurkers on the subject of evolution is to post a few basic links regarding the state of the theory at this time and the general outlines of its history. I used to have such links handy for that purpose but I’ve fallen out of the habit of responding to evolution-deniers. But I agree with you, it’s good to present the case, over and over again, for those who are more open-minded but maybe lacking in some basic familiarity with the subject.

    In general I would say this: a good place to start, if you really are interested in this question, are the essays of Stephen J Gould. Though Gould died in 2002 and many of his essays are written decades ago, they are extremely readable still highly applicable to the discussion.

    Link to this

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