Computers and Electrifying Bacteria

Computers Help Bacteria Clean our Water and Produce Electricity. Computer-based simulations that use an organism’s hereditary information are revealing previously unknown but essential life functions of special bacteria that can be modified to help clean our water and produce electricity for our alternative energy needs.

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Smart computer programs are revolutionizing what we know about and how we can improve the functions of unique bacteria that clean water and even produce electricity. The revolution stems from a computer technology that uses information from a bacteria’s genome, the basis of its hereditary information, to reveal its real-life functions and interactions with the environment. The genome is the collection of DNA bases that are passed from parent to offspring, or original bacterial cell to daughter cells. In a January edition of Nature Reviews just this year, three researchers Mahadeven, Palsson, and Lovley, who range in their experience from physics and computer science to microbiology, describe a computer technology called COBRA that uses a bacteria’s genome to make sense of its real-life activities. COBRA, or Constraint-Based Reconstruction and Analysis, is teaching us many things we did not know about a particularly unique species of bacteria, one with remarkable potentials for bettering our environment.

A unique class of bacteria that has been studied using COBRA is Geobacter_, a tiny organism that plays a big role in removing pollutants from our water and soil, and in producing energy. The COBRA approach imitates what happens in real life for these bacteria using math and computer technology. The mathematical reconstruction or model of Geobacter, built based on its genome as well as experimental data on its real-life activity, is accelerating our progress towards an in-depth understanding of these small yet complex organisms. Computer-based reconstructions are also helping us to harness Geobacter for practical applications like pollution clean-up. Says Professor Lovley, this technology bench/metal.jpg" width=“220” height=“220” class=“mt-image-right” style=“float: right; margin: 0 0 20px 20px;” /> “will help move ‘the study of relations between bacteria and their environments’ from a highly descriptive discipline to a predictive science.” In other words, using computer technology we can predict how Geobacter bacteria behave in real life. Dr. Derek Lovley is indeed an expert on the subject, being the scientist who first identified the curious species of Geobacter that can thrive by chewing up metal oxides (see image of Geobacter bacteria growing on a chunk of iron oxide to the right).

Technology has made this possible. In our age of technology, researchers are often able to predict the physical activity of bacteria through computer reconstructions in less time than it takes to perform experiments in the field. The logical extension of this capability is the use of computer reconstructions to predict which environments will make bacteria like Geobacter perform certain functions more effectively. For example, we might want to predict conditions that help bacteria better clean contaminants out of dirty water or soil. Using technology to predict function is especially important for bacteria types that are difficult to grow in the lab, and thus must be collected from hard-to-get natural soil or water samples. Computer reconstructions can help determine which biological pathways, or series of actions that take place inside the bacteria, are most important to study. Thus, computer technology helps to direct our hands-on studies of these bacteria. This computer-assisted ‘directed research’ is more productive than its ‘trial-and-error’ alternative.

Why Geobacter? The basis for computer reconstruction in bacteria research is the exploration of obscure life functions encoded in the genomes of bacteria with important environmental roles. Geobacter is such a bacteria, being specially adapted to clean contaminants from water or soil and to produce electricity. Geobacter bacteria have specialized appendages that serve as tiny ‘pipes’ that carry electrons from the inside the bacteria to the outside. Once outside the bacteria, these electrons can ‘clean up’ metal contaminants. In another environmentally important process, Geobacter play a role ‘biological batteries’ that use bacteria to produce electricity. The role of Geobacter in these batteries consists of donating electrons, produced during the breakdown of bacterial nutrients, to an electrode, thus producing electricity. While the application of Geobacter in clean-up and energy applications is widespread, the underlying biological pathways of this bacteria that allow its use in these applications had been hazy until the advent of computer-based reconstructions. Computer technology along with laboratory experiments, in repeated cycles, are revealing previously undiscovered aspects of a Geobacter bacteria’s life. Techniques such as COBRA are also allowing researchers to modify these bacteria and their environments in order to create more effective clean-up strategies and more powerful electricity-generating ‘biological batteries’.

We can make Geobacter work for us. Computer-based simulations have not only provided an in-depth understanding of Geobacter activity, but are also providing insights into Geobacter performance in both natural and man-made environments. Recent insights provided by computer reconstructions include how the transport of electrons to the outside of the bacteria affects _Geobacter’_s growth, and how we can ‘pump up’ _Geobacter’_s generation of electrons in energy applications. For example, computer reconstructions have revealed that the bacteria’s transfer of electrons to the outside environment is very energetically taxing, meaning that when Geobacter are busy pumping electrons into the environment, they are not as busy growing and reproducing. This predicted pattern of growth and reproduction is good news for environmental researchers, who don’t have to worry about Geobacter bacteria plugging up groundwater reservoirs when they are used to clean dirty water. Computer reconstructions have also revealed that by starving Geobacter, we can successfully cause decreased bacteria growth and reproduction in favor of increased generation of the electrons needed to produce energy in ‘biological batteries’. Thus, the computer technology is helping us to get the bacteria to more effectively “work for us,” versus working for themselves. No more selfish Geobacter bacteria!

Computer reconstructions match up well with real life. Computer technology approaches used to predict nutrient use and contaminant removal by Geobacter over time matched well with actual physical measurements made on site for pollution clean-up of groundwater. It turns out that we can now use advanced computer technology to predict the real-life functions of bacteria. With this tool we can improve bacteria-mediated pollutant removal, wastewater treatment, and novel bio-energy solutions.

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References:

1. R. Mahadevan, B. Palsson, D. R. Lovley. In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling. Nature Reviews Microbiology 9, 39-50 (January 2011) | doi:10.1038/nrmicro2456

2. ‘Biological Battery’ and general Bacteria Structure images from Wiki Commons

3. Computer-Based Simulation and Discovery process images created and property of Paige Brown

4. All Geobacter images compliments of Dr. Derek Lovley

Mahadevan R, Palsson BØ, & Lovley DR (2011). In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling. Nature reviews. Microbiology, 9 (1), 39-50 PMID: 21132020