12 July 2008

Microbes Rule the World, The Least They Could Do is Give Us All the Energy We Want

...historically, the study of microbes has focused on single species in pure culture, so understanding of these complex communities lags behind understanding of their individual members. NAS_New_Science_of_Metagenomics
It is fortuitous that humans are finally learning the reality behind the community of microbes that rules the world, just at the time that we could use their help. Craig Venter and competitors are trying to create the perfect energy-making microbe. But growing single strains of microbes to make energy from sunlight, waste nutrients, and CO2 may not be the right approach. A community of microbes working together might do a better job. In fact, you might even say it takes a village of microbes to make a fuel.
Unlike the E. coli situation, using just one species may not work well for bioenergy, since, in nature, bacteria do not grow in isolation. In other words, no bacterium is an island. The very biodiversity that fills the Earth with bacteria and offers great bioenergy potential also presents a challenge for engineers. Even if one picks the ideal "bug," growing, maintaining, and optimizing conditions for its use in bioenergy applications remains a daunting challenge in terms of scalability and reliability.

"Microbial communities that are used to harvest energy must be resilient to fluctuations in environmental conditions, variations in nutrient and energy inputs and intrusion by microbial invaders that might consume the desired energy product," say the authors. The key to large-scale success in microbial bioenergy is managing the microbial community so that that the community delivers the desired bioenergy product reliably and at high rate.

In the absence of these molecular techniques, the authors state, our understanding of methanogenic communities progressed through slow, incremental advances over several decades. Today, society cannot wait decades for new bioenergy sources. Fortunately, an array of pre-genomic, genomic, and post-genomic tools is available to understand microorganisms involved in bioenergy production. Taking full advantage of these tools will greatly speed up scientific and technological advances, which is what society most needs.

Genomics provides the base sequence of the entire DNA in an organism, and the complete genome reveals all the possible biological reactions that a microorganism can carry out. In the past, complete genomes were only obtained for those microorganisms that could be isolated into pure culture, but it is now possible to sequence the genomes of uncultivated microorganisms using metagenomics.

To date, approximately 75 genomes are available from microorganisms that have a role in bioenergy production. These include 21 genomes from methane producing archaea, 24 genomes from bacteria that can produce hydrogen or electricity, and 30 genomes from cyanobacteria that are potential biodiesel producers. At least half of the completed microbial genomes that are relevant to bioenergy were released in the past 2 years, and more than 80 bioenergy-related genomes are currently being sequenced. __ScienceDaily_via_NextBigFuture
If you are not familiar with "metagenomics" you are not alone. It is less than a decade old, and like its siblings "synthetic biology" and "systems biology" it is still developing the new tools it will need to take off like a rocket.

The "community microbe" approach to bioenergy makes a lot of sense. One microbe can only carry so many tools to work with, and a robust approach to high-yield bioenergy will require several tools working simultaneously.

I once suggested using multiple microbes for biofuels production, grown individually in a series of bioreactors. I suspect that a combination of the two ideas may be most successful--a series of bioreactors, each containing specialised communities of microbes rather than single cultures. Working out the best ways of separating the desired product from each stage--for transfer to the next bioreactor -- may take some time.

Also, see Brian Wang's excellent overview of microbial approaches to bioenergy.

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