Using bugs to wean the world off fossil fuel

Steve Kretzmann

Donning a pair of gloves and shoving your hand deep into a pile of rotting compost is all in a day’s work for some of the researchers at the University of the Western Cape’s Institute for Microbial Biotechnology and Metagenomics (IMBM).

Donning a white coat and working in a state-of-the art laboratory to isolate a specific enzyme-producing gene found in one of the organisms that live and thrive in the heart of a compost heap comes later.

The need to first dig around in rotting vegetation is because common knowledge tells us that a pile of leaves or grass clippings – or any vegetable matter – left in one place will first get warm, then over time break down to form the nutrient-containing compost that growing plants thrive on.

What some IMBM researchers want to know is which enzymes cause the plant matter to break down and, more specifically, what gene, or sequence of DNA contained in an organism that lives in the heated compost heap, causes the production of that enzyme.

The reason that time, energy and money are spent isolating the enzyme and the gene that produces it is because it can have a direct impact on converting plant matter into biofuel.

Big, multi-national corporations, and governments, are very interested in biofuels at the moment, and will become increasingly interested as the world’s finite reserves of fossil fuels dry up.

Much of the focus on the controversial burgeoning biofuel industry has up to now been on the growing of sugar-rich crops such as sugar cane and maize which can be easily converted into the sugars necessary for the production of ethanol, which can power engines.

But at the same time much of the world, particularly the developing world, is suffering from a lack of – or at the very least a potential lack of – food.

Thus putting aside millions of hectares of arable land to produce crops that will fuel engines rather than filling hungry bellies, is seen to be inhumane, and political suicide for any government with a hungry population.

But if non-edible plant matter produced as an agricultural by-product could be used to produce biofuel there is no question of taking food out of the mouths of those who are hungry, and our global-warming reliance on burning fossil fuels is reduced.

Which leads us back to an IMBM researcher sticking her hand into a pile of compost.

The problem with breaking down waste plant matter into sugars that can then be fermented into bioethanol is that plant matter is insoluble, complex and difficult to process.

Finding the enzymes that speed up this breakdown is the first step to perfecting a process that is economically viable to reproduce on an industrial scale.

To make the enzyme in amounts large enough to be used on an industrial scale, it is almost always necessary to find the gene that creates this enzyme, and to transfer it into a host organism such as Escherichia coli (the work-horse of all molecular biologists).

On a commercial industrial scale, it is necessary for an enzyme supplier to ‘milk’ large quantities of the enzyme from host organisms and to deliver it in barrels to a biofuels factory. This is what IMBM, working in conjunction with leading UK biofuels company TMO Renewables, is aiming at.

The factory would use the enzyme in bioreactors where waste plant matter is broken down into constituent sugars which would then go through a fermentation process before being distilled into ethanol. The ethanol is blended with petrol, and is delivered via the petrol pump into your engine.

Following years of research the IMBM have now identified a “cocktail” of enzymes potentially useful for industrial processes, says Acting Director Marla Tuffin.

Two of these related to the production of biofuel are being prepared for patenting. One, which they’ve provisionally called cellulose, breaks down cellulose and the other, zylanase, breaks down hemicellulose.

Although IMBM’s involvement in the production of biofuels is, in broad terms, very important, it forms only part of the research the Institute’s approximately 40-strong staff and post-graduate students are involved in.

Besides getting acquainted with the micro-organisms (or bugs, as former IMBM Director Prof Don Cowan calls them) that live happily in compost heaps, they also visit some of the most extreme environments on the planet in order to collect samples of the bugs that make themselves at home there.

These include the extremely cold and dry deserts of the Antarctic, the hot Namib Desert, the alkaline salt lakes of Eastern Africa, pH neutral salt pans such as found around Darling up the Cape west coast, and habitats that have been polluted by Acid Mine Drainage and winery or olive processing waste.

Researchers for UWC are also more recently involved in the ambitious PharmaSea project in which researchers from all over the world scour the worlds’ oceans in an effort to find pharmaceutically useful compounds.

The international PharmaSea team are collecting samples by dropping samplers from fishing vessels to trench beds to collect sediment samples. They will then attempt to grow unique microorganisms and isolate novel drug-like molecules that may be useful in the development of medical drugs or cosmetics. PharmaSea researchers will be analysing all sorts of marine bioorganisms, from bacteria to deep-sea sponges to fungi and more, evaluating their potential as novel drug leads.

The UWC researchers, led by Tuffin, with the assistance of Prof Mike Davies-Coleman, (Dean of Science and leading South African expert on the chemical and structural characterisation of natural marine compounds), will be involved in the “Biodiversity Mining” part of the programme. IMBM researchers are looking for novel microorganisms associated with South African marine sponges and sea squirts in an effort to identify new drug-like activities produced by these microorganisms.

Thus researchers at IMBM do, quite literally, travel to the ends of the earth to find organisms adapted to live in the most extreme environments.

Bringing these back home, and finding out what makes them tick – to put it crudely – and what adaptations allow them to survive in these environments, holds a host of fascinating answers to current challenges. – West Cape News