Genetic Engineering vs. Experimental Evolution
Evolugate, a Florida company developing microbes for bioremediation, says that adding microbes to the site of a spill hasn’t worked well before because the microbes haven’t been adapted to the specific environment in which they need to survive. The firm is evolving microbes specifically to survive on oil from the Gulf spill in the Gulf environment by maintaining populations of microbial cells under controlled conditions of growth and environment for an indefinite duration. It says that this is a prerequisite for experimentally evolving natural isolates of wild-type species or recombinant strains.
The company grows the microbes in proprietary continuous cell culture vessels to select microbes that have higher proliferation rates under specific conditions. The innovation behind Evolugate’s continuous culture vessels is that they are engineered to prevent microbes from sticking to the walls, a common strategy by which microbes evade selective pressure in other continuous culture technologies.
The Evolugate technology works via partial dilution: As a culture grows and becomes saturated, a small proportion of the grown culture is replaced with fresh medium, allowing the culture to continually grow at close to its maximum population size. Thomas Lyons, Ph.D., principal research scientist and board member of the firm, told GEN that in adapting the microbes for the Gulf oil spill, “we add more microbes every day to bolster genetic diversity.
“When we first started the culture we saw a die-off, and we expected that the dispersants and oil in the Gulf water-containing medium would kill some microbes. But after one week we saw a huge increase in cell density suggesting that adaptive variants arose. Within two weeks we already have robust growth on oil samples taken from the Gulf.
“The beauty of what we do is that we have built in evolutionary trade-offs: The longer the microbes spend evolving to the oil the less robust they become under other conditions. Once the oil is gone they will lose their competitive advantage and will no longer survive in that environment.”
Dr. Lyons noted that producing such designer microbes through genetic engineering would be hard to pull off. Oil is so full of complicated substances that jamming all the genes needed to digest and metabolize it into a single microbe and then expecting it to reproduce and flourish might be asking too much, he said. Experimental evolution, on the other hand, simultaneously changes metabolic capabilities as well as optimizes growth rates.
He also pointed out that right now the company’s proposal to select and introduce designer oil-eating microbes into the Gulf is in BP’s hands. “It’s in their pipeline, but we are not waiting for a response. We know our approach stands the best chance to make bioremediation work, and we are proceeding accordingly. ”
Genetic engineers did indeed have a shot at enhancing oil-eating microbes. One species of oil eaters in the genus Pseudomonas was used during the Valdez cleanup, but it didn’t work efficiently or very quickly. The oil-eating superbug was developed at General Electric in 1975 by Ananda Mohan Chakrabarty, Ph.D., now distinguished professor of microbiology and immunology at the University of Illinois college of medicine laboratories.
To underscore Dr. Lyons’ point, while there are four oil eaters in this bacterial genus, each uses a different component of the oil as its food source and they all compete with one another when added to the same oil sample. In 1981, Dr. Chakrabarty received a patent on a genetically modified Pseudomonas bacterium that would eat up oil spills, the first patent of its kind; he was the first person to win a patent on a living organism.
Dr. Chakrabarty and his team inserted plasmids from all four species of the oil eaters and put them into a single microbe. While these plasmids would usually not operate together in the same cell, exposing the cell to ultraviolet light caused the plasmids to join into one that could express components of all four pathways of the original plasmids so that several oil components could be broken down.