Genetic engineering was forever changed by a cup of tea made in 2006.
Jill Banfield, a University of California at Berkeley ecosystem scientist and 1999 MacArthur Foundation fellow, had become curious in 2006 about mysterious repeating DNA sequences that were common in microbes that live in some of the planet’s most extreme environments, such as deep-sea heat vents, acid mines and geysers. To explain Crispr/Cas9, she needed to speak with a biochemist and possibly someone local.
The best scientist-location tool available to the highly decorated PhD researcher—a web search—recommended a Berkeley RNA specialist named Jennifer Doudna. Both met up for tea at a cafe on campus. Doudna hadn’t heard of Crispr, a kind of microbial immune system, and was intrigued. So much so that over the next few years she would go on to solve the sequence’s structure, which turned out to be something of a miraculous cut-and-paste tool for DNA. Doudna was awarded half of the 2020 Nobel Prize for Chemistry after her discovery. This opened up a whole new world in genomics.
Banfield, Doudna, and many other co-authors published a paper 15 years ago. This is a significant step towards solving the difficult problem of altering the genomes of microbes that live in complex real-world environments like the soil microbiome and gut microbiome. Complexity of the microbial community has been a significant obstacle in developing technologies to improve agricultural production and avoid diseases. It’s a critical step toward curbing methane, a harmful greenhouse gas that is emitted during rice production.
This work forms part of the Innovative Genomics Institute. Doudna established it to find new uses for Crispr, and other genetic engineering methods to address problems in food production, health and general life. The IGI in July received a $3 million gift from an anonymous donor to pursue climate work, and Banfield’s research on microbial ecosystems is fundamental to that push.
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Soil is “the most difficult ecosystem on the planet to study,” Banfield said. “It’s the most complex. It really was the Holy Grail to be able to get any insights into soil microbial communities.”
Much of the IGI’s climate work is focused on the science of rice, a major source of calories for more than half the world. Rice presents significant challenges to the climate, not only because it is difficult for people to eat enough. It is grown in floodplains. This water reduces oxygen in the soil which allows methane-producing microbes thrive. Rice production accounts for about 2% of global greenhouse gas emissions. It produces up to 34 million tonnes of methane per year. Half of that amount is from India and China.
Rice fields act as smoke stacks to trap soil methane. To stop these emissions scientists must understand microbes. The trouble has been that culturing microbial communities and tinkering with them in a lab with traditional tools “could take years or might fail altogether,” IGI authors write. Their new paper demonstrates that using a Crispr-based system can “accelerate this process to weeks.”
The rice methane pump might need to be shut down. This could require a variety of modifications, including those made to plants or the microbiological network in which roots are grown. Engineered solutions could include the introduction of microbes capable of eating methane in oxygen-free environments to the elimination or complete destruction of specific organisms.
“This is all very blue-sky at the present time,” Banfield said. “First, we want to understand the pieces and how they fit together.”
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Pamela Ronald, a University of California at Davis Professor who studied rice throughout her career and wrote a book about the future of food, is now a University of California at Davis researcher. More than a decade ago she and a colleague identified the gene used to develop flood-tolerant rice that’s now grown by more than 6 million farmers in India and Bangladesh.
Over 130,000 types of rice are available. These genomes might contain overlooked genetic skills scientists can use to graft agricultural varieties into heat resistance or nutrition. Ronald’s lab is looking for changes that, combined with Banfield’s microbial communities, could lead to lower-emission crops. The digestive systems of cattle and other livestock ruminants are an even bigger challenge, as they account for over 5% of the global emission.
There are many options for the agricultural sector to reduce emissions, and Banfield, Ronald, Doudna, and other genetic engineers can create new opportunities.
Lower emissions can be achieved by growing more rice on the same area. Each 1% yield increase also reduces methane emission by approximately 1%. Emissions can be cut by half by flooding rice fields less frequently. Farmers who are able to control the water flow in their fields more efficiently have discovered that alternating dry and wet periods can reduce emissions even further. The other potent greenhouse gas, nitrous oxide, can be produced more during dry periods. Another promising technique is to put rice straw into the fields, or seed the fields with biochar. This will encourage soil carbon storage.
Timothy Searchinger, a senior research scholar at Princeton University’s Center for Policy Research on Energy and the Environment, welcomes progress toward a high-ambition, high-reward genetic-engineering breakthrough in concert with proven real-world techniques—the topic of a policy paper he issued in November.
“It’s entirely a practical challenge,” he said. “How do you actually make this stuff happen? How can you make it happen? The practical challenges are real but that doesn’t mean you can’t get around them.”
Crispr is a promise of practical solutions at the molecular scale. Perhaps even over tea.