Breakthroughs in health and agriculture are possible because of a new method of analyzing how bacteria live.
In 2006, a cup of tea changed the face of genetic engineering forever.
In 2006, Jill Banfield, an ecosystem scientist at the University of California at Berkeley and a 1999 MacArthur Foundation fellow, became intrigued by mysterious repeating DNA sequences found in microbes living in some of the planet’s most extreme environments, such as deep-sea heat vents, acid mines, and geysers. She only wanted a biochemist to explain what Crispr/Cas9 sequences were, and ideally someone who was local.
The best scientist-finding technique available to the highly acclaimed PhD researcher — a Google search — suggested Jennifer Doudna, an RNA specialist at Berkeley. The two met for tea at a campus lunch spot.
Crispr, a type of microbial immune system, was new to Doudna, and she was fascinated. So much so that she went on to unravel the sequence’s structure over the next few years, which turned out to be a miracle cut-and-paste tool for DNA. The finding ushered in a new era of genomics, altering science and a variety of industries, and Doudna was awarded half of the Nobel Prize in Chemistry in 2020.
Banfield, Doudna, and a big team of co-authors have released a work that takes a huge step toward solving the hard challenge of how to study and edit genomes of bacteria living in complex real-world habitats like the gut microbiome or soil, 15 years after their first meeting. The complexity of microbial communities has influenced the evolution of tools to prevent disease and improve agriculture.
It’s an important step in reducing methane emissions, a hazardous greenhouse gas produced during rice production.
The research is part of the Innovative Genomics Institute, which Doudna formed to find new ways to employ Crispr and other genetic engineering techniques to solve problems in health, agriculture, and other fields. Banfield’s research on microbial ecosystems is critical to the IGI’s climate work, which received a $3 million contribution from an anonymous donor in July.
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.
The science of rice, a primary source of calories for more than half of the world’s population, is the subject of most of the IGI’s climate work.
Rice poses a big climatic challenge in addition to the basic issue of ensuring that people have enough. In flooded fields, the crop is grown. That water deprives the soil of oxygen, allowing methane-producing microorganisms to thrive: Rice production emits up to 34 million tons of methane per year, accounting for around 2% of total greenhouse gas emissions. China and India account for half of the total.
Rice fields act as smokestacks for soil methane, and scientists must first understand the bacteria in order to reduce emissions. The problem has been that cultivating microbial communities and working with them in a lab using standard technologies “could take years or might fail altogether,” according to the authors of the IGI report. According to their latest article, adopting a Crispr-based approach can “accelerate this process to weeks.”
Shutting down the rice methane spigot might require any of several alterations, either to the plants themselves or the microbial network into which the roots grow. Engineered solutions might range from introducing microbes that can eat methane in oxygen-free conditions to just flat-out eliminating specific organisms from the soil, the way antibiotics kill disease-causing bacteria.
Shutting down the rice methane spigot might require any of several alterations, either to the plants themselves or the microbial network into which the roots grow. Engineered solutions might range from introducing microbes that can eat methane in oxygen-free conditions to just flat-out eliminating specific organisms from the soil, the way antibiotics kill disease-causing bacteria.
This is all very blue-sky at the present time, Banfield said. First, we want to understand the pieces and how they fit together.
Pamela Ronald is a University of California at Davis professor who has studied rice her entire career and written a book on the future of food. 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.
There are more than 130,000 kinds of rice. Lurking in those genomes may be overlooked evolutionary skills that scientists could graft into agricultural varieties, for heat resistance, nutrition or disease prevention. Ronald’s lab is looking for changes that, combined with Banfield’s microbial communities, could lead to lower-emission crops. An even greater challenge awaits in the digestive tracts of cattle and other ruminants, which are responsible for more than 5% of global emissions.
While Banfield, Ronald, Doudna, and others genetically create new possibilities, the agricultural sector has lots of solutions to reduce emissions in the meantime.
Growing more rice in the same acreage leads to lower emissions; every 1% gain in yield also cuts methane emissions by about 1%. Rice fields that are flooded less frequently can reduce emissions by up to half. Farmers that have a good handle on water flow to their fields have discovered that alternating wet and dry periods during the growing season can significantly reduce emissions. (Unfortunately, dry periods can result in higher nitrous-oxide emissions, which is another potent greenhouse gas.) Plowing rice straw back into fields in the off-season and fertilizing fields with biochar, a type of charcoal, to induce more carbon storage in soil are two other viable strategies.
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 using proven real-world techniques, which was the subject of a policy paper he published in November.
It’s entirely a practical challenge, he said. How do you actually make this stuff happen? What are the incentives to make this happen? The practical challenges are real but that doesn’t mean you can’t get around them.
