Can we hack DNA in plants to help fight climate change?

Using CRISPR genome editing on a few common crops, a team of plant and soil scientists seeks to vastly increase and speed up carbon storage to help fight climate change.

By Madeleine Stone
Published 14 Jul 2022, 15:36 BST
03 rice
University of California, Berkeley microbial ecologist Jill Banfield (right), with lab members Jack Kim and Bethany Kolody, study soil microbes in rice fields at the Rice Experiment Station in Biggs, California. They're working to identify the microbes responsible for methane emissions, as well as those that can store carbon in the soil.
Photograph by Andy Murdock, Innovative Genomics Institute

To prevent dangerous levels of global warming, scientists say it won’t be enough to just stop burning fossil fuels that release carbon into the air. Because it’s virtually impossible for humanity to do that as fast as is now required, we will also need to pull carbon out of the air and secure it.

Plants are among the best tools we have to do this, since these living solar collectors already capture billions of tons of carbon dioxide each year from the atmosphere through photosynthesis. About half of that carbon winds up in roots and eventually the soil, where it can stay for hundreds to thousands of years.

But what if we could create plants and soils that are even better at capturing carbon? With CRISPR genome editing—a revolutionary new molecular biology toolkit that allows scientists to make rapid and precise edits to the DNA code that underpins all life—that might be possible.

Last month, the Innovative Genomics Institute (IGI), a San Francisco Bay area research consortium founded by CRISPR pioneer Jennifer Doudna, began to explore the idea in earnest. With an $11-million (£9.3 million) gift from the Chan Zuckerberg Institute, a team of plant geneticists, soil scientists, and microbial ecologists embarked on a three-year effort using CRISPR to create new crop varieties that photosynthesise more efficiently and funnel more carbon into the soil. Eventually, the researchers hope to create gene-edited rice and sorghum seeds that could—if planted around the globe—pull more than a billion extra tons of carbon out of the air annually.

Seedlings of gene-edited plants grow at the Innovative Genomics Institute, where protocols have been developed to genetically edit over 30 global food crops.
Photograph by Benton Cheung, Innovative Genomics Institute

It’s a tremendously ambitious goal, and the team is likely to face numerous challenges in the lab before its CO2-scrubbing plants can be put in the ground. Additional social, policy, and ethical considerations will determine whether those crops are widely adopted by farmers. But the researchers believe their ambitious project meets the urgency of the climate crisis.

“Climate change is a serious, serious problem,” says Brad Ringeisen, the executive director of the IGI and lead principal investigator on the project. “It’s threatening the entire world. CRISPR can be used to make positive effects on climate, and so we’re going for it.”

Optimising plants

Plants’ ability to sequester carbon naturally begins inside tiny cellular compartments called chloroplasts. There, energy from sunlight is used to strip electrons from water molecules and add them to carbon dioxide, transforming it into glucose, a simple sugar. The plant then uses the organic carbon to grow new leaves, shoots, and roots.

It took hundreds of millions of years for the biochemical machinery behind photosynthesis to evolve. But in recent decades, plant biologists have discovered that the process is surprisingly inefficient. For instance, when it’s very sunny outside, plants will often turn off key proteins involved in collecting photons of light. This helps ensure that they don’t overcommit resources to harvesting sunlight when other factors, like water and nutrients, might limit their growth.

But it’s not necessary for plants to do that, says David Savage, a plant biologist at the University of California, Berkeley and member of the IGI research team. Plants “You can keep photosynthesis at max” and turn that sunlight into stored carbon if humans ensure they are well irrigated and fertilised.

For years, researchers have attempted to improve photosynthesis by using traditional genetic engineering—introducing chunks of DNA from bacteria, or other plants, with desirable traits, into the genes encoding light-harvesting proteins and other biochemical machinery. Editing genomes using Clustered Regularly Interspaced Short Palindromic Repeats, or CRISPR, is different. A system that evolved naturally in bacteria in order to fight viruses, CRISPR is like a pair of molecular scissors that scientists can use to make cut-and-paste edits throughout an organism’s genome without introducing any foreign DNA at all.

Faster and more precise than earlier genetic engineering approaches, CRISPR genome editing opens a door to rapid breakthroughs. “We can start to optimise the pathways [of photosynthesis] in a way that has been completely impossible,” Savage says.

Working first with individual cells, Savage and his colleagues will use CRISPR to make millions of tiny genetic edits to rice, a crop that’s relatively easy to genetically manipulate today, in part because it’s been so well studied for genetic engineering in the past. The researchers will then screen the cells for mutations that could make key steps in photosynthesis more efficient. Eventually, they will take the most promising cell lines and grow actual rice plants to see how their edits hold up.

Based on previously published estimates, Savage believes that stacking multiple beneficial genetic edits together could increase the efficiency of photosynthesis—and hence, the amount of carbon rice plants capture in their tissue—by 30 percent or more.

Deeper in the ground

To boost carbon sequestration in croplands, though, some of that extra carbon needs to get below ground. In parallel research led by crop geneticist Pamela Ronald at the University of California, Davis, researchers will screen a library of 3,200 mutant strains of rice housed at the IGI for varieties with beneficial root traits. These include long-rooted rice strains that can funnel carbon into deeper layers of the soil, as well as strains whose roots release more sugar-heavy molecules, called exudates, that fuel the growth of soil microbial communities.

Once Ronald and her colleagues have identified rice strains with interesting root traits, they hope to use CRISPR genome editing to further optimise those traits.

Wolfgang Busch, a plant biologist at the Salk Institute who leads the Harnessing Plants Initiative, a separate effort to engineer crops with enhanced soil carbon sequestration potential, says that many beneficial root traits already exist in nature. His team, for instance, has identified natural varieties of sorghum that produce more and longer roots. It’s “unquestionable,” Busch says, that these traits can be further manipulated using CRISPR.

But Busch warns that editing those traits in a way that produces unequivocal benefits will be challenging. Genetic manipulations that lead to promising results in a petri dish or greenhouse might not trigger the same outcomes in the field, where environmental conditions are more variable. Edits that offer specific advantages, like deeper rooting, might also have unintended side effects, like altering the timing of seed development. These are all issues that scientists expect to deal with during the research process. Busch says it’s important to account for that when estimating how long it will take to bring new seeds to market.  

“We basically anticipate that most of the stuff we discover in the greenhouse and the lab will fail” to produce the desired effects in the field, Busch says. “The solution is to identify lots of it so some make it through.”

The final frontier

If engineering plants to funnel more carbon underground will be a challenge, ensuring that that carbon remains in the soil long term plunges the project into unknown scientific territory. “That is the hardest part,” Ringeisen says.

A complex community of microorganisms and fungi decomposes the carbon that plants put into soil, transforming it into a huge variety of different compounds. Some of that carbon is fast-burning fuel for microbes, which gobble it up and release carbon dioxide back to the atmosphere. But another portion of the carbon isn’t so easy for microbes to break down, because of its chemistry, its location inside large particles called aggregates, or its tendency to stick to mineral surfaces. These molecules form a stable soil carbon pool that can last decades or longer.

Scientists are still trying to understand how the physical, chemical, and biological diversity of soils shape that stable carbon pool. The soil experts on the IGI research team hope to add to this knowledge base—and ultimately, use what they learn to enhance carbon sequestration.

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On the biology side, UC Berkeley microbial ecologist Jill Banfield and her colleagues will use genomic sequencing tools to investigate the specific microbes and carbon cycling traits in the soil surrounding CRISPR-edited crops. Banfield says she’s particularly interested in looking for microbial species that, like plants, use carbon dioxide directly to create their own food, and ones that produce extracellular polysaccharides—sticky, sugary substances that act like glue, enhancing the formation of carbon-trapping soil aggregates. 

The primary goal of the microbial work, Banfield says, is to develop “foundational knowledge about what's going on in soil” and how editing plants with CRISPR changes that. But in the future, it may also be possible to engineer soil microbes directly. Research that Banfield, Doudna and others published earlier this year demonstrates a CRISPR-based approach to making DNA edits within a diverse microbial community. That’s an enormous leap forward from how microbial gene editing works today: Researchers must first isolate individual species and grow them in the lab, a time-consuming and failure-prone process.

Still, it’s too early to say whether this novel community editing approach can be used to somehow enhance soils. “The soil is the final frontier of that,” Ringesein says. “But it’s something we see as a possibility.”

Counting on atoms

As the microbial research is ongoing, Lawrence Livermore National Laboratory soil scientist Jennifer Pett-Ridge and her colleagues have an all-important task: Counting carbon atoms to make sure the entire concept, from plant cells to soils, actually works.

By placing gene-edited crops in special growth chambers and flooding them with CO2 containing a rare, heavy isotope known as carbon-13, the researchers will be able to see exactly how much carbon their plants are taking up, and where it’s winding up.

“In each of those pools, whether it’s leaves or roots or exudates or microbial cells or even microbial DNA, we can see that carbon-13,” Pett-Ridge says. “And we can quantify how much has been added and how much ends up in each pool.” Pett-Ridge’s team will also be measuring an even rarer radioactive isotope known as carbon-14, which can be used to estimate both the age of soil carbon and how quickly it’s being cycled.

Pett-Ridge’s carbon accounting techniques are “really critical tools that have to be deployed to show attribution,” says Jane Zelikova, the director of the Soil Carbon Solutions Center at Colorado State University. Zelikova isn’t involved with the IGI research effort.

“Lots of people are making claims around increasing soil carbon, but there is a lack of evidence around attribution,” Zelikova says. “Can you actually show that the solution you’ve developed is making measurable impacts on soil carbon stocks, and especially on the molecules that tend to stick around for a long time? Doing that in a rigorous way is key.”

From labs to fields

If the researchers succeed in creating a gene-edited rice variety that enhances soil carbon sequestration, then eventually (and with further funding) they hope to make those same edits in sorghum, a staple food crop across Africa and South Asia. While rice is a useful crop for honing gene editing techniques, deeper-rooted relatives like sorghum can add more carbon into regions of the soil that have the capacity to absorb it.

Ultimately, the researchers intend to launch international field trials that place both CRISPR-edited rice and sorghum seeds in the hands of farmers within 10 years—an ambitious timetable that Zelikova says “matches the urgency of the problem and scale at which we need to find solutions.” IGI Public Impact Director Melinda Kleigman says that ideally, the team will be able to offer farmers seeds that not only enhance carbon sequestration but also provide added benefits, such as increased yields or enhanced soil fertility. “I don't think we're going to have a successful program if all it does is sequester carbon,” Kleigman says. “There needs to be some added benefit to the farmer.”

Even if the team is able to produce seeds that provide multiple benefits, getting farmers to adopt them might not be easy. “Farmers tend to be, as a community, a little bit resistant to new things and change,” Zelikova says. “They want to see things really well-tested and de-risked before they implement them on their own acres.”

Some farmers, and some of their customers, might be wary of a crop that was altered using CRISPR genome editing, still a very new technology. While CRISPR-edited crops aren’t necessarily regulated as “GMOs”—a label typically restricted to organisms containing foreign DNA—a similar perception that they are less desirable than conventional crops might hold back public acceptance. As CRISPR genome editing becomes more widespread, it’s essential that organisations promoting it are transparent about how organisms were altered, Kleigman says. “If people don’t want this in their communities, we should give them an option to opt out.”

But Kleigman suspects that many communities will want crops engineered to fight climate change and thrive in a hotter world. “It is my opinion,” she says, “that we are going to get to the point where there won't be a lot of other options available.”


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