The glassy-winged sharpshooter is a half-inch-long leafhopper that feeds by sticking its straw-like mouth into the watery tissue of plants. The insect is native to northeastern Mexico, but in the late 1980s, it made its way to Southern California. Since its arrival, it has wreaked havoc on the region’s vineyards.
Most of the damage has been caused not by the insect itself, but what it carries with it. The sharpshooter has an unrivaled ability to acquire and spread a pathogenic bacterium, Xylella fastidiosa, which causes a disorder known as Pierce’s disease in grapevines. Stricken plants wither and their grapes shrivel. Over the years, a variety of methods have been used to halt the sharpshooter’s spread, but it is showing increasing resistance to insecticides and represents a significant and growing threat to California’s $55bn wine industry.
“It’s already done its damage on Southern California and it’s now terrifying our grape growers in Central and Northern California,” says Linda Walling, a Professor of Genetics at the University of California, Riverside. In collaboration with colleagues Peter Atkinson and Rick Redak, the team is in the process of bringing a powerful new weapon to bear in the war against the sharpshooter: Gene-editing. Their aim is to make permanent physical changes in the insect that will make it much harder for it to pick up and transfer the Xylella bacterium.
The team’s work is based on CRISPR gene-cutting technology, which was first brought to the world’s attention in a research paper published in 2012. The researchers behind it had observed the way that bacteria snip off and save pieces of DNA from the viruses that attack them, so that they can rapidly identify and defend against those viruses in the future. These virus snippets are stored in the bacteria’s genome, within segments of DNA that have an unusual pattern: Clustered Regularly Interspaced Short Palindromic Repeats, hence the name, CRISPR. When a bacterium encounters a virus that it recognizes, it eliminates it via a dual process. First, it uses a form of ribonucleic acid (RNA) to guide an enzyme toward the viral DNA; then, the enzyme binds to it and breaks the strands of its DNA, incapacitating it.
The researchers made the leap of realizing that different “guide RNAs” could be used like a molecular GPS system to direct the strand-cutting enzymes (called “Cas” enzymes; the one most often used being “Cas9”) to create cuts anywhere in an organism’s genome. In the process, if a new gene is added then the cell will often use this to repair the DNA, effectively allowing scientists to rewrite its genetic code. Over the past decade, billions of dollars have been poured into research using CRISPR in a range of fields. While most of the focus thus far has been on medical applications, there is increasing interest in other areas such as creating disease- and drought-resistant crops or even producing biofuels.
One growing area of research involves applying gene-editing techniques to animals and insects in an agricultural context, to prevent pests and improve productivity and sustainability. Of course, the extent to which this is permissible depends on local legislations; the EU, for example, has notably stricter rules compared to the US.
At UC Riverside, the team of scientists working with glassy-winged sharpshooters has already successfully executed a proof of principle, using CRISPR to knock out genes that control the insects’ eye color. The guide RNA and Cas9 were microinjected into 3mm-long sharpshooter embryos in eggs without removing them from the leaf on which they were laid.
The next stage of the project is more ambitious. What makes the glassy-eyed sharpshooter so adept at unwittingly transferring Xylella is that the bacteria stick to the inside of its mouthparts. The UC Riverside scientists aim to insert genes in the sharpshooter’s genome that will make it harder for the pathogen to bind. As a result, the bacteria will instead be swallowed and pass through and out of the insect.
As they mingle with the local sharpshooter population, the transgenic insects will pass on this new genetic trait. However, the scientists are also adding a further genetic tweak via CRISPR to ensure that the sharpshooter population will ultimately dwindle to manageable levels or even disappear altogether. They will do this by effectively inactivating the insects’ X chromosomes, meaning only males can be produced by mating. The technique, known as “X-shredding”, has been pioneered in mosquitoes, and Walling anticipates a success rate of up to 70 percent.
The glassy-winged sharpshooters are an invasive pest in California, and if they were to disappear altogether in this region, this would be seen as a benefit. However, were one of the transgenic insects somehow able to reach native populations in Texas and beyond, this could pose an existential threat to the entire species. For this reason, the UC Riverside team intends to make the gene drive specific only to the California population of insects.
“It’s perfectly possible,” says Walling. “We have to compare the sequences in the X chromosome of glassy-winged sharpshooters in other populations with the X chromosome in the California population, and find repeated sequences that only exist in the latter. This sort of thing hasn’t been done with mosquitoes, because people are happy to eradicate them. We’re in a different kind of place, because making sure we don’t eradicate glassy-winged sharpshooters in their native environment is really important.”
The team is confident that a field release of their transgenic sharpshooters could be feasible within three or four years, once a series of stringent tests have taken place under controlled conditions—by which time they believe that regulations will be in place to allow the release.
In the context of wider public discourse around the ethical and safety risks associated with gene-editing animals—especially genetically engineering a specific set of genes to spread among a population—the team is already working closely with both growers and state and federal regulatory bodies.
This is a hot-button issue for society, and is threaded with debates along a number of axes: Concerns around the unintended consequences of changing an animal or an ecosystem; the question of “playing god”; and simply the sense that this could be the thin end of the wedge. As technology increasingly merges with biology, opening up ever more profound ways to engineer or co-opt the natural world, these issues are going to come increasingly into focus.
“We have to respect what society feels is right and what regulatory agencies want,” says Walling. “The regulations may be very strict at first, and to be honest I think that’s appropriate. You don’t want to learn from mistakes, you want to learn from something that’s well-controlled.”
According to the United Nations Food and Agriculture Organization, around 40 percent of global crop production is currently lost to plant pests and diseases. Peter Atkinson, Professor of Entomology at UC Riverside and a lead member of the sharpshooter project, believes that gene-editing could have a huge impact in the future. “It could be quite phenomenal,” he says. “We all know that chemical insecticides come at a cost. But now we could actually control or eliminate insect pests of agriculture with no environmental impact at all.”
An emerging avenue of research is opening new possibilities for CRISPR in agriculture. In 2022, scientists at UC Berkeley showed that it is possible to marry the technology with another new science: Metagenomic sequencing. This is a way to analyze communities of microbes (microbiomes) in their own environment. Microbiomes live in, on, and all around us and help to shape our world in significant ways through their collective behavior. For example, an unbalanced human microbiome can underlie health issues such as Alzheimer’s, cardiovascular disease, asthma, and obesity, and microbes also influence the greenhouse gas concentrations responsible for heating the planet.
Until very recently, microbiomes were difficult to study because they do not lend themselves to traditional, culture-based lab research, as the individual microbes within them often cannot exist in isolation. With metagenomic sequencing, on the other hand, samples of whole jumbles of microbes are collected from the environment in which they live, the mass of DNA in this soup is sequenced, and computer algorithms are then used to reconstruct the individual microbes’ genomes.
The UC Berkeley scientists showed that it is possible to carry out targeted CRISPR gene edits within complex microbiomes. As a result, they are now leading a major project at UC Berkeley’s Innovative Genomics Institute, a coalition of leading research institutions aiming to use genome engineering to solve humanity’s greatest problems. Funded to the tune of $70m, “Engineering the Microbiome with CRISPR to Improve our Climate and Health” aims to create a new toolkit that can address global problems in climate and human health through a CRISPR-metagenomic route.
One of the project’s two main strands concerns animal production of methane, a potent greenhouse gas. As much as 65 percent of total methane emissions are attributed to human activities, and more than a third of these come from livestock. So-called “cow burps” are caused by methane-producing microbes in the animals’ guts. The aim of the project is to engineer those microbes—not the cow itself but the microbes within it—to produce less methane. But first some major detective work needs to take place.
“The microbiome in the cow’s rumen [first stomach compartment] has its own collective behavior,” says Dr. Spencer Diamond, a Principal Investigator working on the project. “The actions of hundreds of different microorganisms come together in a network of nutrient sharing and physical interaction to manifest the macro observable traits, such as methane production. So we need to understand how individual species are interacting together and what is the percentage contribution of each to the ultimate outcome that we’re interested in, which is methane production.”
Having identified these specific species of methane-producing microbes, the next challenge is to establish exactly how to engineer their DNA. “There are currently significant knowledge gaps in terms of many species’ complete genomes,” says Diamond.
Another challenge is understanding the possible long-term effects on a cow if it produces less methane. As Professor Ermias Kebreab, one of the leading scientists on the project, points out, there is already some evidence to go on, based on his own research using feed additives to reduce methane emissions in cattle. He has found that when methane production is suppressed, an increase in the production of hydrogen occurs, which causes the digestive fermentation to shift to a different type of fatty acid. That gives the animal more energy, which is a benefit, but the downside is that too much hydrogen can make the cow feel full, and therefore eat less. Some of the gene-editing envisaged by the team will be aimed at engineering certain microbes to use the extra hydrogen themselves.
The final stage is to develop an oral delivery system. This would contain a guide RNA and Cas9 targeting a very specific location in a specific microbe. But how to get it into the microbes? It might be introduced via a bacteriophage, a kind of virus that is particularly adept at infecting microorganisms. An alternative method would be bacterial conjugation (“essentially bacteria sex,” as Diamond puts it), attaching the gene toolkit to bacteria and exploiting the way in which they come together and naturally share genes. It’s hoped that by delivering a one-off treatment to calves, their methane emissions would be reduced for the rest of their lifetime—and the reduction might even be passed on to subsequent generations.
“If we can get all these different steps to work—understanding the microbiology, developing the genetic tools and ultimately the delivery to a cow—it means we could theoretically do it in any microbiome system on the planet,” says Diamond.
The possible benefits would go well beyond agriculture. Indeed, the other main strand of the “Engineering Microbiomes” project concerns childhood asthma: In 2019, scientists discovered a link between the gut microbiome and risk of the condition, and the project aims to modify the asthma-causing genes in the microbiome without disturbing its beneficial functions. This would point the way for treating a whole host of other microbiome-related conditions. But as Diamond points out, microbiomes also control countless biogeochemical processes on the planet, and are used in industrial processes such as wastewater treatment. “Microbial communities are everywhere,” he says, “and we would have a roadmap to control and manipulate those microbiomes for the benefit of humanity and the environment.”
David Rosewell | Group Director for Science and Technology at QinetiQ
Most public opposition to gene editing tends to focus on the danger of the unintended consequences. While gene editing could be an invaluable tool in protecting crops from pests and climate change, it is difficult to fully understand the complex interactions of creatures in the natural world. The ramifications of releasing modified organisms into an ecosystem—or removing one insect from the food chain—are hard to predict and often cause ethical concerns.
While gene editing is a capability that we choose not to involve ourselves with, it is important that we raise the profile of this debate, as adversaries could deliberately abuse it for aggressive and illegal purposes. It takes little imagination to conjure up scenarios in which insect modifications lead to the deliberate ruin of crops or spread of disease, potentially using region-specific targeting to wreak havoc on a certain area. This kind of incident could lead to mass-scale problems for a country and make them vulnerable to other methods of attack.
These are recognized threats that will require continuous monitoring and consideration in order to provide robust protection.
- Mechanical human augmentation. Whether it’s additional limbs or smart exoskeletons, machinery is helping humans upgrade their natural capabilities.
- Power beaming. Sending power wirelessly over long distances could transform everything from electric vehicles to offshore wind farms.
- Biohybrid robots. Combining artificial and organic parts, biohybrid robots offer advantages such as self-repair and agility.
- Neuromorphic computing. Inspired by the brain, neuromorphic chips aim to equal the speed, efficiency, and intelligence of the human mind.
- Hyperspectral imaging. Hyperspectral cameras don’t merely record what something looks like, they can tell you what that thing is made from and help you see what the human eye cannot.
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