In 2012, a group of scientists at University of California Berkeley discovered a tool that has since changed the game of genome engineering.
That tool, called CRISPR – an acronym that stands for clustered regularly interspaced short palindromic repeats – allows us to make targeted, precise changes to DNA in just about any organism and ecosystem on earth. CRIPSR has not only changed how we play the game, it has changed the rules, and carries almost limitless potential for genetic engineering the world around us. Most of the news you hear today probably talks about CRISPR’s ability to treat and prevent human diseases, a realm where it has so far been very successful. But this tool is also revolutionizing how we interact with our environment, and could be instrumental in shaping it in the coming generations.
In its simplest form, CRISPR Cas9 is a little piece of biological machinery that we found inside bacteria, which use it to protect themselves from viruses. When a virus injects its DNA into a cell, CRISPR copies a piece of it and stores it in the cell, kind of like a memory card. Later, if the cell is infected once again by that virus, the CRISPR-saved piece of DNA held by the bacteria matches with the virus DNA, and the enzyme ‘Cas9,’ a type of molecular scissors, cuts the viral DNA, degrading it and keeping the virus from doing any harm.
The research group at Berkeley, led by Jennifer Doudna, discovered that they could use this delivery system to make cuts at specific sites in our DNA, and paste new pieces in. Cool, right? And it gets even cooler: it turns out, we can paste in just about whatever genetic information we want, and therefore have a huge effect on the organism of interest.
A demonstration of the CRISPR-Cas9 genetic editing system currently used in manipulating genomes of a wide variety of organisms. Video by National Geographic.
Using this natural system of cut-and-paste, we can edit many genes in an organism simultaneously and with much greater success than our previous methods, which were inefficient and expensive. Even more impressive, the changes made using CRISPR can be made in germ-line cells, which makes the change permanent and heritable. CRISPR technology is cheaper, easier to use, and more precise than all other genetic editing tools we have today, which makes it a great tool in environmental engineering.
Here are a few of the ways CRISPR is being used in the environmental sphere:
Biofuels
Fossil fuels (like petroleum and natural gas) are running out; fortunately, they are not the only type of energy at our disposal. We have developed extremely efficient fuel sources from things like algae (see this article), corn and sugarcane, but the cheap cost of fossil fuels still makes these new plant-derived fuels less common as energy sources. However, these biofuels represent our next great energy reserve, alongside solar and wind, and CRISPR is likely to be instrumental in making this shift happen.
Many petroleum corporations, realizing that fossil fuels are increasingly becoming limiting resources, have begun investing in biofuel technologies that use CRISPR. Photo credit: Maarten van der Heuvel
Research is currently underway in biofuel-synthesizing organisms like algae and corn to enhance the genes that control the production of these compounds. When optimized, this will allow us to extract more biofuels from these plants at a cheaper cost (most organisms have genes that limit the amount of a substance that they can produce, so by using CRISPR to switch these genes off (or remove them), we are able to make the algae produce more of that substance).
Furthermore, many bacteria are also able to break down decaying plant matter and even human waste into biofuel compounds that we can use in place of fossil fuels. These bacteria are being engineered as a sort of factory to mass produce biofuels. It will take a few more years to get the processed established, but there is little doubt that CRISPR-mediated manipulation of biofuel organisms can help us decrease our reliance on fossil fuels.
Climate adaptation
To take it a step further, CRISPR has the potential to help ameliorate some of our more harmful effects on the environment, like those that are driving climate change. We are trying to use CRISPR to do this by making the natural mechanisms the environment uses to restore itself more efficient. Scientists at the Aarhus University in Denmark are targeting natural sources of methane (an extremely potent greenhouse gas), like cows and the grass they eat, and using CRISPR to edit their methane-producing pathways to release less of it to the environment. Furthermore, we can tweak the organisms that eat methane (see this article) to do so more efficiently, contributing to atmospheric scrubbing.
The symbiosis between coral and their algal symbionts is critical to the survival of coral reefs. Encouraging the health of this partnership could be the key to saving reefs. Photo credit: Marek Okon
CRISPR is also being used to help the key organisms in an ecosystem adapt to climate change. Rachel Levin, a molecular biologist at the Centre for Marine Bio-Innovation in Sydney, Australia is currently trying to engineer Symbiodinium, the microscopic algae that live within coral tissues, to be more tolerant to warming oceans. If this is successful, it could lead to coral reefs that don’t bleach so often, or so severely, and could allow global reefs to begin to recover.
Invasive species
Human transportation across the globe has allowed for the movement of organisms from one environment to another that may not have any natural means of dealing with newcomers. In New Zealand, invasive species like rats and possums have wreaked havoc on natural ecosystems by outcompeting the natural fauna, leading to huge die-offs. CRISPR opens up an interesting and powerful toolbox for dealing with invasive species, primarily through gene drives.
Gene drives can ensure that an edited gene of interest incorporates itself into a population and has the desired effect on the environment. Credit: Tina Hesman Saey
A gene drive is any gene that we add to an organism that will be passed down through generations and codes for a trait that makes that organism (and all of its offspring) less fit: essentially, we are giving it an evolutionary disadvantage. Over a relatively short period of time, that population will decrease due to a losing battle with natural selection.
I know what you’re thinking: what if that gene drive is passed back to the original ecosystem, eliminating that population as well? Very good point: this is why gene drives are extremely controversial. These techniques have the potential to cause environmental cascade effects that we have no way of predicting, and should be used with extreme caution; maybe not at all.
Scientists in New Zealand are currently looking into gene drives as a means of handling their invasive rat and possum crisis, even claiming to eliminate all harmful invasive species by 2050 . This may sound reckless (have no fear, they will not do so without years more research and in-lab testing), but it’s important to recognize that some invasive species, such as the lionfish invasion of the Caribbean, are able to absolutely dismantle ecosystems almost singlehandedly. With no natural predators, animals like the lionfish eat, reproduce and grow unchecked, which is not a natural phenomenon. Some scientists see gene drives using CRISPR as a means of giving back the advantage to an environment that has lost the upper hand.
Lionfish, brought to the Caribbean by shipping vessels from the Indo-Pacific, have caused mass extinctions of plant and animal species in the Caribbean region due to being voracious predators, fundamentally altering the ecosystem. Photo credit: Mathijs Vos
Agriculture
CRISPR is already changing how we grow our food. One of the downsides to a changing global climate is that many ecosystems are becoming more difficult to farm, and minor edits in the DNA of crops could allow them to fare better in changing environments. CRISPR has already been used to create fungus-resistant rice, virus-resistant cucumbers, and mushrooms that don’t brown or bruise; these are small changes, but they may go a long way in helping us produce enough food to support a growing population.
Low-gluten wheat engineered using CRISPR could preserve the taste and texture of wheat products while making them available to gluten-sensitive people. Photo credit: Johnny McClung
Research projects around the world are using CRISPR to try and engineer many of the crops we eat to have a desired effect. By boosting the immune systems of grapes and cacao, scientists are winning in the battle to keep the dreams of wine and chocolate alive. Coffee beans that are naturally decaffeinated have been developed, as the decaffeination process is an expensive one that often affects the coffee flavor. Wheat has even been engineered to carry much lower gluten levels, which will allow those with Celiac’s disease and gluten intolerance to still consume wheat products.
Most of these plants have yet to reach the market and will need to pass through much more rigorous testing before they do. But they are a tribute to the power of CRISPR, and paint a healthier picture for our future.
World hunger
As the population grows, so does our need for food. Currently, we face a massive food waste crisis: we may produce enough food for everyone in the world to live comfortably, but the reality is that much of it goes to waste before it reaches our tables, and those living in poverty often go hungry. Scientists are currently trying to edit plants to more efficiently use water for survival in a drier climate, and even to perform nitrogen fixation on their own (a process usually accomplished only by bacteria), reducing our need for fertilizers. Both of these things could allow us to grow plants in more variable environments, and more easily disperse food to communities that need it.
Even further, we can genetically engineer foods to preserve their shelf life, to be resistant to insects and disease that often make them go bad before reaching the consumer, and to make them more nutrient rich. The reality facing us is a dark one without considering genetic engineering as a tool: with arable land getting more difficult to farm and the population (especially in developing nations) skyrocketing, we will soon be in desperate need for more nutritious, more abundant, and more durable food. CRISPR can help us get there.
Bioplastics
Plastic is without a doubt our most permanent impact on the world around us. The transition to bioplastics might not remove already existing plastics, but it would slow the rate of pollution, which is a start. Photo credit: John Cameron
For right now, most of our plastic is synthesized from petroleum, at great cost to the environment. However, it is well known that bacteria create all kind of compounds that could be useful to us, one of which is a polymer similar to plastic. Researchers are currently trying to identify and enhance the genes inside these bacteria that synthesize bioplastics and their precursors, which will undoubtedly help end our reliance on petroleum.
Furthermore, CRISPR allows us to engineer all kinds of organisms in nature that synthesize compounds of interest, making pharmaceutical compounds like antibiotics, or vitamins like B12, more abundant. By turning simple bacteria into a factory for these compounds (which, in real factories, often use very unsustainable production methods), there is almost limitless potential for an environmentally-conscious and prosperous future.
Bioremediation
Part of our responsibility in the coming years will be to attempt to remedy some of the damage we have done to the environment, mainly through the pollution of our atmosphere and our ecosystems. We already know that some bacteria are capable of degrading plastics, eating greenhouse gases, binding heavy metals, cleaning up oil spills, and more. CRISPR is being used in these organisms to augment the genes responsible for these processes and make them more efficient, giving us potential solutions to the pollution crisis. Imagine having a rapid, bacteria-based solution to a massive oil spill, or being able to efficiently scrub metal pollution from our oceans. All of these things are possible. We may not be able to take back our actions, but we can sure do something about them.
All these things said, CRISPR is a powerful tool, and it is critical that we both treat it with respect, and fully understand the effects of our actions before utilizing it. As discussed before, this becomes even more important in an environmental setting, where a lack of foresight could lead to cascade effects that impact entire ecosystems. In the human realm, regulation of CRISPR technology will be just as important, and controversy abounds surrounding the ethical ramifications of using this tool to edit human beings themselves. On that front, much has yet to be seen. But the reality is that we have already made massive changes to the world around us, and most of them have not been for the better. Maybe, with the right oversight and the right vigilance, CRISPR could be an opportunity to fix some of our mistakes.
- Jason
