How Genetic Engineering Could Save the Coral Reefs
Coral reefs are usually relegated to bit player status in television and movies, providing splashes of background color for "Shark Week," "Finding Nemo," and other marine-based entertainment.
In real life, the reefs are an absolutely crucial component of the ecosystem for both oceans and land, rivaling only the rain forests in their biological complexity. They provide shelter and sustenance for up to a quarter of all marine life, oxygenate the water, help protect coastlines from erosion, and support thousands of tourism jobs and businesses.
Genetic engineering could help scientists rebuild the reefs that have been lost, and turn those still alive into a souped-up version that can withstand warmer and even more acidic waters.
But the warming of the world's oceans -- exacerbated by an El Nino event that occurred between 2014 and 2016 -- has been putting the world's reefs under tremendous pressure. Their vibrant colors are being replaced by sepulchral whites and tans.
That's the result of bleaching -- a phenomenon that occurs when the warming waters impact the efficiency of the algae that live within the corals in a symbiotic relationship, providing nourishment via photosynthesis and eliminating waste products. The corals will often "shuffle" their resident algae, reacting in much the same way a landlord does with a non-performing tenant -- evicting them in the hopes of finding a better resident. But when better-performing algae does not appear, the corals become malnourished, eventually becoming deprived of their color and then their lives.
The situation is dire: Two-thirds of Australia's Great Barrier Reef have undergone a bleaching event in recent years, and it's believed up to half of that reef has died.
Moreover, hard corals are the ocean's redwood trees. They take centuries to grow, meaning it could take centuries or more to replace them.
Recent developments in genetic engineering -- and an accidental discovery by researchers at a Florida aquarium -- provide opportunities for scientists to potentially rebuild a large proportion of the reefs that have been lost, and perhaps turn those still alive into a souped-up version that can withstand warmer and even more acidic waters. But many questions have yet to be answered about both the biological impact on the world's oceans, and the ethics of reengineering the linchpin of its ecosystem.
How did we get here?
Coral bleaching was a regular event in the oceans even before they began to warm. As a result, natural selection weeds out the weaker species, says Rachel Levin, an American-born scientist who has performed much of her graduate work in Australia. But the current water warming trend is happening at a much higher rate than it ever has in nature, and neither the coral nor the algae can keep up.
"There is a big concern about giving one variant a huge fitness advantage, have it take over and impact the natural variation that is critical in changing environments."
In a widely-read paper published last year in the journal Frontiers in Microbiology, Levin and her colleagues put forth a fairly radical notion for preserving the coral reefs: Genetically modify their resident algae.
Levin says the focus on algae is a pragmatic decision. Unlike coral, they reproduce extremely rapidly. In theory, a modified version could quickly inhabit and stabilize a reef. About 70 percent of algae -- all part of the genus symbiodinium -- are host generalists. That means they will insert themselves into any species of coral.
In recent years, work on mapping the genomes of both algae and coral has been progressing rapidly. Scientists at Stanford University have recently been manipulating coral genomes using larvae manipulated with the CRISPR/Cas9 technology, although the experimentation has mostly been limited to its fluorescence.
Genetically modifying the coral reefs could seem like a straightforward proposition, but complications are on the horizon. Levin notes that as many as 20 different species of algae can reside within a single coral, so selecting the best ones to tweak may pose a challenge.
"The entire genus is made up of thousands of subspecies, all very genetically distinct variants. There is a huge genetic diversity, and there is a big concern about giving one variant a huge fitness advantage, have it take over and impact the natural variation that is critical in changing environments," Levin says.
Genetic modifications to an algae's thermal tolerance also poses the risk of what Levin calls an "off-target effect." That means a change to one part of the genome could lead to changes in other genes, such as those regulating growth, reproduction, or other elements crucial to its relationship with coral.
Phillip Cleves, a postdoctoral researcher at Stanford who has participated in the CRISPR/Cas9 work, says that future research will focus on studying the genes in coral that regulate the relationship with the algae. But he is so concerned about the ethical issues of genetically manipulating coral to adapt to a changing climate that he declined to discuss it in detail. And most coral species have not yet had their genomes fully mapped, he notes, suggesting that such work could still take years.
An Alternative: Coral Micro-fragmentation
In the meantime, there is another technique for coral preservation led by David Vaughan, senior scientist and program manager at the Mote Marine Laboratory and Aquarium in Sarasota, Florida.
Vaughan's research team has been experimenting in the past decade with hard coral regeneration. Their work had been slow and painstaking, since growing larvae into a coral the size of a quarter takes three years.
The micro-fragmenting process in some ways raises fewer ethical questions than genetically altering the species.
But then, one day in 2006, Vaughan accidentally broke off a tiny piece of coral in the research aquarium. That fragment grew to the size of a quarter in three months, apparently the result of the coral's ability to rapidly regenerate when injured. Further research found that breaking coral in this manner -- even to the size of a single polyp -- led to rapid growth in more than two-dozen species.
Mote is using this process, known as micro-fragmentation, to grow large numbers of coral rapidly, often fusing them on top of larger pieces of dead coral. These coral heads are then planted in the Florida Keys, which has experienced bleaching events over 12 of the last 14 years. The process has sped up almost exponentially; Mote has planted some 36,000 pieces of coral to date, but Vaughan says it's on track to plant 35,000 more pieces this year alone. That sum represents between 20 to 30 acres of restored reef. Mote is on track to plant another 100,000 pieces next year.
This rapid reproduction technique in some ways allows Mote scientists to control for the swift changes in ocean temperature, acidification and other factors. For example, using surviving pieces of coral from areas that have undergone bleaching events means these hardier strains will propagate much faster than nature allows.
Vaughan recently visited the Yucatan Peninsula to work with Mexican researchers who are going to embark on a micro-fragmenting initiative of their own.
The micro-fragmenting process in some ways raises fewer ethical questions than genetically altering the species, although Levin notes that this could also lead to fewer varieties of corals on the ocean floor -- a potential flattening of the colorful backdrops seen in television and movies.
But Vaughan has few qualms, saying this is an ecological imperative. He suggests that micro-fragmentation could serve as a stopgap until genomic technologies further advance.
"We have to use the technology at hand," he says. "This is a lot like responding when a forest burns down. We don't ask questions. We plant trees."
Two-and-a-half year-old Huckleberry, a blue merle Australian shepherd, pulls hard at her leash; her yelps can be heard by skiers and boarders high above on the chairlift that carries them over the ski patrol hut to the top of the mountain. Huckleberry is an avalanche rescue dog — or avy dog, for short. She lives and works with her owner and handler, a ski patroller at Breckenridge Ski Resort in Colorado. As she watches the trainer play a game of hide-and-seek with six-month-old Lume, a golden retriever and avy dog-in-training, Huckleberry continues to strain on her leash; she loves the game. Hide-and-seek is one of the key training methods for teaching avy dogs the rescue skills they need to find someone caught in an avalanche — skier, snowmobiler, hiker, climber.
Lume’s owner waves a T-shirt in front of the puppy. While another patroller holds him back, Lume’s owner runs away and hides. About a minute later — after a lot of barking — Lume is released and commanded to “search.” He springs free, running around the hut to find his owner who reacts with a great amount of excitement and fanfare. Lume’s scent training will continue for the rest of the ski season (Breckenridge plans operating through May or as long as weather permits) and through the off-season. “We make this game progressively harder by not allowing the dog watch the victim run away,” explains Dave Leffler, Breckenridge's ski patroller and head of the avy dog program, who has owned, trained and raised many of them. Eventually, the trainers “dig an open hole in the snow to duck out of sight and gradually turn the hole into a cave where the dog has to dig to get the victim,” explains Leffler.
By the time he is three, Lume, like Huckleberry, will be a fully trained avy pup and will join seven other avy dogs on Breckenridge ski patrol team. Some of the team members, both human and canine, are also certified to work with Colorado Rapid Avalanche Deployment, a coordinated response team that works with the Summit County Sheriff’s office for avalanche emergencies outside of the ski slopes’ boundaries.
There have been 19 avalanche deaths in the U.S. this season, according to avalanche.org, which tracks slides; eight in Colorado. During the entirety of last season there were 17. Avalanche season runs from November through June, but avalanches can occur year-round.
High tech and high stakes
Complementing avy dogs’ ability to smell people buried in a slide, avalanche detection, rescue and recovery is becoming increasingly high tech. There are transceivers, signal locators, ground scanners and drones, which are considered “games changers” by many in avalanche rescue and recovery
For a person buried in an avalanche, the chance of survival plummets after 20 minutes, so every moment counts.
A drone can provide thermal imaging of objects caught in a slide; what looks like a rock from far away might be a human with a heat signature. Transceivers, also known as beacons, send a signal from an avalanche victim to a companion. Signal locators, like RECCO reflectors which are often sewn directly into gear, can echo back a radar signal sent by a detector; most ski resorts have RECCO detector units.
Research suggests that Ground Penetrating Radar (GPR), an electromagnetic tool used by geophysicists to pull images from inside the ground, could be used to locate an avalanche victim. A new study from the Department of Energy’s Sandia National Laboratories suggests that a computer program developed to pinpoint the source of a chemical or biological terrorist attack could also be used to find someone submerged in an avalanche. The search algorithm allows for small robots (described as cockroach-sized) to “swarm” a search area. Researchers say that this distributed optimization algorithm can help find avalanche victims four times faster than current search mechanisms. For a person buried in an avalanche, the chance of survival plummets after 20 minutes, so every moment counts.
An avy dog in training is picking up scent
Sarah McLear
While rescue gear has been evolving, predicting when a slab will fall remains an emerging science — kind of where weather forecasting science was in the 1980s. Avalanche forecasting still relies on documenting avalanches by going out and looking,” says Ethan Greene, director of the Colorado Avalanche Information Center (CAIC). “So if there's a big snowstorm, and as you might remember, most avalanches happened during snowstorms, we could have 10,000 avalanches that release and we document 50,” says Greene. “Avalanche forecasting is essentially pattern recognition,” he adds--and understanding the layering structure of snow.
However, determining where the hazards lie can be tricky. While a dense layer of snow over a softer, weaker layer may be a recipe for an avalanche, there’s so much variability in snowpack that no one formula can predict the trigger. Further, observing and measuring snow at a single point may not be representative of all nearby slopes. Finally, there’s not enough historical data to help avalanche scientists create better prediction models.
That, however, may be changing.
Last year, an international group of researchers created computer simulations of snow cover using 16 years of meteorological data to forecast avalanche hazards, publishing their research in Cold Regions Science and Technology. They believe their models, which categorize different kinds of avalanches, can support forecasting and determine whether the avalanche is natural (caused by temperature changes, wind, additional snowfall) or artificial (triggered by a human or animal).
With smell receptors ranging from 800 million for an average dog, to 4 billion for scent hounds, canines remain key to finding people caught in slides.
With data from two sites in British Columbia and one in Switzerland, researchers built computer simulations of five different avalanche types. “In terms of real time avalanche forecasting, this has potential to fill in a lot of data gaps, where we don't have field observations of what the snow looks like,” says Simon Horton, a postdoctoral fellow with the Simon Fraser University Centre for Natural Hazards Research and a forecaster with Avalanche Canada, who participated in the study. While complex models that simulate snowpack layers have been around for a few decades, they weren’t easy to apply until recently. “It's been difficult to find out how to apply that to actual decision-making and improving safety,” says Horton. If you can derive avalanche problem types from simulated snowpack properties, he says, you’ll learn “a lot about how you want to manage that risk.”
The five categories include “new snow,” which is unstable and slides down the slope, “wet snow,” when rain or heat makes it liquidly, as well as “wind-drifted snow,” “persistent weak layers” and “old snow.” “That's when there's some type of deeply buried weak layer in the snow that releases without any real change in the weather,” Horton explains. “These ones tend to cause the most accidents.” One step by a person on that structurally weak layer of snow will cause a slide. Horton is hopeful that computer simulations of avalanche types can be used by scientists in different snow climates to help predict hazard levels.
Greene is doubtful. “If you have six slopes that are lined up next to each other, and you're going to try to predict which one avalanches and the exact dimensions and what time, that's going to be really hard to do. And I think it's going to be a long time before we're able to do that,” says Greene.
What both researchers do agree on, though, is that what avalanche prediction really needs is better imagery through satellite detection. “Just being able to count the number of avalanches that are out there will have a huge impact on what we do,” Greene says. “[Satellites] will change what we do, dramatically.” In a 2022 paper, scientists at the University of Aberdeen in England used satellites to study two deadly Himalayan avalanches. The imaging helped them determine that sediment from a 2016 ice avalanche plus subsequent snow avalanches contributed to the 2021 avalanche that caused a flash flood, killing over 200 people. The researchers say that understanding the avalanches characteristics through satellite imagery can inform them how one such event increases the magnitude of another in the same area.
Avy dogs trainers hide in dug-out holes in the snow, teaching the dogs to find buried victims
Sarah McLear
Lifesaving combo: human tech and Mother Nature’s gear
Even as avalanche forecasting evolves, dogs with their built-in rescue mechanisms will remain invaluable. With smell receptors ranging from 800 million for an average dog, to 4 billion for scent hounds, canines remain key to finding people caught in slides. (Humans in comparison, have a meager 12 million.) A new study published in the Journal of Neuroscience revealed that in dogs smell and vision are connected in the brain, which has not been found in other animals. “They can detect the smell of their owner's fingerprints on a glass slide six weeks after they touched it,” says Nicholas Dodman, professor emeritus at Cummings School of Veterinary Medicine at Tufts University. “And they can track from a boat where a box filled with meat was buried in the water, 100 feet below,” says Dodman, who is also co-founder and president of the Center for Canine Behavior Studies.
Another recent study from Queens College in Belfast, United Kingdom, further confirms that dogs can smell when humans are stressed. They can also detect the smell of a person’s breath and the smell of the skin cells of a deceased person.
The emerging avalanche-predicting human-made tech and the incredible nature-made tech of dogs’ olfactory talents is the lifesaving “equipment” that Leffler believes in. Even when human-made technology develops further, it will be most efficient when used together with the millions of dogs’ smell receptors, Leffler believes. “It is a combination of technology and the avalanche dog that will always be effective in finding an avalanche victim.”
Living with someone changes your microbiome, new research shows
Some roommate frustration can be expected, whether it’s a sink piled high with crusty dishes or crumbs where a clean tabletop should be. Now, research suggests a less familiar issue: person-to-person transmission of shared bacterial strains in our gut and oral microbiomes. For the first time, the lab of Nicola Segata, a professor of genetics and computational biology at the University of Trento, located in Italy, has shown that bacteria of the microbiome are transmitted between many individuals, not just infants and their mothers, in ways that can’t be explained by their shared diet or geography.
It’s a finding with wide-ranging implications, yet frustratingly few predictable outcomes. Our microbiomes are an ever-growing and changing collection of helpful and harmful bacteria that we begin to accumulate the moment we’re born, but experts are still struggling to unravel why and how bacteria from one person’s gut or mouth become established in another person’s microbiome, as opposed to simply passing through.
“If we are looking at the overall species composition of the microbiome, then there is an effect of age of course, and many other factors,” Segata says. “But if we are looking at where our strains are coming from, 99 percent of them are only present in other people’s guts. They need to come from other guts.”
If we could better understand this process, we might be able to control and use it; perhaps hospital patients could avoid infections from other patients when their microbiome is depleted by antibiotics and their immune system is weakened, for example. But scientists are just beginning to link human microbiomes with various ailments. Growing evidence shows that our microbiomes steer our long-term health, impacting conditions like obesity, irritable bowel syndrome, type 2 diabetes, and cancer.
Previous work from Segata’s lab and others illuminated the ways bacteria are passed from mothers to infants during the first few months of life during vaginal birth, breastfeeding and other close contact. And scientists have long known that people in close proximity tend to share bacteria. But the factors related to that overlap, such as genetics and diet, were unclear, especially outside the mother-baby dyad.
“If we look at strain sharing between a mother and an infant at five years of age, for example, we cannot really tell which was due to transmission at birth and which is due to continued transmission because of contact,” Segata says. Experts hypothesized that they could be caused by bacterial similarities in the environment itself, genetics, or bacteria from shared foods that colonized the guts of people in close contact.
Strain sharing was highest in mother-child pairs, with 96 percent of them sharing strains, and only slightly lower in members of shared households, at 95 percent.
In Italy, researchers led by Mireia Valles-Colomer, including Segata, hoped to unravel this mystery. They compared data from 9,715 stool and saliva samples in 31 genomic datasets with existing metadata. Scientists zoomed in on variations in each bacterial strain down to the individual level. They examined not only mother-child pairs, but people living in the same household, adult twins, and people living in the same village in a level of detail that wasn’t possible before, due to its high cost and difficulties in retrieving data about interactions between individuals, Segata explained.
“This paper is, with high granularity, quantifying the percent sharing that you expect between different types of social interactions, controlling for things like genetics and diet,” Gibbons says. Strain sharing was highest in mother-child pairs, with 96 percent of them sharing strains, and only slightly lower in members of shared households, at 95 percent. And at least half of the mother-infant pairs shared 30 percent of their strains; the median was 12 percent among people in shared households. Yet, there was no sharing among eight percent of adult twins who lived separately, and 16 percent of people within villages who resided in different households. The results were published in Nature.
It’s not a regional phenomenon. Although the types of bacterial strains varied depending on whether people lived in western and eastern nations — datasets were drawn from 20 countries on five continents — the patterns of sharing were much the same. To establish these links, scientists focused on individual variations in shared bacterial strains, differences that create unique bacterial “fingerprints” in each person, while controlling for variables like diet, demonstrating that the bacteria had been transmitted between people and were not the result of environmental similarities.
The impact of this bacterial sharing isn’t clear, but shouldn’t be viewed with trepidation, according to Sean Gibbons, a microbiome scientist at the nonprofit Institute for Systems Biology.
“The vast majority of these bugs are actually either benign or beneficial to our health, and the fact that we're swapping and sharing them and that we can take someone else's strain and supplement or better diversify our own little garden is not necessarily a bad thing,” he says.
"There are hundreds of billions of dollars of investment capital moving into these microbiome therapeutic companies; bugs as drugs, so to speak,” says Sean Gibbons, a microbiome scientist at the Institute for Systems Biology.
Everyday habits like exercising and eating vegetables promote a healthy, balanced gut microbiome, which is linked to better metabolic and immune function, and fewer illnesses. While many people’s microbiomes contain bacteria like C. diff or E. coli, these bacteria don’t cause diseases in most cases because they’re present in low levels. But a microbiome that’s been wiped out by, say, antibiotics, may no longer keep these bacteria in check, allowing them to proliferate and make us sick.
“A big challenge in the microbiome field is being able to rationally predict whether, if you're exposed to a particular bug, it will stick in the context of your specific microbiome,” Gibbons says.
Gibbons predicts that explorations of microbe-based therapeutics will be “exploding” in the coming decades. “There are hundreds of billions of dollars of investment capital moving into these microbiome therapeutic companies; bugs as drugs, so to speak,” he says. Rather than taking a mass-marketed probiotic, a precise understanding of an individual’s microbiome could help target the introduction of just the right bacteria at just the right time to prevent or treat a particular illness.
Because the current study did not differentiate between different types of contact or relationships among household members sharing bacterial strains or determine the direction of transmission, Segata says his current project is examining children in daycare settings and tracking their microbiomes over time to understand the role genetics and everyday interactions play in the level of transmission that occurs.
This relatively newfound ability to trace bacterial variants to minute levels has unlocked the chance for scientists to untangle when and how bacteria leap from one microbiome to another. As researchers come to better understand the factors that permit a strain to establish itself within a microbiome, they could uncover new strategies to control these microbes, harnessing the makeup of each microbiome to help people to resist life-altering medical conditions.