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It’s not easy being green

The Lemur leaf frog, one of thousands of species of amphibian whose existence is threatened by the fungus Bd

The twenty-first century is a terrible time for frog-lovers. All over the world, these amphibians are hopping out of existence so quickly that even the most optimistic conservationists are furrowing their brows. A third of amphibian species are at risk of extinction. Some of the reasons behind this decline are applicable to all wildlife: habitat loss, pollution, climate change. But amphibians are also plagued by a nemesis that’s all their own: a doomsday fungus called Batrachochytrium dendrobatidis, or Bd for short.

Bd is a frog-killer par excellence. It thickens its victims’ skin, stops them from absorbing salts like sodium and potassium, and triggers the equivalent of a heart attack. Since its discovery in the late 1990s, Bd has spread to six continents. It has shown up everywhere that amphibians exist. And everywhere it shows up, amphibians stop existing. The fungus can destroy entire populations in weeks, and has already consigned dozens of species to history. The sharp-snouted day frog is probably gone. The gastric brooding frog is no more. The Costa Rican golden toad has ribbited its last. Hundreds of others have been exposed. For good reason, Bd has been called “the worst infectious disease ever recorded among vertebrates”. Frogs, toads, salamanders, newts, caecilians: no group of amphibian is exempt. If a new fungus emerged that killed every mammal – every dog, dolphin, elephant, bat and human – we would rightly panic. And biologists who work with amphibians are indeed panicking.

The Panamanian golden frog is thought to be extinct in the wild due to Bd

Afrogalypse now

Bd is a harbinger of things to come. In 2013, scientists described a related fungus, B. salamandrivorans, which attacks salamanders and newts in Europe and North America. Since at least 2006, yet another fungus has been sweeping through North America’s bats, causing a fatal disease called white nose syndrome and littering caves with millions of corpses. For decades now, corals have been hit by epidemic after epidemic. These infectious diseases of wildlife are emerging ever more quickly, and humans are at least partly to blame. On planes, boats and boots, we carry pathogens around the world with unprecedented speed, overwhelming new hosts before they can acclimatise and adapt. The rise of Bd is a perfect example. Yes, it is virulent. Yes, it represses the immune systems of amphibians. But it’s still just a fungus, and amphibians have been dealing with fungi for some 370 million years. This isn’t their first rodeo. They are fumbling this particular ride because they have already been weakened by changing climate, introduced predators and environmental pollutants. Add a destructive and quickly spreading disease into the mix and the future suddenly looks exponentially bleak.

But amphibian specialist Reid Harris has hope. Harris has discovered a possible way of protecting these animals from their fungal foes. In the early 2000s, he found that the red-backed and four-toed salamanders – two small, sinuous species from the eastern US – are covered in a rich cocktail of antifungal chemicals. These substances aren’t made by the animals themselves but by the bacteria on their skin. They might help to protect the salamanders’ eggs from fungi that would otherwise thrive in the humid underground nests. And as Harris later found, they can also stop Bd from growing. Perhaps, he thought, this explained why some lucky amphibian species seem to resist the killer fungus: their skin microbiomes act as symbiotic shields. And perhaps, he hoped, those microbes could help to save vulnerable species from the looming Amphibiageddon.

On the other side of the US, Vance Vredenburg was entertaining the same hope. He had been studying the mountain yellow-legged frogs of California’s Sierra Nevada, and was becoming despondent as Bd hit the area. “It was unbelievable,” he says. “The fungus would go from not being there at all to wiping out an entire basin.”

“It would be great to figure out every little detail but we don’t have time. If we take time, the frogs won’t be around any more. We’re working in a crisis”

One after another, in quick succession, dozens of sites emptied of frogs. But not everywhere. In an alpine lake at Mount Conness, yellow-legged frogs were infected with Bd but still resolutely hopping around. Bd kills by overwhelming its hosts with tens of thousands of spores, but these frogs were carrying just a few dozen each. The supposedly lethal fungus that was filling other lakes with upturned cadavers was proving to be, at worst, a mild nuisance at Conness. At this site, and a few others, something was resisting Bd’s advance. And when Vredenburg heard about Harris’s experiments, he suddenly knew what. By swabbing the skins of the Conness frogs, he confirmed that they carried the same antifungal bacteria that Harris saw in his salamanders. One bacterial species stood out, both for its protective powers and for its colour: blackish-purple, ominous but darkly beautiful. It was called Janthinobacterium lividum. But everyone just refers to it as J-liv.

In lab tests, Vredenburg and Harris confirmed that J-liv can indeed protect certain frogs from Bd – but how? Does it kill the fungus directly by making antibiotics? Does it stimulate the frogs’ own immune system? Does it reshape the frogs’ native microbiome? Does it simply take up space in the skin, physically preventing the fungus from taking hold? And if it is so useful, why is it only found on some frogs and not others? And why is it relatively rare even when it is present?

“It would be great to figure out every little detail but we don’t have time,” says Vredenburg. “If we take time, the frogs won’t be around any more. We’re really working in a crisis.” Forget the details. What mattered was that the bacterium worked, at least in the cosy confines of a lab. Would it also work in the wild?

Vance Vredenburg at work in his laboratory at San Francisco State University’s department of biology

The battle of Dusy Basin

At the time, Bd was creeping fast across the Sierra Nevada, covering around 700 metres a year. By charting its advances, Vredenburg predicted that it would next hit Dusy Basin, a site some 11,000 feet above sea level, where thousands of yellow-legged frogs remained oblivious to the encroaching doom. It was the perfect place to put J-liv’s powers to the test. In 2010, Vredenburg and his team hiked to Dusy Basin and grabbed every frog they could find. They found J-liv on the skin of one individual, and grew it into rich, thriving cultures. They then baptised some of the other captured individuals in this bacterial broth. The rest, they left in containers that just had pond water. After a few hours, they released all the frogs to fate and fungus.

“The results were phenomenal,” says Vredenburg. As predicted, Bd arrived that summer. The fungus took its usual toll on the frogs that had just been soaked in pond water – dozens of spores became thousands of spores, and each frog became an ex-frog. But in the animals that were dunked in J-liv, the fatal accumulation of spores not only plateaued early, it often reversed. A year later, around 39 per cent of them were still alive, while their peers were all dead. The trial had worked. The team had successfully protected a wild population of vulnerable frogs with a microbe. And they had established J-liv as a probiotic: a term that is most commonly linked to yoghurts and supplements, but really applies to any microbe that can be applied to a host to improve its health.

But conservationists can’t very well catch and inoculate every amphibian that’s threatened with Bd – that would be all of them. Instead, Harris is thinking about seeding soils with probiotics so that any passing frog or salamander would automatically dose itself. Alternatively, threatened frogs that are already being bred in captivity could be dosed in the lab before being released as a group. “There is a lot of potential,” says Vredenburg, “but this is not a silver bullet. Like any complex problem, we can’t expect it to be a winner all the time.” Indeed, Matthew Becker, one of Harris’s former students, found that the same approach failed completely with captive Panamanian golden frogs. This species is a ghost in a bumblebee’s colours: a gorgeous black-and-yellow creature that has already been exterminated from the wild by Bd. Today, it exists only in zoos and aquariums and cannot be reintroduced to Panama as long as Bd persists. J-liv, despite its initial promise, won’t help with that.

“Bd has been called ‘the worst infectious disease ever
recorded among vertebrates’. Frog, toad, salamander: no amphibian is exempt”

Perhaps that was predictable. Even closely related animals can carry very different microbiomes. There’s no reason to suppose that a bacterium that colonises one species will thrive on another, or that there would ever be a universal probiotic that shields every amphibian.

J-liv might live in salamanders and frogs throughout the US, but it’s not native to Panama and has no evolutionary history with the golden frog. With the acuity of hindsight, shoving an American microbe onto a Panamanian frog seems overly optimistic, not to mention a bit imperialist. Undaunted, Becker travelled to Panama to find a better probiotic. He surveyed the skin microbiomes of the golden frog’s closest relatives, and found several indigenous species that stopped Bd from growing – at least in Petri dishes.

Unfortunately, none of these native microbes would colonise the golden frogs either, and none of them bested the fungus in real conditions. There was one sign of hope: against all expectations, five of Becker’s golden frogs were naturally resistant to Bd. Their skin microbes differed from those of the frogs that had died, and Becker is now trying to identify the protective bacteria within these communities. Harris is doing similar work in Madagascar, an amphibian Shangri-La that Bd has only just invaded. He is trying to find local bugs that can block Bd and persist on skins when artificially added. Becker and Harris aren’t trying to create any new symbioses or introduce bacteria from one part of the world to another. “We’re just augmenting locally occurring bacteria,” Harris says.

Even if they identify good candidates, they still need to work out how to get these bacteria to stick on the frogs. A simple bath may not be enough. Timing might be important, since the transformation from tadpole to adult sweeps a frog’s skin clean of microbes, like a fire burning through a forest. It creates a barren world that must be recolonised. This is the time when the animals are most at risk from Bd but it might also be the perfect moment to add probiotics. Perhaps these foreign microbes might more easily integrate into tumultuous, reassembling communities than into fixed, stable ones. Other subtleties probably matter, too. What about the microbes that already live on the skins of different amphibians: would they block or complement the incipient probiotics? What about the host’s immune system: would it allow the boosted microbial populations to persist on the skin, or correct them towards a different state?

The details, it turns out, do matter. They could mean the difference between success or failure, preservation or extinction.


Further reading: Ed Yong is the author of I Contain Multitudes: The Microbes Within Us and a Grander View of Life, published by Bodley Head at £20

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