Macrocosm: Microbes Provide New Way Of Tracking Wildlife

CHRISTOPH BURGSTEDT/SCIENCE PHOTO LIBRARY

Sam Pannoni is something of a psychic. Give him an artifact of the past, and he can tell you where it came from. He can tell you if it belonged to someone with a large family, if they ate a lot or a little, even whether they had any chronic health defects.

But what separates him from the mystics is that the token he needs isn’t a palm or a lock of hair. What he needs is a fecal sample, and the subjects of his divination are elk in the Greater Yellowstone Ecosystem and muskox in Greenland.

Pannoni, a PhD candidate at the University of Montana, has been researching landscape genetics for the past seven years, from undergraduate all the way through his current six year track towards completing a doctorate. He finds himself drawn to parts of the world that are smaller than he can see that affect the world around him. And the gut microbiome certainly falls into that description.

What is the gut microbiome?

Picture a thriving community - it can be a lush forest, a pond full of fish, or a suburban neighborhood. All the members contribute to the continued survival of the group; no one takes too much, and the population flourishes as a result.

Now shrink that community down past the view of the naked eye, where each member is about 1 or 2 microns in diameter - about 1/100,000th the width of your fingernail. Make sure everyone in there can survive at a very specific pH and heat, and place that interwoven collection of bacteria, viruses, protozoa, and fungi into the stomach and intestines of a mammal. That’s the gut microbiome.

The gut microbiome has received a serious spotlight over the past 15 years. Between 2013 and 2017, nearly 13,000 publications focused on the gut microbiota were published. The gut microbiome plays an important role in nutrient and mineral absorption, as would be expected, but also plays an important role in protection against diseases that enter through our mouths during food intake. Through tests on different system models, like germ-free mice, scientists have learned that the types of microscopic organisms in our guts can influence what long-term diseases we may acquire, like diabetes and asthma. Even food allergies can be influenced by what flourishes in our guts.

How does this connect to landscape ecology?

Pannoni finds this interesting, but ultimately not what he’s really fascinated with for his research. He’s looking at the gut microbiomes of ungulates - large mammals with hooves - in colder parts of North America and Greenland. He fondly recalls exciting days of gathering samples of scat in Yellowstone park in the middle of winter on skis, or waiting for elk for days atop a windy ridgetop.

After finding his samples, he travels back to his lab, where he ends up spending most of his days looking at code and finding relationships between the data he’s gathered and the attribute values of his subjects. Through this, he can track where a herd is moving, how old the members of that herd are, how much an individual has eaten, and whether the population is going to face major predation. He compares his results to existing tracking methods - those done by a helicopter or a radio chip - and sees how close they are.

From what his research can say so far, they’re remarkably close. His research is still in the committee stage, but he anticipates that it will be published within the next six months. This could be revolutionary for population tracking in the future. Instead of an expensive and loud helicopter following around populations and possibly interfering with their movements and reproduction, scientists could move into an area after a population travels through it, gather scat, and be able to tell which elk were still alive from a previous reading, whether they were eating well, and how interbred the population was.

“Ideally, we won’t have to be as invasive in the future,” Pannoni says. Then, jokingly, “It does break my heart a little bit, since we won’t be using that cool ‘Batman’ net gun from a helicopter anymore, but it’s better for the elk.”

His hope is that this innovative new method won’t be used in its current state, but will be changed multiple times as it is tested and reviewed in many different environments. But this isn’t all his work has done. Pannoni and his colleagues came across an interesting development as they tested microbiome samples from dead and living elk, which may have long-reaching impacts for evolution and ecology alike.

Is the microbiome a true indicator of health?

Wolves in Yellowstone kill elk once every 3 or 4 days to survive. Hunting an elk is a dangerous and costly endeavor. Wolves course, which means they chase their prey over long distances to figure out if the animal is easy or hard to kill. If it’s difficult to kill, and the wolves miscalculate, they could end up dying to the elk’s heavy hooves or investing a very limited reserve of energy into a fruitless chase. Wolves need a way to tell which elk will go down without much of a fight, so they make use of two senses: sight and smell.

And, Pannoni has measured, they also may sense the microbiome of the creature they’re chasing.

Pannoni found significant differences in the microbiomes of dead and living elk, suggesting that wolves are selectively picking elk with different microbiomes. This could mean one of two things, he says. The microbiome could be a true indicator of health, meaning that wolves are true arbitrators of natural selection. Elk that are healthy are not eaten by wolves, allowing them to carry on their genes (and beneficial microbiota) to the next generation, while those that are unhealthy and weak are killed before they can add themselves to the gene pool. This is the truest expression of Darwinian natural selection; a find like this could support the argument that organisms that are better adapted to their environment will survive and produce more offspring. This, in short, would tie microbiota to the field of evolution.

This could also mean that wolves can sense the microbiome of an elk and be able to tell through the scent of a sprinting elk whether it is weaker or stronger. This would expand the field of wildlife studies to an incredible degree. Wolves may have a better nose than we thought. Does this extend to all animals? How many species can smell a microbiome, and could we utilize this sense when working with our own microbiota?

Pannoni knows his work isn’t finished yet. The information he’s found with his PhD project needs to be checked again and again. If he wants this to be widely used, it will need to be proven to be generally applicable to all populations of a given species, or always reliable in a given season.

“The way I see it, this is spreading awareness of its plausibility,” he says. “In its current phase, I'm the only person who has touched it, and I’ve only used one method. When more people do it and more people collaborate on it, it’ll be something I don’t even recognize. That's where I’m hoping it goes.”