A Bee’s Eye View Of Cities’ Microbiomes

7:49 minutes

a person in a white bulky bee suit pulls out a frame from a beehive with two hands. bees cover the frame and fly around the hive
Credit: U.S. Department of Agriculture

When you want to look at the microbial health of a city, there are a variety of ways to go about it. You might look at medical records, or air quality. In recent years, samples of wastewater have been used to track COVID outbreaks. Studies of urban subway systems have involved painstaking swabs of patches of subway muck. But now, researchers are offering another approach to sample a city’s environment—its beehives.  

A report recently published in the journal Environmental Microbiome used the bees foraging in a city to provide information about the town’s bacteria and fungi. The researchers found that by looking at the debris in the bottom of a beehive, they could  learn about some of the environments in the blocks around the hives. The microbes they collected weren’t just species associated with flowers and plant life, but included organisms associated with ponds and dogs. The team found that the hive samples could reveal changes from one neighborhood to another in a city, and in the microbial differences between different cities—samples taken in Venice, for instance, contained signals associated with rotting wood that were not seen in samples from Tokyo. 

Elizabeth Henaff, an assistant professor in the NYU Tandon School of Engineering at New York University and a co-author of the report, joins SciFri’s Kathleen Davis to talk about what bees and microbes can tell us about the cities we share.

Further Reading

Segment Guests

Elizabeth Henaff

Dr. Elizabeth Henaff is an assistant professor in the NYU Tandon School of Engineering at New York University in New York, New York.

Segment Transcript

KATHLEEN DAVIS: This is Science Friday. I’m Kathleen Davis. When you want to look at the health of a city, there are a bunch of ways that you can go about it. You can look at medical records or maybe air quality. Or in recent years, samples of wastewater have been used to track COVID outbreaks. But now, researchers are offering another approach to sample a city’s environment. It’s beehives. Using the bees foraging in a city to provide information about the bacteria and the fungi there.

Joining me now is Elizabeth Henaff. She is an assistant professor in the NYU Tandon School of Engineering at New York University. She’s a co-author of a report on the approach that was recently published in the journal Environmental Microbiome. Welcome to Science Friday.

ELIZABETH HENAFF: Glad to be here.

KATHLEEN DAVIS: So you study environmental microbiomes. Before we get to the bees, can you explain to me what does this mean?

ELIZABETH HENAFF: So we think of the environmental microbiome as a population of microorganisms. So that’s both bacteria but also viruses and also protists that can be found in the environment that we interact with. There’s a kind of emerging body of literature that shows that human health and well-being is tightly related to our relationship with our own microbiome, our gut microbiome, our skin microbiome, for example. And the human microbiome interacts with and is sculpted by the environmental microbiome.

KATHLEEN DAVIS: So let’s get to the buzzy news in your study. What makes bees such a good way to study the microbiome of a city?

ELIZABETH HENAFF: Well, the challenge with studying the microbiome of a city is that a city is a very large surface area to cover. And the tool that we have used most commonly to take biological samples for microbiological studies is the swab that we’re all overly comfortable with or uncomfortable with. But the size of that tool is not quite adjusted to the size of the thing that we want to study. So a swab allows us to sample maybe a square foot area of a particular environment.

But if we want to get the read of a microbiome of, say, a whole block or a whole neighborhood, that tool isn’t quite well adapted to that particular resolution, that particular size. And so we were really looking for some kind of system that existed in a city already that would allow us to collect aggregate information about the microbiome of a larger area, so say a block or a neighborhood.

And so that’s how we got to thinking about bees. Because basically, bees are doing what we’ve in the past asked armies of undergrad students to do when we’re running these citywide studies, which is to go out into the environment, interact with things, and always come back to the same place.

And so it turns out that bees are coming back with a lot more information or material than what they set out to forage, and we’re able to use some of the material that the bees recover to understand the microbial fingerprint of the environment they’re foraging in.

KATHLEEN DAVIS: So it sounds like they’re not just picking up the bacteria on flowers, for example. Are they kind of picking up just whatever is out there?

ELIZABETH HENAFF: Yeah, so our assumption was that bees were going to come back with plant-related microorganisms because that’s what they’re most frequently physically interacting with. But it turns out that they were recovering microbes from all sorts of other environments. So say, aquatic environments if there happened to be a body of water nearby, or also mammalian systems like human-related microbes or even dog-related microbes.

The bees are really traversing this kind of rich three-dimensional microbial environment as they’re foraging. And so as they’re traversing these microbial clouds, they’re bringing back that microbial information and then depositing it at the bottom of the hive when they enter the hive, and then we’re able to collect that material.

KATHLEEN DAVIS: So you studied hives in several different cities, including New York, Tokyo, Venice, and Sydney, Australia. What sort of differences did you find?

ELIZABETH HENAFF: So what we saw looking at those cities across the globe is that different cities have different microbial signatures as seen by honeybees. Perhaps most interesting is that even within a city, different neighborhoods will have different microbial signatures.

KATHLEEN DAVIS: Did you find anything in this debris that signaled, oh, this makes sense to find this sort of microbe in, say, this Tokyo hive, or this makes sense to have found in this Venice hive. I mean, were there any things that really gave you a sense of place that you found in this debris?

ELIZABETH HENAFF: I think the example for that would be the study that we did in Venice. So one of the main organisms that we recovered in Venice was a fungus related to wood rot, which makes sense because Venice is a city built on wooden pilings, submerged wooden pilings. So it makes sense historically and architecturally.

KATHLEEN DAVIS: So zooming out, I mean, now that we know this, where do we go from here? I mean, do you see a future where humans could regularly look at hives and maybe see that there’s a disease floating around a city?

ELIZABETH HENAFF: Yeah, I mean, so there’s obviously some constraints to this method that we’re well aware of. One of the constraints being is that there is a bee season, at least in more northern parts of the world like New York City. So bees are active only from the end of spring to the beginning of fall. And so as far as using this as an epidemic surveillance method, that’s one of the constraints.

We also don’t know what our false negative rate is. So we don’t know what is out there but we’re not recovering. But we do know that the genomic data or genetic data that we’re able to recover is rich enough to be able to identify certain types of pathogens.

But maybe even more so than using this as a surveillance mechanism, what’s really interesting to me is that this is a study and an approach that allows us to think of cities as kind of multi-species assemblages. That actually, cities, we think of them as designed for humans and by humans, but they are very much inhabited by a whole host of other species. And it’s looking at the interactions of those species, so in this case, insects, and microbes, and humans all together, that we’re able to kind of approach them and study them as a biological superstructure.

KATHLEEN DAVIS: Are there other species that you think might have a future as good samplers? I mean, I’m just thinking of things like bird nests or other creatures that move around a lot and collect things.

ELIZABETH HENAFF: So there’s examples in the literature of people using leeches.


ELIZABETH HENAFF: As a way to study, to get aggregate information from other organisms in an ecosystem. So leeches, as being bloodsucking organisms, and then if you collect a leech, and you can assess the genomic signatures of the blood of the different species that that leech has extracted from, you can get a read of biodiversity in that area. And that’s been used really successfully to monitor for endangered species that are maybe hard to identify or to count in other ways.

Obviously, we can’t use leeches in New York City, and I’m really glad that is actually not a method that’s available to us. But there are other examples of using one organism as a proxy measure for understanding a whole other ecosystem that it’s interacting with.

KATHLEEN DAVIS: Fascinating stuff. Elizabeth Henaff, assistant professor in the NYU Tandon School of Engineering at New York University. Thank you so much for joining me.

ELIZABETH HENAFF: Thank you so much.

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