Night Hike: Following Microbes Into the Dark
- Heather McSharry, PhD
- 3 hours ago
- 19 min read
Summary
As daylight fades, the infectious-disease landscape begins to change. In the final episode of From Sunrise to Starlight, we follow a summer trail into the dark to explore mosquitoes and ticks, wildlife and bats, artificial light, and the hidden relationships among microbes, vectors, hosts, and the environments they share. Along the way, we discover why time and behavior matter to transmission and why understanding the risks around us can make the natural world more fascinating, not more frightening.
Listen here or scroll down to read full episode.
Also available on all major podcast platforms
Full Episode
Citation list is after my signature at the end of the post.
COLD OPEN
There is a particular moment on a summer evening when the landscape begins to change. The sun may not be completely gone yet. There is still enough light to see the trail ahead, enough to distinguish individual trees and patches of vegetation, enough that you probably haven't reached for a flashlight. But the day is ending. The temperature begins to fall. Shadows stretch across the ground. Colors lose some of their intensity. Birds that were active during the day become quieter, and other sounds begin taking their place. Like crickets, frogs, and the first persistent whine of a mosquito somewhere near your ear.
And if you keep walking as dusk gives way to darkness, you enter a landscape undergoing a shift change. Animals that spent the heat of the day sheltering begin to emerge. Predators take advantage of darkness. Prey respond to it. Insects become active on schedules that have been shaped by millions of years of evolution.
And while all of that is happening, we become steadily less capable of seeing it.
So let's follow a trail through that transition—from the last light of evening, through the woods after dark, all the way to a lake beneath the stars.
This is Night Hike: Following Microbes Into the Dark
WHEN DAY BECOMES NIGHT
At we hit the trail, it's dusk, which feels like an in-between time because, for us, it is. The working day is ending. Summer heat finally starts loosening its grip, and the part of the day when we're expected to be active begins giving way to the part when we're supposed to wind down.
Ecologically, though, sunset means something else. For example, predators and prey adjust their behavior around one another, and insects that attracted very little of our attention during the afternoon become more noticeable. Among them are some of the most important disease vectors on Earth.
Mosquitoes are an obvious part of a summer evening, but saying that mosquitoes “come out at night” is one of those statements that sounds perfectly reasonable until you look more closely at mosquito biology.
There are thousands of mosquito species, and they do not all keep the same schedule.
Some Aedes mosquitoes—including species capable of transmitting viruses such as dengue, Zika, chikungunya and yellow fever—are generally associated with daytime biting. We called them daybiters in Galveston. Their activity can be particularly strong during portions of the morning and late afternoon, although the exact pattern varies among species, locations and environmental conditions.
Many Culex mosquitoes operate on a different schedule. Species involved in transmission of West Nile virus often become particularly active around dusk and into the night. And many of the Anopheles mosquitoes responsible for transmitting human malaria feed predominantly during evening and nighttime hours.
Those differences help determine when transmission can occur. A vector can't transmit a pathogen to a host it never encounters. For mosquito-borne transmission to happen, a competent mosquito has to be present. The pathogen has to be circulating. A susceptible host has to be available. And somewhere in that chain of events, the behavior of vector and host has to bring them together. That makes time part of the infectious-disease landscape.
Think about what happens as people move through a summer day. In the morning and early afternoon, we're outside swimming, heading to work, picnicking. During the hottest part of the afternoon, we usually spend more time indoors. Then evening arrives. Temperatures become tolerable again depending on where you live. People return to patios, parks, yards and trails. At exactly the same time, the activity of some mosquito species increases and the overlap is what's important for this story.
And mosquitoes searching for a host also experience this landscape differently than we do. We rely heavily on vision, and as daylight disappears, the amount of information we can extract from our surroundings decreases. Mosquitoes can use a combination of cues to locate potential hosts. Carbon dioxide from our breath provides information that an animal is nearby. At closer range, body heat, odors and other chemical cues can help guide them toward us.
Darkness may be taking information away from the person walking down the trail but it doesn't necessarily take useful information away from the mosquito looking for that person. And that distinction gets us to something important about infectious-disease ecology.
“Are there mosquitoes here?” is a reasonable question. It's just not enough. We should also ask: Which mosquitoes are here? When do they feed? What hosts do they prefer? Where do they reproduce? How far do they travel? Which pathogens are they capable of transmitting? Are those pathogens actually circulating here? And when are they outside in the same places as us?
Change one of those variables and you change the opportunity for transmission. Of course, being outside at dusk doesn't mean you're inevitably going to acquire a mosquito-borne infection. Most mosquito bites don't transmit disease. The actual risk depends on geography, season, mosquito species, pathogen circulation, host susceptibility, and a long sequence of biological events inside both vector and host.
So my point isn't that dusk is dangerous. Dusk is the start of the best time of day if you ask me. My point is that dusk changes the ecological equation. And mosquitoes aren't the only arthropods worth thinking about as daylight disappears.
As we follow our trail into the woods, the remaining sunlight beneath the canopy disappears first. Eventually, we reach the point where we need a flashlight, and suddenly the world around us contracts. Ahead in the flashlight beam, there's maybe twenty feet of trail. Turn the beam toward the side and we see tree trunks, leaves and tangled vegetation. Point it toward the ground and we see our boots, rocks, grass, and whatever happens to fall inside that narrow circle of light.
Everything else is still there but we're receiving less sensory information about it. That's particularly interesting if you happen to be hiking with a dog. Gypsy, for example, experiences this trail very differently than I do. I try staying in the middle of the path and avoid walking into branches. She's staying closer to the vegetation, following scents I can't detect and investigating every patch of grass that appears to contain information of enormous importance.
We technically occupy the same environment but we don't encounter it in the same way.
And somewhere along the edge of that trail might be another arthropod waiting for exactly that kind of contact, only it has no wings and gives us no obvious announcement that we've encountered it at all.
OUTSIDE THE BEAM
Ticks are remarkably good at going unnoticed. And contrary to one persistent bit of tick mythology, they don't perch in trees waiting to drop onto unsuspecting hikers. Most encounters begin much closer to the ground.
A tick searching for a host may climb onto vegetation and wait near the tip of a blade of grass, leaf or stem, holding on with its rear legs while extending its front pair. This behavior is called questing. When a suitable animal brushes past, the tick grabs on.
Which means I don't have to step off the trail and go wandering dramatically through the undergrowth to encounter one. I just have to touch the right piece of vegetation.
When that happens, I swing the flashlight toward my leg and don't see anything. But that doesn't mean much. Depending on the tick, its species and its life stage, what I'm looking for could be very small. An immature tick can be easy to overlook even in broad daylight let alone at night.
And once a tick gets onto a host, it doesn't necessarily attach immediately. It can spend time moving across clothing, fur or skin before finding a place to feed. That's one reason the end of a hike matters so much. A tick check after you've been in tick habitat is an important and simple response to a possible exposure that can be difficult to notice while it's happening. Showering after coming indoors can also help remove unattached ticks and give you another opportunity to look. Clothing and gear deserve attention too.
And tonight, I don't just have myself to check, I have Gyspy.
And she's discovered something irresistible at the edge of the path. I have no idea what.
She pushes her nose into the vegetation.
“Come on.”
Compared to Gypsy, I'm upright, several feet above the ground, trying to keep my boots on the trail. She's covered in fur, considerably closer to the vegetation and deeply committed to investigating every smell within reach.
It's no secret that dogs can pick up ticks, and some tick-borne pathogens can infect them too. Depending on where you live, veterinary tick prevention can be an important part of protecting a dog that spends time outdoors. And checking a dog after a hike can reveal a hitchhiker before it has much opportunity to settle in.
But there's another reason I'm paying attention to where Gypsy goes. She expands the boundaries of my encounter with this landscape. I can stay carefully in the middle of the trail while she investigates the edge. Something that never touches my pant leg can still attach to her fur. And later, when we're back in the car or at home, the boundaries between her environment and mine get blurred.
That doesn't make dogs some sort of dangerous delivery system for ticks but it illustrates that the relevant environment isn't always limited to the ground directly beneath your own feet. Sometimes another host connects you to it.
But keep in mind that darkness didn't suddenly put the ticks here. Although nighttime conditions can affect their questing behavior. Ticks and vegetation were here before sunset. Gypsy would have stuck her nose into all of it at noon too. What darkness changed is my ability to watch any of it happen. During the day, I can watch where Gypsy is going while still seeing what's ahead. At night, that world collapses.
At night, every time I choose one thing to illuminate with the flashlight, I stop seeing something else. A flashlight feels as though it restores vision in the dark, but it doesn't restore daylight. It creates a small, intensely visible world surrounded by an enormous amount of missing information. And that makes the night feel empty in a way it really isn't. The organisms beyond the beam are still there.
And if we here a sound, maybe I stop and Gypsy doesn't. Maybe the sound or whatevmade the sound is less interesting than the smell she's currently investigating.
I appreciate the reassurance and keep going.
And later on the trail, I sweep the flashlight across the ground alongside it and something reflects back. Then another. Tiny points of pale blue-green light suspended just above the forest floor. I stop again. This time, I know exactly what I'm looking at. Spider eyeshine. If you were with us for an earlier Outbreak After Dark, you may know exactly what I'm looking at too.
“Nope. We've already done that episode, Gypsy.”
The spiders can keep this section of trail. Because somewhere farther ahead, something much larger is moving through the dark. And Gypsy senses it before I do.
SOMETHING IN THE WOODS
Gypsy freezes. Her head up, ears forward, as she looks intently into the trees.
I look but see nothing of course. Then I hear it.
Something moving through leaves. So I turn the flashlight toward the sound. I can see a tree trunk, branches, and brush, but nothing that explains it.
Gypsy is still staring. And for a moment, the difference between the two, other than the obvious of course...becomes well...more obvious.
I'm trying to solve this almost entirely with my eyes. Gypsy isn't. Dogs inhabit an extraordinary sensory world built heavily around smell. Their hearing also extends beyond ours in important ways. She may have detected an animal before I ever heard the first leaf move, and she's receiving information about it that I don't have access to.
I'm standing here with a flashlight trying to force the nighttime landscape to behave like daytime. Gypsy doesn't need it to.
Somewhere ahead, leaves move again. This time, farther away. Whatever it was seems to be leaving. Good. Let's keep going.
Ok so for a substantial portion of the animal world, nighttime is when their day begins.
Nocturnality offers animals several advantages. Darkness can provide protection from predators—or cover for predators themselves. Cooler nighttime temperatures can reduce heat stress and water loss. And for some animals, being active when humans are less active allows them to avoid us.
So as we move deeper into the woods at night, we're entering a period when animals we rarely notice during the day may be feeding, hunting, traveling or searching for mates.
That doesn't mean they're searching for us. Or hunting us. They're living their life.
And that's worth emphasizing because infectious-disease discussions about wildlife can become distorted quickly. A raccoon isn't a rabies diagnosis. A rodent isn't a hantavirus exposure. A bat flying overhead isn't an emergency.
Wildlife can maintain pathogens capable of infecting humans, but the existence of a pathogen in an animal population and an actual human exposure are not the same things. Transmission requires a route. For rabies, that generally means saliva or neural tissue from an infected mammal reaching broken skin or a mucous membrane, most often through a bite. Just being near a wild mammal isn't enough.
For hantaviruses, the relevant interface is different. In the Americas, human infection is generally associated with exposure to infected rodent urine, droppings or saliva, often when contaminated material is disturbed and infectious particles become airborne. A mouse running across a trail in front of me is not the same exposure as entering an enclosed space where infected rodents have been living.
So, the takeaway is that yes, the animal matters, and of course the pathogen matters, but the encounter matters too. And that can get lost when we reduce zoonotic disease to lists of animals.
Well, Gypsy has decided the unidentified thing in the woods no longer deserves her attention. Which is convenient, because something else just crossed through the flashlight beam. Not on the ground. Above us. A quick movement against the remaining faint light in the sky. Then another. Oh cool! Bats.
There are few animals that have acquired a more disproportionate place in our infectious-disease imagination. Bats are important reservoirs for a number of viruses, and they are enormously important to the study of emerging infectious disease. But that fact can obscure what bats are actually doing on an ordinary summer night. Mostly, they're being bats. Many species are hunting insects. Yay! Go bats!
A night of foraging can involve enormous numbers of insect pursuits and captures, depending on the species and conditions. They navigate and hunt in darkness using sensory abilities dramatically different from ours, including echolocation in many species. And while I'm down here mildly irritated that mosquitoes have discovered me, insect-eating bats overhead are doing something I can enthusiastically support. And let me reiterate...their presence above this trail does not constitute a rabies exposure. Hearing one nearby does not constitute a rabies exposure. I'm not saying there's zero risk with bats, but the concern begins when there has been potential direct contact.
Direct contact with a bat deserves careful attention because bites or scratches can sometimes be small or difficult to recognize. If direct contact may have occurred—or if the circumstances make it difficult to know—public-health or medical professionals can help determine whether the encounter qualifies as a rabies exposure. That's important to file away.
But out here? They're flying. I'm walking. Gypsy is sniffing. Our paths overlap without intersecting. So the takeaway here is that sharing an ecosystem with an animal isn't the same thing as being exposed to its pathogens.
Up ahead the trail curves, and through a gap between the trees I can see more sky.
We've been walking long enough that the last traces of twilight are gone. When I switch the flashlight away from the trail, the darkness feels complete. So, because it's what I do, I stop for a moment and turn the light off.
And see nothing. But, because of my amazing hearing aids my senses aren't completely gone. I can hear insec the wind, Gypsy breathing somewhere beside me, and a faint movement of leaves. But visually, for the first few seconds, I see nothing at all. Then my eyes begin trying to make something of it. The trunks nearest me emerge first as darker shapes against darkness. A patch of sky appears between branches. A few stars become visible. And somewhere above those trees, bats continue hunting without any need for the light I'm missing. Gypsy continues smelling whatever extraordinary archive of information this trail apparently contains. The nocturnal world is functioning perfectly well. I'm the one who turned off the sense I was relying on.
Turn the flashlight back on and the trail reappears. So we keep moving. And somewhere farther ahead, another kind of light begins to appear between the trees. Not moonlight. Not starlight. Something distinctly human. A porch light. A trail shelter. A building near the lake. Whatever its source, it's a small pool of artificial light sitting in the middle of the darkness. And we aren't the only ones who can see it.
FOLLOWING THE LIGHT
Artificial light has become such an ordinary part of human life that it's easy to think of it as something we add to an environment without fundamentally changing that environment. For us, light makes nighttime easier to navigate.
For other organisms, though, artificial light is a different kind of information. Anyone who has ever switched on an outside light on a summer night has seen the most obvious example. Insects arrive. We usually describe this by saying insects are attracted to light, but the biology is more interesting than that.
Responses to light vary enormously among insects, and researchers are still working out the mechanisms behind some of the behaviors we see. Many insects use natural light sources as orientation cues. Artificial light can interfere with those systems. It can alter flight behavior, draw insects away from other activities or concentrate them in places where they otherwise might not have gathered.
Recent work has even challenged the simple idea that insects are deliberately flying toward artificial light. For some flying insects, artificial light appears to disrupt orientation behaviors that normally help them determine which direction is up. And the effects of artificial light aren't universal. Wavelength, intensity, the surrounding environment, and the species all play a role.
And we have to consider those factors when we bring infectious disease into the story.
It would be easy to look at a cloud of insects around a light on a summer night and construct a very simple chain: Light attracts insects. Some insects transmit pathogens.
Therefore, outdoor lights attract disease. But biological chains are rarely that convenient.
Not every insect approaching a light bites humans. Not every biting insect is a competent vector. Not every vector responds to artificial light in the same way.
But the point here is that artificial light at night can alter insect activity, movement and community structure. And that makes it interesting from an infectious-disease perspective. I mean, Anything that changes where organisms spend time, when they're active or which species encounter one another has the potential to change ecological relationships.
Ok, as our trail continues, we leave that artificial light behind and the trees begin to thin. And eventually, another sound becomes distinguishable beneath the insects and wind. Water.
We've reached the lake.
THE LAKE
This is where our August day comes full circle. We started From Sunrise to Starlight beside a lake.
Now we've arrived at a different lake and from the opposite direction. The sun is gone. The water beyond the shoreline is almost completely dark. And I promise I'm not going to repeat everything that might be living in it.
But arriving here after dark gives us a very different way to think about the same environment because the darkness has taken much of that information away.
That could make the lake feel threatening but it doesn't have to. Personally, this is exactly the sort of place where I'd want to go swimming. The only thing better might be a night dive along the cliffs of Maui.
Alas, tonight we're here...and it's beautiful and after a swim I can have the snack I packed... nonperishable of course.
My point is that understanding an environment isn't the same thing as being afraid of it. In fact fear is often a product of ignorance...the less we know about something the more we fear it. I mean we see that play out every day.
But for this podcast, learning and understanding are meant to arm us against fear and also bolster our confidence in making decisions to protect ourselves. And neither mean living in fear. Knowing that natural water contains microorganisms doesn't mean we never swim in a lake. Knowing ticks live in vegetation doesn't mean we never walk through the woods. Knowing mosquitoes can transmit pathogens doesn't require spending summer behind a sealed window.
Risk isn't binary. We make decisions using information. Where are we? What are the current conditions? Are there recreational-water advisories? What risks are relevant in this particular place? What are we planning to do? What precautions make sense? And sometimes, after considering all of that, we get in the water.
There is one important difference after dark, though, and it has very little to do with infectious disease. Swimming at night removes many of the visual cues we normally use to assess our surroundings. Depth, underwater obstacles, changing conditions and even our position relative to shore can become harder to judge. So whether a particular place is appropriate for night swimming depends on the setting, conditions and rules we will check beforehand of course. And experience in the location during the day so you're familiar with it is important too. So follow your passion... but take your brain with you.
And this brings us back to this lake in the night. And since the depths of the water are unknowable to us at this moment, let's look up instead.
Above us, we finally have something we've been missing beneath the trees.
The sky. To see the stars, the most useful thing we can do with our flashlight now is turn it off. And wait. And while we're looking up, everything we've encountered along the way keeps going. And Gypsy is still paying attention to things I can't see.
The night hasn't become still. We have.
WHILE YOU WERE LOOKING UP
When we stop moving through the landscape for a while, I'm reminded that when it comes to infectious disease, we should we stop thinking only about pathogens and start thinking about relationships. Because questions about all the variables at play, give us a better basis for deciding where the risk is, what deserves our attention, and what doesn't.
So tonight, we can sit beside a lake knowing perfectly well that our surroundings are teeming with life of all sizes and shapes, even some that under different conditions could present a risk. And we can still enjoy being here.
FROM SUNRISE TO STARLIGHT
From the first light on the water to a picnic beneath the afternoon sun and now a dark lake beneath the stars, we've spent this summer day looking for the biological world hidden inside ordinary moments.
There is more happening in an ordinary summer day than we could ever possibly see.
Well, we made it, from sunrise to starlight. And eventually, we'll turn the flashlight back on, retrace the trail, and I'll check myself—and Gypsy—for ticks when we get home.
But not yet. For now, the lake is dark. The woods are carrying on behind us, the stars overhead are brighter than ever, and Gypsy and I are both dying for a swim.
Thanks for being here. Don't forget to sign up for my free weekly newsletter, Field Notes, where I continue the conversation on the episode, share things I’m paying attention to and outbreak updates, and peek behind-the-scenes. Until next week, stay healthy, stay informed, and spread knowledge, not diseases.
Annotated Citations
Each citation is annotated to explain how the source connects to the episode and to help listeners who want to explore the science in greater depth.
Accessing the literature: Whenever possible, I've linked directly to free full-text articles and books that are legally available online. All papers in this list are open access.
Fabian S. T., et al. (2024). Why flying insects gather at artificial light. Nature Communications.
➡This study uses high-speed three-dimensional tracking to examine how flying insects behave around artificial light and offers a fascinating alternative to the familiar idea that insects are just attracted to it. The researchers found evidence that artificial light can disrupt insects' normal orientation to the sky, helping explain the circling and trapping behaviors we see around lights at night.
🆓 Open access
Rivas G. B. S., et al. (2018). Effects of light and temperature on daily activity and clock gene expression in two mosquito disease vectors. Journal of Biological Rhythms.
➡This study examines how light, temperature, and internal biological clocks interact to shape daily activity in two important mosquito vectors. It provides a closer look at the biological rhythms behind when mosquitoes are active, and why time of day can become part of the ecology of vector-borne disease.
🆓 Open access
Wolkoff, M., Fyie, L., & Meuti, M. (2023). Light pollution disrupts seasonal differences in the daily activity and metabolic profiles of the Northern house mosquito, Culex pipiens. Insects.
➡This study looks at how light pollution can alter daily activity and seasonal biology in Culex pipiens, an important vector of West Nile virus. It provides an interesting connection between two ideas explored in this episode: the timing of mosquito activity and the ecological consequences of changing the natural nighttime environment.
🆓 Open access
Eisen, R. J., & Piesman, J. (2012). What do we need to know about disease ecology to prevent Lyme disease in the northeastern United States? Journal of Medical Entomology.
➡This review examines the ecology underlying Lyme disease risk, including interactions among ticks, hosts, pathogens, habitat, and human exposure. It's a useful example of why preventing vector-borne disease requires understanding the entire transmission system rather than focusing on the pathogen or vector alone.
🆓 Open access
Gomes-Solecki, M. (2014). Blocking pathogen transmission at the source: reservoir targeted OspA-based vaccines against Borrelia burgdorferi. Frontiers in Cellular and Infection Microbiology.
➡Lyme disease exists within an ecological network connecting Borrelia burgdorferi, ticks, wildlife reservoirs, and ultimately humans. This article explores an unusual prevention strategy aimed at interrupting that cycle in reservoir hosts rather than waiting until the pathogen reaches people. It's a particularly interesting illustration of how understanding transmission ecology can reveal places where the chain might be broken.
🆓 Open access
Diaz, J. H. (2021). Regional rodent-borne infectious diseases in North America: what wilderness medicine providers need to know. Wilderness & Environmental Medicine.
➡This review covers important rodent-associated infections in North America and the circumstances that create risk in wilderness settings. For hantaviruses in particular, it helps explain why exposure to contaminated rodent urine, droppings, or saliva—especially when contaminated material is disturbed—is more relevant than just sharing an outdoor environment with rodents.
🆓 Open access
Byers, K. B. (2018). Zoonotic infections from hantavirus and lymphocytic choriomeningitis virus (LCMV) associated with rodent colonies that were not experimentally infected. Applied Biosafety.
➡This article examines hantavirus and LCMV in the context of rodent colonies and provides additional background for understanding how the route of exposure determines whether an encounter is meaningful from an infectious-disease perspective.
🆓 Open access
Mahroo, O. A. (2023). Visual electrophysiology and “the potential of the potentials”. Eye.
➡This article provides technical background on retinal physiology and visual electrophysiology, including the different contributions of rods and cones to vision. It helps explain why the nighttime landscape gradually becomes visible again even though the amount of light around us hasn't suddenly increased.
🆓 Open access
Ruseckaite, R., et al. (2011). Human scotopic dark adaptation: comparison of recoveries of psychophysical threshold and ERG b-wave sensitivity. Journal of Vision.
➡This study examines how visual sensitivity recovers after exposure to light and provides a deeper look at the physiology of rod-mediated vision. It's the science behind the familiar experience of turning off a flashlight beneath a dark sky, waiting, and gradually discovering that more and more stars were visible all along.
🆓 Open access
https://iovs.arvojournals.org/article.aspx?articleid=2121165
Ellis, J., et al. (2024). 2022 AAHA canine vaccination guidelines: 2024 update. Journal of the American Animal Hospital Association.
➡These veterinary guidelines provide broader context for protecting dogs from infectious diseases and considering prevention according to lifestyle and exposure risk. For the parts of this episode involving Gypsy, they're a reminder that bringing a dog onto the trail adds another host—and another set of preventive-health considerations—to the ecological picture.
🆓 Open access
https://jaaha.kglmeridian.com/view/journals/aaha/60/6/article-p1.xml
Comments