Cave diving, microbes, and slime: A love story

Some people decorate their offices with flowers, family photos, or art. Jennifer Macalady prefers bottles of sludge.

“They’re super cool,” she says, peering at what, at a glance, looks like someone’s smoothie that’s been left out for several days. 

The jars actually contain self-sustaining microbial ecosystems known as Winogradsky columns. In the light, layered colors emerge. There’s a purple layer from a sulfur-eating phototroph, a black shade from pyrite, and a green tint from cyanobacteria. A closer inspection reveals a weird and sinuous beauty.

The bottles are fitting decorations for a slime-obsessed scientist who delves into the most-overlooked environments on Earth. As a researcher at Pennsylvania State University, Dr. Macalady studies the underground, out-of-sight, and microscopic world of life in cave slime. Through these subterranean life-forms, she probes the biggest mysteries of biology. Her work is helping to broaden our view of where life can be found both on Earth and beyond.

“Because we don’t see [microbes], we don’t have this gut feeling for how much a part of Earth’s life they are,” says Dr. Macalady, noting that we’ve barely begun to know even the tip of the iceberg of microbial species. “There is an enormous amount of potential to learn new and useful things about Earth life by continuing to pick away at this iceberg.”

The biology below

Dr. Macalady is a tough scientist to pigeonhole. She’s a geomicrobiologist, a biogeochemist, and an astrobiologist. Her fieldwork takes her to the depths of caves in Italy, Mexico, the Bahamas, and the United States. Her research shifts between the nanoscale and the ecosystem scale.

“Jenn has a great balance of combining the pursuit of something that just interests her with asking really big transcending questions, and having fun along the way,” says Jan Amend, a geobiologist at the University of Southern California who is currently working on a paper with Dr. Macalady. 

It’s that curiosity – and her love of slime – that led Dr. Macalady to perhaps the most pivotal moment of her career: a visit to Frasassi, an Italian cave system perfect for studying the sulfur cycle in subsurface environments. There, she fell in love with caves. 

Tourists exclaim over the stalactites and stalagmites in the upper caverns of Frasassi, but Dr. Macalady went lower, through slippery mud and a strong smell of sulfide until she found a different kind of beauty.

“I was absolutely smitten, just starry-eyed,” Dr. Macalady recalls of her first visit in 2002. “There was so much slime of so many different kinds, on every surface.” She lost track of time and stayed below for eight hours. “It was a completely transformative experience.”

Some cave environments come closest to replicating what the Earth was like billions of years ago, as life was just beginning. In caves, Dr. Macalady looks for microbial communities and biofilms that rely on chemical reactions, rather than light. Scientists think some of the first life-forms evolved away from light and with little oxygen. 

“We don’t know how life emerged on Earth, but we know it did,” says Dr. Amend. “We don’t know if there’s life on another planetary system, but it seems like there might be conditions out there somewhere where life would persist. These are fundamentally exciting questions – the kind of questions children ask from day one.”

Unearthing a whole new world

In a field where so much is still unknown – biologists estimate we’ve identified less than 1% of microbial species on Earth – there’s plenty to explore. And the terrestrial subsurface, Dr. Macalady says, is arguably the least-explored habitat on the planet.

“There’s a tremendous amount of potential for humanity, for understanding life on a planet, just picking away at this blackness that is microbial life on Earth,” she says.

That can mean regularly finding new species of microbes, many of which Dr. Macalady and her colleagues sequence genetically. Using an electron microscope, they make “micrographs,” visual renderings that help scientists see patterns and understand how various microbes and minerals work together.

Dr. Macalady is fascinated by individual microbes and how their communities appear. In her office, she points to photos of white feathery specimens in hot sulfuric caves, to fuzzy brown microbial masses in Frasassi that “are like being on the inside of a teddy bear,” and to a stretchy white substance in a hot cave that she calls “silk,” which seems to stabilize the normally unstable elemental sulfur. 

One new species of cyanobacteria grew with such distinctive purple tufts and Muppet-like hair that Dr. Macalady and her colleagues decided to name it after Jim Henson. 

Primarily, she’s interested in understanding the rules that govern these microbes: why multiple species that seem to have the same function coexist in the same niche; how microbes make pyrite, a mineral key to the Earth’s past; and whether we can learn enough about these microbial communities to successfully predict, in a previously unexplored place, what life might be there.

Out of the box biology

Despite science fiction imaginings, most scientists believe that if extraterrestrial life is discovered, it will look a lot like simple, microbial life on Earth. But such a discovery requires understanding the origins and bounds of life as we know it. 

That’s where cave slime comes in. Subsurface microbiology underpins some of astrobiologists’ thinking about where they might find life on other worlds – particularly in places where sunlight might not reach. 

“You can have a really exciting biosphere underground,” says Dr. Macalady. “You don’t need light; you don’t need oxygen. You just need chemical energy.”

On Earth, it’s those lightless, least-explored places that entice Dr. Macalady. She’s enlisted cave divers to reach the most extreme environments, and she’s learned to navigate complex vertical and horizontal ropes – “nylon highways” – that guide her deep below the surface.  

While she loves the adventure of caving, it’s the single-celled organisms, and the communities they create, that are the real exploration for her.

“We’re walking around with our microbial biomes in a sea of microbes in the soil and the microbiomes of plants,” says Dr. Macalady. With her research, she says, “we’re trying to bring Earth life into focus.”