‘It’s Hard to Believe You’re Still on Earth’
How the secrets of the deep sea may help reveal life beyond Earth
Although his work takes him to some of the most inhospitable places on Earth, Professor of Microbiology James “Jim” Holden is warm and welcoming, as his students can attest. His research into the microbes that thrive near hydrothermal vents on the ocean floor is helping to shed light on the origins of life on our planet—and, through a partnership with NASA, the search for life in other parts of the solar system. Whether traveling to the bottom of the ocean to collect samples in a submarine or mentoring students back in the lab, his zest for his work is obvious. “It’s a fun way to make a living,” he admits.
Forces of nature
In his office, housed inside his lab in Morrill Science Center, Holden is animated and easy with a smile as he speaks about his research. On the wall behind him hangs an eye-catching multi-canvas painting depicting an undersea vent in shades of blue, gray, and gold—a gift from a former student. “I teach a class called A Sea of Microbes, which talks about social issues related to marine microbiology, and then I have the students somehow express what they’ve learned in the class,” he says. When one student answered that prompt with a painting, he liked it so much that he asked to keep it. It’s been proudly displayed in his office for 10 years.
Much like the painting’s half-dozen canvases, which come together in different shapes and sizes to form a complete picture, Holden’s varied interests have converged into a rich career. Growing up camping near lakes and rivers, he developed an early appreciation for being around the water. “The bigger the body of water, the better,” he says. At the time, famed oceanographer Jacques Cousteau was bringing footage of ocean life to the masses through his popular television shows, and Holden was entranced.
Then, just before his 14th birthday, Mount St. Helens erupted on May 18, 1980. One of the most powerful volcanic explosions ever recorded in North America, it sent over 540 tons of ash eastward across the continent. From his home in Spokane, Washington—about 250 miles east of the volcano—Holden saw its effects firsthand. “It was a crystal-clear, blue-sky day, and we watched this gray-brown cloud slowly move towards us,” he recalls. “By midafternoon, it was pitch-black, and, like it was snowing, this really fine ash came down over the house.”
“It was fascinating for me that this could happen, and especially so close to home,” adds Holden. Later that summer, he and his family visited friends who lived near the volcano and traveled to see the blast zone. “There were houses that were buried up to the eaves in ash. I saw a car that was wrapped around a tree so that the front and rear bumpers were touching each other.”
Holden fed his fascination by collecting issues of National Geographic and other magazines that covered the eruption. And in college, his two interests intersected when he learned about volcanoes at the bottom of the ocean. “I loved oceans, I loved volcanoes, and here they were together,” he says. “And the fact that you had all this life thriving around these deep-sea volcanoes, that was it for me. I was hooked.”
“ I feel safer in the submarine than I do sometimes driving on Route 9.”
Into the depths
Scientists used to believe that any life on the dark ocean floor would have to be fed by nutrients raining down from above, where photosynthesizing organisms near the surface formed the basis of the food chain. That all changed when famed marine geologist Robert Ballard and his crew discovered a hydrothermal vent for the first time in 1977. Cameras sent 8,000 feet below the surface turned up a shocking discovery: Life was thriving down in the depths. Thanks to the nutrients and chemicals provided by that hydrothermal vent, the ecosystem hosted its own food chain containing everything from single-celled microbes to tube worms the size of a person.
Today, scientists of many stripes turn to that vital ecosystem for answers to their questions about biology, chemistry, geology, and more. Holden’s work focuses specifically on the microorganisms that thrive at high temperatures around thermal vents. His two basic questions: How do these organisms work, and what effects do they have on their environment? To answer these questions, Holden starts by going straight to the source.
Roughly every other summer, he heads out to sea with a team of other researchers to visit Axial Seamount, the Northeast Pacific’s most active submarine volcano, located about 300 miles off the coast of Oregon. Holden was first introduced to the site during his PhD program at the University of Washington, and he’s been visiting ever since. On these two- to four-week voyages, Holden—along with other microbiologists, chemists, geologists, geophysicists, and biologists who study larger organisms—collect samples by remotely controlled or human-occupied submarines (the latter named Alvin). “I love going out to sea, and I’ve been to the bottom of the ocean 11 times in Alvin,” says Holden.
“You are sitting in this little cramped metal sphere, but you get down to the bottom, and you look out the window, and it’s hard to believe you’re still on Earth,” says Holden. Incredible mineral structures loom all around, with water venting out at a temperature of three and a half times the boiling point at the surface. “And there’s life there. The rocks are just covered in life.”
Traveling to the ocean floor in a two-person submersible may sound intimidating, but unlike at the surface, where Holden has occasionally found himself in big storms with 50-foot waves (“Thankfully, I don’t get seasick, but still, that was quite a ride,” he says), his experience down deep has been calm. “The people who run these submarines are so incredibly professional that everything runs very smoothly,” he says. With a laugh, he adds, “I feel safer in the submarine than I do sometimes driving on Route 9.”
Holden and his team collect samples of rock, water, and microorganisms and begin working with them immediately when they get back up to the ship, doing incubations and chemical analyses and trying to isolate new organisms. In the window of just a few weeks at sea, every moment counts. “We work 24 hours a day,” says Holden. Then, once he’s back on land, the research begins in earnest. “Well, after a little bit of a rest,” he says, laughing.
“Until we get back to shore, we don’t really know what happened. So, we are excited to get back and begin processing the samples,” he says. “The fun just begins when you get back from the expedition.”
What makes them tick
In the lab, Holden and his students examine the hundreds or thousands of samples collected. Replicating the conditions where the microorganisms normally grow, the researchers make synthetic seawater and provide the other chemicals the microbes need. They create mathematical models of the microbes’ growth and try to isolate new organisms—his lab has found seven new species so far. “We’ll begin to take these organisms apart, look at their proteins and other molecules inside the cell to try and understand how these organisms tick,” he says. “How are they capable of living under these harsh conditions at temperatures that no other life can live at?”
Holden and his team also explore ways to detect these organisms. “What effect do they have on the oceans or the neighboring environment?” he asks. “And what does this tell us about life on the early Earth, the first half billion years of Earth’s existence?”
That’s where NASA comes in. “Exploration of the deep sea and exploration of space both started about the same time in the 1960s,” says Holden, “and by the 1990s, we realized that the two fields were really running parallel to one another.” That’s because oceans were discovered on other moons in our solar system, with a strong possibility that they might contain deep-sea volcanoes.
Holden, in the right place at the right time, was a PhD student when space scientists and oceanographers were starting to work together. Today, he’s on his sixth grant from NASA to help prep space missions on what to look for in places like Jupiter’s moon Europa and Saturn’s moon Enceladus. “We’re in such an amazing period in history where there are so many exciting things happening in the area of planetary science,” he says. When NASA sends spacecraft to the oceans on these moons, they can look for environmental changes identified by Holden’s lab to determine whether the moon might be habitable, meaning it’s capable of supporting life, or even inhabited, meaning life is actually present.
“When I was studying oceanography as a graduate student and undergraduate, there was only one ocean at the time that we thought about: the one here on Earth,” he says. Now, the field has expanded to include other oceans in our solar system. “It changes the whole idea of what it means to be an oceanographer.”
The discoveries made deep in the ocean also have implications for us right here on Earth. “One of the most important enzymes in biotechnology came from these high-temperature organisms,” says Holden. “You do a COVID test, or you collect DNA from a crime scene, and you’ve got to make copies of it in a test tube, and the enzyme that’s responsible for that comes from the high-temperature organisms that I study.”
One of the organisms Holden’s lab has identified is good at breaking down sugars and proteins—a possible solution for handling organic waste, which can produce climate-warming gases as it decomposes. The lab has worked with White Lion Brewing Company in Springfield to break down its organic-rich brewery waste, as well as waste milk from cows being treated for infections at local dairy farms. The process has the added benefit of producing hydrogen as a waste product—“one of the energy compounds of the future,” says Holden.
“There are still things to figure out.”
The next generation
Speaking of the future, Holden is helping to ensure that the next generation of researchers is capable and productive. For all his accomplishments, discoveries, and deep-sea adventures, he doesn’t hesitate when asked about his proudest achievement. “What I’m proudest of are the students that I’ve been able to mentor,” he says. “It’s the best part of the job.”
“What’s an exciting day for me?” he asks. “It’s discovery. It’s when a student comes to you and says, ‘Hey, I’ve got this really cool result that I want to show you,’ especially if it’s unexpected. Seeing the excitement in the student and having those 'aha' moments are the days that make the job totally worth it.”
His students’ regard for him is just as clear. “He’s so passionate about his work, it was kind of hard not to love what we did, just because he would get so excited,” says Briana Kubik ’25PhD. She didn’t have any microbiology experience before joining the lab, but Holden saw a need for her background in computational work. “I was really interested in using mathematical modeling to be able to describe biological systems,” she says. Holden was willing to teach her the basics, and Kubik centered her dissertation on interspecies competition in deep-sea hydrothermal environments.
“Jim is a really important person in my life,” says Gabby Rizzo ’23, who was excited to discover she could combine her interests in microbiology and space. Now a PhD student at the University of Nebraska–Lincoln, Rizzo started out assisting Kubik before moving on to her own project characterizing a new species from the hydrothermal vents. Methanothermococcus jasoni is only the third species to be characterized from its genus, and it earned Rizzo a prestigious SETI Forward Award, which recognizes outstanding undergraduates and helps them pursue careers in the search for life beyond Earth.
Nathaniel Scott ’25, ’27MS has been working in Holden’s lab since his undergraduate days, studying sulfur-breathing bacteria and the enzymes they use to break down hydrogen for energy. Though excited by this work, he says his greatest discovery is his love for research. “I came into it just trying to get some experience and maybe get a job after college. And now I’m going to grad school and planning on doing even more grad school.”
But Holden taught all three students more than just scientific techniques and concepts. “He’s kind of shown me how to mentor,” says Scott. “He’s a really good example to me of somebody who’s both a productive scientist and somebody who cares about their students and really takes the time to understand them and be there for them in ways that are sometimes hard to come by in academia.”
“Jim was an amazing mentor to me, and he trained [Kubik] to be an amazing mentor,” says Rizzo. “She mentored me really well, and now I get to be a mentor to undergraduates.” She adds, “I wish everybody could have a Jim.”
Looking toward his own future, Holden hopes to keep going out to sea and building on the research he’s already done. “What’s the next important question?” he asks. It might involve microorganisms found in other environments. “I love doing deep-sea work, but there are a lot of parallel, similar types of projects that can be done that are literally closer to home.” For example, that enzyme that paved the way for COVID tests and DNA collection? It was found not only on the ocean floor but also in the hot springs at Yellowstone National Park. “Maybe they come from a salt marsh, or maybe they come from the gut of a human being,” he says of potential future discoveries. “What can we take from what we’ve learned about the deep sea and apply it to other types of questions? I think that there are a lot of exciting possibilities.”
“I wasn’t born too late,” he says. “There are still things to figure out.”
