A view of the ocean floor from Alvin. Image: Rachel Smith/Motherboard

Methane-Eating Ocean Microbes Could Play a Major Role in Climate Change

Caltech geobiologist and MacArthur Fellow Victoria Orphan sheds light on the tiny single-celled organisms that help keep Earth’s climate in check.

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Sep 27 2018, 5:05pm

A view of the ocean floor from Alvin. Image: Rachel Smith/Motherboard

THE MOST UNKNOWN is Motherboard's love letter to the scientific process. For the next nine weeks, we'll be profiling the people trying to answer science's most difficult questions. Our feature-length documentary is now available on Netflix, and bonus episodes are available on YouTube.


In the great hierarchy of childhood dream careers, marine biologist is likely to be right up there with astronaut and firefighter. But while most water babies go on to pursue other professions, Victoria Orphan never wavered from her goal to become a “mirne bilogest,” as she spelled it as a grade-schooler in her copy of Dr. Seuss’s My Book About Me.

Image: Victoria Orphan/TEDx

“In general, I just feel much more at home in the water,” Orphan told me. “I’m sure my blood pressure drops every time I hop in.”

Given this ingrained childhood passion, it’s no surprise that Orphan pursued a career in marine biology, earning a BA and PhD from UC Santa Barbara in 1994 and 2001 respectively. What was unexpected, however, was the type of ocean ecosystem that came to captivate her interest: Methane-breathing microbes that live in some of the most remote depths of the sea.

“Like most kids, I think I was excited by the charismatic megafauna, as we tend to call them—dolphins, fish, things like that,” Orphan said. “But what I’m doing now is studying the smallest lifeforms in the ocean, that you can’t see with your naked eye. In many ways, I find this to be the most fascinating and exciting part of research today.”

Orphan, who now serves as the James Irvine Professor of Environmental Science and Geobiology at the California Institute of Technology (Caltech), was able to indulge her love of the sea from an early age. The daughter of a physicist and a literature teacher, she grew up in San Diego, California, with the Pacific Ocean as her playground.

Enchanted by the marine world, she recreated it in her bedroom, decorating the walls with drawings of aquatic life and sketching out the hull of a ship on the ceiling. It was an early premonition of how familiar the submerged view of boats would be to Orphan later in life, when deep sea dives in submersibles like Alvin became a regular part of her worklife.

The submersible craft Alvin being lowered into the sea. Image: Lindsay Blatt/Motherboard

Orphan’s interest in the ocean’s tiniest lifeforms was sparked after observing seawater under a microscope as an undergraduate student. Swarms of normally invisible organisms, illuminated by fluorescent dye, were suddenly brought into sharp relief before her eyes. The sight, like stars in the night sky, was a gateway drug to the enormously consequential—but barely understood—world of marine microbes.

It’s a paradoxical reality that these seemingly humble lifeforms exert a far greater influence on Earth’s processes than ocean megastars like whales, sharks, squids, and octopuses. Large aquatic animals affect their ecosystems, of course, but if you want to meet the creatures that are really running the show on the grandest scales and over the longest time frames, you need a microscope.

“Microbes are typically portrayed as these sort of negative entities, like germs that make you sick, and I was really fascinated to find out that microorganisms are all around us and they are really critical for the health of the planet,” Orphan explained. “They cycle all of the major elements and chemicals that we depend on. That hooked me and I haven’t looked back since.”

She began her work with microbes by sampling deep oil reservoirs where extremophiles, a class of organisms that can survive punishing conditions, metabolize harsh chemicals in near-boiling temperatures. Orphan was drawn to these creatures partly because their abilities are so gnarly, but also because of their potential to mitigate damage from human-created environmental disasters, like oil spills.

“I wanted to know not only which types of organisms were able to live in these environments but how they were affecting the chemistry around them and responding to the physical and chemical environment,” she said. “It’s really this interplay of biology, chemistry, and environmental impacts that I find to be most exciting and one of the more challenging things to figure out in natural ecosystems.”

This interest in the broader context surrounding microbial life led her to specialize as a geobiologist, which is a scientist that studies interactions between abiotic environments, the non-living, physical parts of a habitat, and the living creatures that occupy them. Oil reservoirs served as an excellent primer on microbial influence over habitats (and vice versa), and also how human activity folds another layer of complexity into these natural dynamics. But another group of microbes—albeit with some similarities to the oil-eaters—eventually became the focus of Orphan’s career.

It is a common cliché that we know more about the surface of the Moon than we do about the deep ocean. That is particularly true when it comes to methane seeps, habitats where the gas leaks from the seafloor, sometimes a mile or more below the surface.

To the untrained eye, these seeps look sterile, littered with unassuming carbonate rocks. But as shown in Motherboard’s The Most Unknown, a documentary that follows scientists as they shadow researchers in other fields, experts see something completely different at these depths. For Orphan and her colleagues, the otherworldly seeps are brimming with vibrant ecosystems filled with single-celled organisms—mostly from the Archaea and bacteria families—that live off of methane emanating from the seafloor, sulfates in the seawater, and symbiosis with each other.

A yeti crab. Image: Lindsay Blatt/Motherboard

“This is one of these processes that for many years was thought to be not very favorable for supporting life because it doesn’t give a lot of energy,” Orphan said. “But in reality, what we see is that there are thriving microbial communities that are making a living off of using this process, and they’re doing it through this very tight collaboration. We’ve been interested in understanding more about how they’re sharing energy and the diversity of different organisms that have figured out a solution to working together to carry out this process.”

Deep sea methane seeps were not even discovered until the 1980s, so research into their inhabitants is very much a frontier science. But what has become ominously clear is that these extremophiles may be especially relevant in the era of human-driven climate change. Methane is a potent greenhouse gas, and these microbes are preventing enormous quantities of it from reaching the atmosphere by metabolizing runoff from the seeps. If these deep sea communities are disrupted by human activity, the floodgates could open, with potentially disastrous consequences.

How all this might play out is still an “open question,” Orphan said. She uses that phrase many times in our conversation, hinting at the many secrets and superpowers of these ecosystems, and at the “non-linear” nature of scientific inquiry.

“[Science] oftentimes is this circuitous path and there’s as many failures as successes,” she said. “It’s all building on progressive research, both in your own lab and other people’s findings. But sometimes it takes years, decades even, to make discoveries that get condensed into a few publications, so you miss the whole backstory.”

Extracting answers from the seeps, for instance, requires collaboration between specialists in marine exploration technologies, geobiology, microbiology, genetics, chemistry, paleobiology, and more. Rock samples collected by submersibles are examined for isotopic signatures that can shed light on the past evolution of these communities, contextualizing how they function today.

Orphan’s team has also mastered the art of secondary-ion mass spectrometry (SIMS), a technique that can resolve the molecular composition of these organisms down to one or two nanometers of detail. This innovative line of research earned her a MacArthur Fellowship—also known as the “genius grant”—in 2016, among many other honors.

More recently, advances in genome sequencing have enabled scientists to comb through seafloor samples for DNA, providing new windows into the genetic programming that enables methane-oxidizing ecosystems to function.

“It’s kind of an exciting time with the sequencing technologies,” Orphan said. “It’s sort of a merger of being able to look through the lens of their DNA, and also looking at their actual metabolic activities and the chemical cues in the environment that tell a big picture story of how these organisms are operating in the deep sea environment.”

That excitement is palpable in The Most Unknown, when astronomer Rachel Smith joins Orphan onboard the research vessel Atlantis, and takes a dive in Alvin to the seafloor off the coast of Costa Rica. Sharing the deep ocean environment with people who have never seen it before is one of the biggest perks of the job for Orphan, and you can sense that thrill when Smith embarks on her adventure to the deep, accompanied by Orphan’s colleague Erik Cordes.

“It really is a great bonding moment to be able to go into Alvin with someone who has never dove before, and watch their excitement, going through the twilight and seeing the seafloor for the first time,” Orphan said. “You feel very privileged to be one of very few people who have gotten to see the seafloor first hand. It’s just a thrill. It never ever gets old, to be able to go down in Alvin.”

Atlantis, Orphan's research vessel. Image: James Murray/Motherboard

Smith clearly shared that thrill, and compared the diving experience to traveling in a spaceship to another planet. In fact, this connection between marine extremophiles and extraterrestrial habitats has been made more explicit in recent years, as discoveries are made about ocean worlds like Saturn’s moon Enceladus and Jupiter’s moon Europa, which might contain similar environments to those in the deep sea.

Orphan has been interested in this astrobiological angle of her research for years, and did a postdoc at NASA’s Ames Research Center with a focus on exobiology. Her role as senior scientist at the Center for Dark Energy Biosphere Investigations, an NSF-funded research group focused on the bizarre life-forms that live below the deep seafloor, also inspires her to imagine how similar ecosystems might exist in extraterrestrial habitats.

“It’s a very exciting time to have all of this effort and interest in ocean worlds and the potential that we might actually get to explore places like Europa or Enceladus,” she said. “It piques my interest as an explorer and I see huge parallels between the unexplored deep ocean and what we might find in these exotic outer world environments.”

NASA’s interest in developing autonomous exploration platforms for extreme places on Earth is a “win-win situation,” she added, because “we can learn a lot about this amazing environment on our own planet and also develop technologies that might be useful for future spaceflight missions.”

The search for extraterrestrial life provided a clear overlap in interests for Smith and Orphan, but she also found common ground with physicist Jun Ye, the next link in The Most Unknown’s scientific chain, when he hosted Orphan at his laboratory at the University of Colorado at Boulder. Ye works with atomic clocks, the most accurate timekeeping devices ever made, and demonstrated how his team manipulates strontium atoms to make precision measurements.

“I actually was really pleasantly surprised to see how many commonalities there were just in terms of the challenges in thinking about how do you unravel something that you can’t necessarily see, but you know is there,” Orphan noted.

At one point in the segment, Ye points out that he and his colleagues anthropomorphize the atoms, often calling the elemental particles “he” or “she.” Likewise, Orphan told me that she and her colleagues have their own pet names for the microbes they bring up from the methane seeps.

“They tend to have certain traits associated with them so we actually have given them first-person names as a way of just identifying them, to make it more fun—Igor, Susie, it sticks in your mind better than some label or number,” she said. “We definitely end up adding a little bit of a personal spin on our research. Of course this would never come out in the scientific publications, but in the lab it’s fun to talk about these guys as our friends and family.”

That sense of camaraderie, between researchers and their microbial subjects, is another major perk of Orphan’s job. The kid with the nautically-themed bedroom now looks forward to the long stretches of time she gets to spend on real research vessels, bonding with fellow ocean-obsessed adventurers.

“You have your own little community on a ship for weeks at a time so it’s a very intimate and exciting experience, driven by lots of caffeine and little sleep,” she said. “It selects for certain personality types.”

“In order to be able to do the kind of ecosystem-level science you really need people from a bunch of different disciplines to come together. The ones that are successful, I think, are the ones that are willing to share their expertise, stretch their thinking, and extend creativity outside of their own small world to understand the bigger picture.”