Mapping Microbes: Seeking Carbon-Capturing Bacteria Off a Remote Japanese Island

What if the solutions to some of the world’s biggest problems were microscopic? From devouring carbon dioxide to digesting plastics, certain microbes have evolved traits that could rewrite our environmental future. In Mapping Microbes, we join forces with scientists, explorers, and local changemakers as they traverse the world in search of microbial adaptations to climate change, ocean acidification, biodiversity loss, and beyond.

One hundred miles southwest of Tokyo, a volcanic island rises from the depths of the Philippine Sea.

Sculpted by the heat, gases, and chemicals of the Earth’s core, Shikinejima is home to bubbling CO₂ vents, highly acidic waters, and a rainbow of metallic green and orange-brown hot springs. Over billions of years, organisms have adapted to the island’s inhospitable conditions and found ways to thrive within its constraints.

Nowadays, its rocky cliffs are dotted with lush greenery, tropical flowers, and unique wildlife—but it’s the island’s invisible residents that caught the attention of the Two Frontiers Project (2FP). 

The 2FP team travels the world to find and collect microbes adapted to conditions that mirror a changing climate. For their Carbon Initiative, they look to bacteria that thrive in high-CO₂ conditions like those on Shikinejima. They then study these microbes to see if they possess helpful adaptations for reducing carbon dioxide in the atmosphere. 2FP’s small, agile non-profit research team previously sampled microbial life in carbonated springs of Colorado’s Rocky Mountains and volcanic plumes in the Aeolian Islands off Sicily before landing on Shikinejima this summer.

“This site was unlike anywhere else in the world—certainly [unlike] anywhere we’ve sampled,” says 2FP’s Executive Director, Dr. Braden Tierney.

We caught up with the team to learn about Shikinejima’s extraordinarily resilient microbial life, how they conducted first-of-its-kind sampling on it, and what their findings could mean for climate adaptation in Japan and beyond.

Preparing for the Unknown

Before setting off to Shikinejima last August, the 2FP team studied existing research on the island’s ecology and worked with on-the-ground researcher Dr. Sylvain Agostini (who has been studying the island’s evolving geochemistry since 2014) and long-time partner Dr. Marco Milazzo (a University of Palermo Professor of Ecology who specializes in how marine ecosystems adapt to climate change).^1,2 

As part of the International CO₂ Natural Analogues Network (ICONA), these collaborators had critical knowledge of how carbon dioxide and acidification impacted the island’s ecosystems. Now, 2FP’s work would contribute a critical new layer: knowledge of the microbial life that underpins these ecosystems.

The team also worked closely with the island’s Head of Fisheries, Mr. Kiyoshi Onuma, to ensure their work respected—and ultimately benefited—the locals who depend on the island’s natural resources like fish and coral. 

This preparation provided clues about where to start looking for interesting microbial life and how to collect it without disrupting the surrounding community.

This expedition would be the team’s most ambitious and logistically challenging to date. In addition to collecting terrestrial microbial samples, they would also be doing underwater sampling—the first time tackling both sampling regimens at the same site. 

After months of planning, the team arrived in Shikinejima equipped with hundreds of pieces of scientific equipment, coolers full of dry ice, and SCUBA gear. Finally, their survey of the island’s mysterious microbial life could begin.  

“Upon deciding to do this, we knew it was going to take a lot of time, effort, and communication,” says 2FP’s  Director of Operations, Krista Ryon. “It would require everyone to use everything in their skillset to complete every task they were assigned.”

To understand the magnitude of this undertaking, consider the collection process for a single sample:

Once a team member identifies an area with potentially interesting microbial life, they collect a small piece of sediment, water, or biomass from it and place it in a 50ml test tube. Then, they write an extremely detailed description of where the sample came from, what time of day it was collected, measure the surrounding water chemistry, etc. (the metadata). Any labeling or measurement mistakes could disconnect the sample from this critical contextual information, rendering it useless. (And remember: They’re doing this about 50 times a day, on land and underwater.) 

Next, the sample needs to be immediately cooled to slow microbial activity, processed in the lab, and then kept frozen to keep it alive for future study. Once it’s been frozen, allowing it to thaw, says 2FP’s Director of R&D, Dr. James Henriksen, would be like waking a hibernating bear in a cage without food or water: “It wouldn’t last very long.” 

In addition to freezing certain samples for future study, the team also planned to sequence (analyze the genetic material of) some microbes in real time to gain insights into their properties. The hitch: There was no sterile laboratory on the island—so they had to bring along the equipment to rig their own. 

They were able to transform a former fish processing room in the University of Tsukuba’s field research station into a cutting-edge lab using their signature modular science system. This portable kit contains supplies for microbial sampling, genetic analysis, and culturing, and it’s what allows 2FP to conduct science in resource-limited environments around the world. 

Science in Motion

As soon as the team got to Japan, they knew the weather would further complicate their already complex work. Tropical storm warnings lingered after a typhoon that threatened their arrival, and temperatures on Shikinejima approached 100 degrees Fahrenheit with 80-100% humidity.

“I was struck by the experience of being at the whim of nature,” says Erin Miller, expedition participant and the Senior Manager of SeedLabs. “In a typical lab, it’s perfectly cleaned, controlled, and air-conditioned. Here, there were insects, typhoons, and megaquake warnings.” 

Each morning, the group would brave the elements to explore different parts of the island by land and sea. The multidisciplinary team included experts in marine biology, genomics, data science, microbial ecology, and more. Instead of operating in silos, they combined their expertise to form one “meta-scientist,” working together to study the micro and macro life on the island.

Through it all, they stayed flexible and open to surprise. “We always come in with a plan for what we want to sample and what we want to study while we’re there—but it always changes,” says Ryon. 

When Henriksen’s microbiology background made him suspect that certain colors of onsens (natural hot springs) might be teeming with greenhouse gas-fixing microbes, for example, they focused their attention there.

When Ryon, an environmental genomics specialist, realized that certain corals had somehow found a way to adapt to highly acidic waters off the island’s coast, they were sure to take plenty of samples of them.

After long, sweaty, mosquito-ridden days in the field, the team returned to the makeshift lab to start processing, cataloging, storing, and sequencing until the wee hours of the morning—the first time genetic sequencing was done on the island of Shikinejima.  

“I like to think of science as asking questions of nature,” says Miller. “With everyone’s collective knowledge, we were able to ask such robust questions and get such great answers.” 

During meal breaks, they’d learn from local partners about how the island’s larger ecosystem might be contributing to the unique adaptations they were finding in the lab. 

“Doing scientific research all over the world in these remote places, you really learn to rely on the people who make that part of the world their home,” says Henriksen.

All said and done, the team was able to collect and prepare to sequence 168 samples of bacteria from the island’s water, sediment, and coral—microscopic souvenirs that could prove highly valuable to the scientific community.

Beyond the Field

The 2FP team is now in the process of adding the Shikinejima samples to their Living Database, an extensive biobank of microbial samples from extreme environments around the world, which they describe as the “crown jewel” of their work. This repository includes a cryopreserved sample of the complete microbial ecology from each location, paired with a detailed map of its genetic makeup.

Other researchers will be able to request to receive samples of these microbes so they can study them in their own labs. “Our plan is to lend this data to the world,” says Ryon.

This type of transparency and data sharing is practically unheard of in the scientific community, which is often veiled in secrecy and competition. By making their work available to others, the 2FP team hopes it will help fuel faster and more effective solutions. 

“We’re not just doing science for the sake of doing science. We’re trying to solve problems,” says Tierney.

The team is optimistic about the potential of many of the microbes they identified on Shikinejima. Henriksen is giddy as he describes certain cyanobacteria they found, for example. This type of photosynthetic bacteria is difficult to grow in a lab but can be very effective at absorbing or converting carbon dioxide. Usually, he’d be lucky to walk away from an expedition with one species of cyanobacteria of interest. “But from Shikinejima,” he smiles, “we are growing 50-plus.” 

Ryon says she’s eager to see how the bacteria from the island’s heat- and acidity-resistant coral could go on to help other reefs around the world survive as ocean conditions change. This microbial knowledge will also go back to benefit the people who live on Shikinejima—many of whom, notes Agostini, depend on the health of fisheries and coral for their livelihoods. 

“That is how we fight helicopter science. As an organization, we’re dedicated to using open science to broaden impact across different populations,” Tierney says.

“This [information] is not for profit or for commercialization. It’s meant to be shared,” he adds.

The Shikinejima expedition shows how collaborative, innovative, and transparent science can drive large-scale solutions. It also serves as a lesson in interspecies learning—a reminder that microbes have valuable insights to share when we are curious enough to listen.

Explore More From The Two Frontiers Project Here:

• The Bacteria That Could Help the World Curb The Climate Crisis
• Meet the Microbes of Your Home

Photographs by John Kowitz and Nobu Arakawa.