SeedLabs

SeedLabs is the environmental research division of Seed Health. Founded on the notion of One Health—that human health and environmental health are intertwined and interdependent—we advance emergent environmental research and microbial innovations to recover ecosystems impacted by human activity and address some of the greatest challenges presented by climate change.

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Community Science
Carbon Dioxide
Methane
Coral
Soil
Honey Bees
Plastics

01Community Science

Creating opportunities for public engagement in microbiome science.

Research Collaborators

The Two Frontiers Project

Can taking a more communal approach to science drive solutions and inspire hope?

At SeedLabs, we believe that science can and should happen anywhere—not just in the lab. As such, we invite the public to participate in our research projects by describing and, in some cases, sampling the microbial life around them. Community science is a key way to spark public excitement in the sciences, grow communities invested in health and sustainability, and, ultimately, build more robust and comprehensive datasets. It proves that, much like microbes, we are stronger and more adaptive when we work together.

Status of Research

To date, SeedLabs has partnered with The Two Frontiers Project on three initiatives that engage community scientists across the U.S.:

The Extremophile Campaign: At Home invited participants to sample microbes from “everyday extreme” environments in their homes (think: piping-hot coffee machines and eternally damp dishwashers). The Two Frontiers Project is now investigating whether this tapestry of at-home microbial life possesses adaptations to increasingly common environmental conditions, such as rising temperatures and heightened radiation, and could help power the future of climate solutions. This project is in the sequencing and analysis phase, and is no longer accepting samples.

Learn more on Cultured.

The Extemophile Campaign: In the Wild expanded upon our At Home work, inviting participants to help identify and map overlooked high-CO₂ sites in their regions, including hot springs. This project is in the sequencing and analysis phase, and is no longer accepting samples.

Project ReefLink engaged a critical but untapped frontier for coral research: aquariums. For this initiative, SeedLabs and The Two Frontiers Project called on home hobbyists and professional aquarists to submit coral samples from their tanks for microbial analysis. Like the human microbiome, the microorganisms that live in and on coral are essential for their health and resilience.

Reef tanks present a uniquely accessible and controlled environment in which to study corals and their microbiomes. By studying the microbiomes of cultivated aquarium coral, we hope to identify microbial patterns, signatures of imbalance, or taxa that may help revive threatened coral reefs in the wild. This project is in the sequencing and analysis phase, and is no longer accepting samples.

Learn more on Cultured

02Carbon Dioxide

Could ‘extreme’ microbes steward the future of carbon capture?

Research Collaborators

The Two Frontiers Project

Could ‘extreme’ microbes steward the future of carbon capture?

Rising atmospheric carbon dioxide levels are a major concern for life on Earth, fueling rapid changes across our planet. In addition to reducing CO₂ emissions, we need solutions for capturing the greenhouse gas from the environment and storing it or converting it into usable materials¹—and that’s where microbes could come in.

Microbes have been evolving on the planet for at least 3.6 billion years, further optimizing their physiology with every round of cell division. A key aspect of microbial physiology is their ability to survive just about anywhere, living off whatever resources are available. Certain species have developed ways to survive and thrive in extreme and inhospitable conditions, including high-CO₂ environments like hot springs and hydrothermal vents.

The Two Frontiers Project (2FP), founded by Dr. Braden Tierney, Krista Ryon, and Dr. James Henriksen, is an non-profit research initiative devoted to “scientifically exploring” the world in search of microbes that could help solve humanity’s greatest challenges. They hypothesize that the places on Earth with the highest CO₂ likely house the organisms that are best at consuming it.

Their carbon initiative aims to discover these carbon-eating microbes living in extreme environments across the planet.

The team is also creating a first-of-its-kind, open-source ‘living database’ of extreme microbiomes, combining DNA sequencing data with a biobank of distinct environmental and biological samples. This comprehensive dataset will help scientists better understand microbial diversity and its potential applications for climate resilience.

SeedLabs provides catalytic funding, strategic partnership, and science communication support to advance 2FP’s mission. In collaboration, we aim to tap into the power of microbes for novel solutions to the climate crisis.

Status of Research

To date, under our SeedLabs partnership, 2FP has completed four research expeditions to uncover microbes in high CO₂ areas across the globe.

CARBON1 took place at the Aeolian Islands off the coast of Sicily to sample microbial life in the volcanic, highly acidic hydrothermal CO₂ vents near the small island of Vulcano.

CARBON2 traversed Colorado—a state famous for its hot and carbonated springs—to collect, sequence, and culture microbial samples from deep in the Rocky Mountains. With Oxford Nanopore's MinION system, the team carried out a novel approach for sequencing DNA in the field and designing enrichment media onsite for targeted isolation of carbon-capture-efficient microbes.

CARBON3 returned to Sicily’s Aeolian Islands to explore the unique underwater CO₂ seeps known as the Smoking Land where cold-water hydrothermal vents create an extraordinary bubbling, acidic environment that dramatically shapes local ecosystems. To access the microbial life thriving at these remarkable sites, the team tested innovative sampling methods and performed technically demanding dives, capturing rare insights from one of the ocean’s most challenging habitats.

CARBON4 journeyed to Shikinejima, a remote island off the coast of Japan, to study its extraordinary landscape shaped by CO₂ seeps. The area’s volcanic activity creates terrestrial hot springs and bubbling acidified waters, offering a rare opportunity to understand how life adapts to higher levels of CO₂. The expedition team navigated challenging conditions to capture critical scientific samples, providing valuable insights into how microbes might help marine ecosystems respond to ocean acidification in the coming decades.

Learn more on Cultured.

These expeditions have led to several new findings, including the discovery of a never-before-seen microbe highly efficient at consuming CO₂, demonstrating traits that could potentially outperform leading carbon-capturing organisms (particularly in terms of biomass production). The team lovingly nicknamed the organism 'Chonkus' for its large size. This finding was published in the scientific journal Applied and Environmental Microbiology.²

Additionally, the research team’s early analysis has identified 46 microbial consortia from corals in high-CO₂ environments with traits potentially linked to coral colonization and resilience to CO₂-driven ocean acidification. These findings could pave the way for microbial innovations to protect coral reefs and strengthen coastal resilience, helping sustain local fishing industries and global economies. The samples and associated data will be added to 2FP’s open-source living database for further study.

Learn more on Cultured

1 Intergovernmental Panel on Climate Change. (2022). Carbon dioxide removal (CDR): IPCC AR6 Working Group III factsheet. https://www.ipcc.ch/report/ar6/wg3/downloads/outreach/IPCC_AR6_WGIII_Factsheet_CDR.pdf

2 Schubert, M. G., Tang, T.-C., Goodchild-Michelman, I. M., Ryon, K. A., Henriksen, J. R., Chavkin, T., Wu, Y., Miettinen, T. P., Van Wychen, S., Dahlin, L. R., Spatafora, D., Turco, G., Guarnieri, M. T., Manalis, S. R., Kowitz, J., Hann, E. C., Dhir, R., Quatrini, P., Mason, C. E., Church, G. M., … Tierney, B. T. (2024). Cyanobacteria newly isolated from marine volcanic seeps display rapid sinking and robust, high-density growth. Applied and environmental microbiology, 90(11), e0084124. https://doi.org/10.1128/aem.00841-24

03Methane

Studying microbial approaches to capturing and transforming methane at scale.

The Two Frontiers Project

Could methane-consuming microbes help us more rapidly respond to climate change?

Following successful carbon dioxide expeditions, The Two Frontiers Project (2FP) set its sights on another climate change catalyst: methane.

Methane (CH₄) gas is rapidly building up in our atmosphere, and its contribution to global warming is 86 times greater than that of CO₂ over a 20-year period.¹But unlike carbon dioxide, methane is short-lived (it only persists for 10-12 years before being broken down), making CH₄reductions a climate solution with a fast and decisive payoff.²

Most methane emissions are anthropogenic (human-caused), driven primarily by fossil fuel production, industrial agriculture, and landfill waste. However, the gas is also released naturally in the environment from features like wetlands, permafrost, and gas seeps.

Some microbes, known as methanotrophs, have evolved ways to consume methane as an energy source to survive in these conditions. The 2FP team wondered: Could these organisms provide a blueprint for capturing and transforming methane on a global scale?

Status of Research

To date, with the support of SeedLabs, 2FP has completed two research expeditions to collect microbes in high-methane areas across the globe. Now, they are analyzing the samples in the lab for climate-relevant adaptations—and sharing their findings with the wider scientific community as they go.

METHANE1 traveled to Scoglio d’Africa off the coast of Italy to collect microbes from high-methane underwater mud volcanoes with local collaborators. In Italy, 2FP successfully deployed a new method for collecting methane-consuming microbes without disrupting their ability to grow.

METHANE2 ventured to the Buzău region of Romania to look for methane-consuming microbes in otherworldly land features like mud volcanoes and eternal flames. While there, the team tested a new low-cost, portable tool for measuring methane gas in the environment to quickly locate methanotrophic activity.

Learn more on Cultured

¹ Jackson, R. B., Abernethy, S., Canadell, J. G., Cargnello, M., Davis, S. J., Féron, S., Fuss, S., Heyer, A. J., Hong, C., Jones, C. D., Matthews, H. D., O’Connor, F. M., Pisciotta, M., Rhoda, H. M., De Richter, R., Solomon, E. I., Wilcox, J. L., & Zickfeld, K. (2021). Atmospheric methane removal: A research agenda. Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences, 379(2210), 20200454. https://doi.org/10.1098/rsta.2020.0454

² United Nations Environment Programme, & Climate and Clean Air Coalition. (2021). Global methane assessment: Benefits and costs of mitigating methane emissions. United Nations Environment Programme.

04Coral

Using microbiology to increase reef resilience.

Research Collaborators

Raquel Peixoto, PhD, MSc

KAUST

The Two Frontiers Project

CitSci.org

Coral Morphologic

Could microbiome manipulation and probiotics help save corals?

Coral reefs are one of the most biodiverse ecosystems on Earth. They sustain 25% of marine life,¹ and their function in the economics, health, and protection of human ecosystems is equally vital.

Coral is a ‘holobiont’—an animal host and the many microbes living in or on it, which function together as a single unit.² These microbes—algal symbionts, and a variety of bacteria, archaea, fungi, and viruses—are vital partners for coral survival. They help corals get nutrients and energy, protect them from disease, and support their ability to withstand stressful conditions. Without them, corals lose much of their strength and resilience. When a coral is exposed to stressors like heat, acidity, pollution, or disease, its partnership with microbes and algae can break down.³ As these colorful symbionts are lost, the coral turns pale or white—a process called bleaching—that leaves it weakened and susceptible to death.

Due to increasing anthropogenic (human-caused) ocean warming, acidification, and pollution, the relationship between coral and its resident microbes has never been more at risk. If current trends in greenhouse gas emissions continue, we stand to lose 90% of the world’s coral in the coming decades.⁴ It doesn’t have to be this way.

In 2020, SeedLabs began to investigate microbiological approaches to coral conservation. First, we partnered with advisor Dr. Raquel Peixoto, Associate Professor of Marine Science at KAUST, on her lab’s work to develop a next-generation “coral probiotic” that leverages beneficial bacteria to help restore and regenerate these critical ecologies. Then, in partnership with The Two Frontiers Project (2FP), we set out to learn from the highly resilient coral and microbial life thriving around volcanic CO₂ seeps off the coasts of Italy and Japan. We’ve also advanced this research through our coral-focused community science project.

Status of Research

Carbon Stress: Volcanic CO₂ seeps are natural environments that mimic future ocean warming and acidification. The lifeforms that can withstand their harsh conditions may possess adaptations that could help other corals survive in a warming world. To date, SeedLabs and 2FP have conducted expeditions to sample coral and microbial life in carbon-rich environments in Sicily and Japan. Sample analysis is currently underway, with early findings identifying dozens of microbial consortia with traits potentially linked to coral colonization and resilience to ocean acidification.

Coral Probiotics: Dr. Piexoto’s lab conducted studies in the Coral Probiotics Village, a specialized underwater laboratory in the Red Sea. Early results showed promise in using coral probiotics to prevent bleaching, enhance calcification, and support coral growth and resilience, and Dr. Peixoto’s lab continues to advance this research.

Learn more on Cultured

¹ Timmers, M. A., Jury, C. P., Vicente, J., Bahr, K. D., Webb, M. K., & Toonen, R. J. (2021). Biodiversity of coral reef cryptobiota shuffles but does not decline under the combined stressors of ocean warming and acidification. Proceedings of the National Academy of Sciences, 118(39). https://doi.org/10.1073/pnas.2103275118

² Margulis, L., & Fester, R. (1991). Symbiosis as a source of evolutionary innovation. MIT Press.

³ Schul, M. D., Smyth, A., Patterson, J. T., Zangroniz, A. N., Krueger, S. L., & Meyer, J. L. (2024). The coral holobiont: A brief overview of corals and their microbiome (EDIS Publication SL520/SS733). University of Florida Institute of Food and Agricultural Sciences. https://edis.ifas.ufl.edu/publication/SS733

⁴ Klein, S. G., Roch, C., & Duarte, C. M. (2024). Systematic review of the uncertainty of coral reef futures under climate change. Nature Communications, 15, 2224. https://doi.org/10.1038/s41467-024-42809-5

05Soil

Sprouting soon. Check back mid-2026.

06Honey Bees

Developing probiotics to improve honey bee resilience.

Research Collaborators

Gregor Reid, PhD, MBA

Scientific Advisor

Brendan A. Daisley, PhD

PostDoc, University of Guelph

Could beneficial microbes help save honey bees?

The honey bee (Apis mellifera L.) is one of our most vital insect pollinators, responsible for nearly a third of our global food crops.¹ Yet widespread pesticide use, along with climate change, disease, and habitat loss, have contributed to a stark reduction in honey bee populations over the past decade.²

Seed Scientific Board Member, Dr. Gregor Reid, and SeedLabs collaborator, Dr. Brendan Daisley, identified three probiotic strains—Lactiplantibacillus plantarum Lp39, Lacticaseibacillus rhamnosus GR-1, and Apilactobacillus kunkeei BR-1—with the potential to improve innate immune response, provide resistance against infection, and reduce the use of toxic pesticides.³

So, we developed The BioPatty™, formulated with these three probiotic strains and delivered it to A. mellifera hives.

Early results showed promise. Hives that were administered the BioPatty™ demonstrated a significantly lower pathogen load in both adult bees and in larvae than those without. Initial field trial observations were then reproduced in laboratory experiments, indicating that our three-strain probiotic could improve honey bee survival against Paenibacillus larvae infection, directly inhibit P. larvae cells in vitro, and modulate innate immunity of honey bees.

The team has since developed the probiotic blend in a spray-based delivery format that has been applied in field studies and shown to support bee resistance against pathogens.

Status of Research

Since 2018, the formulation has undergone three field trials—including the largest ever conducted on a honey bee probiotic. Over the course of several years, independent researchers from the University of Guelph, Western University, and the University of California, Davis (UC Davis) observed its long-lasting benefits to honey bees that correspond with shifts in immune signaling, microbiota composition, pathogen infestation, and overall colony size.

The findings were published in the ISME Journal in 2023 and demonstrated the probiotic’s effectiveness in reducing levels of pathogens and parasites, enhancing immune defense and survival, mitigating antibiotic-induced dysbiosis, and improving key measures of hive productivity.⁴ The findings reinforce the promise of microbes to support at-risk ecosystems impacted by human activity and the climate crisis. The formulation is currently being studied in a field trial.

¹ Lactobacillus spp. attenuate antibiotic-induced immune and microbiota dysregulation in honey bees Brendan A. Daisley, Andrew P. Pitek, John A. Chmiel, Shaeley Gibbons, Anna M. Chernyshova, Kait F. Al, Kyrillos M. Faragalla, Jeremy P. Burton, Graham J. Thompson & Gregor Reid Commun Biol 3, 534 (2020). https://doi.org/10.1038/s42003-020-01259-8

² Missing Microbes in Bees: How Systematic Depletion of Key Symbionts Erodes Immunity 

Brendan A. Daisley, John A. Chmiel, Andrew P. Pitek, Graham J. Thompson, Gregor Reid

Trends in Microbiology, S0966-842X(20)30185-2; (2020). https://doi.org/10.1016/j.tim.2020.06.006 

³ Novel probiotic approach to counter Paenibacillus larvae infection in honey bees

Brendan A. Daisley, Andrew P. Pitek, John A. Chmiel, Kait F. Al, Anna M. Chernyshova, Kyrillos M. Faragalla, Jeremy P. Burton, Graham J. Thompson, Gregor Reid The ISME Journal, 14(2), 476–491; (2020). https://doi.org/10.1038/s41396-019-0541-6

⁴ Daisley, B.A., Pitek, A.P., Torres, C. et al. Delivery mechanism can enhance probiotic activity against honey bee pathogens. ISME J 17, 1382–1395 (2023). https://doi.org/10.1038/s41396-023-01422-z

07Plastics

Growing bioengineered bacterial strains to reduce plastic waste on space missions.

What if a microbe could help change the future of plastic?

The UN has called the accumulation of plastics a planetary crisis. Plastic is rampant in our environment, and it’s even becoming a problem in outer space. Plastic waste used by astronauts is building up inside spacecraft, posing a growing challenge to long space missions. Recycling isn’t enough to fix the plas tic crisis—we need new solutions for cleaning up waste.

In collaboration with researchers from institutions including MIT Media Lab Space Exploration Initiative, the National Renewable Energy Laboratory, and Harvard Medical School, we developed and tested an autonomous bioreactor system that degrades single-use polyethylene terephthalate (PET) plastic and upcycles it into the components of a new, environmentally benign material (‘new plastic’) using bacteria and enzymes.

The system first introduces PET to a specialized enzyme, which breaks it down into organic compounds, then utilizes a bioengineered bacterial strain—Pseudomonas putida KT24401—to convert these compounds into β-ketoadipic acid (BKA)—a high performance nylon monomer which can then be 3D printed into various objects for use on Earth or in space (think: sneakers, shirts, chairs, even a spacesuit).¹

On November 26th, 2022, the bioreactor was transported to the International Space Station (ISS) for further testing—so we could better understand the unique impacts of microgravity and radiation on the bacteria’s upcycling abilities. The biological system was aboard the ISS for 43 days before completing its space flight on January 8, 2023.

Status of Research

The results from this mission have been published in the open-source journal NPJ Microgravity.²

Once in orbit, the autonomous system proceeded through a pre-programmed experiment schedule, enabling culturing and data collection on the effect of spaceflight on microbes without the need for human intervention or astronaut resources for one month.

In service of democratizing biological science in space, this paper outlines how other researchers can build their own iterations of the system (which was constructed from 3D-printed and commercially available components).

By sharing the learnings from this mission in an open-source journal, SeedLabs and collaborators hope to help catalyze future plastic upcycling initiatives that use microbes.

As we move towards continued exploration of the cosmos, microbes’ upcycling capabilities offer a promising tool for the future of space exploration. Furthermore, they could help solve the plastic crisis here on Earth, too.

Learn more on Cultured

Research Collaborators

Xin Liu, Pat Pataranutaporn, Benjamin Fram, Allison Z. Werner, Sunanda Sharma, Nicholas P. Gauthier, Erika Erickson, Patrick Chwalek, Kelsey J. Ramirez, Morgan A. Ingraham, Natasha P. Murphy, Krista A. Ryon, Braden T. Tierney, Gregg T. Beckham, Christopher E. Mason, Ariel Ekblaw

MIT Media Lab Space Exploration Initiative

National Renewable Energy Laboratory

Harvard Medical School

1 Werner, A. Z., Avina, Y. C., Johnsen, J., Bratti, F., Alt, H. M., Mohamed, E. T., Clare, R., Mand, T. D., Guss, A. M., Feist, A. M., & Beckham, G. T. (2025). Adaptive laboratory evolution and genetic engineering improved terephthalate utilization in Pseudomonas putida KT2440. Metabolic engineering, 88, 196–205. https://doi.org/10.1016/j.ymben.2024.12.006

2 Development and flight-testing of modular autonomous cultivation systems for biological plastics upcycsling aboard the ISS. Liu, X., Pataranutaporn, P., Fram, B., Werner, A. Z., Sharma, S., Gauthier, N. P., Erickson, E., Chwalek, P., Ramirez, K. J., Ingraham, M. A., Murphy, N. P., Ryon, K. A., Tierney, B. T., Beckham, G. T., Mason, C. E., & Ekblaw, A. npj Microgravity 11, 23 (2025). https://doi.org/10.1038/s41526-025-00463-2