Newly discovered cyanobacteria could help sequester carbon from oceans and factories

An international coalition of researchers from the United States and Italy has discovered a novel strain of cyanobacteria, or algae, isolated from volcanic ocean vents that is especially adept at growing rapidly in the presence of CO₂  and readily sinks in water, making it a prime candidate for biologically-based carbon sequestration projects and bioproduction of valuable commodities. This strain, nicknamed “Chonkus,” was found off the coast of the island of Vulcano in Sicily, Italy — an environment in which marine CO₂ is abundant due to shallow volcanic vents. The discovery is described in a paper published today in Applied Environmental Microbiology.

“Dissolved carbon is relatively dilute compared to all the other molecules in the ocean, and that limits the growth of photosynthetic organisms that live there. We decided to investigate what happens when you alleviate that limiting factor by going to a place with plenty of carbon, where some organisms could have evolved the ability to use it to galvanize their growth,” said co-corresponding author Max Schubert, Ph.D., who was a staff scientist at the Wyss Institute at Harvard University when the work was conducted and is now Lead Project Scientist at Align to Innovate. “This naturally occurring strain of cyanobacteria has several traits that could be useful to humans, including highly dense growth and a natural tendency to sink in water, making Chonkus a particularly interesting organism for future work on decarbonization and biomanufacturing.”

From the shallow sea to the lab bench

Schubert and fellow corresponding author Braden Tierney, Ph.D. first met as bench neighbors in the lab of Wyss Core Faculty member George Church, Ph.D. nine years ago, but didn’t start collaborating until both were later working at Harvard Medical School (HMS) in 2016. Schubert, a microbiologist who was interested in building tools for directed evolution of bacteria and their genomes, submitted a proposal to the HMS Consortium for Space Genetics’ 2019 Symposium on Climate Change to bring this work to cyanobacteria. He won the top prize, which funded his early forays into applying his tools to cyanobacteria to investigate their potential to help fix and sequester carbon.

Meanwhile, Tierney, who was then a postdoc co-advised by Schubert’s advisor Church, was sent a paper by a friend about shallow seeps - areas on the ocean floor where gasses seep into the water but are shallow enough to receive sunlight - and realized that there might be photosynthetic microbes living in those environments that had evolved to be adept at capturing dissolved CO₂ from the water. He made connections with Marco Milazzo, Ph.D. and Paola Quatrini, Ph.D., both professors at the University of Palermo in Sicily, who were actively studying nearby, accessible shallow seeps. Tierney secured funding for a collecting expedition from SeedLabs, and reached out to Schubert for help understanding and working with the cyanobacteria that could be present in that environment.

Tierney and Schubert assembled a coalition that ultimately included scientists from the Wyss Institute, HMS, Weill Cornell Medical College, Colorado State University, University of Wisconsin-Madison, MIT, the National Renewable Energy Laboratory in Colorado, and multiple institutions in Palermo, Italy. The group launched a field expedition to the ocean off the coast of Vulcano where they donned SCUBA suits and collected water samples from a CO₂-rich shallow seep. They then shipped tubes of the seawater across the Atlantic to Boston, where scientists led by Schubert isolated and characterized the microbes living in the samples.

One microbe’s bug is a feature for humanity

To coax their target cyanobacteria to grow, the researchers replicated the conditions a fast-growing cyanobacteria would thrive in: warm temperatures, lots of light, and plenty of CO₂. After isolation from enrichment cultures, two strains of fast-growing cyanobacteria were discovered: UTEX 3221 and UTEX 3222. The team chose to focus on UTEX 3222 due to its single-celled growth, which made it easier to compare to existing cyanobacteria strains.

UTEX 3222 produced larger colonies than other known fast-growing cyanobacteria strains, and its individual cells were larger as well – thus the moniker Chonkus. It also grew to higher density than existing strains, appeared to harbor carbon-containing storage granules in its cells, and had a higher overall carbon content than other strains: all potentially valuable traits for applications like carbon sequestration and bioproduction. Most interestingly, Chonkus rapidly settled into a dense pellet resembling “green peanut butter” at the bottom of its sample tubes, while other strains remained suspended. This behavior is especially valuable for industrial processing, as concentrating and drying biomass currently accounts for 15-30% of production costs.

“Many of the traits that we observed in Chonkus aren’t inherently useful in their natural environment, but are very useful to humans. Aquatic organisms naturally grow at very low density, but being able to grow to a high density at higher temperatures is very helpful in the industrial environments that we use to manufacture many goods and products, and can help sequester more carbon,” said Tierney. “An incredible amount of microbial diversity exists out there in the world, and we believe it’s more efficient to seek out the microbes that have already evolved to succeed in human-relevant environments rather than trying to engineer all of the traits we want into lab-grown E. coli bacteria.”

The team is excited about the many applications that could be addressed with Chonkus or modified versions of the microbe. Many organizations are investigating the use of fast-growing organisms for carbon sequestration, and Chonkus could one day join their ranks. Several products are currently manufactured in algae, like omega-3 fatty acids, the antioxidant astaxanthin, and spirulina, and could be made more efficiently in a strain that grows quickly and densely. And the fact that cyanobacteria directly harvest carbon from their environment to grow means that they can couple the processes of carbon sequestration and biomanufacturing together in a single organism. Samples of UTEX 3222 and UTEX 3221 are cryopreserved and publicly available for other researchers to use from the Culture Collection of Algae at the University of Texas, Austin.

Inspired by the success of their first expedition, Tierney has since co-founded a non-profit organization with paper co-authors Krista Ryon and James Henriksen called The Two Frontiers Project, which aims to study how life thrives in extreme environments through next-generation scientific expeditions. The group has already completed subsequent expeditions to hot springs in Colorado, the Smoking Lands in the Tyrrhenian Sea, the coral reefs of the Red Sea, and others. The organization is focused on microbes that have uses for three major applications: carbon capture, CO2 upcycling for sustainable products, and coral ecosystem restoration.

“The traits inherent in the naturally evolved cyanobacteria strains described in this research have the potential to be used both in industry and the environment, including biomanufacturing of useful carbon-based products or sinking large volumes of carbon to the ocean floor. While further modifications could be made to enhance these microbes’ abilities, harnessing billions of years of evolution is a significant leg up in humanity’s urgent need to mitigate and reverse climate change,” said Church, who is also the Robert Winthrop Professor of Genetics at HMS and a Professor of Health Sciences and Technology at Harvard and MIT. “But it’s very important to ‘build the seatbelts before you build the car’ – our lab also studies bio-containment approaches that help contain and control these kinds of experiments.”

“The Wyss Institute was founded on the belief that Nature is the best source of innovation on the planet, and that emulating its principles is the key to driving positive impact. I’m proud of this team for getting out of the lab and seeking Nature’s best ideas where they’ve already developed. This is a wonderful example of how our new Sustainable Futures Initiative is pursuing out-of-the-box approaches to confront climate change - the biggest challenge of our generation,” said Wyss Founding Director Don Ingber, M.D., Ph.D., who is also the Judah Folkman Professor of Vascular Biology at HMS and Boston Children’s Hospital and the Hansjörg Wyss Professor of Biologically Inspired Engineering at Harvard’s John A. Paulson School of Engineering and Applied Sciences.

Additional authors of the paper include Tzu-Chieh Tang, Isabella Goodchild-Michelman, Krista Ryon, James Henriksen, Theodore Chavkin, Yanqi Wu, Teemu Miettinen, Stefanie Van Wychen, Lukas Dahlin, Davide Spatafora, Gabriele Turco, Michael Guarnieri, Scott Manalis, John Kowitz, Raja Dhir, Paola Quatrini, Christopher Mason, and Marco Milazzo.

This research was supported by the US Department of Energy (DOE) under grant no. DE-FG02-02ER63445 and by the National Science Foundation (NSF) award no. MCB-2037995, SEED Labs, the WorldQuant Foundation, the Scientific Computing Unit (SCU) at Weill Cornell Medical College, and the International CO2 Natural Analogues (ICONA) Network.