Throughout the ocean, billions and billions of plant-like microbes make up an invisible floating forest. As they drift, the microorganisms use sunlight to absorb carbon dioxide from the atmosphere. Collectively, these photosynthetic plankton, or phytoplankton, absorb almost as much carbon dioxide as the world’s terrestrial forests. A measurable portion of their carbon-capturing muscles comes from Prochlorococcus–an emerald-colored free-floating phytoplankton that is the most abundant in the oceans today.
But Prochlorococcus didn’t always inhabit open water. It is likely that the ancestors of the microbe were stuck near the coasts, where nutrients were abundant and the organisms lived in common microbial mats on the seafloor. So how did the descendants of these coastal inhabitants end up becoming today’s photosynthetic centers of the open ocean?
MIT scientists think rowing was the key. In a new study, they suggest that the ancestors of Prochlorococcus acquired the ability to attach themselves to chitin—the degraded molecules of ancient exoskeletons. Microbes rode on passing flakes, using the particles as rafts to venture far out to sea. These chitin rafts may also have provided essential nutrients, feeding and sustaining microbes throughout their journey.
Thus, generations of fortified microbes have had the opportunity to evolve new capabilities to adapt to the open ocean. Eventually, they would have evolved to a point where they could jump ship and survive like the floating ocean dwellers that live today.
“If Prochlorococcus and other photosynthetic organisms had not colonized the ocean, we would be looking at a very different planet,” says Roger Brackmann, a research scientist in MIT’s Division of Earth, Atmospheric and Planetary Sciences (EAPS). “It was the fact that they were able to attach themselves to these chitinous rafts that enabled them to establish a foothold in an entirely new and enormous part of the planet’s biosphere, in a way that changed the Earth forever.”
Brackmann and his collaborators present their new “chitin raft” hypothesis, along with experiments and genetic analyzes that support the idea, in a study appearing this week in PNAS.
MIT co-authors are Giovanna Capovella, Greg Fournier, Julia Schwartzman, Zinda Lu, Alexis Yelton, Elaina Thomas, Jack Payette, Kurt Castro, Otto Cordero, and MIT Professor Sally (Penny) Chisholm, along with colleagues from multiple institutions including Including the Woods Hole Oceanographic Institution.
Prochlorococcus is one of two major groups that belong to a class known as picocyanobacteria, and are the smallest photosynthetic organisms on the planet. The other group is Synechococcus, a closely related microbe that can be found abundantly in ocean and freshwater systems. Both organisms make a living through photosynthesis.
But it turns out that some strains of Prochlorococcus can adopt alternative lifestyles, particularly in low-light areas where photosynthesis is difficult to maintain. These microbes are “heterotrophic,” using a combination of other carbon capture strategies to grow.
Researchers in Chisholm’s lab were looking for signs of mixed feeding when they stumbled upon a gene common to several modern strains of Prochlorococcus. The gene encoded the ability to break down chitin, a carbon-rich substance that comes from the scaled shells of arthropods, such as insects and crustaceans.
“It was very strange,” says Capovila, who decided to dig deeper into the discoveries when she joined the lab as a postdoc.
For the new study, Capovilla ran experiments to see if Prochlorococcus could actually break down chitin in a beneficial way. Previous work in the laboratory showed that the chitin-degrading gene appeared in Prochlorococcus strains that live in low-light conditions, and in Synechococcus. The gene was missing in Prochlorococcus, which inhabits more sunlit regions.
In the lab, Capovilla introduced chitin particles into samples from low-light and high-light strains. It found that microbes containing the gene could degrade chitin, and of those, only the low-light-adapted Prochlorococcus seemed to benefit from this breakdown, as it also seemed to grow faster as a result. Microbes can also attach themselves to chitin flakes—a finding that particularly interested Brackmann, who studies the evolution of metabolic processes and the ways they shaped Earth’s environment.
“People always ask me: How did these microbes colonize the early oceans?” He says. “And while Geo was doing these experiments, there was this ‘aha’ moment.”
Could this gene have been present, Brackmann wondered, in the ancestors of Prochlorococcus, in a way that allowed coastal microbes to latch on to and feed on chitin, riding on the flakes at sea?
It’s all in the timing
To test the new “chitin raft” hypothesis, the team looked to Fournier, who specializes in tracing genes across microbial species throughout history. In 2019, Fournier’s lab generated an evolutionary tree for those microbes that display the chitin-degrading gene. From this tree, they note a trend: Microbes begin to use chitin only after arthropods become abundant in a given ecosystem.
For the chitin raft hypothesis to prove, the gene must have been present in the ancestors of Prochlorococcus shortly after the arthropods began colonizing marine environments.
The team looked at the fossil record and found that aquatic species of arthropods became plentiful in the early Paleozoic, about half a billion years ago. According to the Fournier evolutionary tree, this also occurs around the time of the appearance of the chitin-degrading gene in the common ancestors of Prochlorococcus and Synecococcus.
“The timing is very strict,” says Fournier. “Marine systems are becoming inundated with this new type of organic carbon in the form of chitin, just as the genes used for this carbon are spread across all different types of microbes. And the movement of these chitin molecules suddenly opened up the opportunity for the microbes to really make it in the open ocean.”
The appearance of chitin may be particularly beneficial to microbes that live in low-light conditions, such as the coastal sea floor, where ancient pycocyanobacteria are thought to have lived. For these microbes, chitin would have been a much-needed source of energy, as well as a way out of their shared coastal niche.
Once out at sea, Brackmann says, the raft-gathering microbes were robust enough to evolve other ocean-dwelling adaptations. After millions of years, the organisms are ready to “take the reins” and evolve into the free-floating, photosynthetic Prochlorococcus that exists today.
“In the end, it’s about ecosystems evolving together,” Brackman says. “With these chitin rafts, both arthropods and cyanobacteria were able to expand into the open ocean. Ultimately, this helped give rise to modern marine ecosystems.”
This research was supported by the Simons Foundation, an EMBO Long-Term Fellowship, and the Human Frontier Science Program. This paper is a contribution from the Simons Collaboration on Ocean Processes and Ecology (SCOPE).