Field work on South Africa's "living rocks" reveals rapid carbon capture in extreme conditions

by Clarence Oxford
Los Angeles CA (SPX) Dec 16, 2025
South Africa preserves some of the oldest traces of life on Earth in rocky, layered formations known as microbialites, which resemble coral reefs but are built by microbes that turn dissolved minerals into solid rock. Along the country's southeastern coast, researchers examined modern microbialites that continue to accrete new layers as calcium-rich groundwater seeps from coastal sand dunes.

An international team led by Bigelow Laboratory for Ocean Sciences and Rhodes University has now quantified how these living structures absorb carbon and convert it into calcium carbonate. Reporting in Nature Communications, the scientists linked measured carbon uptake rates to the genetic makeup of the microbial community, revealing how these mats use both photosynthesis and other metabolic pathways to fix carbon around the clock.

"These ancient formations that the textbooks say are nearly extinct are alive and, in some cases, thriving in places you would not expect organisms to survive," said Senior Research Scientist Rachel Sipler, the study's lead author. "Instead of finding ancient, slow growing fossils, we've found that these structures are made up of robust microbial communities capable of growing quickly under challenging conditions."

Because fossil microbialites can be billions of years old, scientists have long struggled to reconstruct how the organisms that built them interacted with their environment. The team turned to modern analogues, carrying out multiple field expeditions to four microbialite systems in South Africa's Eastern Cape that are fed by hard, calcium-rich groundwater emerging from dunes.

"The systems here are growing in some of the harshest and most variable conditions," Sipler said. "They can dry out one day and grow the next. They have this incredible resiliency that was compelling to understand."

Measurements showed that these microbialites precipitate calcium carbonate quickly, allowing the structures to extend vertically by nearly two inches per year. The work indicates that living microbialites can build substantial rock mass on human timescales, rather than existing only as slowly accumulating relics.

One of the most striking results was evidence of strong carbon uptake at night. Although these systems were assumed to depend entirely on photosynthesis, repeated experiments demonstrated that nocturnal uptake rates can match daytime levels, indicating that microbes are using non-photosynthetic metabolic pathways to fix carbon in the absence of light, similar to communities at deep-sea hydrothermal vents.

From daily measurements, the researchers estimate that the microbialites absorb the equivalent of nine to 16 kilograms of carbon dioxide per square meter each year. Scaled up, a tennis court-sized patch of microbialites would take up as much CO2 annually as roughly three acres of forest, placing these mats among the most efficient biological systems for long-term carbon storage observed in nature.

"We're so trained to look for the expected. If we're not careful, we'll train ourselves to not see the unique characteristics that lead to true discovery," Sipler said. "But we kept going out and kept digging into the data to confirm that the finding wasn't an artifact of the data but an incredible discovery."

The team is now comparing microbialites with other carbon-rich microbial ecosystems such as coastal marshes, which also take up carbon at comparable rates but store it in organic matter that can be more easily broken down. By contrast, microbialites trap carbon in stable mineral phases, and the researchers are using their combined expertise to explore how environmental conditions and community composition control the eventual fate of carbon in these different systems.

"If we had just looked at the metabolisms, we would have had one part of the story. If we had just looked at carbon uptake rates, we would have had a different story. It was through a combination of different approaches and strong scientific curiosity that we were able to build this complete story," Sipler said. "You never know what you're going to find when you put people from different backgrounds with different perspectives into a new, interesting environment."

The study drew initial support from internal funding at Bigelow Laboratory intended to launch new use-inspired projects. Additional funding came from the South African National Research Foundation, the Gordon and Betty Moore Foundation, and the International Development and Research Centre.

Research Report:Integration of multiple metabolic pathways supports high rates of carbon precipitation in living microbialites