Study showcases resilience and rapid growth of “living rocks”

South Africa is home to some of the oldest evidence of life on Earth, contained in rocky, often layered outcroppings called microbialites. Like coral reefs, these complex “living rocks” are built up by microbes absorbing and precipitating dissolved minerals into solid formations.

A new study, co-led by researchers at Bigelow Laboratory for Ocean Sciences and Rhodes University, suggests that these microbialites aren’t just surviving — they’re thriving.

The paper, recently published in Nature Communications, quantifies how microbialites along the South African coast take up carbon and turn it into fresh layers of calcium carbonate. They show how these structures utilize photosynthesis and chemical processes to absorb carbon day and night, relating those rates for the first time to the genetic makeup of the microbial community. The findings highlight just how efficient these microbial mats are at removing dissolved carbon from their environment and sequestering it into stable mineral deposits.

“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.”

Scientists have struggled to understand how these microbial communities interact with their environment based on data from fossilized remains of microbialites — some of which are billions of years old. Fortunately, living microbialites are still widely distributed.

Inspired by how these mats can produce compounds with direct human use, Sipler and her colleagues aimed to understand the underlying geochemical processes at play in this novel environment. Across several field expeditions over multiple years, the team examined four microbialite systems in southeastern South Africa where calcium-rich hard water seeps out of coastal sand 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.”

The team found that these systems were precipitating calcium carbonate rapidly, estimating that the structures can grow almost two inches vertically every year.

More surprising was the finding of carbon uptake day and night. These systems have long been assumed to be driven solely by photosynthesis, so Sipler says they were surprised to find nighttime uptake rates as high as during the day. After repeating their experiments several times, the researchers confirmed that the microbes are utilizing metabolic processes other than photosynthesis to absorb carbon in the absence of light, similar to how microbes living in deep-sea vents survive.

Based on daily rates of carbon uptake, the team estimates that these microbialites can absorb the equivalent of nine to 16 kilograms of carbon dioxide every year per square meter. That’s like a tennis court-sized area absorbing as much CO2 every year as three acres of forest, making these systems one of the most efficient biological mechanisms 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.”

Coastal marshes are similar to microbialites in that they’re a microbial mat ecosystem that’s been found to take in carbon at a similar rate. Yet, marsh microbes put all of that energy into organic matter, which can be easily broken down compared to stable, mineral structures. Given those differences, the team is continuing to investigate how environmental factors and variations in microbes present influence the fate of carbon in these different microbial systems, using the interdisciplinary expertise and international perspective of the research team.

“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 research was partially supported by internal funding from Bigelow Laboratory to kickstart new use-inspired research. Other sources of funding include the South African National Research Foundation, the Gordon and Betty Moore Foundation, and the International Development and Research Centre.