Discovering South Africa's Living Rocks and Their Carbon-Capturing Power

Along the rugged southeastern coastline of South Africa, near areas like Schoenmakerskop in the Eastern Cape, researchers have uncovered formations that look like ordinary layered rocks but are alive with microbial activity. These structures, known as microbialites or 'living rocks,' are built by communities of microorganisms that thrive in the harsh supratidal zone—where rocks are battered by waves, baked by intense ultraviolet radiation, and subjected to extreme temperature swings and desiccation. Unlike typical carbon sinks such as forests, which store carbon in organic matter, these microbialites lock away carbon dioxide (CO2) as stable mineral carbonate, creating permanent geological storage.

The recent breakthrough comes from a collaborative study led by scientists at Rhodes University in Makhanda (formerly Grahamstown) and the Bigelow Laboratory for Ocean Sciences in the United States. Published in December 2025 in the prestigious journal Nature Communications, the research quantifies for the first time how these ancient-style ecosystems function in modern times, absorbing carbon not just during the day but continuously, around the clock.

Rhodes University's Pivotal Role in Unlocking Microbial Secrets

Rhodes University, a leading institution in South African higher education known for its strong emphasis on environmental and marine sciences, played a central role through Professor Rosemary A. Dorrington from the Department of Biochemistry, Genetics and Microbiology. Dorrington, a marine biologist with expertise in microbial ecology, co-led the fieldwork and genetic analyses that revealed the diverse bacterial communities powering these rocks. Her team's contributions highlight Rhodes' commitment to tackling global challenges like climate change through innovative research.

This study builds on years of Rhodes-led investigations into South African microbialites, including prior work on their prokaryote communities and biogeochemical processes. For aspiring researchers, Rhodes offers programs in microbiology and environmental science, with opportunities to engage in cutting-edge fieldwork. Explore research jobs or university jobs in South Africa to join such impactful projects.

Mechanisms Behind Day-and-Night Carbon Absorption

Microbialites form through biomineralization, where microbes extract dissolved inorganic carbon (DIC) from seawater or freshwater seepage and precipitate it as calcium carbonate (CaCO3). During daylight hours, photosynthetic bacteria and cyanobacteria raise the local pH by consuming CO2, promoting carbonate formation. Remarkably, the study found that nighttime uptake accounts for up to 80% of daytime rates, driven by light-independent processes like sulfide oxidation and other chemolithoautotrophic pathways.

• Photosynthesis (day): Cyanobacteria fix CO2, increasing alkalinity for CaCO3 precipitation.
• Chemosynthesis (night): Bacteria use alternative electron donors like hydrogen sulfide.
• Multiple pathways: Diverse metabolisms ensure continuous productivity despite environmental stresses.

Genetic sequencing revealed a rich microbiome, including Proteobacteria, Bacteroidetes, and Cyanobacteria, enabling this integrated metabolic network.

Quantifying the Carbon Sequestration Potential

The team's field measurements using flux chambers and isotope tracing showed these microbialites absorb between 9 and 16 kilograms of carbon per square meter annually—equivalent to 33-59 kg of CO2. This rate is 50 to 100 times higher than that of tropical rainforests per unit area, positioning them as champion natural carbon sinks. Growth rates reach 0.5 to 1 mm per year, far exceeding many ancient analogs.

In South Africa's context, where coastal ecosystems face threats from climate change and development, scaling these findings could contribute significantly to national carbon goals. For context, if expanded across suitable habitats, they might sequester thousands of tons of CO2 yearly.

Photo by mohamad rajab zade on Unsplash

Thriving in South Africa's Harsh Coastal Extremes

Supratidal zones in South Africa experience desiccation for weeks, UV exposure 10 times higher than open ocean, and salinity fluctuations. Yet, these microbialites not only survive but grow rapidly, demonstrating remarkable resilience. The study at sites like Cape Hangklip underscores how groundwater-fed freshwater influences their formation, distinct from marine stromatolites.

This adaptability offers lessons for bioengineering carbon capture in extreme environments worldwide.

Innovative Methods from Field to Lab

Researchers deployed benthic chambers to measure real-time DIC fluxes, combined with metagenomic sequencing on an Oxford Nanopore MinION sequencer for community profiling. Radiocarbon dating confirmed active layering, while microsensor profiles mapped pH and oxygen gradients within the mats. Rhodes' facilities supported sample processing and analysis.

• Flux measurements: Day/night DIC uptake.
• Genomics: Functional genes for carbon fixation.
• Geochemistry: CaCO3 precipitation verification.

Implications for Global Climate Strategies

These findings challenge assumptions that modern microbialites are relics, revealing them as dynamic carbon stores. In South Africa, with its biodiversity hotspots and climate vulnerabilities, protecting these systems aligns with national strategies under the Paris Agreement. Potential applications include nature-based solutions for coastal restoration.

Stakeholders from government to industry can leverage this for blue carbon credits. Learn more about higher ed career advice in environmental sciences.

Rhodes University: A Hub for Environmental Innovation

Rhodes University's involvement exemplifies its prowess in interdisciplinary research, from microbiology to geochemistry. Past projects on stromatolites have paved the way, training PhD students in molecular ecology. For South African academics, this underscores opportunities in grant-funded marine research via the National Research Foundation (NRF).

Check academic opportunities in South Africa or research jobs to contribute.

Photo by clement proust on Unsplash

Future Directions and Challenges Ahead

Upcoming work may explore scaling microbialite-inspired bioreactors or monitoring climate impacts. Challenges include habitat loss from urbanization. Rhodes plans expanded genomic studies and modeling for global predictions.

Engaging with Rhodes University Research Opportunities

This study highlights why institutions like Rhodes attract global talent. Students and professors interested in carbon sequestration research can pursue postgraduate programs or faculty positions. Visit Rate My Professor for insights on Rhodes faculty, higher ed jobs, and career advice. Share your thoughts in the comments below.