Microbes Fix Massive Amounts of Carbon without Sunlight in Earth’s Deep Subsurface Biosphere

May 11, 2021. By Kolemann Lutz

Researchers sampled and compared the bacterial community composition of hot springs with the deep-subsurface subduction geochemistry in Costa Rica. Metagenomic DNA analysis suggests that vast underground forests of chemolithoautotrophs and microbial ecosystems fix and transform CO2 into biomass without any sunlight via chemical redox reactions. These subsurface microbes are estimated to sequester up to 1.4 × 10^10 mol of carbon per year, which would decrease the total carbon delivered to the mantle by up to 22%.

Subduction zones are the regions where tectonic plates interact and move carbon between the interior and exterior of Earth. Because of the extremely high pressures and temperatures involved, this process is thought to occur without microbes. In the early 2020’s, scientists learned that microbes extend far deeper into Earth's crust than previously thought.

Deeply sourced hydrogen and methane in fluids are though to be important energy and carbon sources supporting the largest microbial habitat on Earth, the deep subsurface biosphere. Microbes in the deep biosphere, where temperatures are around 122 °C, can reside at least 5 km below the continental surface and 10.5 km below the sea surface.

On Earth, the carbon cycle is at equilibrium on the surface through a combination of tectonic processes that buries carbon, volcanism which releases it, and biology to mediate carbon transfer. As subducting slabs can range from 20–150 km in depth, volatiles and elements mobilized from the descending slab and mantle can be altered by interactions with the deep-subsurface biosphere on their trek to the Earth’s surface.

Developed over billions of years of evolution, chemolithoautotroph bacteria sequester vast quantities of carbon primarily from their unique metabolism and diet, which allows them to make energy without sunlight. Chemolithoautotrophy bacterial communities can be viewed as vast underground dynamic forest. Researchers hypothesize that the upward mobility of deeply sourced fluids may connect microorganisms such as chemolithoautotrophs to the deep tectonic processes below.

A team of 46 scientists from 19 institutions demonstrate that a vast microbial ecosystem primarily eats the carbon, sulfur, and iron chemicals produced during the subduction of the oceanic plate beneath Costa Rica. The interdisciplinary and international team tested these theories and results by sampling microbial communities brought to the surface in 21 natural hot springs. In work funded by the Deep Carbon Observatory and the Alfred P. Sloan Foundation, researchers compared the bacterial community composition with the deep-subsurface geochemistry from a 200km subduction segment in Costa Rica.

They conducted a co-occurrence network analysis of metagenomic DNA sequences of carbon metabolism across each bacterial community in the hot springs. Enzymes are present in three carbon-fixation pathways (rTCA, Calvin–Benson–Bassham and Wood–Ljungdahl) and they cluster around the key gene in each pathway. For example, gene-clique B contains all the genes necessary for rTCA, ATP, citrate lyase, and 2-oxoglutarate synthase and is the only gene clique that correlates consistently with subsurface geochemical parameters.

Chemolithoautotrophs that use the reverse tricarboxylic acid cycle (rTCA) as well as abundances of metagenomic rTCA genes correlate with concentrations of slab-volatilized carbon. This suggests that chemolithoautotroph communities in the subsurface ecosystem fix and chemically transform the slab-derived CO2 into biomass at high pressures from energy during chemical redox (reduction-oxidation) reactions.

The team discovered that this autotrophic microbial ecosystem sequesters significant amounts of carbon generated during subduction that would otherwise escape to the atmosphere.

“Even if only 30% of the cells are chemolithoautotrophs, we calculate that this subsurface microbial ecosystem could sequester 1.4 × 10^9 to 1.4 × 10^10 mol of carbon per year, which would decrease the total carbon delivered to the mantle by 2 to 22%”, mentions lead author Katherine M. Fullerton from the Microbiology Department at the University of Tennessee, Knoxville.

Carbon availability is the most important corollary for diversity in bacterial cliques found on the surface. Research suggests that the availability of volatilized carbon during subduction is the limiting factor for bacterial community composition.

Metagenomic results suggest that the biomass production is primarily produced through the rTCA cycle and is limited by dissolved inorganic carbon (DIC) availability from deeply sourced fluids, since calcite (CaCO3) deposition dominates the forearc subsurface carbon sink.

As mentioned in the research published in April 2021 in the Journal of Nature Geoscience, "If other convergent margins lack such a strong calcite sink, chemolithoautotrophs would no longer be limited by DIC availability, suggesting that the biological carbon sink could compensate for the calcite carbon sink in other systems."

Findings have implications for the understanding of carbon reservoir changes, carbon sequestration to the mantle with crustal carbon sequestration and, planetary redox balance and long-term climate stability.

Mars presently has no active tectonic system, a significant biosphere, oceans, or carbon-based soil ecosystem. Multiple data sources indicate an active hydrogeological history of Mars and chemolithoautotrophs-suited environments during the Noachian period around 4.1 and about 3.7 billion years ago (Gya).

The discovery and improved understanding of biological interactions in the deep carbon cycle on Earth holds the potential to facilitate natural carbon sequestration and to help recreate subsurface biospheres on other planets such as Mars.

Novel methods to spawn microbial subsurface environments on Mars, to prime subsurface biospheres with carbon, nitrogen, oxygen, and hydrogen. Alternatively, chemolithoautotroph genes and organisms hold great potential to capture carbon without any energy source except the carbon biomass.

Better understanding the genomes of chemolithoautotrophs might help enable microbes to adapt to the deep subsurface Martian environment with less fertile soil, less water, reduced pressure, temperatures, 3/8Gs, and DIC availability.

To develop the research on sequestering large quantities of carbon, further research is demanded to geoengineer a subsurface carbon cycle, biosphere, and carbon sinks to create a more life-friendly carbon cycle on planet Mars.


Fullerton, K.M., Schrenk, M.O., Yücel, M. et al. Effect of tectonic processes on biosphere–geosphere feedbacks across a convergent margin. Nat. Geosci. (2021). https://doi.org/10.1038/s41561-021-00725-0

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