Deciphering subsurface carbon fixation

Project Information

SUBCARB

Grant agreement ID: 101154017

DOI

10.3030/101154017

Project closed

EC signature date 2 May 2024

Start date 1 June 2024

End date 31 May 2026

Funded under

• Marie Skłodowska-Curie Actions (MSCA)

Total cost

No data

EU contribution

€ 172 750,08

Coordinated by

UNIVERSITA DEGLI STUDI DI NAPOLI FEDERICO II
Italy

Periodic Reporting for period 1 - SUBCARB (Deciphering subsurface carbon fixation)

Reporting period: 2024-06-01 to 2026-05-31

Summary of the context and overall objectives of the project

The subsurface of our planet, the vast zone of rock and sediment beneath the soil and seafloor, hosts an immense and still poorly understood reservoir of microbial life. It is estimated to contain around 15% of all biomass on Earth, yet most of this life lives without sunlight, relying instead on chemical energy from rocks and fluids to sustain itself. A key open question is how much carbon dioxide these subsurface microorganisms convert into living matter through processes known as carbon fixation, and how this contributes to the planet's overall carbon cycle, the same cycle that governs atmospheric CO2 levels and, ultimately, climate.

Understanding this hidden part of the carbon cycle matters for several reasons. First, it helps complete the picture of how carbon moves between the atmosphere, the surface, and deep geological reservoirs over long timescales, information relevant to climate models and to the European Union's broader climate objectives, including the European Green Deal. Second, it can reveal whether subsurface carbon capture and storage strategies, increasingly considered as tools to fight climate change, might interact with existing microbial communities and their metabolism. Third, because subsurface microorganisms often use ancient, non-canonical strategies to fix carbon rather than the more familiar plant-like photosynthesis pathway, studying them offers a window into some of the earliest forms of metabolism to have evolved on Earth, with implications for understanding the origin and limits of life more broadly, including in extreme environments elsewhere in the Solar System.

Despite its importance, no comprehensive, global picture of how carbon fixation strategies are distributed across subsurface environments existed prior to this project. Previous studies were limited to individual sites or regions, making it impossible to determine whether the strategies used by subsurface microorganisms follow consistent patterns linked to their physical and chemical surroundings, such as temperature, oxygen availability, or the composition of the fluids they inhabit.

The overall objective of this project was to address this gap by systematically surveying subsurface carbon fixation across a wide range of geological settings worldwide, and by linking the microbial strategies observed to the environmental conditions in which they occur. The ultimate goal was to produce a predictive, quantitative understanding of subsurface carbon fixation that could serve as a baseline for future research, environmental monitoring, and climate-relevant carbon budgeting.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

The project's central activity was a large-scale, top-down survey of carbon fixation strategies across subsurface environments worldwide. Fieldwork focused on naturally occurring seeps, springs and hydrothermal features that provide a direct window into deep subsurface fluids without the need for costly drilling. Samples of fluids, sediments and, where present, biofilms were collected at 176 such sites across diverse geological settings, together with on-site physicochemical measurements and an extensive characterisation of the surrounding geochemistry, spanning more than 50 variables including major ions, trace metals, dissolved gases and noble gases.

From these samples, 242 new subsurface metagenomes (genetic surveys of entire microbial communities) were generated, adding to 170 subsurface metagenomes already available from previous work. A single, consistent computational pipeline was developed to identify and quantify carbon fixation pathways across this combined dataset of 412 subsurface metagenomes, and to compare it against more than 1,000 metagenomes from marine, freshwater and soil environments at the surface.

This analysis showed that subsurface environments host a greater abundance and a greater diversity of carbon fixation strategies than surface ecosystems, and that the specific strategy favoured at a given site is closely tied to local environmental conditions (e. g. temperature and the availability of oxygen). Building on this, a computational framework was developed to translate these genetic signals into a quantitative estimate of carbon fixation activity, and to combine it with existing measurements and with estimates of the volume of habitable subsurface fluids worldwide. This produced the first global, data-driven estimate of continental subsurface carbon fixation, on the order of 2.65 billion tonnes of carbon per year, a flux an order of magnitude larger than the carbon released to the surface through volcanic activity.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

This project moves substantially beyond the previous state of the art, which consisted of isolated studies documenting carbon fixation in individual subsurface sites or regions, without a consistent, quantitative link to the environmental conditions driving pathway selection. By combining a uniform, global-scale survey with an integrated geochemical dataset, the project delivered the first comprehensive functional map of subsurface carbon fixation strategies and their environmental drivers.

Its most significant single result is the first global, metagenomics-based estimate of continental subsurface carbon fixation, around 2.65 billion tonnes of carbon per year. This figure exceeds narrower estimates previously derived from geochemical approaches, and falls within the range independently estimated for chemosynthesis in the ocean, providing an important cross-check between two very different methods. It establishes, for the first time, a quantitative baseline against which the contribution of the deep subsurface biosphere to the global carbon cycle can be assessed and refined.

Beyond this headline result, the project produced a reusable computational framework that converts standard metagenomic sequencing data into a quantitative index of carbon fixation potential. Because it relies only on genomic data and is not tied to any specific site or sampling campaign, this framework can, in principle, be applied by other researchers to any subsurface, soil, or marine dataset, extending its usefulness well beyond the scope of this project.

To fully translate these results into further scientific and societal uptake, several needs can be identified. Experimental, laboratory-based validation of the genomically inferred pathway responses to environmental change, originally envisaged but not carried out within this project, would strengthen the causal link between environmental conditions and microbial strategy. Extending the geochemical survey into marine subsurface settings, currently under-represented relative to continental sites, would improve the global estimate's completeness. Finally, engagement with environmental monitoring bodies and industry stakeholders would help translate the open-source analysis pipeline into practical tools, for instance to support the environmental assessment of subsurface carbon capture and storage strategies, or to identify microbial strains of biotechnological interest for sustainable carbon-based production.