Soils do more than store carbon from plant residues. Beneath our feet, vast communities of microbes quietly pull carbon dioxide from the air and convert it into organic matter, helping regulate climate and sustain agricultural productivity. A new study reveals that this overlooked microbial process is strongly influenced by soil type, plant roots, and biochar, a carbon rich material increasingly promoted for sustainable farming.
In research published in Biochar, scientists examined how autotrophic soil microbes that fix carbon dioxide through the Calvin cycle respond to biochar additions in two contrasting agricultural systems: flooded rice paddies and well aerated upland croplands. The team focused on key microbial genes, known as cbbL and cbbM, that encode the enzyme RubisCO, which drives biological carbon fixation.
"Our results show that paddy soils, especially around plant roots, are hotspots for microbial carbon fixation," said corresponding author Xiaomin Zhu. "These microbes are actively capturing carbon dioxide in ways that have been largely ignored in soil carbon research."
Using field experiments in China, the researchers combined molecular analyses, enzyme activity measurements, and microbial community sequencing. They found that microbes carrying the cbbL gene dominated carbon fixation in both soil types, but paddy soils supported much higher overall activity. Flooded conditions, shifting redox states, and rice root exudates created ideal microenvironments for autotrophic microbes to thrive.
The rhizosphere, the narrow zone of soil surrounding roots, emerged as a critical zone for carbon capture. In paddy fields, RubisCO enzyme activity was consistently higher near roots than in bulk soil, confirming that plant microbial interactions amplify soil carbon assimilation.
Biochar, produced by heating crop residues in low oxygen conditions, played a complex role. Rather than simply increasing carbon fixation across the board, biochar selectively reshaped microbial communities. In paddy soils, biochar reduced the abundance of microbes carrying the cbbM gene, which are less common but closely linked to high RubisCO activity under low oxygen conditions.
"Biochar does not just add carbon to soil," Zhu explained. "It changes which microbes are active and how carbon flows through the soil system. That can create tradeoffs between different microbial pathways of carbon fixation."
The study also revealed strong links between microbial carbon fixation and nitrogen cycling. Soil nitrogen forms, redox conditions, and enzyme activities emerged as major drivers controlling which microbial groups dominated. In paddy soils, inorganic nitrogen and redox potential strongly regulated microbial carbon fixation, while in upland soils, microbial biomass and labile carbon and nitrogen pools played a larger role.
Importantly, the researchers found that carbon fixation by these microbes was tightly coupled with other biogeochemical processes, including nitrogen reduction, iron cycling, methane metabolism, and even arsenic detoxification. This highlights the broader ecological importance of autotrophic microbes beyond carbon storage alone.
"These microbes sit at the crossroads of many nutrient cycles," said Zhu. "Managing soils to support them could deliver multiple benefits, from climate mitigation to improved soil health and crop resilience."
The findings suggest that strategies aimed at enhancing soil carbon sequestration should account for microbial pathways that operate independently of plant inputs. Biochar remains a promising tool, but its impacts depend strongly on soil type, water management, and nutrient status.
By uncovering how biochar and farming systems shape microbial carbon fixation, the study provides new insight into how agricultural soils can be managed to better support climate smart agriculture and long term carbon storage.
===
Journal Reference: Jiang, H., Han, S., Zhang, H. et al. Calvin cycle driven autotrophic CO2-fixation traits and autotrophic microbial communities in paddy (Anthrosol) and upland (Vertisol) soils: rhizosphere effects and impacts of biochar. Biochar 7, 118 (2025).
https://doi.org/10.1007/s42773-025-00538-z
===
About Biochar
Biochar is the first journal dedicated exclusively to biochar research, spanning agronomy, environmental science, and materials science. It publishes original studies on biochar production, processing, and applications—such as bioenergy, environmental remediation, soil enhancement, climate mitigation, water treatment, and sustainability analysis. The journal serves as an innovative and professional platform for global researchers to share advances in this rapidly expanding field.
