A study published in the journal Biochar examined how autotrophic microbes that use the Calvin cycle to fix carbon dioxide respond to biochar in flooded rice paddies and well aerated upland croplands in China. The researchers tracked two functional genes, cbbL and cbbM, which encode forms of the enzyme RubisCO that catalyzes 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, molecular analyses, enzyme activity assays, and microbial community sequencing, the team found that cbbL carrying microbes dominated carbon fixation in both soil types but were much more active in paddy soils. Flooded conditions, changing redox states, and carbon rich exudates from rice roots created favorable microenvironments for these autotrophic microbes.
The rhizosphere, the narrow zone of soil surrounding roots, showed consistently higher RubisCO activity than bulk soil in paddy fields, indicating that root associated microbial communities amplify soil carbon assimilation. This highlights root influenced microsites as important contributors to carbon cycling in rice based systems.
Biochar, produced by heating crop residues under low oxygen, did not simply boost carbon fixation uniformly but instead reshaped microbial communities. In paddy soils, biochar reduced the abundance of microbes carrying the cbbM gene, which, although less common, are associated with high RubisCO activity in low oxygen environments.
"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 identified connections between microbial carbon fixation and nitrogen cycling, with soil nitrogen forms, redox conditions, and enzyme activities acting as major controls on which microbial groups prevail. In paddy soils, inorganic nitrogen and redox potential regulated autotrophic carbon fixation, whereas in upland soils microbial biomass and labile carbon and nitrogen pools were more influential.
Microbial carbon fixation was linked to other biogeochemical processes including nitrogen reduction, iron cycling, methane metabolism, and arsenic detoxification. These associations indicate that autotrophic microbes contribute not only to carbon storage but also to broader soil function and contaminant dynamics.
"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 indicate that strategies to increase soil carbon sequestration should incorporate microbial pathways that operate independently of direct plant carbon inputs. Biochar remains a tool for climate related agriculture, but its effects depend strongly on soil type, water management, and nutrient status.
By clarifying how biochar and contrasting farming systems shape autotrophic microbial communities and Calvin cycle based carbon fixation, the study provides guidance for managing agricultural soils for long term carbon storage and multiple ecosystem services.
Related Links
Biochar Editorial Office, Shenyang Agricultural University
Carbon Worlds - where graphite, diamond, amorphous, fullerenes meet
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