Metagenomic and 14 C tracing evidence for autotrophic microbial CO2 fixation in paddy soils

Abstract

Autotrophic carbon dioxide (CO₂ ) fixation by microbes is ubiquitous in the environment and potentially contributes to the soil organic carbon (SOC) pool. However, the multiple autotrophic pathways of microbial carbon assimilation and fixation in paddy soils remain poorly characterized. In this study, we combine metagenomic analysis with ¹⁴ C-labelling to investigate all known autotrophic pathways and CO₂ assimilation mechanisms in five typical paddy soils from southern China. Marker genes of six autotrophic pathways are detected in all soil samples, which are dominated by the cbbL genes (67%-82%) coding the ribulose-bisphosphate carboxylase large chain in the Calvin cycle. These marker genes are associated with a broad range of phototrophic and chemotrophic genera. Significant amounts of ¹⁴ C-CO₂ are assimilated into SOC (74.3-175.8 mg ¹⁴ C kg^-1 ) and microbial biomass (5.2-24.1 mg ¹⁴ C kg^-1 ) after 45 days incubation, where more than 70% of ¹⁴ C-SOC was concentrated in the relatively stable humin fractions. These results show that paddy soil microbes contain the genetic potential for autotrophic carbon fixation spreading over broad taxonomic ranges, and can incorporate atmospheric carbon into organic components, which ultimately contribute to the stable SOC pool.