Soil Microbes Transform Inorganic Carbon Into Organic Carbon by Dark Fixation Pathways in Desert Soil

Soil inorganic carbon (SIC) represents the main soil carbon pool in drylands with a high geologic residence time for carbon sequestration. Recent studies have shown that SIC is not stable as previously supposed, and can be employed by certain microbes and transformed into organics in soils; however, this transformation remains largely unexplored. We performed in situ 13C tracing in desert bulk soil and employed metagenomics to predict the microbial metabolic processes associated with carbon transformation. The tracing data showed that the 13C signature profile in soil organic carbon (SOC) originated from SIC with a carbon transformation content of 6.881 mg m−2 during the feeding periods, corresponding to a rate of 3.276 μg kg−1 d−1. Metagenomic analysis identified genes encoding enzymes related to microbial CO2 and HCO3− fixation, accounting for 0.448% (based on Kyoto Encyclopedia of Genes and Genomes database) and 0.668% (based on Evolutionary genealogy of genes: Non‐supervised Orthologous Groups database) of all ascertained genes. Soil microbes, from a broad taxonomic range, harboring these genes mainly contributed toward chemoautotrophic and heterotrophic carbon fixation. Our results demonstrated that the microbes employed the chemoautotrophic and heterotrophic pathways, namely, dark microbial pathways, for SIC transformation into SOC. Although the amount of SOC derived from the dark microbial fixation process was not assessed, the present study highlights a neglected carbon transformation process mediated by soil microbes in drylands and provides insights into carbon transformation of SIC to SOC in dryland soil. Key Points Soil inorganic carbon may be employed by certain microbes and transformed into organics; however, this remains largely unexplored We performed in situ 13C tracing in the desert soil and predicted associated metabolisms by metagenomics The study highlights a neglected carbon transformation process from inorganic to organic carbon mediated by soil microbes in drylands