Identification of fungal populations assimilating rice root residue-derived carbon by DNA stable-isotope probing

Abstract Determining the underlying mechanisms of microbes having in biogeochemical processes is a research hotspot, but the specific taxa that undergo exogenous carbon (C) utilization remain ambiguous. Soil microcosm was established to identify fungal populations that can utilize root residue-derived C by using DNA-stable isotope probing coupled with Illumina MiSeq-based sequencing of ribosomal markers. Major fungal populations associated with C assimilation were affiliated with phyla Basidiomycota and Ascomycota. A succession of C consumers was observed over time from genera Talaromyces and Masariosphaeria to the more enriched genera, like Bulleromyces and Arnium. Additionally, LEfSe analysis of the enriched 13C in fungal DNA further showed that fungi in orders Sordariales and Eurotiomycetes, families Lindgomycetaceae, Montagnulaceae and Onygenaceae, and genera Staphylotrichum and Penicillium were key microbes in fresh C utilization in this paddy soil. The results help improving our understanding about the mechanisms of root residue-derived C cycling and emphasizing the importance of this huge amount C utilization.