Linking stable soil carbon and microbes using rapid fractionation and metagenomics assays – First results screening fungal inoculants under wheat crops

Abstract

Increasing soil carbon in agricultural systems can help mitigate and eventually reverse climate change. Soil microorganisms play a key role in regulating soil carbon accrual and stability. Questions remain about the link between microbes and soil carbon outcomes and how to leverage microbial processes. Here we screen microbial inoculation (endophytic fungal isolates) regarding their effects on soil carbon in a wheat pot trial using a rapid soil carbon fractionation assay and link the results with microbial community structure and function observations. Under the specific chemical and biological conditions of the plant-soil-environmental system, two of the 17 fungi tested increased soil carbon in close proximity to the roots by ∼15 %. This increase was associated with the medium stable, soil aggregate organic matter fraction (up to +21 %) and also mineral-associated organic matter, the long-term soil carbon storage (+10 %). Some of these changes were linked to a shift in predicted functional genes (whole metagenome, long read sequencing) and an increase in bacterial and fungal biomass (phospholipid fatty acid analysis). Microbial inoculation did not induce a statistically significant shift in the microbial composition (metagenomics), which, instead, correlated with the labile, particulate organic matter pool. While it is unclear whether the two endophytes directly influenced soil carbon cycling or had an indirect effect, through altering existing microbial processes, it demonstrates their potential for positive impacts on soil carbon that needs confirming in field trials. The combination of high throughput assays we present here could further help link carbon stability with microbial indicators and build more accurate soil carbon models.