Determination of Microbial Biomass in Soil using Digital Droplet PCR (ddPCR)

Soil represents the largest terrestrial pool of organic carbon, yet more than 133 Gt of carbon has been lost from soils over the past two centuries. Accurate quantification of soil microbial biomass, particularly fungi and bacteria, the primary decomposers driving carbon and nutrient cycling, is essential for understanding soil ecological functioning and health. Conventional approaches, including chloroform fumigation extraction and PLFA analysis, are limited by high sample requirements and uncertainties associated with converting biochemical markers into microbial biomass estimates. Here, we present an optimized workflow for quantifying bacterial and fungal abundance in soil using digital droplet PCR (ddPCR) targeting the 16S and 18S rRNA genes. The method enables absolute quantification of microbial gene copies, conversion to cell numbers using gene copy number correction factors, and subsequent estimation of microbial biomass carbon. We applied this protocol to soils from five globally distributed agricultural systems differing in soil texture, land use, and organic matter content. ddPCR-derived estimates were compared with conventional chloroform fumigation estimates of microbial biomass carbon. ddPCR provided high-resolution quantification of microbial abundance and produced broader and more sensitive estimates of F:B ratios across soil types than whole genome sequencing. Although ddPCR-derived MBC showed only a weak correlation with chloroform fumigation values, this method offers an effective molecular approach for assessing microbial biomass and ecological indicators such as the F:B ratio. This protocol provides a reproducible and scalable strategy for integrating microbial abundance measures with compositional analyses to advance soil health assessment.