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

Area of Science:

• Soil ecology
• Molecular biology
• Environmental science

Background:

• Soils store vast terrestrial organic carbon, but significant losses have occurred.
• Accurate quantification of soil microbial biomass (fungi and bacteria) is vital for soil health and carbon cycling.
• Conventional methods for microbial biomass estimation have limitations in sample requirements and accuracy.

Purpose of the Study:

• To present an optimized digital droplet PCR (ddPCR) workflow for absolute quantification of bacterial and fungal abundance in soil.
• To enable conversion of gene copies to cell numbers and estimate microbial biomass carbon.
• To compare ddPCR-derived microbial biomass carbon with conventional chloroform fumigation methods.

Main Methods:

• Utilized digital droplet PCR (ddPCR) targeting 16S (bacteria) and 18S (fungi) rRNA genes for absolute quantification.
• Applied a workflow to convert gene copy numbers to cell counts and estimate microbial biomass carbon (MBC).
• Compared ddPCR results with chloroform fumigation estimates across five diverse agricultural soil systems.

Main Results:

• ddPCR provided high-resolution quantification of microbial abundance and sensitive fungal:bacterial (F:B) ratio estimates.
• ddPCR-derived MBC showed a weak correlation with chloroform fumigation values.
• The ddPCR method proved reproducible and scalable for soil microbial assessment.

Conclusions:

• ddPCR is an effective molecular approach for assessing soil microbial biomass and ecological indicators like the F:B ratio.
• This protocol offers a reproducible and scalable strategy for soil health assessment.
• ddPCR advances soil ecological studies by integrating microbial abundance with compositional analyses.