Because of its sensitivity, accuracy and precision, digital PCR (dPCR) is rapidly rising among nucleic acid quantification techniques, especially in disciplines such as microbiology where high sensitivity and precision are necessary. Here, we report three case studies about using dPCR to quantify microbes in plant and soil microbiology:
- Endophyte-Pathogen Interactions: dPCR validation of next-generation sequencing (NGS) results, confirming a higher abundance of beneficial Firmicutes in plant resistance to Fusarium verticillioides infection.
- Soil Fertilization Effects: dPCR accurately quantified bacterial populations, revealing that digestates rich in pig slurry enhanced soil microbial abundance more than mineral fertilizers or controls.
- Plant Pathogen Diagnostics: Existing qPCR assays (SYBR Green and TaqMan) were adapted to dPCR, demonstrating comparable sensitivity and greater precision for detecting the pathogen Xylella fastidiosa. The TaqMan assay proved more reliable, and dPCR offered cost and time advantages due to absolute quantifications and higher throughput.
Across all cases, nanoplate-based dPCR proved effective for absolute microbial quantification, offering increased accuracy, sensitivity and efficiency for both research and diagnostic applications in plant health.