Quantitative PCR for measuring biomass of decomposer fungi in planta

• Biomass of two wood-degrading fungi was estimated using ergosterol and rDNA.
• The two biomarkers were compared on three types of wood substrate.
• For both biomarkers, conversion factors varied between species, wood type and decay stage.
• Change in hyphal dimension between agar and wood partially explained such difference.
• A constant conversion factor cannot be assumed as default for either method.

The biomass of brown and white rot fungi were estimated using ergosterol and quantitative PCR (qPCR). Each biomass estimate was compared with biomass measured gravimetrically from liquid cultures, as well as from three wood substrata at two decay stages. Fungal morphological changes in two different substrata, agar and pine, were measured using a chitin-specific fluorophore and confocal microscopy. In liquid culture, the two fungal isolates had significantly different biomass conversion factors for both methods. In wood colonized for 3 wks, qPCR yielded a lower estimate than did ergosterol, while at week 8 it yielded a higher estimate. Changes in average fungal cell dimensions partially explained differences between the two methods. Overall, our results suggest that a constant conversion factor cannot be assumed as default for either method. Instead, it demonstrates the importance of standardizing wood species, decay class, fungus-specific conversion factor, and DNA extraction protocol in order to properly estimate fungal biomass in woody substrata.