Estimated decrease in alpha diversity, measured as Shannon Index (H’), for different incubation treatments and markers. A short and gentle lysis (B1, LT1) recovers diversity values closer to the actual values of the original sample measured in biomass with the 16S marker (blue) and an increase in lysis time and chemical aggressiveness of the buffer returns more distant values. With COI (orange), this effect is dependent only on the lysis buffer. The decrease in alpha diversity compared to the mock samples based on number of individuals is greater than based on biomass, but they reproduce the same pattern. The black line indicates H’(mock community) = H’(metabarcoding sample).