Does the number of cells of individual strains correlate with their contribution to the total substrate turnover within a microbial community?

The contribution of individual bacterial strains within a mixed microbial community to the overall turnover of a specific compound is often assessed using qPCR data quantifying strain-specific 16S rRNA or functional genes. Here we compare the results of a qPCR based approach with those of compound specific stable isotope analysis (CSIA), which relies on strain-specific magnitudes of kinetic isotope fractionation associated with the biotransformation of a compound. To this end, we performed tetrachloroethylene (PCE) transformation experiments using a synthetic binary culture containing two different Desulfitobacterium strains ( Desulfitobacterium hafniense strain Y51; C,PCE = −5.8‰ and Desulfitobacterium dehalogenans strain PCE1; C,PCE = −19.7‰). Cell abundances were analyzed via qPCR of functional genes and compared to strain-specific PCE turnover derived via carbon isotope fractionation. Repeated spiking of an initially strain Y51 dominated synthetic binary culture with PCE led to a steadily increasing contribution of strain PCE1 to PCE turnover ( C,initial = −5.6 ± 0.6‰ to C,final = −18.0 ± 0.6‰) which was not or only weakly reflected in the changes of the cell abundances. The CSIA data further indicate that strain-specific PCE turnover varied by more than 75% at similar cell abundances of the two strains. Thus, the CSIA approach provided new and unexpected insights into the evolution of the metabolic activity of the single strains within a synthetic binary culture and indicates that strain-specific substrate turnover appears to be controlled by physiological and enzymatic properties of the strains rather than their cell abundance. In a synthetic binary culture, cell numbers derived by qPCR did not reflect the contribution of individual strains to the total substrate turnover.