Dear Dr. Berninger,

We recently published a paper using this kind of qPCR approach to detect difference of fungi and bacteria before and after fishponds in streams (Four et al. 2017 in freshwater biology). We also firstly looked for this type of proxy, but it appears that it is difficult to give a proxy between copy number and biomasses as the number of copy vary in intra- and between species but also between bacterial and fungal kingdoms (as suggested by Manerkar et al. (2008):“Estimating bacterial and fungal biomasses from relative DNA values is much more uncertain. Copy numbers rRNA operons per fungal cell are largely unknown for most species, making quantification of fungal biomass from a mixed community very difficult [3, 9, 20]. For example, copy numbers in the subphylum Pezizomycotina cary between 50 and 100 [37]. If we apply this to the current study and assume an average of 75 copies per fungal and an average of 7.5 per bacterial genome, the number of bacterial cells would exceed that of fungal cells by a factor of between five and ten times”). As the variation numbers of operons in species community and of different species are still poorly known (in my knowledge) I think that we can't use this indicator:

· as a proxy of abundance or biomass

· neither to compare the number of gene copy between bacteria and fungi.

Hope that can help,

See you,

Brian Four