If for example effects of root exudation on soil microbial community dynamics are to be investigated, it is important to consider the different temporal scales of the processes to be correlated. Root exudation varies with plant development stage and shows diurnal patterns, whereas community changes on a DNA level may not be detectable on such a short temporal scale. Any patterns of a single sampling time point would rather represent a legacy community that established around plant roots than the current state of a community that can be linked to root exudation (composition, rate) measured at the same time point.
Another soil parameter that might mask the detection of community shifts is intrinsically linked with microbial turnover: relic or environmental/exogenous DNA . Relic DNA is extracellular DNA from nonviable cells that has leaked into the environment and that is thought to persist in soils for months to years \cite{Levy_Booth_2007,Carini_2016}. Relic DNA has been estimated to comprise between 30% and 97% of the amplifiable soil DNA pool and has been successfully removed from soil samples via the application of DNases or propidium monoazide \cite{Lennon_2018,Carini_2020}. The latter study found greater differences in soil communities across several timepoints where relic DNA was removed as compared to samples where relic DNA was still present. Consequently, the presence of relic DNA may complicate the interpretation of sequencing data by over- or under-estimating microbial diversity which may be of particular concern when temporal dynamics are key to the scientific question.
Alternatively, ribosomal RNA (rRNA) amplicon sequencing via complementary DNA (cDNA) synthesis may be used to analyze microbial communities without bias of relic DNA (e.g. \cite{Vieira_2019}. The lifetime of rRNA in soils is relatively short and has been estimated to range from days to a few weeks depending on biogeochemical parameters such as temperature, pH, and water saturation \cite{Schostag_2020,Blazewicz_2013}. Thus, rRNA-targeted amplicon sequencing may increase the chances of capturing dynamics within soil microbial communities over time, however caution should still be directed to the persistence of relic DNA and rRNA in soil. If community dynamics are to be investigated in shorter time periods (e.g. minutes, hours) we suggest combining amplicon sequencing with methods for targeting the metabolically active cell fraction (as discussed in section XYZ Improving Ecological Insights).