This is an interesting study, and research addressing the controls on ‘relic DNA’ concentrations in soils is important! We provide the following comments in an effort to strengthen the manuscript for publication:
1. Clarification of the pH effect on relic DNA is important - conflicting information exists in the text (lower pH soils have more relic DNA; Lines 207-208, Table 1) and figure S7 (lower pH soils have more similar communities after PMA treatment). Given these relationships, it appears that your data suggest a negative relationship between the quantity of relic DNA and community dissimilarity. Is this the case? In our opinion the presentation of the data obscures this point. For example, samples are ordered differently in Fig. 1 and 2, and regression of community dissimilarity against pH is in the supplement. Why not directly regress community dissimilarity against relic DNA quantity?
2. Why was relic DNA quantity converted to a binary variable for regression with edaphic factors (Table 1, Fig. S6)? Why was 20% chosen as a cutoff for relic DNA presence/absence? If the assumption is that PMA treatment is not quantitative this should be discussed prominently in the manuscript, as this affects interpretation of results.
3. Sample storage should be discussed more explicitly as this could potentially affect the number of viable cells. How long were samples stored before PMA treatment? In addition, a test of the effect of soil moisture on relic DNA quantity would be useful for interpreting the data as this could be an important determinant of the number of viable cells.
4. A broader discussion of the significance of these findings for other biogeographical work on soil microbes would be valuable, as it calls into question the validity of earlier DNA-based approaches (e.g., how diversity relates to soil properties).
-- Kevin Geyer, Eric Morrison, Serita Frey (University of New Hampshire)