We conducted mixed effects models (R package: nlme) to examine the difference in Q10 values between the topsoil and the subsoil. In the model, site and soil depth were set as fixed factors, and depth nested in replicate was treated as a random factor. Having detected no interaction effect between site and soil depth (table S1), we used paired t tests to compare the means of physicochemical properties between the topsoil and the subsoil. Linear regression models were then performed to identify the relationships of Q10 with aggregate protection and microbial communities. Before the analyses, the variance inflation factor (VIF) was calculated to assess the collinearity of the variables (acceptable collinearity VIF ≤ 2) (58). On the basis of this criterion, the collinearity between SOC distribution in macroaggregates and microaggregates could be partly omitted (VIF = 1.6), whereas the relative abundance of fungal PLFAs was closely correlated with F/B (VIF = 4.4), and thus, only the former was included in the model.

To further analyze the relative importance of different variables, we conducted variation partitioning analysis (R package: vegan) to partition the effects of aggregate protection and microbial communities on Q10 in various C pools. △Q10 (Q10 topsoilQ10 subsoil, the difference in Q10 between the topsoil and the subsoil) for the two manipulative experiments was then calculated to test the role of aggregate protection and microbial communities. A positive value of △Q10 represents larger Q10 in the topsoil, while a negative value represents larger Q10 in the subsoil. The means of △Q10 between control and crush/inoculation treatments were compared using paired t tests. The decrease in △Q10 compared with the control indicates that crush/inoculation treatment reduces the difference in Q10 between the topsoil and the subsoil and vice versa. All of the statistical analyses were conducted with R version 3.2.1 (59), with a significance level of 0.05.

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