Soil sampling and sample processing
During 2019, from mid-April to mid-June, we collected soil samples from 44 sites representing the main five forest habitat types of the Troodos mountain range (described above, Figure 1; Table S1). Our sampling scheme covered the full extent of the distribution and altitudinal range that the five tree species exhibit on Troodos, spanning over 65 km along an east-west axis and 1500 m of elevation range (Figure 1; Table S1). We collected two soil samples per sampling site corresponding to the superficial (1 m2 of leaf litter and humus, 5 cm depth) and the deep layer (30 cm diameter, 30 cm depth, comprising ~20 liters of soil) as described in Arribas et al. (2021b). The 88 soil samples were subsequently processed using a standardized flotation-Berlese-flotation protocol to extract the soil mesofauna as detailed in Arribas et al. (2016, 2021b). This protocol allows the retrieval of two subsamples of bulk arthropod specimens, divided according to their body size (typically Acari and Collembola vs. Coleoptera) which are suited for ‘clean’ extraction of whole organism community DNA. During bulk-sample processing, we additionally selected ‘voucher’ specimens of Acari, Collembola and Coleoptera representing broadly the morphological variation observed in these groups across samples. A total of 176 bulk subsamples and 344 ‘voucher’ specimens were preserved at -20°C in ethanol 100% for molecular analyses.