CONCLUSIONS
This study highlights the power of haplotype-level community metabarcoding, enabled by the application of stringent filtering strategies, for the description of spatial biodiversity patterns of complex communities in understudied regions (Cyprus) and environments (soil), overcoming previous limitations of the taxonomic impediment, low-resolution data and noise due to the presence of spurious sequences. The wide implementation of harmonised field, lab and bioinformatic protocols for community metabarcoding of unexplored assemblages will increase the comparability of datasets from across the globe (Arribas et al., 2021a), providing the basis for broad-scale analyses of metacommunity patterns that would enable drawing more general conclusions on the consistency or context-dependency of ecological processes across spatial scales and fractions of biodiversity. Additionally, the ease with which all species in local communities can be characterised at the population genetic level using metabarcoding with stringent filtering raises the prospect for modelling demographic processes for each of the component species (Overcast, Emerson, & Hickerson, 2019; Overcast et al., 2021). Such an approach has the potential to elucidate historical and contemporaneous community responses to environmental heterogeneity and dispersal limitation at a much finer resolution than the summary statistics currently applied in whole-community metabarcoding.