Daisuke Fujiki

The overabundance of sika deer has become a significant threat to plant communities across Japan. As a result of the deer overgrazing, rare plants are undergoing a demographic bottleneck, leading to a loss of genetic diversity. Genetic diversity is crucial for the reproductive success of self-incompatible plants, and it also provides evolutionary potential, which increases their long-term population viability. Therefore, it is essential to appropriately manage the remaining genotypes to conserve local genetic resources. In this study, we exemplify this, via a conservation genetic analysis of Parasenecio peltifolius populations impacted by deer. Genetic data revealed that the small populations confined to isolated refugial sites consisted of effectively single genets. Recent reproductive failures in these populations may be attributed to the loss of genotypic diversity. Despite the bottlenecks, the remaining genets exhibited high individual heterozygosity, which is a good indicator that they have not been affected by severe inbreeding. Hybrid simulations suggested that interpopulation outbreeding between the unique genotypes can be a viable option to promote sexual reproduction and re-establish genetic diversity within the local populations. Establishing artificial progenies in botanical gardens can serve as a vital genetic resource for the long-term viability of threatened P. peltifolius populations.

Almost all ecosystems are open systems, meaning that significant changes in one ecosystem can lead to unexpected changes in others. Deer overabundance has become a problem worldwide, leading to forest degradation that has impacts on not only terrestrial, but also aquatic ecosystems. This study aims to investigate the regional-scale importance of large herbivores in inter-ecosystem interactions by examining the effects of deer-induced forest degradation on fish populations. We selected similar-scale catchments from river systems in Hyogo, Japan, that differed in the time since deer-induced forest degradation. Conventional surveys for fish densities and microhabitat environments were conducted in 23 catchments, and surveys using quantitative eDNA metabarcoding were conducted in 95 catchments. We examined the relationships between fish population densities, microhabitats, and time since forest degradation, considering confounding effects. Data from 8 and 17 fish taxa detected by snorkeling and eDNA methods, respectively, were available for statistical analysis. Snorkeling-counts (Individuals/1 m transect) and eDNA concentrations (Copies/L) in river water were strongly correlated. Fine sediments on riverbeds were increased in the 3–15 years following forest degradation and decreased after 16 years. Population densities of sand-preferring fishes, as inferred from both eDNA and snorkeling, reasonably followed this pattern. These patterns may be caused by the depletion of fine sediments on mountain slopes. The results of this study suggest that deer-induced worldwide alternation may also occur in aquatic ecosystems.

Ungulate overbrowsing is a growing problem in forests worldwide due to its prolonged and pervasive impact on plant biodiversity and ecosystem functioning. It has been shown that overbrowsing not only reduces plant species diversity and biomass (i.e., direct effects) but also causes a loss of associated trophic levels that could potentially feedback to influence plant community structure (i.e., indirect effects). One of the primary pathways of such indirect effects that have not been fully examined is the impact of overbrowsing on soil microorganisms. Recent studies have shown that soil microorganisms maintain vegetation diversity and drive succession, so it is of critical importance to understand how soil microbial communities might be affected by or protected from the deer impact. To assess the consequence of creating artificial grazing refugia on the structure and composition of soil microbial communities, we compared the distribution and abundance of soil microbial taxa (bacteria, archaea, fungi) at the fenced versus unfenced control sites in the context of a catchment-scale field experiment in Japan. The eDNA metabarcoding analysis of soil microbial communities showed that the numbers of archaea and basidiomycetes fungal species were greater in the fenced site than in the control, while no such pattern was found for bacteria and ascomycetes fungi. Despite the lack of significant influence of the fence treatment on taxonomic composition in the soil fungal communities, their functional guild composition was influenced by the fenced treatment, with significant changes in the abundance of animal pathogens. Thus, although the effect of fencing on soil microbial communities is characterized by complex responses that vary from taxon to taxon, our work suggests that creating ecosystem-scale refugia from deer overgrazing might help sustain certain, if not all, taxa of soil microbial communities.