Agriculture provides a wide range of ecosystem services and has the potential to contribute to biodiversity conservation. In Japan, many of the resources associated with agroecosystems are threatened by farmland abandonment. Identifying where and to what extent agricultural ecosystem services and farmland biodiversity are affected by farmland abandonment is essential for developing effective strategies to counter the potential loss of these services and the biological communities that support them. Our study aimed to examine how a set of indicators for ecosystem services and biodiversity linked to agroecosystems (proportions of land dedicated to rice production and other agricultural production, proportion of agricultural land on slopes potentially providing landscape aesthetics, proportion of villages promoting rural tourism, and densities of forest edges and irrigation ponds in agricultural land) are distributed at the municipal level across the Japanese Archipelago, and to analyze their spatial patterns in relation to the distribution of farmland abandonment. It was hypothesized that hotspots of agricultural ecosystem services and farmland biodiversity occur in areas at risk of farmland abandonment owing to shared drivers. The cluster analysis identified four distinct ecosystem service bundle types, two of them representing areas specializing in agricultural production, while the other two provided high levels of cultural services and habitats for diverse biological communities. The latter two bundles were located in hilly and mountainous areas and accounted for 58% of rice production, 27% of other agricultural production, 77% of landscape aesthetics, 77% of rural tourism, 64% of forest edges, and 87% of irrigation ponds in Japan. In support of the hypothesis, farmland abandonment was pronounced in these areas, with 64% of recently abandoned fields located where 44% of agricultural land was found. This spatial overlap suggests that substantial losses of ecosystem services and biodiversity may occur if current patterns of farmland abandonment continue. In order to prevent large-scale losses of agricultural ecosystem services and farmland biodiversity, measures to counteract the ongoing abandonment trends should prioritize hilly and mountainous areas, and future studies should further evaluate the multiple functions of agricultural areas to improve policies that aim to ensure sustainable development of rural areas in Japan.
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