Seasonal Shifts in Soil Microbiome Structure Are Associated with the Cultivation of the Local Runner Bean Variety around the Lake Mikri Prespa

SIMPLE SUMMARY: The “Prespa beans” are an important leguminous crop for the agricultural economy of the rural areas surrounding the lake Mikri Prespa. However, agricultural intensification and climate change have a negative impact on the available arable land, soil microbiome and, consequently, crop productivity. This study investigated the effects of seasonal changes on soil microbiome associated with runner bean cultivation. The results indicated that the presence of the runner bean and the soil processes affecting the carbon cycle differentially shaped the structure of the soil microbial community. Ultimately, this study highlights the importance of investigating soil microbiome in agriculture and is expected to contribute to future research for the development of novel preservation strategies for native soil ecosystem services. ABSTRACT: Leguminous crops play a key role in food production and agroecosystem sustainability. However, climate change and agricultural intensification have a significant impact on the available arable land, soil microbiome functions, and ultimately, crop productivity. The “Prespa bean” (Phaseolous coccineous L.) is an important leguminous crop for the agricultural economy of the rural areas surrounding the lake, Mikri Prespa, which is of significant ecological importance. The seasonal effects on soil microbiome structure, diversity and functions associated with the runner bean cultivation were investigated using 16S rRNA amplicon sequencing. The results indicated that the presence of the runner bean differentially shaped the soil microbial community structure. The runner bean was implicated in the recruitment of specific bacteria, by favouring or excluding specific classes or even phyla. Soil functions involved in nutrient availability and carbon metabolism, among other pathways, were associated with microbiome–plant interactions. The temporal relative abundance shifts could be explained by the impact of soil organic matter, the fertilization regime, and the equilibrium in carbon metabolic processes. This research has shown the effect of runner bean cultivation on the soil microbiome which, in future, may potentially contribute to research into sustainable agricultural productivity and the protection of soil ecosystem services.