Organ-specific microbiomes in natural Lotus corniculatus populations: Metacommunity dynamics in the plant endosphere

The structure of plant microbial communities vary due to a broad range of factors such as host and environmental factors, abiotic and biotic perturbations, and various assembly processes occurring at multiple tempo-spatial scales. In natural environments plant microbial communities are constantly exposed to such perturbations and processes. Thus, to attain a systemic understanding of the ecology of plant microbiomes, it is essential to study assembly processes that influence patterns of microbial community structures in natural environments. In this study we examined bacterial, fungal, and eukaryotic communities in plant organs of Lotus corniculatus in natural populations at seven grassland sites for four years. We used the framework of metacommunity theory of ecology to understand assembly processes that shape community structures and variations by defining microbial communities associated with the roots, shoots, flowers, and seeds as distinct communities linked by dispersal. In this study we show the organ-specificity of plant endophytic communities. Our findings suggest that selective filtering by plant organs, microbial interactions, as well as abiotic and biotic factors at tempo-spatial scales result in distinct core microbiomes of plant organs. In addition, transmission of microorganisms from within and outside the plant hosts accounts for the distinct yet overlapping organ microbiomes. We could provide a comprehensive knowledge of the stochastic and deterministic assembly processes that shape plant microbial communities in natural conditions. Understanding these ecological processes is essential for harnessing beneficial effects of plant-associated microbial communities on plant productivity, resilience, and pathogen defense.