Multidimensional sampling framework reveals plant-driven effects on microbial spatial heterogeneity and niche differentiation in a natural ecosystem.

Background: The identification of complex spatial patterns of microbial communities in relation to their ecological niches is fundamental to understanding the mechanisms of ecological interactions among diverse organisms. This study introduces a novel three-dimensional (3D) sampling approach to examine the spatial dynamics of microbial populations and niche differentiation influenced by plant-mediated effects in natural ecosystem.

Results: Microbial communities across horizontal and vertical dimensions were systematically mapped, and we found that the total microbial diversity, particularly among eukaryotes, increased more than ten-fold compared to that obtained via single-grid sampling, emphasizing the importance of spatial heterogeneity in shaping microbial dynamics. Moreover, the 3D framework enabled us to identify taxa specifically associated with particular plants, offering insights into plant-microbe interactions, pathogen prevalence, and ecological consequences of plant-driven effects on local communities.

Conclusions: Collectively, these findings demonstrate that 3D sampling approach provides a reproducible and scalable methodology for investigating microbial spatial heterogeneity, pathogen ecology, and niche differentiation in natural environments.