Ecophylogenetic patterns of rhizosphere bacterial community assembly in Pisum spp. (Fabaceae, Fabeae) reveal strong ecological filtering

Plant-microorganisms interactions are among the oldest biotic relationships and play a fundamental role in shaping biological systems. These associations involve several and diverse species, each evolving on different timescales. Understanding these interactions requires approaches that integrate both the ecological dynamics and evolutionary processes, which drive the adaptation of plants and microorganisms. We investigated bacterial community assembly dynamics associated with four diverse Pisum spp. accessions grown in greenhouse conditions on soil. Bacterial DNA was extracted from bulk soil, rhizosphere, rhizoplane, and endosphere microhabitats across three plant growth stages, followed by full-length 16S rRNA gene sequencing. Bacterial communities varied in diversity, composition and structure across microhabitats and growth stages. Ecophylogenetic analyses indicated strong plant-induced ecological filtering, with community assembly across space and time structured by phylogenetic constraints. This illustrates the role of plant-defined ecological niches in shaping bacterial communities, where selective recruitment favors specific and closely related lineages. Our findings suggest that an ecophylogenetic framework provides valuable insights into plant–microbiota dynamics by integrating ecological and evolutionary processes, thereby offering a powerful perspective to investigate the co-adaptation of plants and their associated microbiota.