Seed bacterial microbiota: transmission, community assembly, and prospects for engineering heritable functions in crops

Abstract

Seeds represent specialized, low-biomass microbial niches that facilitate the transmission of the plant-associated microbiota from one generation to another. Residing as both epiphytes and endophytes, seed-associated bacteria contribute to microbial community assembly during the seed-to-seedling transition. Recent integration of single-seed omics and synthetic bacterial communities has moved the field beyond descriptive surveys to identify the microbial drivers of plant germination success and early-life resilience. Despite this potential, the establishment and persistence of seed-borne bacteria are often constrained by competition with soil-derived microbiota. Seedling bacterial community assembly is further shaped by host genotype, domestication history, and maternal environmental conditions. In this review, we synthesize the mechanisms of bacterial transmission from flowering through seedling emergence and evaluate the functional capacity of the seed holobiont. We define the ecological parameters for the successful recruitment of engineered seed-based consortia into the soil-plant continuum, providing an experimental roadmap to move seed-based technologies from the laboratory to the field. Ensuring the functional stability of these heritable microbial traits will be essential for stabilizing agricultural productivity under increasing climatic volatility.