The plant microbiome: From ecological foundations to precision microbial engineering for sustainable agriculture.

Plants are best understood as evolutionary holobionts, in which the host and its associated microbiomes operate as an integrated unit to influence growth, health, and stress resilience. This comprehensive review synthesizes the most current knowledge of plant-associated microbiomes across key ecological compartments, including the rhizosphere, endosphere, phyllosphere, and seeds, highlighting their assembly drivers, functional mechanisms, and translational potential. We dissect the molecular foundations of rhizobial and arbuscular mycorrhizal (AM) symbioses, the plant-AM fungus-bacterium continuum, alongside emerging concepts including the aerial root mucilagesphere, phyllosphere homeostasis, and the pathobiome. We further explore host genetic, metabolic, and environmental determinants of microbiome assembly, and present cutting-edge methodologies ranging from quantitative profiling to artificial intelligence-driven synthetic community design. Finally, we outline a strategic blueprint for harnessing standardized synthetic microbiomes and precision microbiome engineering to advance sustainable agriculture. This integrative framework bridges fundamental ecology with practical applications, delineating a path toward climate-resilient crop production.