Biodiversity faces serious threats and to effectively protect it, we must understand the ecological processes that shape and structure it in natural communities. Nevertheless, it remains unclear how assembly processes influence the observed species diversity and coexistence among interconnected trophic levels. Thus, for my dissertation research I used a multitrophic system of flowers, their bee partners, and their associated microbes to explore the mechanisms underlying the process of community assembly through the lenses of microbial transmission ecology. Combining experiments, field data, and bioinformatics, this research emphasizes the intricate relationships and dependencies that define these systems. In Chapter 1 I investigate the bidirectional transmission of lactic acid bacteria (Apilactobacillus micheneri) between bees (Osmia lignaria) and flowers (Phacelia tanacetifolia). I learned that bees not only acquire but also deposit beneficial microbes onto flowers, thereby substantiating the environmental transmission hypothesis and highlighting the critical role of bees and flowers as vectors and filters within their ecosystems. In Chapter 2 I build on these findings by analyzing how the floral resources collected by mother bees influence the microbial communities associated to wild bee pollen provisions. By employing shotgun metagenomics, I discovered that maternal foraging patterns affect the microbial symbionts present in the pollen provisions, thereby impacting subsequent generations and emphasizing the importance of floral diversity in shaping these microbial landscapes. Finally, for Chapter 3 I extend the scope of my research to consider how these interactions affect biodiversity at broader spatial scales, specifically spatial variation of biodiversity (β-diversity). By exploring multitrophic dependencies across different ecological regions—namely the Santa Monica Mountains and the Channel Islands in Southern California—I illustrated how multitrophic assembly is a key mechanism driving variation in β-diversity and propose a new framework for including multitrophic perspectives into community assembly theory. Overall, this dissertation contributes to a deeper understanding of how symbiotic and ecological interactions across multiple trophic levels influence microbial transmission and community dynamics, providing valuable insights for conservation strategies and ecological management of multitrophic systems.