Rhizosphere microbiomes play a fundamental role in mediating nutrient cycling, supporting plant growth, and shaping the functional ecology of soils. Despite growing recognition of their importance, the mechanisms through which microbial communities interact with plants, respond to biological amendments, and vary across management contexts remain poorly understood. The goal of this dissertation research is to advance our understanding of plant-microbiome interactions by integrating genomic, multi-omics combining metagenomics and metaproteomics, and phenotypic approaches across multiple cropping systems and scales. Specifically, this dissertation consists of four objectives: 1) investigating the synergistic effects of polyphosphate-accumulating organism-enriched microbiomes and arbuscular mycorrhizal fungi on plant nutrient uptake and rhizosphere community dynamics in sorghum; 2) characterizing the phenotypic and compositional patterns of rhizosphere microbial communities across conventional and organic farming systems using an integrated Raman spectroscopy and microbiome approach; 3) examining how plant developmental stage shapes rhizosphere microbial genomic and functional responses to mycorrhizal and bacterial co-inoculation in tomato; and 4) investigating how beneficial microbial consortia restructure rhizosphere networks and plant nutrition in New York City urban tomato production using metaproteomic profiling. The first chapter growth chamber study demonstrated that microbiomes derived from enhanced biological phosphorus removal systems can establish in the sorghum rhizosphere and synergistically enhance plant growth and nutrient acquisition when combined with arbuscular mycorrhizal fungi, with single-cell Raman microspectroscopy and network analysis revealing corresponding shifts in microbial phenotypes and community connectivity. The second chapter regional farm survey conducted across farms in New York State showed that farming system was the dominant driver of rhizosphere microbial community structure and phenotype across diverse crop species and sites, with distinct microbial phenotypic profiles and network architectures characterizing organic and conventional systems. The third chapter growth chamber study revealed that tomato developmental stage is a critical but underappreciated modulator of rhizosphere microbial functional responses to inoculation, with co-inoculation effects of arbuscular mycorrhizal fungi and phosphate-solubilizing bacteria on microbial activity and community composition varying substantially between the flowering and fruiting stages. The fourth chapter field study conducted across three urban farms in New York City demonstrated that co-inoculation of arbuscular mycorrhizal fungi and phosphate-solubilizing bacteria restructures rhizosphere microbial networks and stimulates nutrient acquisition and cycling functions in urban compost-based production systems, as resolved through metagenome-informed metaproteomic profiling. Overall, our work shows that plant-microbiome interactions are highly dynamic, shaped by the interplay of microbial consortia, plant developmental context, and production management. These studies are among the first to integrate single-cell phenotyping with multi-omics approaches to demonstrate how microbial consortia interact with diverse crops to jointly determine rhizosphere community outcomes across production systems. Our research provides new mechanistic insight into how microbiomes mediate plant nutrient acquisition and advances the conceptual and methodological foundation for microbiome-informed strategies in sustainable crop production.