The enormous potential of the phytobiome for better plant growth and productivity is an essential tool for sustainable agronomic practices for eco-friendly cultivation processes. However, microbes in relation to plants, environment, omics, and their interactions are still to be clearly explored. Current predictive formulae like niche origin, ecological traits, evolution, genetics or heterosis, and resource trades are not mutually exclusive. This chapter mainly emphasizes on phytobiome related to soil fertility, nutrient cycling, plant growth, and soil health. Plant-associated phytobiome such as rhizospheric and phyllospheric played a significant role in the enhancement of plant growth and yield. These organisms form multifarious networks that are established and regulated through nutrient cycling, competition, antagonism, and chemical communication mediated by a diverse array of signaling molecules. The integration of knowledge of signaling mechanisms with that of phytobiome members and their networks will lead to a new understanding of the fate and significance of these signals at the ecosystem level. Such an understanding could lead to new biological, chemical, and breeding strategies to improve crop health and productivity. Soil organic matter (SOM) is a heterogeneous mixture of materials that range in the stage of decomposition from fresh plant residues to highly decomposed material known as humus. SOM is made of organic compounds that are highly enriched in carbon. Though half of the global population depends on fertilizer N, atmospheric N fixation by rhizospheric microbes is essential for plant productivity in low N soils. Many plants form symbiotic associations between their roots and specialized fungi in the soil known as mycorrhizae; the roots provide the fungi energy in the form of carbon, while the fungi provide the plant with often-limiting nutrients such as phosphorus. Besides, some soil microbiomes play a crucial role in the solubilizing stable form of potassium and micronutrients by releasing some metabolites which act as chelating agents. We explain recent information and cracks in these areas using phytobiomes.