In recent years, plant‐associated microbiota has received considerable attention for their ability in crop improvement, productivity and stability. All plants, and nearly all plant tissues, are inhabited by a variety of microorganisms. Many of them offer benefits to the plants, by improving nutrient uptake, increasing plant growth under adverse environmental conditions and preventing pathogen attack. In return microorganisms have access to a carbon‐rich food supply and shelter from host and the surrounding environment. The interaction between plant and microorganism is quite complex. Best elucidated symbiotic systems are legumes and the nitrogen fixing rhizobium and host plants and mycorrhiza fungi, a and their influence on crop management, soil parameters and climatic effects are well studied. In addition, the knowledge about plant‐endophyte, plant‐epiphyte, and plant‐ rhizosphere flora is rapidly growing. Numerous species of plant growth promoting bacteria form biofilm when colonizing roots, which can affect bio‐geochemical processes and can result in increased availability of poorly available mineral nutrients. Four major groups of microorganisms are considered as beneficial to plants: arbuscular mycorrhizal fungi (AMF), plant growth promoting rhizobacteria (PGPR), nitrogen‐fixing rhizobia, which are usually not considered to be PGPR, and microbial biocontrol agents, which are composed of viruses, bacteria, yeasts and fungi. The integration of beneficial plant-microbe and microbiome interactions may represent a promising sustainable solution to improve agricultural production. The response is mediated and linked with several molecules, generally messenger molecules which activate the pathogen-responsive genes coding for antimicrobial compounds or enzymes. However, the responses specifically a gene-for-gene interaction recognition system by triggering a biochemical attack and programmed cell death. A synthetic biology approach to design microbial consortia combining desired mechanisms, pathways and interactions is a promising approach. New biotechnological products are currently being developed based on stimulation of the plant defense response, and on the use of plant-beneficial bacteria for biological control of plant diseases (biopesticides), abiotic stresses and for plant growth promotion (biofertilizers). Modern technologies such as next-generation sequencing (NGS), omics approaches (metagenomics, transcriptomics, proteomics, metabolomics), and computational tools enable the understanding of community-level molecular aspects of the PM interactions governing the plant traits.