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Bacterial endophytes are a class of endosymbiotic microorganisms widespread among plants that colonize intercellular and intracellular spaces of all plant compartments and do not cause plant disease or significant morphological changes. Plant and endophytic bacteria association includes vast diversity of bacterial taxa and plant hosts and in this review we present an overview of taxonomic composition of endophytes identified in common agricultural crops. Further, during the last decade, new aspects of the microbial diversity have emerged with application of new metagenomic analysis methods in studies of bacterial endophytes. Endophytic bacteria community structure is influenced by plant genotype, abiotic and biotic factors such as environment conditions, microbe – microbe interactions and plant – microbe interactions. Agricultural practices, such as soil tillage, irrigation, use of pesticides and fertilizers have a major effect on function and structure of soil and endophytic microbial populations. Therefore, the use of agricultural practices that maintain natural diversity of plant endophytic bacteria is becoming an important element of sustainable agriculture that could ensure plant productivity and quality of agricultural production. The diverse endophytic microbial communities play integral and unique role in the functioning of agroecosystems. Endophytic bacteria have been shown to have several beneficial effects on their host plant, including growth promoting activity, modulation of plant metabolism and phytohormone signalling that leads to adaptation to environmental abiotic or biotic stress. Use of endophytic bacteria presents a special interest for development of agricultural applications that ensure improved crop performance under cold, draught or contaminated soil stress conditions or enhanced disease resistance.

Bacterial endophytes in agricultural crops and their role in stress tolerance: a review