Assessment of the structural and functional diversities of plant microbiota: Achievements and challenges – A review

•History about the discovery of endophytes with the focus on Azospirillum and related diazotrophs.•Contribution of approaches to reach highest resolution of microbial diversity assessment.•Differentiation of beneficial A. brasilense and opportunistic human pathogen R. fauriae.•Osmoadaption and oxygen tolerance as major traits for endophytic bacteria.•Bacteria-plant communication with focus on bacterial N-acyl homoserine lactones.