The plant is colonized by a plethora of microorganisms such as fungi, bacteria, archaea, oomycetes, and viruses that are detrimental or beneficial for their hosts (Hardoim et al. 2015; Brader et al., 2017). Some of these microorganisms colonize the plant surfaces before to enter inside plant tissues and form assemblages of subcommunities in various organs. Each step of the colonization of some of these microorganisms has been studied using single cells or natural communities. Different fluorescence techniques such as the use of tagged strains, fluorescence in situ hybridization or general staining techniques coupled with confocal microscopy have enabled to determine the colonization of these microorganisms (Compant et al., 2010). As an example, fungal colonization of a pathogen associated with grapevine has been revealed in Pierron et al (2015) and results have shown in which the niches the pathogenic strain could be present.

For bacteria, tagging of strains have been also done and a thorough understanding of the niches and ways of colonization of some specific plant-associated bacteria has been revealed (Compant et al., 2010; Escobar Rodríguez et al., 2018).

Different microbes have been detected crossing from different plant surfaces to inner tissues. Using general staining or specific targeting FISH, natural communities have been also visualized.