IntroductionThe endosphere of a plant is an interface containing a thriving community of endobacteria that can affect plant growth and potential for bioremediation.Eichhornia crassipesis an aquatic macrophyte, adapted to estuarine and freshwater ecosystems, which harbors a diverse bacterial community. Despite this, we currently lack a predictive understanding of howE. crassipestaxonomically structure the endobacterial community assemblies across distinct habitats (root, stem, and leaf).MethodsIn the present study, we assessed the endophytic bacteriome from different compartments using 16S rRNA gene sequencing analysis and verified thein vitroplant beneficial potential of isolated bacterial endophytes ofE. crassipes.Results and discussionPlant compartments displayed a significant impact on the endobacterial community structures. Stem and leaf tissues were more selective, and the community exhibited a lower richness and diversity than root tissue. The taxonomic analysis of operational taxonomic units (OTUs) showed that the major phyla belonged to Proteobacteria and Actinobacteriota (> 80% in total). The most abundant genera in the sampled endosphere wasDelftiain both stem and leaf samples. Members of the family Rhizobiaceae, such as in both stem and leaf samples. Members of the family Rhizobiaceae, such asAllorhizobium- Neorhizobium-Pararhizobium-Rhizobiumwere mainly associated with leaf tissue, whereas the generaNannocystisandNitrospirafrom the families Nannocystaceae and Nitrospiraceae, respectively, were statistically significantly associated with root tissue.Piscinibacter and Steroidobacterwere putative keystone taxa of stem tissue. Most of the endophytic bacteria isolated fromE. crassipesshowedin vitroplant beneficial effects known to stimulate plant growth and induce plant resistance to stresses. This study provides new insights into the distribution and interaction of endobacteria across different compartments ofE. crassipesFuture study of endobacterial communities, using both culture-dependent and -independent techniques, will explore the mechanisms underlying the wide-spread adaptability ofE. crassipesto various ecosystems and contribute to the development of efficient bacterial consortia for bioremediation and plant growth promotion.