Endophytic bacterial communities associated with halophytic plants in southern Tunisia

In the arid regions of southern Tunisia, soil and irrigation water salinity are the main serious issues that threaten agriculture. The potential of endophytic bacteria in providing salt-tolerance has not been investigated. Twenty-two plants and their corresponding soils were collected from five sites in two governorates kebili and Gabes. Significant differences in soil physicochemical properties were observed between sampling sites. The soils are generally poorly developed, non-fertile (with very low organic matter and high CaCO3 levels), and highly saline, leading to limited cultivation potential. Molecular identification of plants revealed nine different families and 14 genera, with the Amaranthaceae family being the most prominent, including Atriplex spp. (2), Bassia spp. (2), Suaeda spp. (4), and Halocnemum spp. (1). Bacterial community studies were conducted of both culturable and non-culturable endophyte communities inhabiting the green and root compartments of different halotolerant plants. Endophytic microbiome compositions differed between above-ground and below-ground tissues within the same plant family. A higher prevalence of three phyla Proteobacteria (67.80%), Firmicutes (14.06%), and Actinobacteria (6.57%) was detected across all samples. At the genus level, Acinetobacter , Halomonas, Kushneria, Pseudomonas, Psychrobacter, Stenotrophomonas , and Streptomyces formed the common core microbiome. PICRUSt gene prediction highlighted multiple KEGG functional pathways, indicating the role of these bacteria in plant adaptability under extreme conditions. Leveraging the microbiome of halophilic plants with specific species could be a valuable tool for enhancing plant adaptation during salt-degraded soil restoration