We examined Salicornia europaea, a non-mycorrhizal halophyte associated with specific and unique endophytic bacteria and fungi. Microbial community structure was analyzed at two sites differing in salinization history (anthropogenic and naturally saline site), in contrasting seasons (spring and fall) and in two plant organs (shoots and roots) via 16S rRNA and ITS amplicon sequencing. We observed distinct communities at the two sites, and in shoots and roots, while the season was of no importance. The bacterial community was less diverse in shoots libraries than in roots, regardless of the site and season, whereas no significant differences were observed for the fungal community. Proteobacteria and Bacteroidetes dominated bacterial assemblages and Ascomycetes were the most frequent fungi. A root core microbiome OTU belonging to genus Marinimicrobium was identified. We detected a significant influence of the Salicornia bacterial community on the fungal one by means of co-correspondence analysis. Additionally, pathways and potential functions of the bacterial community in S. europaea were inferred and discussed.
We can conclude that bacterial and fungal microbiomes of S. europaea are determined by the origin of salinity at the sites. Bacterial communities seemed to influence fungal ones, but not the other way around, which takes us closer to understanding of interactions between the two microbial groups. Additionally, the plant organs of the halophyte filter the microbial community composition.
Importance Endophytes are particularly fascinating because of their multifaceted lifestyle i.e. they may exist as either free-living soil microbes or saprobic ones or pathogens. Endophytic communities of halophytes may be different than those in other plants because salinity acts as an environmental filter. At the same time, they may contribute to the host's adaptation to adverse environmental conditions, which may be of importance in agriculture.
