We examined Salicornia europaea, a nonmycorrhizal halophyte associated
with specific and unique endophytic bacteria and fungi. The 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 internal transcribed spacer 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 shoot 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 operational taxonomic unit belonging to the
genus Marinimicrobium was identified. We detected a significant influence of the Salicornia
bacterial community on the fungal one by means of cocorrespondence analysis.
In addition, pathways and potential functions of the bacterial community in Salicornia
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. In addition, the plant organs of the halophyte filter the microbial
community composition
