Abstract
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.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.
Highlights
We examined Salicornia europaea, a nonmycorrhizal halophyte associated with specific and unique endophytic bacteria and fungi
Salinization history is a critical factor for S. europaea endophytic community structure
The reason can be that the interior of the halophyte tissues provides a relatively stable and protective environment for diverse communities of endophytic microbes compared to the saline soil, which is subject to wide fluctuations in the osmotic potential [29]
Summary
We examined Salicornia europaea, a nonmycorrhizal halophyte associated with specific and unique endophytic bacteria and fungi. 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. We can conclude that bacterial and fungal microbiomes of S. europaea are determined by the origin of salinity at the sites. Endophytic communities of halophytes may be different than those in other plants because salinity acts as an environmental filter. The two sites are only 40 km from one another, and the soil physicochemistry is similar, apart from the salinity origin This system gives a unique opportunity to observe differences due to the various times of plant host-microbiome coevolution. We first hypothesized that the Salicornia endophytic community composition at the two sites would be different, but a set of common microorganisms (a core microbiome) can be delineable
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