Bacterial and Fungal Endophytic Microbiomes of Salicornia europaea

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.

Keywords: 16S rRNA and ITS amplicon sequencing; endophyte; halophyte; microbial community structure; soil salinity.

FIG 1

Species richness, diversity, and evenness in different test sites and plant organs for OTUs constructed at 0.03 dissimilarity for bacterial and fungal sequences. (a and b) Shannon’s H′; (c and d) Shannon’s E; (e and f) observed number of OTUs. Robust ANOVA test with the Tukey’s post hoc analysis was used to assess the significance of differences between test sites and plant organs. Variants labeled with the same letters are not significantly different (P ≤ 0.05).

FIG 2

Analysis of log-transformed and Wisconsin double-standardized Bray-Curtis dissimilarity matrix for endophytic bacterial and fungal communities associated with S. europaea, respectively. (a and c) CCA (canonical correspondence analysis); (b and d) NMDS (nonmetric multidimensional scaling analysis). Circles represent OTUs; their fill color denotes consensus taxonomy at the family level (bacteria) and genus level (fungi). The size reflects abundance. Squares, S1 samples; triangles, S2 samples; green, shoots; brown, roots. Arrows in the CCA graphs denote soil parameters that were significantly associated with the community structure.

FIG 3

Endophytic bacterial community structure at class (a) and genus (b) levels among the two test sites and plant organs.

FIG 4

Significantly represented bacterial classes. (a) Alphaproteobacteria; (b) Cytophagia; (c) Epsilonproteobacteria; (d) Sphingobacteriia. Whiskers denote the standard errors of the mean. Significant differences (P < 0.05), assessed using robust ANOVA and Tukey’s HSD test, are indicated by asterisks.

FIG 5

Significantly represented bacterial genera. (a) Kushneria; (b) Saccharospirillum; (c) Arcobacter; (d) Halomonas. Whiskers denote standard errors of the mean. Significant differences (P < 0.05), assessed using robust ANOVA and Tukey’s HSD test, are indicated by asterisks.

FIG 6

Endophytic fungal community structure at family (a) and species (b) levels among the two test sites and plant organs.

FIG 7

Significantly represented fungal taxa. (a) Pleosporaceae; (b) Paradendryphiella arenariae. Whiskers denote standard errors of the mean. Significant differences (P < 0.05), assessed using robust ANOVA and Tukey’s HSD test, are indicated by asterisks.

FIG 8

PICRUSt analysis of bacterial sequences. Box-and-whisker plots for most significantly different KEGG Orthology (KO) categories. Error bars represent standard errors of the mean of each given category abundance in different sample types. For sites S1 and S2, “-r” indicates “root” and “-s” indicates “shoot.”

FIG 9

CoCA of bacterial versus fungal communities’ plot of sites. Bacterial sites are displayed as circles, fungal ones as squares. The circle color denotes organ: green, shoots; and red, roots. Respective bacterial and fungal communities are connected with arrows. Arrow length conveys the strength of community association: the longer the arrow, the weaker the association.