Together throughout the year: seasonal patterns of bacterial and eukaryotic microbial communities in a macrotidal estuary

Abstract

Background: Estuaries are complex ecosystems linking river and marine environments, where microorganisms play a key role in maintaining ecosystem functions. In the present study, we investigated monthly 8 sites at two depth layers and over a one-year period the bacterial and eukaryotic community dynamics along the Seine macrotidal estuary (Normandy, France). To date, the taxonomy of the microbial diversity present in this anthropized estuary remains elusive and the drivers of the microbial community structure are still unknown.

Results: The metabarcoding analysis of 147 samples revealed both a high bacterial and eukaryotic diversity, dominated by Proteobacteria, Bacteriodota, Actinobacteriota and Bacillariophyta, Spirotrichea, Dinophyceae, respectively. Along the estuary we only detected significant spatial patterns in the bacterial and eukaryotic community compositions for three and two months out of twelve, respectively. However, we found a clear seasonal effect on the diversity of both microbial communities driven by physical and chemical variables that were fluctuating over the year (temperature, irradiance, river flow). Biotic associations were also significant drivers of both alpha and beta diversity. Throughout the year, we identified a diverse and abundant core microbiota composed of 74 bacterial and 41 eukaryotic OTUs. These regionally abundant species include habitat generalists encompassing heterotrophs, phototrophs and consumers. Yet, many of these core OTUs remain taxonomically and functionally poorly assigned.

Conclusions: This molecular survey represents a milestone in the understanding of macrotidal estuary dynamics and the Seine ecosystem, through the identification of putative markers of ecosystem functioning. It also identifies seasons and biotic associations as main drivers of the Seine estuary microbiota and reveals the importance of a core microbiota throughout the year.

Keywords: Longitudinal gradient; Metabarcoding; Season; Seine River; Trophic interactions.

Fig. 1

Localization of the eight sites sampled monthly for one year along the Seine estuary

Fig. 2

Overview of the taxonomic distribution of the ten major (A) bacterial phyla and (B) eukaryotic clades (rank-2 level based on the PR2 classification system) present in the 147 samples. Each point represents the relative abundance (% of the number of reads) of each clade in a sample

Fig. 3

Microbial OTU richness. Mean predictor importance (% of increase of mean squared error) of environmental drivers on microbial OTU richness for (A) the bacteria and (B) the eukaryotes. Only the variables represented by red barplots are significant (P < 0.05). Temporal evolution of the (C) bacterial and (D) eukaryotic richness across the year. The horizontal black dashed line represents the median richness of the whole dataset. The blue line represents a regression fitted using the “gam” method. Shaded areas correspond to the point wise 95% confidence interval on the fitted values. SPM: suspended particulate matter; TEP: transparent polymeric substances; EPS: extracellular polymeric substances

Fig. 4

Correlation biplot based on a RDA ordination of the (A) bacterial and (B) eukaryotic communities constrained by the environmental variables. Only the environmental variables retained by forward selection (P < 0.05) are presented

Fig. 5

Core microbiota. Taxonomic distribution and mean relative abundance of the core OTUs of the (A) bacterial and (B) eukaryotic communities. Vertical black lines correspond to median values. Seasonal variations of the relative abundance of core microbiota for (C) the bacterial and (D) the eukaryotic communities. Statistical comparisons were computed with Kruskal–Wallis test followed by Dunn’s test with Bonferroni adjustment

Fig. 6

Core microbiota. Heatmap showing the Pearson correlations between the core bacterial and core eukaryotic OTU abundances. The color code for OTU taxonomy is similar to the one used for Fig. 5. Refer to Table S3 for the complete taxonomic assignment of these OTUs