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 commu...
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BMC
2025-01-01
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| Series: | Environmental Microbiome |
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| Online Access: | https://doi.org/10.1186/s40793-025-00664-y |
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| author | Vincent Hervé Jérôme Morelle Josie Lambourdière Pascal Jean Lopez Pascal Claquin |
| author_facet | Vincent Hervé Jérôme Morelle Josie Lambourdière Pascal Jean Lopez Pascal Claquin |
| author_sort | Vincent Hervé |
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| description | 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. |
| format | Article |
| id | doaj-art-862bcf4b8d574cc3b2ff99f0673ed6a5 |
| institution | Kabale University |
| issn | 2524-6372 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
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| series | Environmental Microbiome |
| spelling | doaj-art-862bcf4b8d574cc3b2ff99f0673ed6a52025-01-26T12:53:21ZengBMCEnvironmental Microbiome2524-63722025-01-0120111510.1186/s40793-025-00664-yTogether throughout the year: seasonal patterns of bacterial and eukaryotic microbial communities in a macrotidal estuaryVincent Hervé0Jérôme Morelle1Josie Lambourdière2Pascal Jean Lopez3Pascal Claquin4Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFoodDepartment of Biology and CESAM—Centre for Environmental and Marine Studies, University of AveiroUMR BOREA, Muséum National d’histoire Naturelle, CNRS-8067, Sorbonne Université, IRD, Université de Caen Normandie, Université des AntillesUMR BOREA, Muséum National d’histoire Naturelle, CNRS-8067, Sorbonne Université, IRD, Université de Caen Normandie, Université des AntillesUniversité de Caen Normandie, Laboratoire MERSEA UR 7482, Centre de Recherches en Environnement CôtierAbstract 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.https://doi.org/10.1186/s40793-025-00664-yMetabarcodingSeine RiverLongitudinal gradientSeasonTrophic interactions |
| spellingShingle | Vincent Hervé Jérôme Morelle Josie Lambourdière Pascal Jean Lopez Pascal Claquin Together throughout the year: seasonal patterns of bacterial and eukaryotic microbial communities in a macrotidal estuary Environmental Microbiome Metabarcoding Seine River Longitudinal gradient Season Trophic interactions |
| title | Together throughout the year: seasonal patterns of bacterial and eukaryotic microbial communities in a macrotidal estuary |
| title_full | Together throughout the year: seasonal patterns of bacterial and eukaryotic microbial communities in a macrotidal estuary |
| title_fullStr | Together throughout the year: seasonal patterns of bacterial and eukaryotic microbial communities in a macrotidal estuary |
| title_full_unstemmed | Together throughout the year: seasonal patterns of bacterial and eukaryotic microbial communities in a macrotidal estuary |
| title_short | Together throughout the year: seasonal patterns of bacterial and eukaryotic microbial communities in a macrotidal estuary |
| title_sort | together throughout the year seasonal patterns of bacterial and eukaryotic microbial communities in a macrotidal estuary |
| topic | Metabarcoding Seine River Longitudinal gradient Season Trophic interactions |
| url | https://doi.org/10.1186/s40793-025-00664-y |
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