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Prokaryotic community diversity in the sediments of saline lagoons and its resistance to seasonal disturbances by water level cycles

  • Sediments, Sec 4 • Sediment-Ecology Interactions • Research Article
  • Published:
  • volume 21pages 3169–3184 (2021)
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Apart from having high concentrations of salt, some natural saline wetlands also go through cyclical fluctuations in water level. They are frequently considered vulnerable habitats. In the last decades, the reduction of rainfall in many areas, coupled with fertilizer overuse, is transforming wetlands, especially in climates with a pronounced dry season. We studied a seasonally flooded saline wetland, and focused on the changes in the microbial communities.


High-throughput sequencing was used to explore the diversity and structure of the prokaryotic communities present in the surface sediments. A water and soil salinity gradient along different lagoons in the wetland complex was observed.


Salinity affected both microbial richness and composition. The highest microbial richness was observed in lagoons with lower salinity. Statistical analysis suggests that the differences in community composition were associated with differences in salinity level, although an anthropic disturbance (increasing levels of soil organic matter, SOM) that was present predominantly in one lagoon also had a noticeable effect. Sorting of samples using beta diversity distances revealed that differences among communities were due to the distinct habitats, that is, a lagoon’s salinity and SOM, not water level cycles. Differences between flooded and dry-out seasons were also explored and the linear model showed that only a small number of OTUs (2.5%) had statistical differences between seasons.


Our findings will help in understanding the effects that both salinity and drying-out periods, which are increasing problems worldwide, may have on microbial communities and their resistance to seasonal fluctuations in water levels.

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We want to thank Mariano Rodríguez, director of the “Reserva Natural de Las Lagunas de Villafáfila,” for all his collaboration and assistance.

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All authors have contributed significantly to the project and merit to be included as co-authors.

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Correspondence to Luis E. Sáenz de Miera.

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The authors declare no competing interests.

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Responsible editor: Terrence H. Bell

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Supplementary Information

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Supplementary file1 Supplementary Table S1. Description of the linear models used in the analysis to test the effect of lagoon and water level factors, as well as their interaction. Description of mixed models used to explore the water level factor, considering sample localization as a random effect. Response variables analyzed with these models included: Phsyco-Chemical parameters; indexes of alpha diversity; position of communities on the first three axes of the PCoAs for the two estimated distances; and logarithm of the relative abundance of each OTU. Significant P-values are in light salmon, and those with P < 10–6 are in dark salmon color. Samples grouped by lagoon and water level stage (season) are depicted using a color gradient in magenta. The names of species with OTUs that have more than 90% identity with NCBI’s RefSeq 16S databases are also shown. (PDF 2.11 MB)


Supplementary file2 Supplementary Figure S1. Boxplots showing relative abundance of certain taxa for the salty and the non-salty lagoons. Abundance represented as the logs of normalized reads. Different patterns among lagoons can be appreciated. See text for a more detailed explanation. (PDF 18 KB)


Supplementary file3 Supplementary Figure S2. Boxplots of taxonomically far distanced taxa, with higher frequency during the flooded stage (F) or dried-out stage (D). Abundance represented as the logs of normalized reads. Taxa more frequent in F were Deltaproteobacteria, Bacteroidia, and Planctomycetaceae; while in D were: Actinobacteria, Cytophagia, and Group 21 of Acidobacteria. (PDF 16 KB)

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Sáenz de Miera, L.E., Gutiérrez-González, J.J., Arroyo, P. et al. Prokaryotic community diversity in the sediments of saline lagoons and its resistance to seasonal disturbances by water level cycles. J Soils Sediments 21, 3169–3184 (2021).

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