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Distinctive Patterns in the Taxonomical Resolution of Bacterioplankton in the Sediment and Pore Waters of Contrasted Freshwater Lakes

  • Environmental Microbiology
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Abstract

Bacteria assemblages in lake sediments play a key role in various biogeochemical processes, yet their association with interstitial pore waters has been scarcely investigated. In this study, we utilized Illumina next-generation amplicon sequencing of the 16S rRNA gene to characterize the seasonal bacterial communities in the sediments and pore waters of three contrasted temperate freshwater lakes, namely Pavin, Aydat, and Grangent (French Massif Central). Despite occupying seemingly similar habitats, bacterial communities differed substantially between sediments and pore waters at all seasons with low sharing of operational taxonomic units (OTUs, 6.7 to 20.3%) between them. Sediment-associated bacteria were more rich and diverse than pore water bacteria, indicating a high heterogeneity in the sediment microhabitat. The changes in both sediment and pore water bacterial communities were lake and season specific. The bacterial community showed distinct differences between the lakes, with larger presence of strict anaerobes such as Syntrophus, Syntrophorhabdus, and Sulfuricurvum in the pore water and sediments of Pavin responsible for carbon and sulfur cycling. In both Aydat and Grangent, the hgcI_clade dominated throughout the study period in the pore waters. The higher representation of lesser-known transient members of lake communities such as Methylotenera in the pore waters of Aydat, and Clostridium and Sulfuricurvum in the pore and sediments of Grangent, respectively, were observed during the period of temporary anoxia in summer caused by lake stratification. Our study revealed that in the investigated lakes, the prevailing environmental factors across time and space structured and influenced the adaptation of bacterial communities to specific ecological niches.

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Acknowledgements

JK was supported by a postdoctoral fellowship from the Université Clermont Auvergne (formerly Université Blaise Pascal), Clermont Ferrand (France). We thank J. Colombet and F. Perriere for their technical assistance in flow cytometry and nutrient analysis respectively. We appreciate the two reviewers for their time, effort, and valuable contributions to this manuscript.

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  1. J. Keshri

    Present address: Institute of Postharvest and Food Sciences, Agricultural Research Organization, Volcani Centre, 50250, Bet Dagan, Israel

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  1. Laboratoire Microorganismes: Génome et Environnement, UMR CNRS 6023, Université Clermont-Auvergne, 1 Impasse Amélie Murat, BP 80026, 63178, Aubière Cedex, France

    J. Keshri, A. S. Pradeep Ram & T. Sime-Ngando

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  1. J. Keshri
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Correspondence to A. S. Pradeep Ram.

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Keshri, J., Pradeep Ram, A.S. & Sime-Ngando, T. Distinctive Patterns in the Taxonomical Resolution of Bacterioplankton in the Sediment and Pore Waters of Contrasted Freshwater Lakes. Microb Ecol 75, 662–673 (2018). https://doi.org/10.1007/s00248-017-1074-z

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