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Diel Rhythm Does Not Shape the Vertical Distribution of Bacterial and Archaeal 16S rRNA Transcript Diversity in Intertidal Sediments: a Mesocosm Study

  • Environmental Microbiology
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Abstract

In intertidal sediments, circadian oscillations (i.e., tidal and diel rhythms) and/or depth may affect prokaryotic activity. However, it is difficult to distinguish the effect of each single force on active community changes in these natural and complex intertidal ecosystems. Therefore, we developed a tidal mesocosm to control the tidal rhythm and test whether diel fluctuation or sediment depth influence active prokaryotes in the top 10 cm of sediment. Day- and nighttime emersions were compared as they are expected to display contrasting conditions through microphytobenthic activity in five different sediment layers. A multiple factor analysis revealed that bacterial and archaeal 16S ribosomal RNA (rRNA) transcript diversity assessed by pyrosequencing was similar between day and night emersions. Potentially active benthic Bacteria were highly diverse and influenced by chlorophyll a and phosphate concentrations. While in oxic and suboxic sediments, Thaumarchaeota Marine Group I (MGI) was the most active archaeal phylum, suggesting the importance of the nitrogen cycle in muddy sediments, in anoxic sediments, the mysterious archaeal C3 group dominated the community. This work highlighted that active prokaryotes organize themselves vertically within sediments independently of diel fluctuations suggesting adaptation to physicochemical-specific conditions associated with sediment depth.

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Acknowledgements

This research was supported by a PhD grant from the Charente Maritime Department and by the national program CPER 2006-2013 (Contrat Projet Etat Région) of Charente Maritime, the French national program EC2CO (CAPABIOC, 2012-2014), and the CNRS organism. The tidal mesocosms were built by M. Prineau and N. Lachaussée. We acknowledge the Molecular and the Cytometry Core Facilities at LIENSs laboratory. The authors are grateful to A. Leynaert (LEMAR, Brest, France) for the rhizon technique, to P. Pineau (LIENSs, La Rochelle, France) for the nutrient measurement, and to N. Lachaussée (LIENSs, La Rochelle, France) for field sampling. We also thank V. Becquet, C. Dussud, M. Bréret, J.C. Gama de Matos, and J. Lavaud (LIENSs, La Rochelle, France) who help us during the experiment. We thank N. Taib and JC. Charvy (LMGE, Clermont-Ferrand, France) for their help in phylogenetic analyses.

Author information

Authors and Affiliations

  1. Université de La Rochelle – CNRS, UMR 7266, LIENSs, 2 rue Olympe de Gouges, 17000, La Rochelle, France

    C. Lavergne, C. Dupuy & H. Agogué

  2. School of Biochemical Engineering, Pontificia Universidad Católica Valparaíso, Avenida Brasil, 2085, Valparaíso, Chile

    C. Lavergne

  3. CNRS, UMR5557 Ecologie Microbienne, Université Lyon 1, INRA, UMR1418, 69220, Villeurbanne Cedex, France

    M. Hugoni

  4. Muséum National d’Histoire Naturelle, UMR BOREA, Sorbonne Universités, UPMC Univ Paris 6, CNRS 7208, IRD 207, UCN, UA, Station de Biologie Marine, 29900, Concarneau, France

    C. Hubas

  5. Clermont Université, Université Blaise Pascal, LMGE, BP 10448, 63000, Clermont-Ferrand, France

    D. Debroas

  6. CNRS, UMR 6023, LMGE, 63171, Aubière, France

    D. Debroas

Authors
  1. C. Lavergne
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  2. M. Hugoni
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  3. C. Hubas
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  4. D. Debroas
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  5. C. Dupuy
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  6. H. Agogué
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Corresponding author

Correspondence to C. Lavergne.

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The authors declare no conflict of interest.

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Lavergne, C., Hugoni, M., Hubas, C. et al. Diel Rhythm Does Not Shape the Vertical Distribution of Bacterial and Archaeal 16S rRNA Transcript Diversity in Intertidal Sediments: a Mesocosm Study. Microb Ecol 75, 364–374 (2018). https://doi.org/10.1007/s00248-017-1048-1

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  • DOI: https://doi.org/10.1007/s00248-017-1048-1

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