Microbial Ecology

, Volume 75, Issue 4, pp 875–887 | Cite as

Flooding Duration Affects the Structure of Terrestrial and Aquatic Microbial Eukaryotic Communities

  • Oliver RöhlEmail author
  • Nadine Graupner
  • Derek Peršoh
  • Martin Kemler
  • Moritz Mittelbach
  • Jens Boenigk
  • Dominik Begerow
Environmental Microbiology


The increasing number and duration of inundations is reported to be a consequence of climate change and may severely compromise non-adapted macroorganisms. The effect of flooding events on terrestrial and aquatic microbial communities is, however, less well understood. They may respond to the changed abiotic properties of their native habitat, and the native community may change due to the introduction of alien species. We designed an experiment to investigate the effect of five different flooding durations on the terrestrial and aquatic communities of eukaryotic microorganism, using the AquaFlow mesocosms. With amplicon sequencing of the small subunit (SSU) and internal transcribed spacer (ITS) rRNA gene regions, we analyzed community compositions directly before and after flooding. Subsequently, they were monitored for another 28 days, to determine the sustainability of community changes. Our results revealed a temporary increase in similarity between terrestrial and aquatic communities according to OTU composition (operational taxonomic unit, serves as a proxy for species). Increased similarity was mainly caused by the transmission of OTUs from water to soil. A minority of these were able to persist in soil until the end of the experiment. By contrast, the vast majority of soil OTUs was not transmitted to water. Flooding duration affected the community structure (abundance) more than composition (occurrence). Terrestrial communities responded immediately to flooding and the flooding duration influenced the community changes. Independent from flooding duration, all terrestrial communities recovered largely after flooding, indicating a remarkable resilience to the applied disturbances. Aquatic communities responded immediately to the applied inundations too. At the end of the experiment, they grouped according to the applied flooding duration and the amount of ammonium and chloride that leached from the soil. This indicates a sustained long-term response of the aquatic communities to flooding events.


Flooding duration Terrestrial eukaryotes Aquatic eukaryotes Mesocosm experiment Metabarcoding High-throughput sequencing 



The Stiftung Mercator (Pr-2013-0036) is acknowledged for financial support of the AquaFlow experiment. We want to thank Thomas Korte and Andreas Mölls from the Emschergenossenschaft und Lippeverband (eglv; Dortmund, NRW, Germany) for access to the Emscher River, Marcus Kamplade from the Grünflächenamt Bochum for providing access to soil, the technical staff of the botanical garden UDE for assistance and equipment, as well as Prof. Dr. Hardy Pfanz for the access to the autoclave, Marisa Bartling for assisting in the experimental phase of this study, Andreas Brachmann (LMU Munich) for amplicon library sequencing, and Marco Guerreiro for assistance with bioinformatic problems. We would like to thank Alistair McTaggart (FABI, University of Pretoria) for critical language revision of the manuscript.

Author Contributions

OR, DB, NG, and JB designed the AquaFlow experiment, which was conducted by OR and NG. Laboratory work was conducted by OR and NG. DP supported the HTS library preparation conducted by OR. OR analyzed the data with support by DP, MM, and MK. OR wrote the manuscript with guidance and support of MK, DP, and DB. All authors discussed and commented on the final version of the manuscript.

Compliance with Ethical Standards

Conflict of Interest

The authors declare that they have no conflict of interest.

Supplementary material

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Copyright information

© Springer Science+Business Media, LLC 2017

Authors and Affiliations

  1. 1.AG Geobotany, Faculty of Biology and BiotechnologyRuhr Universität BochumBochumGermany
  2. 2.Department of Biodiversity, Faculty of BiologyUniversity of Duisburg-EssenEssenGermany
  3. 3.AG Ökologie der Pflanzen; Institute of BiologyFreie Universität BerlinBerlinGermany

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