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Front. Microbiol. | doi: 10.3389/fmicb.2018.02794

Drying and rainfall shape the structure and functioning of nitrifying microbial communities in riverbed sediments

  • 1Leibniz-Institut für Gewässerökologie und Binnenfischerei, Germany
  • 2Universidad del País Vasco, Spain
  • 3University of Greifswald, Germany
  • 4Friedrich Loeffler Institute of Medical Microbiology, University Medicine Greifswald, Germany
  • 5Humboldt-Universität zu Berlin, Germany
  • 6Department of Ecogenomics and Systems Biology, Universität Wien, Austria
  • 7Lawrence Berkeley National Laboratory (LBNL), United States

Non-flow periods in fluvial ecosystems are a global phenomenon. Streambed drying and rewetting by sporadic rainfalls could drive considerable changes in the microbial communities that govern stream nitrogen (N) availability at different temporal and spatial scales. We performed a microcosm-based experiment to investigate how dry period duration (0, 3, 6 and 9 weeks) and magnitude of sporadic rewetting by rainfall (0, 4 and 21mm applied at end of dry period) affected stocks of N in riverbed sediments, their nitrifyingammonia-oxidizing bacteria (AOB) and archaea (AOA) microbial communities and rates of ammonia oxidation (AO), and emissions of nitrous oxide (N2O) to the atmosphere. While ammonium (NH4+) pool size decreased, nitrate (NO3-) pool size increased in sediments with progressive drying. Concomitantly, the relative and absolute abundance of nitrifying microbialAOB and, especially, AOA groups (assessed by 16S rRNA gene sequencing and quantitative PCR of ammonia monooxygenase genes, respectively) increased, despite an apparent decrease of AO rates with drying. An increase of N2O emissions occurred at early drying before substantially dropping until the end of the experiment. Strong rainfall of 21 mm increased AO rates and NH4+ in sediments, whereas modest rainfall of 4 mm triggered a notable increase of N2O fluxes. Interestingly, such responses were detected only after 6 and 9 weeks of drying. Our results demonstrate that progressive drying drives considerable changes in in-stream N cycling and the associated nitrifying microbial communities, and that sporadic rainfall can modulate these effects. Our findings are particularly relevant for N processing and transport in rivers with alternating dry and wet phases – a hydrological scenario expected to become more important in the future.

Keywords: intermittent, Stream, Nitrification, Ammonia-oxidation, AOA, AOB, NOB, Comammox

Received: 13 Jul 2018; Accepted: 30 Oct 2018.

Edited by:

Graeme W. Nicol, Université de Lyon, France

Reviewed by:

Annika C. Mosier, University of Colorado Denver, United States
Martina Herrmann, Friedrich-Schiller-Universität Jena, Germany  

Copyright: © 2018 Arce, von Schiller, Bengtsson, Hinze, Jung, Eloy Alves, Urich and Singer. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Maria Isabel Arce, Leibniz-Institut für Gewässerökologie und Binnenfischerei, Berlin, Germany,