Depth matters: effects of precipitation regime on soil microbial activity upon rewetting of a plant-soil system

  • The ISME Journalvolume 12pages10611071 (2018)
  • doi:10.1038/s41396-018-0079-z
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Changes in frequency and amplitude of rain events, that is, precipitation patterns, result in different water conditions with soil depth, and likely affect plant growth and shape plant and soil microbial activity. Here, we used 18O stable isotope probing (SIP) to investigate bacterial and fungal communities that actively grew or not upon rewetting, at three different depths in soil mesocosms previously subjected to frequent or infrequent watering for 12 weeks (equal total water input). Phylogenetic marker genes for bacteria and fungi were sequenced after rewetting, and plant-soil microbial coupling documented by plant 13C-CO2 labeling. Soil depth, rather than precipitation pattern, was most influential in shaping microbial response to rewetting, and had differential effects on active and inactive bacterial and fungal communities. After rewetting, active bacterial communities were less rich, more even and phylogenetically related than the inactive, and reactivated throughout the soil profile. Active fungal communities after rewetting were less abundant and rich than the inactive. The coupling between plants and soil microbes decreased under infrequent watering in the top soil layer. We suggest that differences in fungal and bacterial abundance and relative activity could result in large effects on subsequent soil biogeochemical cycling.

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This research was supported by funding from the ANR (project INCITE, ANR-13-JSV7-0004), the European Commission (Career Integration Grant FP7-MC-CIG #618010) and the Conseil Régional de Bourgogne to RB. IE was supported in part by an INRA Ph.D. fellowship (Département Environnement et Agronomie). AG acknowledges support by an SNF grant (31003A_159866). We thank François Nuge and Xavier Buisson for kindly letting us use their soil, Michel Laderach (Dijon Céréales) for providing the seeds, Karine Palavioux, Céline Bernard, Franck Zenk, Damien Gironde, and Noureddine El Mjiyad for help in the greenhouse, Jérôme Fromentin for the ultracentrifuge, Samuel Jacquiod for sharing on functional response groups, Livio Antonielli for bioinformatics discussions, Virginie Bourion for root scans, Florian Bizouard for grinding, Marielle Adrian and Marie-Claire Héloir for the Li-6400, Arnaud Coffin and Marjorie Ubertosi for soil retention data. Matthieu Barret kindly provided the bacterial mock community, assembled within the MetaBAR project funded by the INRA MEM Metaprogramme.

Author information

Author notes

    • Amy Welty

    Present address: Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA


  1. Agroécologie, INRA, AgroSup Dijon, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France

    • Ilonka C. Engelhardt
    • , Amy Welty
    • , David Bru
    • , Nadine Rouard
    • , Marie-Christine Breuil
    • , Aymé Spor
    •  & Romain L. Barnard
  2. Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA

    • Steven J. Blazewicz
  3. Swiss Federal Research Institute WSL, Zuercherstr. 111, 8903, Birmensdorf, Switzerland

    • Arthur Gessler
    •  & Lucía Galiano
  4. Forest History, Physiology and Genetics Research Group, Universidad Politecnica de Madrid, Ciudad Universitaria s/n, 28040, Madrid, Spain

    • José Carlos Miranda


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Conflict of interest

The authors declare that they have no conflict of interest.

Corresponding author

Correspondence to Romain L. Barnard.

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