Plant and Soil

, Volume 422, Issue 1–2, pp 67–79 | Cite as

Assembly of seed-associated microbial communities within and across successive plant generations

  • Samir Rezki
  • Claire Campion
  • Philippe Simoneau
  • Marie-Agnès Jacques
  • Ashley Shade
  • Matthieu BarretEmail author
Regular Article


Background and aims

Seeds are involved in the transmission of microorganisms from one plant generation to another and consequently may act as the initial inoculum source for the plant microbiota. In this work, we assessed the structure and composition of the seed microbiota of radish (Raphanus sativus) across three successive plant generations.


Structure of seed microbial communities were estimated on individual plants through amplification and sequencing of genes that are markers of taxonomic diversity for bacteria (gyrB) and fungi (ITS1). The relative contribution of dispersal and ecological drift in inter-individual fluctuations were estimated with a neutral community model.


Seed microbial communities of radish display a low heritability across plant generations. Fluctuations in microbial community profiles were related to changes in community membership and composition across plant generations, but also to variation between individual plants. Ecological drift was an important driver of the structure of seed bacterial communities, while dispersal was involved in the assembly of the fungal fraction of the seed microbiota.


These results provide a first glimpse of the governing processes driving the assembly of the seed microbiota.


Seed-associated microbial community Heritability Community assembly Dispersal Ecological drift 



This research was supported by grant awarded by the Region des Pays de la Loire (metaSEED, 2013 10080) and the Michigan State University Plant Resilience Institute. The authors wish to thanks Gloria Torres-Cortes for manuscript assessment, Emmanuelle Laurent, Julie Gombert and Vincent Odeau (Fédération Nationale des Agriculteurs Multiplicateurs de Semences - FNAMS) for their help with all the field experiments, Aude Rochefort for the preparation of the sequencing library and Muriel Bahut from the platform ANAN of SFR Quasav for launching the MiSeq runs.

Compliance with ethical standards

Conflict of interest

The authors declare no conflict of interest.

Supplementary material

11104_2017_3451_MOESM1_ESM.pdf (546 kb)
ESM 1 (PDF 546 kb)


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Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  • Samir Rezki
    • 1
  • Claire Campion
    • 1
  • Philippe Simoneau
    • 2
  • Marie-Agnès Jacques
    • 3
  • Ashley Shade
    • 4
  • Matthieu Barret
    • 3
    Email author
  1. 1.IRHS, INRA, AGROCAMPUS-Ouest, Université d’AngersBeaucouzéFrance
  2. 2.INRA, UMR1345 Institut de Recherches en Horticulture et SemencesBeaucouzéFrance
  3. 3.UMR1345 Institut de Recherches en Horticulture et SemencesUniversité d’AngersBeaucouzéFrance
  4. 4.Department of Microbiology and Molecular Genetics; Program in Ecology, Evolutionary Biology, and Behavior; The DOE Great Lakes Bioenergy Research Center; and The Plant Resilience InstituteMichigan State UniversityEast LansingUSA

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