Original Article | Published:

Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits

The ISME Journal volume 11, pages 22442257 (2017) | Download Citation

Abstract

Plant domestication was a pivotal accomplishment in human history, but also led to a reduction in genetic diversity of crop species compared to their wild ancestors. How this reduced genetic diversity affected plant–microbe interactions belowground is largely unknown. Here, we investigated the genetic relatedness, root phenotypic traits and rhizobacterial community composition of modern and wild accessions of common bean (Phaseolus vulgaris) grown in agricultural soil from the highlands of Colombia, one of the centers of common bean diversification. Diversity Array Technology-based genotyping and phenotyping of local common bean accessions showed significant genetic and root architectural differences between wild and modern accessions, with a higher specific root length for the wild accessions. Canonical Correspondence Analysis indicated that the divergence in rhizobacterial community composition between wild and modern bean accessions is associated with differences in specific root length. Along the bean genotypic trajectory, going from wild to modern, we observed a gradual decrease in relative abundance of Bacteroidetes, mainly Chitinophagaceae and Cytophagaceae, and an increase in relative abundance of Actinobacteria and Proteobacteria, in particular Nocardioidaceae and Rhizobiaceae, respectively. Collectively, these results establish a link between common bean domestication, specific root morphological traits and rhizobacterial community assembly.

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Acknowledgements

JEP-J was financially supported by the Department of Science, Technology and Innovation of Colombia—COLCIENCIAS through the doctoral grant 568-2012-15517825. JMR and VJC were supported by the Dutch STW-program ‘Back to the Roots’ and RM by CNPq 443112/2014-2. We are grateful for the expert help from Dr O Toro (RIP), Dr D DeBouck and LG Santos at the International Centre for Tropical Agriculture (CIAT, Cali, Colombia) in the selection of the bean accessions. We are also grateful to HA Pérez and JA Osorio for collecting the soil for the greenhouse experiments. We thank G Bongiorno and NM Robles for their valuable help in root phenotyping and JN Paulson for his expert advice in using the R package metagenomeSeq., this is publication 6290 of the NIOO-KNAW.

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Author notes

    • Mirte Bosse

    Present address: Animal Breeding and Genomics Centre, Wageningen University, P.O. box 338, 6700 AH Wageningen, The Netherlands.

Affiliations

  1. Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands

    • Juan E Pérez-Jaramillo
    • , Víctor J Carrión
    • , Mattias de Hollander
    •  & Jos M Raaijmakers
  2. Institute of Biology, Leiden University, Leiden, The Netherlands

    • Juan E Pérez-Jaramillo
    •  & Jos M Raaijmakers
  3. Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands

    • Mirte Bosse
  4. Department of Genetics, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo (USP), Piracicaba, São Paulo, Brazil

    • Luiz F V Ferrão
    •  & Antonio A F Garcia
  5. Institute of Biology, University of Antioquia, Medellín, Colombia

    • Camilo A Ramírez
  6. Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, Embrapa Environment, Jaguariúna, Brazil

    • Rodrigo Mendes

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Competing interests

The authors declare no conflict of interest.

Corresponding author

Correspondence to Jos M Raaijmakers.

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DOI

https://doi.org/10.1038/ismej.2017.85

Supplementary Information accompanies this paper on The ISME Journal website (http://www.nature.com/ismej)

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