Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits
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 genet...
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Published in | The ISME Journal Vol. 11; no. 10; pp. 2244 - 2257 |
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Main Authors | , , , , , , , , |
Format | Journal Article |
Language | English |
Published |
England
Nature Publishing Group
01.10.2017
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Subjects | |
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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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AbstractList | 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. 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. 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. |
Author | Pérez-Jaramillo, Juan E de Hollander, Mattias Ferrão, Luiz F V Ramírez, Camilo A Mendes, Rodrigo Raaijmakers, Jos M Carrión, Víctor J Garcia, Antonio A F Bosse, Mirte |
Author_xml | – sequence: 1 givenname: Juan E surname: Pérez-Jaramillo fullname: Pérez-Jaramillo, Juan E organization: Institute of Biology, Leiden University, Leiden, The Netherlands – sequence: 2 givenname: Víctor J surname: Carrión fullname: Carrión, Víctor J organization: Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands – sequence: 3 givenname: Mirte orcidid: 0000-0003-2433-2483 surname: Bosse fullname: Bosse, Mirte organization: Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands – sequence: 4 givenname: Luiz F V surname: Ferrão fullname: Ferrão, Luiz F V organization: Department of Genetics, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo (USP), Piracicaba, São Paulo, Brazil – sequence: 5 givenname: Mattias surname: de Hollander fullname: de Hollander, Mattias organization: Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands – sequence: 6 givenname: Antonio A F surname: Garcia fullname: Garcia, Antonio A F organization: Department of Genetics, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo (USP), Piracicaba, São Paulo, Brazil – sequence: 7 givenname: Camilo A surname: Ramírez fullname: Ramírez, Camilo A organization: Institute of Biology, University of Antioquia, Medellín, Colombia – sequence: 8 givenname: Rodrigo orcidid: 0000-0002-9817-4118 surname: Mendes fullname: Mendes, Rodrigo organization: Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, Embrapa Environment, Jaguariúna, Brazil – sequence: 9 givenname: Jos M surname: Raaijmakers fullname: Raaijmakers, Jos M organization: Institute of Biology, Leiden University, Leiden, The Netherlands |
BackLink | https://www.ncbi.nlm.nih.gov/pubmed/28585939$$D View this record in MEDLINE/PubMed |
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ContentType | Journal Article |
Copyright | Copyright Nature Publishing Group Oct 2017 Copyright © 2017 International Society for Microbial Ecology 2017 International Society for Microbial Ecology Wageningen University & Research |
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Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Present address: Animal Breeding and Genomics Centre, Wageningen University, P.O. box 338, 6700 AH Wageningen, The Netherlands. |
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SubjectTerms | Abundance Agricultural land Animal Breeding and Genetics Animal Breeding and Genomics Beans Biodiversity Communities Community composition Crop diversification Divergence Domestication Fokkerij en Genetica Fokkerij en Genomica Genetic diversity Genetic Variation Genotyping Highlands Humans Leerstoelgroep Fokkerij en genetica Microbiota Original Phaseolus - microbiology Phaseolus vulgaris Phenotyping Plant Roots - microbiology Relative abundance Rhizosphere Species diversity WIAS |
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Title | Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits |
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