Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia
Abstract Background Modern crop varieties are typically cultivated in agriculturally well-managed soils far from the centers of origin of their wild relatives. How this habitat expansion impacted plant microbiome assembly is not well understood. Results Here, we investigated if the transition from a...
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| Format: | Article |
| Language: | English |
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BMC
2019-08-01
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| Series: | Microbiome |
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| Online Access: | http://link.springer.com/article/10.1186/s40168-019-0727-1 |
| _version_ | 1819160152761171968 |
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| author | Juan E. Pérez-Jaramillo Mattias de Hollander Camilo A. Ramírez Rodrigo Mendes Jos M. Raaijmakers Víctor J. Carrión |
| author_facet | Juan E. Pérez-Jaramillo Mattias de Hollander Camilo A. Ramírez Rodrigo Mendes Jos M. Raaijmakers Víctor J. Carrión |
| author_sort | Juan E. Pérez-Jaramillo |
| collection | DOAJ |
| description | Abstract Background Modern crop varieties are typically cultivated in agriculturally well-managed soils far from the centers of origin of their wild relatives. How this habitat expansion impacted plant microbiome assembly is not well understood. Results Here, we investigated if the transition from a native to an agricultural soil affected rhizobacterial community assembly of wild and modern common bean (Phaseolus vulgaris) and if this led to a depletion of rhizobacterial diversity. The impact of the bean genotype on rhizobacterial assembly was more prominent in the agricultural soil than in the native soil. Although only 113 operational taxonomic units (OTUs) out of a total of 15,925 were shared by all eight bean accessions grown in native and agricultural soils, this core microbiome represented a large fraction (25.9%) of all sequence reads. More OTUs were exclusively found in the rhizosphere of common bean in the agricultural soil as compared to the native soil and in the rhizosphere of modern bean accessions as compared to wild accessions. Co-occurrence analyses further showed a reduction in complexity of the interactions in the bean rhizosphere microbiome in the agricultural soil as compared to the native soil. Conclusions Collectively, these results suggest that habitat expansion of common bean from its native soil environment to an agricultural context had an unexpected overall positive effect on rhizobacterial diversity and led to a stronger bean genotype-dependent effect on rhizosphere microbiome assembly. |
| first_indexed | 2024-12-22T16:51:55Z |
| format | Article |
| id | doaj.art-34a4dee21dd54875b6225919267ccf88 |
| institution | Directory Open Access Journal |
| issn | 2049-2618 |
| language | English |
| last_indexed | 2024-12-22T16:51:55Z |
| publishDate | 2019-08-01 |
| publisher | BMC |
| record_format | Article |
| series | Microbiome |
| spelling | doaj.art-34a4dee21dd54875b6225919267ccf882022-12-21T18:19:34ZengBMCMicrobiome2049-26182019-08-017111610.1186/s40168-019-0727-1Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from ColombiaJuan E. Pérez-Jaramillo0Mattias de Hollander1Camilo A. Ramírez2Rodrigo Mendes3Jos M. Raaijmakers4Víctor J. Carrión5Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW)Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW)Institute of Biology, University of AntioquiaEmbrapa Meio AmbienteDepartment of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW)Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW)Abstract Background Modern crop varieties are typically cultivated in agriculturally well-managed soils far from the centers of origin of their wild relatives. How this habitat expansion impacted plant microbiome assembly is not well understood. Results Here, we investigated if the transition from a native to an agricultural soil affected rhizobacterial community assembly of wild and modern common bean (Phaseolus vulgaris) and if this led to a depletion of rhizobacterial diversity. The impact of the bean genotype on rhizobacterial assembly was more prominent in the agricultural soil than in the native soil. Although only 113 operational taxonomic units (OTUs) out of a total of 15,925 were shared by all eight bean accessions grown in native and agricultural soils, this core microbiome represented a large fraction (25.9%) of all sequence reads. More OTUs were exclusively found in the rhizosphere of common bean in the agricultural soil as compared to the native soil and in the rhizosphere of modern bean accessions as compared to wild accessions. Co-occurrence analyses further showed a reduction in complexity of the interactions in the bean rhizosphere microbiome in the agricultural soil as compared to the native soil. Conclusions Collectively, these results suggest that habitat expansion of common bean from its native soil environment to an agricultural context had an unexpected overall positive effect on rhizobacterial diversity and led to a stronger bean genotype-dependent effect on rhizosphere microbiome assembly.http://link.springer.com/article/10.1186/s40168-019-0727-1Common beanWild and modern accessionsDomesticationRhizosphereCore microbiomeNetworks |
| spellingShingle | Juan E. Pérez-Jaramillo Mattias de Hollander Camilo A. Ramírez Rodrigo Mendes Jos M. Raaijmakers Víctor J. Carrión Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia Microbiome Common bean Wild and modern accessions Domestication Rhizosphere Core microbiome Networks |
| title | Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia |
| title_full | Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia |
| title_fullStr | Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia |
| title_full_unstemmed | Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia |
| title_short | Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia |
| title_sort | deciphering rhizosphere microbiome assembly of wild and modern common bean phaseolus vulgaris in native and agricultural soils from colombia |
| topic | Common bean Wild and modern accessions Domestication Rhizosphere Core microbiome Networks |
| url | http://link.springer.com/article/10.1186/s40168-019-0727-1 |
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