Nitrogen Fertilizers Shape the Composition and Predicted Functions of the Microbiota of Field-Grown Tomato Plants
The microbial communities thriving at the root−soil interface have the potential to improve plant growth and sustainable crop production. Yet, how agricultural practices, such as the application of either mineral or organic nitrogen fertilizers, impact on the composition and functions of these commu...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
The American Phytopathological Society
2019-11-01
|
| Series: | Phytobiomes Journal |
| Online Access: | https://doi.org/10.1094/PBIOMES-06-19-0028-R |
| _version_ | 1818284895077662720 |
|---|---|
| author | Federica Caradonia Domenico Ronga Marcello Catellani Cleber Vinícius Giaretta Azevedo Rodrigo Alegria Terrazas Senga Robertson-Albertyn Enrico Francia Davide Bulgarelli |
| author_facet | Federica Caradonia Domenico Ronga Marcello Catellani Cleber Vinícius Giaretta Azevedo Rodrigo Alegria Terrazas Senga Robertson-Albertyn Enrico Francia Davide Bulgarelli |
| author_sort | Federica Caradonia |
| collection | DOAJ |
| description | The microbial communities thriving at the root−soil interface have the potential to improve plant growth and sustainable crop production. Yet, how agricultural practices, such as the application of either mineral or organic nitrogen fertilizers, impact on the composition and functions of these communities remains to be fully elucidated. By deploying a two-pronged 16S rRNA gene sequencing and predictive metagenomics approach, we demonstrated that the bacterial microbiota of field-grown tomato (Solanum lycopersicum) plants is the product of a selective process that progressively differentiates between rhizosphere and root microhabitats. This process initiates as early as plants are in a nursery stage and it is then more marked at late developmental stages, in particular at harvest. This selection acts on both the bacterial relative abundances and phylogenetic assignments, with a bias for the enrichment of members of the phylum Actinobacteria in the root compartment. Digestate-based and mineral-based nitrogen fertilizers trigger a distinct bacterial enrichment in both rhizosphere and root microhabitats. This compositional diversification mirrors a predicted functional diversification of the root-inhabiting communities, manifested predominantly by the differential enrichment of genes associated to ABC transporters and the two-component system. Together, our data suggest that the microbiota thriving at the tomato root−soil interface is modulated by and in responses to the type of nitrogen fertilizer applied to the field. |
| first_indexed | 2024-12-13T01:00:04Z |
| format | Article |
| id | doaj.art-3c93298cf7224a19a5cb174c5978bb37 |
| institution | Directory Open Access Journal |
| issn | 2471-2906 |
| language | English |
| last_indexed | 2024-12-13T01:00:04Z |
| publishDate | 2019-11-01 |
| publisher | The American Phytopathological Society |
| record_format | Article |
| series | Phytobiomes Journal |
| spelling | doaj.art-3c93298cf7224a19a5cb174c5978bb372022-12-22T00:04:42ZengThe American Phytopathological SocietyPhytobiomes Journal2471-29062019-11-013431532510.1094/PBIOMES-06-19-0028-RNitrogen Fertilizers Shape the Composition and Predicted Functions of the Microbiota of Field-Grown Tomato PlantsFederica CaradoniaDomenico RongaMarcello CatellaniCleber Vinícius Giaretta AzevedoRodrigo Alegria TerrazasSenga Robertson-AlbertynEnrico FranciaDavide BulgarelliThe microbial communities thriving at the root−soil interface have the potential to improve plant growth and sustainable crop production. Yet, how agricultural practices, such as the application of either mineral or organic nitrogen fertilizers, impact on the composition and functions of these communities remains to be fully elucidated. By deploying a two-pronged 16S rRNA gene sequencing and predictive metagenomics approach, we demonstrated that the bacterial microbiota of field-grown tomato (Solanum lycopersicum) plants is the product of a selective process that progressively differentiates between rhizosphere and root microhabitats. This process initiates as early as plants are in a nursery stage and it is then more marked at late developmental stages, in particular at harvest. This selection acts on both the bacterial relative abundances and phylogenetic assignments, with a bias for the enrichment of members of the phylum Actinobacteria in the root compartment. Digestate-based and mineral-based nitrogen fertilizers trigger a distinct bacterial enrichment in both rhizosphere and root microhabitats. This compositional diversification mirrors a predicted functional diversification of the root-inhabiting communities, manifested predominantly by the differential enrichment of genes associated to ABC transporters and the two-component system. Together, our data suggest that the microbiota thriving at the tomato root−soil interface is modulated by and in responses to the type of nitrogen fertilizer applied to the field.https://doi.org/10.1094/PBIOMES-06-19-0028-R |
| spellingShingle | Federica Caradonia Domenico Ronga Marcello Catellani Cleber Vinícius Giaretta Azevedo Rodrigo Alegria Terrazas Senga Robertson-Albertyn Enrico Francia Davide Bulgarelli Nitrogen Fertilizers Shape the Composition and Predicted Functions of the Microbiota of Field-Grown Tomato Plants Phytobiomes Journal |
| title | Nitrogen Fertilizers Shape the Composition and Predicted Functions of the Microbiota of Field-Grown Tomato Plants |
| title_full | Nitrogen Fertilizers Shape the Composition and Predicted Functions of the Microbiota of Field-Grown Tomato Plants |
| title_fullStr | Nitrogen Fertilizers Shape the Composition and Predicted Functions of the Microbiota of Field-Grown Tomato Plants |
| title_full_unstemmed | Nitrogen Fertilizers Shape the Composition and Predicted Functions of the Microbiota of Field-Grown Tomato Plants |
| title_short | Nitrogen Fertilizers Shape the Composition and Predicted Functions of the Microbiota of Field-Grown Tomato Plants |
| title_sort | nitrogen fertilizers shape the composition and predicted functions of the microbiota of field grown tomato plants |
| url | https://doi.org/10.1094/PBIOMES-06-19-0028-R |
| work_keys_str_mv | AT federicacaradonia nitrogenfertilizersshapethecompositionandpredictedfunctionsofthemicrobiotaoffieldgrowntomatoplants AT domenicoronga nitrogenfertilizersshapethecompositionandpredictedfunctionsofthemicrobiotaoffieldgrowntomatoplants AT marcellocatellani nitrogenfertilizersshapethecompositionandpredictedfunctionsofthemicrobiotaoffieldgrowntomatoplants AT cleberviniciusgiarettaazevedo nitrogenfertilizersshapethecompositionandpredictedfunctionsofthemicrobiotaoffieldgrowntomatoplants AT rodrigoalegriaterrazas nitrogenfertilizersshapethecompositionandpredictedfunctionsofthemicrobiotaoffieldgrowntomatoplants AT sengarobertsonalbertyn nitrogenfertilizersshapethecompositionandpredictedfunctionsofthemicrobiotaoffieldgrowntomatoplants AT enricofrancia nitrogenfertilizersshapethecompositionandpredictedfunctionsofthemicrobiotaoffieldgrowntomatoplants AT davidebulgarelli nitrogenfertilizersshapethecompositionandpredictedfunctionsofthemicrobiotaoffieldgrowntomatoplants |