Nitrogen Fertilisers Shape the Composition and Predicted Functions of the Microbiota of Field-Grown Tomato Plants

Federica Caradonia, Domenico Ronga, Marcello Catellani, Cleber Vinícius Giaretta Azevedo, Rodrigo Alegria Terrazas, Senga Robertson-Albertyn, Enrico Francia, Davide Bulgarelli

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Abstract

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 fertilisers, 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 fertilisers 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 fertiliser applied to the field.

Original languageEnglish
JournalPhytobiomes Journal
Early online date14 Aug 2019
DOIs
Publication statusE-pub ahead of print - 14 Aug 2019

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nitrogen fertilizers
tomatoes
microhabitats
rhizosphere
minerals
ABC transporters
Actinobacteria
Solanum lycopersicum
organic fertilizers
sustainable agriculture
microbial communities
soil
genes
ribosomal RNA
developmental stages
plant growth
phylogeny
microbiome

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Caradonia, Federica ; Ronga, Domenico ; Catellani, Marcello ; Azevedo, Cleber Vinícius Giaretta ; Alegria Terrazas, Rodrigo ; Robertson-Albertyn, Senga ; Francia, Enrico ; Bulgarelli, Davide. / Nitrogen Fertilisers Shape the Composition and Predicted Functions of the Microbiota of Field-Grown Tomato Plants. In: Phytobiomes Journal . 2019.
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Nitrogen Fertilisers Shape the Composition and Predicted Functions of the Microbiota of Field-Grown Tomato Plants. / Caradonia, Federica; Ronga, Domenico ; Catellani, Marcello ; Azevedo, Cleber Vinícius Giaretta ; Alegria Terrazas, Rodrigo; Robertson-Albertyn, Senga; Francia, Enrico; Bulgarelli, Davide.

In: Phytobiomes Journal , 14.08.2019.

Research output: Contribution to journalArticle

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AU - Catellani, Marcello

AU - Azevedo, Cleber Vinícius Giaretta

AU - Alegria Terrazas, Rodrigo

AU - Robertson-Albertyn, Senga

AU - Francia, Enrico

AU - Bulgarelli, Davide

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