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

Federica Caradonia (Lead / Corresponding author), Domenico Ronga, Marcello Catellani, Cleber Vinícius Giaretta Azevedo, Rodrigo Alegria Terrazas, Senga Robertson-Albertyn, Enrico Francia (Lead / Corresponding author), Davide Bulgarelli (Lead / Corresponding author)

Research output: Contribution to journalArticlepeer-review

21 Citations (Scopus)
97 Downloads (Pure)


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.

Original languageEnglish
Pages (from-to)315-325
Number of pages11
JournalPhytobiomes Journal
Issue number4
Early online date14 Aug 2019
Publication statusPublished - 2019


  • Crop productivity
  • Digestate
  • Fertilizers
  • Metagenomics
  • Microbiota
  • Nitrogen
  • Rhizosphere and phyllosphere
  • Root
  • Solanum lycopersicum
  • Yield

ASJC Scopus subject areas

  • Plant Science
  • Ecology, Evolution, Behavior and Systematics
  • Agronomy and Crop Science
  • Ecology
  • Molecular Biology


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