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

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 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. [Formula: see text] Copyright © 2019 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

A footprint of plant eco-geographic adaptation on the composition of the barley rhizosphere bacterial microbiota

“…The pooled amplicon library was submitted to the Genome Technology group, The James Hutton Institute (Invergowrie, UK) for quality control, processing and sequencing as previously described 23 , 63 , 64 . Briefly, samples were sequenced using an Illumina MiSeq platform with the 2 × 150 bp chemistry.…”

A footprint of plant eco-geographic adaptation on the composition of the barley rhizosphere bacterial microbiota

“…The pooled amplicon library was submitted to the Genome Technology group, The James Hutton Institute (Invergowrie, UK) for quality control, processing and sequencing as previously described 25,64–66 . Briefly, samples were sequenced using an Illumina MiSeq platform with the 2 × 150bp chemistry.…”

Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities

“…As such, the abundances of viral populations and, consequently, the structure of viral communities are inherently linked to the compositional trends of coexisting host communities [ 18 – 20 ]. In agricultural soils, rhizosphere processes can alter microbial diversity by actively promoting or inhibiting the recruitment of select taxa [ 21 , 22 ], and soil amendments can further affect microbiome structure [ 23 ]. Understanding whether viral communities display similar trends to those of other microbiota is essential for unraveling the potential of host–virus interactions to affect microbially influenced soil properties.…”