Rhizobacteriome Diversity and Morphophysiological Features of Three Tomato Plant Varieties Under Nitrogen Deficiency

The increasing biogeochemical imbalance of nitrogen (N) heightens the importance of studying rhizosphere bacteria, which aid crop nutrient uptake, and their responses to N deficiency. The aim of the study was to assess variety-specific responses of the tomatoes and their associated rhizobacteriome to low N availability. Three determinant varieties of Solanum lycopersicum L. were cultivated in pot-scale experiment during 10 weeks on low-fertility substrate (sod-podzolic soil:peat:clay:sand, 1:1:1:2, v/v), half of which were supplemented with ammonium nitrate (60 mg N kg−1 in total). A comprehensive methodology was employed, including 16S rRNA metagenomic Nanopore sequencing, quantitative assessment of N-cycling bacteria, and analysis of plant growth, photosynthetic pigments, total N in biomass, and fine root architecture. Results demonstrated that N deficiency significantly reduced plant biomass and photosynthetic pigments. The rhizosphere contained a diverse community of N-transforming bacteria (38 identified genera), whose composition and relative abundance were strongly influenced by both tomato variety and N fertilization. Nitrogen application increased the abundance of N-fixers and altered alpha-diversity in a variety-dependent manner. Significant correlations were found between the abundance of key bacterial genera (e.g., Stenotrophomonas, Rhizobium) and N parameters in plants and substrates. The study concludes that the response of the tomato rhizobacteriome to N availability is variety-specific, which is important for the development of microbiome management strategies for enhancing N use efficiency.