Microbial inoculants reshape cherry tomato fruit metabolome and boost quality traits

The study, published in Plant Molecular Biology, used untargeted metabolomic profiling and fruit volatile analysis on the cultivar ‘Pusa Cherry 1’ to compare how different microbial interventions elicit distinct metabolic responses.

The team tested the cyanobacterium Anabaena laxa and a mesocarp-associated bacterium, Enterobacter cloacae, both alone and in combination. Treatment with A. laxa raised fruit lycopene content by 1.13-fold compared with untreated control fruits. E. cloacae had a broader effect on antioxidant-related compounds, increasing lycopene by 1.07-fold, phenolics by 1.5-fold and flavonoids by 2.54-fold. When the two organisms were inoculated together, phenolics rose 1.25-fold and flavonoids 1.68-fold over control fruits.

Untargeted metabolome analysis of the treated fruits revealed that A. laxa enriched spermidine and benzoquinone, and the authors interpret this as a likely induction of the plant’s antioxidant defense system and hormonal modulation, associated with enhanced lycopene content and accumulation of benzenoid-derived floral volatiles.

Fruits treated with E. cloacae showed high lycopene, flavonoid and ascorbic acid content, along with carotenoid- and lipoxygenase-derived fruity volatiles. The researchers suggest these changes may be linked to stimulation of sphingolipid metabolism, lipoxygenase-mediated oxylipin synthesis and accumulation of S-adenosyl methionine, patterns they interpret as pointing to jasmonate- and ethylene-mediated induced systemic resistance.

Co-inoculation of the two microbes produced yet another metabolic profile. Fruits from the combined treatment showed enrichment of alpha-ketoglutarate, amines, purines and pyrimidines, alongside S-adenosyl methionine, sphingolipid and rutin accumulation. Notably, the combined treatment was also accompanied by a 20.4 percent increase in fruit yield, suggesting that the metabolic changes did not come at the expense of productivity.

According to the authors, the two microbes elicited distinct modes of defense system activation and coordinated hormonal responses, which influenced the fruit’s overall ripeness, nutritional and sensory quality, as well as yield. The study’s key message is that microbial interventions modulate the intricate networking of the fruit metabolome, improving quality through coordinated regulation of primary and secondary metabolism and fruit hormonal activity in cherry tomato.

The work was motivated by the potential of bio inputs to enhance the organoleptic attributes of tomato, particularly their nutraceutical benefits and export potential. The researchers developed stimulatory microbial formulations and then assessed how each intervention differentially elicited metabolites in the fruit, combining metabolic profiling with volatile analysis to capture both nutritional and sensory dimensions of quality.

The findings illustrate that the choice of microbial inoculant matters: rather than a generic boost, each organism steered fruit metabolism along a different path, with A. laxa favoring lycopene and floral volatile accumulation, E. cloacae favoring a broad antioxidant and fruity volatile profile, and the combination favoring primary metabolite enrichment together with higher yield. As the study is based on a single cherry tomato cultivar under the reported experimental conditions, the authors’ mechanistic interpretations, including the proposed hormonal and defense-related pathways, are presented as likely associations supported by the metabolomic data rather than directly demonstrated causal pathways.

Subject of Research: Metabolomic profiling of cherry tomato fruit quality under single and combined microbial inoculations

Article Title: Metabolomic profiling unveils differential modulation of tomato fruit quality by microbial interventions

Article References: Varsha, D., Shukla, S., & Prasanna, R. (2026). Metabolomic profiling unveils differential modulation of tomato fruit quality by microbial interventions. Plant Molecular Biology, 116(6), Article 107. https://doi.org/10.1007/s11103-026-01775-x

Image Credits: AI Generated

DOI: 10.1007/s11103-026-01775-x

Keywords: tomato, metabolomics, microbial inoculants, Anabaena laxa, Enterobacter cloacae, lycopene, flavonoids, fruit volatiles, plant defense, fruit yield, cherry tomato, bioinputs