| Summary: | Tomato is the main vegetable cultivated under soilless culture systems (SCSs); production of organic tomato under SCSs has increased due to consumer demands for healthier and environmentally friendly vegetables. However, organic tomato production under SCSs has been associated with low crop performance and fruit quality defects. These agricultural deficiencies could be linked to alterations in tomato plant microbiota; nonetheless, this issue has not been sufficiently addressed. Thus, the main goal of the present study was to characterize the rhizosphere and phyllosphere of tomato plants cultivated under conventional and organic SCSs. To accomplish this goal, tomato plants grown in commercial greenhouses under conventional or organic SCSs were tested at 8, 26, and 44 weeks after seedling transplantation. Substrate (<i>n</i> = 24), root (<i>n =</i> 24), and fruit (<i>n =</i> 24) composite samples were subjected to DNA extraction and high-throughput <i>16S rRNA</i> gene sequencing. The present study revealed that the tomato core microbiota was predominantly constituted by Proteobacteria, Actinobacteria, and Firmicutes. Remarkably, six bacterial families, <i>Bacillaceae</i>, <i>Microbacteriaceae</i>, <i>Nocardioidaceae</i>, <i>Pseudomonadaceae</i>, <i>Rhodobacteraceae</i>, and <i>Sphingomonadaceae</i>, were shared among all substrate, rhizosphere, and fruit samples. Importantly, it was shown that plants under organic SCSs undergo a dysbiosis characterized by significant changes in the relative abundance of <i>Bradyrhizobiaceae</i>, <i>Caulobacteraceae</i>, <i>Chitinophagaceae</i>, <i>Enterobacteriaceae</i>, <i>Erythrobacteraceae</i>, <i>Flavobacteriaceae</i>, <i>Nocardioidaceae</i>, <i>Rhodobacteraceae</i>, and <i>Streptomycetaceae</i>. These results suggest that microbial alterations in substrates, roots, and fruits could be potential factors in contributing to the crop performance and fruit quality deficiencies observed in organic SCSs.
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