Opportunistic bacteria in greenhouse Solanaceous plants – assessment by new generation sequencing methods

Relevance. In recent years, there has been an alarming increase in the number of human and animal disease cases caused by opportunistic microorganisms. These pathogens are often found in agricultural plants, which serve as natural reservoirs for them. The mechanisms of plant damage caused by these pathogens are similar to those of human and animal pathogenic bacteria.As the ecology of these pathogenic bacteria has been studied, data has been obtained that clearly shows the possibility of their long-term survival and reproduction in plants, without any signs of loss of their virulence towards the main host organism.

Methodology. Tomato and potato plant samples (39 in total) were collected from 12 different greenhouses in the Moscow region. Genomic DNA and RNA were isolated using appropriate kits. Standard primers were used to amplify the hypervariable V3-V4 region of the 16S ribosomal RNA gene. Sequencing was performed on the Illumina platform. The obtained sequencing data was processed by a program written using the QIIME 1.9.1 algorithm. An open-reference Opec classification algorithm (OTU) was used, with a classification threshold of 97%.

Results. In this paper, we consider experimental evidence for the latent survival of opportunistic bacteria using both metagenome analysis of the bacterial community on protected plants and bacteriophage population analysis, which is used as an indicator of the presence of target species in the environment.

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