Phylogeny and Molecular Characterisation of Bacterial Pathogens Associated with Selected Tomato (Solanum lycopersicum L.) Varieties in Enugu State

Abstract

Abstract

Objective: The study aimed to investigate the increasing threat posed by bacterial pathogens to tomato (Solanum lycopersicum L.) crops, with a specific focus on the roles of Acinetobacter nosocomialis, Corticimicrobacter populi, and Sphingobacterium thalpophilum. The research focused on the phylogenetic and molecular characterization of bacterial isolates recovered from the symptomatic leaves and fruits of three tomato hybrids (Muna, Cobra, and Platinum) and one local cultivar (Yollins) grown in southeastern Nigeria.

Method: Isolates were analysed using 16S rRNA gene sequencing and multilocus sequence analysis (MLSA) to determine their genetic relationships. The study evaluated the distribution of these bacteria across the four specific tomato varieties and conducted molecular screening to identify functional genes associated with virulence and plant interaction, specifically those linked to biofilm formation, secretion systems, and the degradation of plant cell walls.

Result: The analysis revealed distinct ecological clustering, with A. nosocomialis (a Gram-negative member of the A. calcoaceticus–baumannii complex) primarily found in the Muna and Platinum varieties. In contrast, the recently described actinobacterium C. populi and the beneficial bacterium S. thalpophilum were more prevalent in Yollins and Cobra. Several of these isolates were confirmed to carry genes necessary for biofilm formation and plant cell wall degradation. This finding marks the first official report of C. populi in West African tomatoes, along with the identification of S. thalpophilum, which is known to enhance antioxidant activity and root metabolism under salinity stress.

Conclusion: The study concludes that diverse bacterial species, ranging from opportunistic pathogens to beneficial growth enhancers, inhabit tomato varieties in southeastern Nigeria. The presence of virulence-linked genes in A. nosocomialis and C. populi underscores an emerging phytosanitary risk. These results emphasise the urgent need for ongoing pathogen monitoring and the development of breeding strategies tailored to the unique microbial profiles of specific tomato hybrids and local cultivars to ensure crop resilience.

Keywords: Solanum lycopersicum, Acinetobacter nosocomialis, Corticimicrobacter populi, Sphingobacterium thalpophyilum, phylogenetics, molecular characterisation,