Metagenomic analysis of tomato rhizosphere microbiomes detects Ralstonia phage sequences in Kenyan agricultural soils

Bacterial wilt caused by Ralstonia solanacearum species complex is a major constraint in tomato production in Kenya, resulting in yield losses of up to 100% in heavily infested fields. This study used high-throughput shotgun metagenomic sequencing approach to characterize the rhizosphere microbiomes of tomato plants in three of the major production areas in Kenya (Kirinyaga, Kiambu, and Laikipia counties) focusing on detecting Ralstonia phage sequences. Soil samples were collected from the rhizosphere of bacterial wilt-infected tomato plants, and microbial DNA was extracted using a modified phenol-chloroform protocol and sequenced using Illumina NovaSeq platform. Taxonomic profiling revealed diverse microbial communities dominated by Actinobacteria and Proteobacteria. Four Ralstonia species were confirmed ( R. insidiosa , R. pickettii , R. mannitolilytica and R. wenshanensis ). Sequences similar to the R. solanacearum species complex were also detected but were too short for species-level confirmation. Metagenomic analysis detected sequences matching four previously described Ralstonia phages (RSL1, RSIBR3, Anchaing, and Cimandef). Functional annotation demonstrated abundant metabolic pathways, energy production systems, and stress response mechanisms, indicating highly adaptive microbial communities in the tomato rhizosphere. This study provides baseline data on rhizosphere microbiome composition in Kenyan tomato production systems and identifies Ralstonia phage sequences that could guide future isolation and host-range studies. If future work shows that these phages are active against Ralstonia , they could contribute to locally adapted biocontrol approaches that reduce reliance on chemical pesticides.