Tomato rhizosphere soil microbiome companion planting with Basil or Cilantro

Companion planting is well known for efficient management in suppressing soil-borne phytopathogens. However, the effects of companion planting on soil microbial composition and antibiotic resistance genes (ARGs) remain largely unclear. In this study, we assessed the changes of soil microbiome and ARGs frequencies for tomato growing soils companion planting with basil (TB) or cilantro (TC) by using metagenome approach. The abundance of phytopathogen Ralstonia solanacearum was significantly lower in TC or TB treatments than in tomato monoculture soils (TT). A significantly enrichment of Pseudomonas, Aquabacterium, and Flavobacterium and depletion of Nocardioides and Streptomyces was observed in TC treatment. Interestingly, both TC and TB companion planting reduced the absolute abundance and the number of subtypes of ARGs. TC soil showed the lowest numbers of unique ARG subtype genes, especially the ARGs resistant to vancomycin and rifamycin, and multidrug resistance. Furthermore, Network analysis further revealed that Nocardioides and Streptomyces were potential hosts of ARGs, whereas Flavobacterium negatively correlated with mdtG, suggesting a suppressive effect in reducing ARGs. Together, our results suggest that companion planting of tomato with basil or cilantro can reduce the risk of ARG accumulation, a feasible farming management tool to promote soil and plant health in sustainable agriculture.