Bio-organic fertilizers containing potential biocontrol strains suppress bacterial soft rot and reshape soil microbial communities in cucumbers

Bacterial soft rot disease poses a serious threat to cucumber production. Bio-organic fertilizers containing antagonistic beneficial microorganisms have emerged as promising approaches for enhancing plant disease resistance. However, the underlying mechanisms by which these fertilizers suppress bacterial soft rot disease remain unclear. This study aimed to explore the fundamental patterns of bio-organic fertilizer regulation of bacterial and fungal community assembly in cucumbers and their relationships with bacterial soft rot resistance through a field experiment involving four different types of bio-organic fertilizer treatments. The plant health and soil fertility increased significantly under all treatments. The combination of Chinese medicine residue with bio-organic fertilizer demonstrated the most pronounced effects among all treatments. Shifts in bacterial and fungal community structure induced by bio-organic fertilizers are crucial in suppressing bacterial soft rot disease. In particular, bio-organic fertilizers recruit more beneficial microorganisms with antimicrobial activity and promote plant growth traits. Following bio-organic fertilizer application, the bacterial network displays greater complexity than the fungal network. Structural equation models have demonstrated the influence of bio-organic fertilizer application on specific microflora that drives modifications in soil physicochemical properties. Altering key soil physicochemical factors such as total nitrogen and total phosphorus is vital for promoting the suppressive effect of bio-organic fertilizers on bacterial soft rot. Thus, the effectiveness of bio-organic fertilizers stems from a combination of the actual antagonistic activities of the inoculated biocontrol agents and the promotion of indigenous beneficial microbial groups. This dual mechanism not only suppresses the growth of pathogens directly but also strengthens the soil’s overall microbial ecosystem, thereby promoting plant health and resistance to diseases.