Bio-organic substitution in red soil: An optimal strategy for inhibiting plant diseases and improving soil health

Partial substitution of chemical nitrogen fertilizer with organic manure, known as organic substitution, is widely recognized as an effective method to enhance soil quality, fertility, and microbial diversity. We assessed the effects of organic substitution strategies—farmyard manure (NF), commercial organic manure (NC), and bio-organic manure ( Trichoderma viride Pers. ) (NT)—on soil microbial community composition and structure in tobacco ( Nicotiana tabacum L. ) fields in Yunnan province. Bacterial alpha diversity was significantly higher under organic substitution strategies (NF, NC, NT) than under synthetic chemical fertilizer (SN). Beta diversity analysis confirmed that organic substitution strategies significantly altered bacterial community structure. Organic substitution strategies reduced the relative abundance of Ralstonia , lowering the risk of tobacco wilt disease. The NT strategy significantly enriched Gammaproteobacteria , particularly Clostridia , whereas NF increased Actinobacterota , potentially improving soil health. In contrast, Fusarium abundance was higher under NC and NF strategies compared to SN, with NT showing the lowest abundance. The NC strategy also exhibited the highest discrimination in the pathogen order Sordariales , suggesting that NC and NF may inadvertently increase plant disease risk. This study demonstrates that organic substitution strategies reshape microbial communities. Specifically, the NT strategy improves disease suppression and soil fertility, making it a promising approach for sustainable tobacco production. • Organic substitutes increased bacterial diversity and altered community structure. • Commercial organic substitution increased fungal species but reduced its diversity. • Commercial- & farm-organic substitutions increased the risk of plant diseases. • Bio-organic substitution improves pathogen suppression and soil fertility. • Bacteria are involved in N cycling, while fungi contribute to P cycling.