Phyllosphere microbiome responses to nano-berberine and chemical fungicides in powdery mildew infected strawberry

Meng Yang¹Tao He¹Romy Moukarzel²Man Li¹Mei Li¹Zengxiu Zhang¹Yiyi He¹Yixiang Liu¹Lei Yu³Shusheng Zhu¹Fei Du^1*

• ¹Yunnan Agricultural University, Kunming, China
• ²Lincoln University, Lincoln, New Zealand
• ³Kunming University, Kunming, China

Strawberry powdery mildew, caused by the obligate biotroph Podosphaera aphanis, is a major threat to commercial strawberry production, reducing both yield parameters and fruit quality. While chemical fungicides remain a standard control method, their non-target effects on phyllosphere microbial communities have raised important ecological and environmental concerns. Nano-pesticides are increasingly applied in plant disease management, however, their influence on the composition and functional potential of phyllosphere microbial communities remains poorly understood. In this study, we compared the field-level effects of a nano-berberine formulation (BBR-M) and conventional chemical fungicides (e.g., bupirimate) on the strawberry phyllosphere microbiota using high-throughput sequencing, bioinformatics analysis, and microbial isolation techniques. The nano-berberine formulation (BBR-M) used in this study was provided by a collaborative group, with synthesis and physicochemical characteristics consistent with those previously reported for this material. The results showed that nano-fungicide application significantly reduced the disease index of powdery mildew and markedly decreased its incidence in field-grown strawberries, ultimately lowering leaf disease incidence to 5.06% with a control efficacy of 96.81%. Furthermore, nano-fungicides and conventional chemical fungicides treatments were associated with distinct impacts on the phyllosphere microenvironment of strawberry. Application of BBR-M was associated with a more structured and potentially stable microbial community, characterized by increased fungal diversity and higher modularity in co-occurrence networks. In contrast, bupirimate treatment increased microbial complexity but coincided with reduced network stability. A strain of Bacillus siamensis—a genus identified as a core taxon within the BBR-M phyllosphere network—was subsequently isolated from nano-berberine–treated leaves and exhibited strong antagonistic activity against Colletotrichum nymphaeae. Field assays showed that this strain effectively suppressed strawberry powdery mildew with 98.18% control efficacy. Collectively, these findings provide important insights into the ecological safety and functional implications of novel pesticide technologies, underscoring the potential of nano-fungicides and native biocontrol agents for sustainable strawberry disease management.