Multifactorial suppression of Erwinia amylovora by the apple flower endophyte Pantoea agglomerans AFF2001

Fire blight, caused by Erwinia amylovora , represents a significant threat to apple and pear production worldwide. The negative environmental impact of copper and the emergence of antibiotic resistance have led to the development of more eco-friendly management strategies for E. amylovora . It is now well established that apple flowers harbour bacterial taxa capable of limiting the ability of E. amylovora to colonise floral tissues. Because apple flowers are the primary infection sites of E. amylovora , their endophytic microbiota are reservoirs of potential biological control agents. In this study, endophytic bacteria were isolated from healthy apple flowers (Malus domestica cv. Golden Delicious) collected in Trentino and screened for their ability to control E. amylovora . Based on 16S rRNA gene sequencing, the bacterial isolates mainly belonged to the families Enterobacteriaceae, Pseudomonadaceae and Microbacteriaceae. Among the tested bacterial strains, Pantoea agglomerans AFF2001 exhibited the highest efficacy in suppressing E. amylovora on newly opened apple flowers and immature pear slices. In vitro and in planta assays were combined to investigate interactions between P. agglomerans AFF2001 and E. amylovora . The selected bacterial strain showed a significant contact-dependent inhibition of E. amylovora growth. It significantly acidified a stigma-mimicking medium, thereby reducing the viability and motility of E. amylovora cells. Furthermore, active competition for iron was associated with increased siderophore production by P. agglomerans AFF2001 in the presence of E. amylovora . The analysis of the P. agglomerans AFF2001 genome identified biosynthetic gene clusters responsible for producing siderophores and toxic secondary metabolites, as well as genes encoding a Type VI secretion system that may be involved in contact-dependent antagonism. Random transposon mutagenesis with pUT-miniTn5-Km revealed that genes involved in regulatory pathways, motility, and amino acid biosynthesis contribute to the biocontrol activity of P. agglomerans AFF2001. These results demonstrate that suppression of E. amylovora by P. agglomerans AFF2001 involves multiple interacting mechanisms, including nutrient and iron competition, environmental acidification, interference with the plant pathogen motility, and contact-dependent interactions. The findings emphasise apple flower endophytes as a valuable reservoir of biological control agents and identify P. agglomerans AFF2001 as a promising candidate for the development of sustainable fire blight management strategies.