Microbiome legacy influences necrosis formation in Diplodia sapinea-infected Scots pine shoots

Fungal endophytes are important members of the holobiont of all plants, including that of Scots pine (Pinus sylvestris), potentially affecting host performance. One of the most important pathogens of Scots pine in Europe is Diplodia sapinea, which causes necrotic lesions and is becoming increasingly prevalent in northern regions. Although endophytes are known to affect plant performance, it remains unclear whether naturally established fungal communities in Scots pine shoots can modulate D. sapinea-induced necrosis. Using a field experiment, we tested the hypothesis that exclusion of airborne fungal inoculum shapes the endophytic community in shoots of pine seedlings, and that such alterations in this community influence the necrosis-inducing capacity of D. sapinea.

In the field site, airborne fungal inoculum was reduced in half of the saplings by covering shoots with mesh bags. Covered (bagged) and free (unbagged) shoots were transported to the laboratory and inoculated with D. sapinea. The morphology and physiological status of the shoots were monitored using a multispectral 3D scanner, and the necrotic lesion development was assessed. The propagule exclusion resulted in endophytic communities with slightly lower richness, while shoots showed no detectable morphological or physiological differences prior to inoculation. Shoots inoculated with D. sapinea developed clear necrotic lesions, which were significantly larger in covered shoots than in the free ones. Long-read Oxford Nanopore metabarcoding revealed that community shifts following inoculation were more pronounced in covered shoots. Community composition clearly separated necrotic and healthy tissues.

Our findings suggest that the structure of the resident fungal endophytic community may influence the extent of necrotic lesions caused by D. sapinea in Scots pine shoots. A more established, diverse fungal community was associated with smaller lesion sizes, whereas shoots exposed to lower propagule pressure developed larger lesions following inoculation. These results highlight the functional role of fungal community assembly in shaping disease outcomes and suggest that endophyte-based approaches may provide new opportunities for improving disease resistance in forest tree species. The results also suggest that endophytic status may need to be considered when lesion size is used to evaluate resistance to pathogens in tree breeding programs.