Arbuscular mycorrhizal fungi (AMF) are symbiotic fungi crucial for plant health, enhancing nutrient uptake, diversity, and resistance to biotic and abiotic stresses. Their role in plant disease suppression is well-documented, making them key players in sustainable agriculture. While the impact of agricultural practices (organic vs. conventional) on AMF communities is debated, the influence of plant health status remains understudied, with existing research often focusing on single agricultural systems. This study examined the effects of plant health status on AMF communities in lavender (*L. angustifolia*) and lavandin (*L. intermedia*) grown under both organic and conventional practices in France. These lavender systems are affected by yellow decline, caused by the phytoplasma ‘*Candidatus* Phytoplasma solani’, which significantly impacts plant productivity. The study hypothesized that AMF colonization, diversity, and composition would be influenced by plant health status, with variations depending on agricultural practice and plant species.

Previous research has highlighted the relationship between root-associated fungal communities and plant health. Studies on *Pisum sativum* (pea) and *Salix* (willow) have shown increased AMF abundance and diversity in healthy plants. However, these studies lacked the comparative analysis of different agricultural management systems. Organic farming, with its crop rotation, cover cropping, and reduced pesticide/fertilizer use, is often associated with greater AMF colonization and diversity. Conversely, conventional farming's high inputs can negatively impact AMF communities. Conflicting results exist regarding the impact of agricultural practices on AMF communities, suggesting potential interaction with other factors like plant health status.

The study was conducted in four fields (two species × two agricultural practices) in southeastern France. Twelve root samples were collected from healthy and diseased plants (2 years old) in each field. Mycorrhizal colonization was assessed microscopically using the MYCOCALC program. DNA was extracted from pooled root samples and AMF-specific primers (FLR3 and FLR4) were used to amplify the partial large subunit region for Illumina sequencing. Bioinformatic analysis using OBItools involved read assembly, filtering, MOTU clustering (98% similarity), and taxonomic assignment. Statistical analyses included Levene's test, Student's t-tests, Wilcoxon tests, Multiple Factor Analysis (MFA), and PERMANOVA to evaluate the effects of plant health status, agricultural practice, and plant species on AMF colonization, diversity, and community structure. The composition of the most abundant MOTUs (present in at least 2/3 of samples) was compared between healthy and diseased plants using a Chi-squared test.

Mycorrhizal root colonization was significantly higher in healthy plants of both lavender and lavandin, regardless of agricultural practice. This difference was more pronounced in lavender (approximately 30% in healthy vs. 5-15% in diseased plants). In lavender, under conventional practice, plant health status significantly impacted AMF abundance and richness, with higher values in healthy plants. This effect was not observed in organic lavender or lavandin under either practice. Multiple Factor Analysis revealed distinct AMF communities associated with healthy and diseased lavender, but not lavandin. Analysis of abundant MOTUs showed that four MOTUs per species were significantly more abundant in healthy plants under both practices. Specific MOTUs such as *Funneliformis mosseae* and *Glomus macrocarpum*, known for alleviating stress, were more abundant in healthy plants.

The study's findings demonstrate a clear link between plant health status and AMF communities. Healthy plants exhibited greater mycorrhizal colonization, potentially due to differences in root exudates or carbon supply. The stronger effect in lavender compared to lavandin suggests a role of host plant identity. The interaction between plant health status and agricultural practice on AMF diversity in lavender indicates the complexity of the relationships involved. The identification of specific AMF MOTUs associated with healthy plants suggests the potential for using these fungi as biocontrol agents to enhance plant resistance to phytoplasma and other stresses.

This research underscores the importance of plant health status in shaping root AMF communities. The results reveal species-specific responses and the modifying influence of agricultural practices. The identification of specific AMF MOTUs enriched in healthy plants opens avenues for developing biocontrol strategies to enhance plant health and resilience. Future research should focus on the mechanisms underlying these interactions and testing the potential of specific AMF as biocontrol agents in field settings.

The study focused on a limited number of lavender and lavandin cultivars and geographical locations. The relatively small sample size might limit the generalizability of the findings to other systems. The study focused on characterizing AMF communities based on molecular data, which may not fully reflect the functional diversity or interactions within the community.