Biology subjects

Rabiey, M.

Publications and source records attributed to Rabiey, M..

4 recordsLinked to original sources

bioRxiv2026

Mutations in bacterial regulatory genes are linked with chronic ash tree infections

Long term chronic infections of plants by bacterial pathogens are largely unknown. Understanding how pathogens adapt during chronic infection provides a key insight to pathogen evolutionary strategy both for persistence and survival, but also for potential future outbreaks. Pseudomonas savastanoi pv. fraxini (Psf), a member of phylogroup 3 within the Pseudomonas syringae species complex, causes canker disease in European ash (Fraxinus excelsior). Infections persist for years within the bark parenchyma, where bacteria are enclosed in cavities that contribute to the gradual expansion of host periderm. This pathosystem therefore provides an opportunity to examine pathogen evolution in a long-lived, largely unmanaged host. We combined population genomics and phenotypic analysis of 124 Psf strains collected from six sites across the UK. Phylogenetic analysis revealed a highly clonal population, with only 833 core genome SNPs across a 5.3 Mb genome, and a relatively small accessory genome largely shaped by gain and loss of large mobile genetic elements. Despite this limited genomic diversity, mutations were enriched in regulatory genes, including two-component systems, chemotaxis proteins, and cell envelope-associated loci. Notably, the global regulator gacA/S was independently mutated multiple times within the same clonal lineage. These mutations, typically small deletions, were associated with changes in motility, nutrient utilisation, stress tolerance, and virulence across genetic backgrounds. As a result, phenotypic heterogeneity was observed within otherwise clonal populations, including within individual lesions. These findings indicate that repeated mutation of regulatory systems represents a key mechanism of adaptation in this chronic plant-pathogen interaction, enabling phenotypic diversification despite limited sequence divergence. This study provides a microevolutionary perspective on P. syringae populations in the phyllosphere and highlights the role of regulatory variation in the evolution of low-virulence, ecologically restricted pathogens.

microbiology↗

bioRxiv2026

Managing the phyllosphere: Agronomic practices influence the ecology and evolution of Pseudomonas syringae in cherry orchards

Bacterial canker, caused the Pseudomonas syringae species complex, is a major constraint on sweet cherry production worldwide. However, the influence of agronomic practices on pathogen ecology, dispersal and evolution under field conditions remains poorly understood. Here, we combined a factorial-design field experiment with whole-genome sequencing to investigate the effects of polytunnel covering and nitrogen fertigation on phyllosphere populations and the dynamics of a key pathogen, P. syringae pathovar syringae 9644 (Pss9644) in young cherry trees. Epiphytic P. syringae populations initially resembled those in surrounding woodland environments. Over time, pathogenic phylogroup 2d lineages became dominant, particularly on uncovered trees. Diversity of P. syringae populations was higher in uncovered treatments. Polytunnel covering markedly altered community composition and limited rain-splash dispersal of Pss9644 from stem cankers to leaves, thereby interrupting a key stage of the disease cycle. By contrast, nitrogen fertigation had no detectable effect on phyllosphere community structure, but enhanced plant growth and reduced lesion expansion following inoculation. Whole-genome sequencing of re-isolated Pss9644 strains revealed limited short-term genomic diversification, with single-nucleotide polymorphisms detected in 22 re-isolates. In total, 36 mutations were identified across the chromosome although no mutation affected virulence or motility. Taken together, our results show that agronomic practices influence both pathogen ecology and disease outcomes through distinct mechanisms: polytunnel covering primarily limits pathogen dispersal and reshapes phyllosphere communities, while nitrogen fertigation enhances plant growth and reduces disease severity. These findings highlight the potential to integrate canopy management and nutrient strategies to mitigate bacterial canker risk in commercial cherry production.

microbiology↗

bioRxiv2025

The cause-effect conundrum of local-scale site and soil factors in acute oak decline (AOD)

Background and aimsAcute oak decline (AOD), a decline syndrome affecting mature oaks, involves bacterial pathogens which likely act as opportunists under host stress. Trees displaying symptoms (bleeding cankers) appear in localized clusters, not whole stands. This study investigates the potential involvement of local-scale factors, in interaction with large-scale environmental drivers, in influencing onset and progression of AOD. MethodsAOD-symptomatic (n=30) and asymptomatic trees (n=30) across three UK oak woodlands were assessed for tree characteristics, their surrounding context, and soil properties. ResultsTree health status was linked to significant differences in soil and tree properties across sites. Symptomatic trees exhibited greater loss of crown density, lower local stand (0-20 m) basal area and shallower depth to gleying. Significant differences in soil properties included lower concentrations of Olsen P, total N, and exchangeable Mg in symptomatic trees, alongside higher exchangeable Fe, especially at 40-50 cm depth. Depth to gleying and exchangeable Fe were identified as the most influential predictors of AOD. ConclusionsAOD symptomatic trees may experience seasonal soil water saturation closer to the surface compared to asymptomatic trees, resulting in a higher proportion of their roots being exposed to an anoxic, iron-reducing environment. This study is the first to report such an association between gleying depth, likely seasonal water saturation, and symptom status for AOD. It is unclear whether water balance and associated soil nutrient variations are predisposing factors or consequences of declining tree health, though the identified local-scale factors likely contribute to AOD. A feedback loop is conceptualised where declining tree health worsens soil conditions, creating a negative cycle that accelerates tree decline.

ecology↗

bioRxiv2024

Exploring the Exclusive Isolation of Pseudomonas syringae in Peltigera Lichens via metabolite analysis and growth assays

The specific association of the potentially plant-pathogenic Pseudomonas syringae with Peltigera lichens raises questions about the factors driving this host specificity. To explore this, the metabolic profile of seven lichen species belonging to three genera (Cladonia, Peltigera, and Stereocaulon) was analysed using LC-MSMS. Additionally, we assessed the growth of P. syringae strains in media supplemented with extracts from each lichen species. This revealed that Peltigera exhibits lower metabolite richness compared to other genera, but shows a higher chemical investment in specific compounds. Growth kinetics showed comparable P. syringae growth across lichen-supplemented media, except for C. arbuscula and Cladonia sp., where the former exhibited lower growth rates. Inhibition assays with lichen extracts showed no inhibition of P. syringae. The lichen metabolome is predominantly composed of lipids and organic acids. Furthermore, specific compounds, such as aminoglycosides, may facilitate P. syringae presence in Peltigera by inhibiting Bacillus subtilis and other antagonists. Additionally, compounds absent in Peltigera, like anthracene, might serve as a carbon source inhibitors like B. velezensis.

microbiology↗