Biology subjects

Jackson, R. W.

Publications and source records attributed to Jackson, R. W..

11 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↗

bioRxiv2024

Genetic dissection of the tissue-specific roles of type III effectors and phytotoxins in the pathogenicity of Pseudomonas syringae pv. syringae to cherry

When compared with other phylogroups (PGs) of the Pseudomonas syringae (Ps) species complex, Ps pv. syringae strains within PG2 have a reduced repertoire of type III effectors (T3Es) but produce several phytotoxins. Effectors within the cherry pathogen Pss9644 were grouped based on their frequency in strains from Prunus as: the conserved effector locus (CEL) common to most Ps pathogens; a CORE of effectors common to PG2; a set of PRUNUS effectors common to cherry pathogens; and a FLEXIBLE set of T3Es. Pss9644 also contains gene clusters for biosynthesis of toxins syringomycin/syringopeptin and syringolin A. After confirmation of virulence gene expression, mutants with a sequential series of T3E and toxin deletions were pathogenicity tested on wood, leaves and fruits of sweet cherry (Prunus avium) and leaves of ornamental cherry (Prunus incisa). The toxins had a key role in disease development in fruits but were less important in leaves and wood. An effectorless mutant retained some pathogenicity to fruit but not wood or leaves. Striking redundancy was observed amongst effector groups. The CEL effectors have important roles during the early-stages of leaf infection and acted synergistically with toxins in all tissues. Deletion of separate groups of T3Es had much more effect in Prunus incisa than in sweet cherry. Mixed inocula were used to complement the toxin mutations in trans and indicated that strain mixtures may be important in the field. Our results highlight the niche-specific role of toxins in cherry tissues and the complexity of effector redundancy in the pathogen Pss9644.

microbiology↗

bioRxiv2021

The role of L-arabinose metabolism for Escherichia coli O157:H7 in edible plants

Arabinose is a major plant aldopentose in the form of arabinans complexed in cell wall polysaccharides or glycoproteins (AGP), but comparatively rare as a monosaccharide. L-arabinose is an important bacterial metabolite, accessed by pectolytic microorganisms such as Pectobacterium atrosepticum via pectin and hemicellulose degrading enzymes. However, not all plant-associated microbes encode cell wall degrading enzymes, yet can metabolise L-arabinose, raising questions about their use of and access to the glycan in plants. Therefore, we examined L-arabinose metabolism in the food-borne pathogen Escherichia coli O157:H7 (isolate Sakai) during its colonisation of plants. L-arabinose metabolism (araBA) and transport (araF) genes were activated at 18 {degrees}C in vitro by L-arabinose and expressed over prolonged periods in planta. Although deletion of araBAD did not impact the colonisation ability of E. coli O157:H7 (Sakai) on plants, araA was induced on exposure to spinach cell wall polysaccharides. Furthermore, debranched and arabinan oligosaccharides induced ara metabolism gene expression in vitro, and stimulated modest proliferation, while immobilised pectin did not. Thus, E. coli O157:H7 (Sakai) can utilise pectin/AGP- derived L-arabinose as a metabolite, but differs fundamentally in ara gene organisation, transport and regulation from the related pectinolytic species P. atrosepticum, reflective of distinct plant- associated lifestyles.

microbiology↗

bioRxiv2021

Extreme parallel evolution of flagellar motility is facilitated by synonymous sequence

Mutational hotspots can determine evolutionary outcomes and make evolution repeatable. Hotspots are products of multiple evolutionary forces including mutation rate heterogeneity, but this variable is often hard to identify. In this work we reveal that a powerfully deterministic genetic hotspot can be built and broken by a handful of silent mutations. We observed this when studying homologous immotile variants of the bacteria Pseudomonas fluorescens, AR2 and Pf0-2x. AR2 resurrects motility through highly repeatable de novo mutation of the same nucleotide in >95% lines in minimal media (ntrB A289C). Pf0-2x, however, evolves via a number of mutations meaning the two strains diverge significantly during adaptation. We determined that this evolutionary disparity was owed to just 6 synonymous variations within the ntrB locus, which we demonstrated by swapping the sites and observing that we were able to both break (>95% to 0% in AR2) and build (0% to 80% in Pf0-2x) a powerfully deterministic mutational hotspot. Our work reveals a fundamental role for silent genetic variation in determining adaptive outcomes.

evolutionary biology↗

bioRxiv2021

Muscle coordination retraining inspired by musculoskeletal simulations: a study on reducing knee loading

Humans typically coordinate their muscles to meet movement objectives like minimizing energy expenditure. In the presence of pathology, new objectives gain importance, like reducing loading in an osteoarthritic joint, but people often do not change their muscle coordination patterns to meet these new objectives. Here we use musculoskeletal simulations to identify simple changes in coordination that can be taught by providing feedback of electromyographic activity to achieve a therapeutic goal--reducing joint loading. Our simulations predicted that changing the relative activation of the redundant ankle plantarflexors could reduce knee contact force during walking, but it was unclear whether humans could re-coordinate redundant muscles during a complex task like walking. With simple biofeedback of electromyographic activity, healthy individuals reduced the ratio of gastrocnemius to soleus muscle activation by 25{+/-}15% (p=0.004). The resulting "gastrocnemius avoidance" gait pattern reduced the late-stance peak of simulation-estimated knee contact force by 12{+/-}12% (p=0.029). Simulation-informed muscle coordination retraining could be a promising treatment for knee osteoarthritis and a powerful tool for optimizing coordination for a variety of rehabilitation and performance applications.

bioengineering↗

bioRxiv2019

Foot strike pattern during running alters muscle-tendon dynamics of the gastrocnemius and the soleus

Running is thought to be an efficient gait due, in part, to the behavior of the plantar flexor muscles and the elastic energy storage in the Achilles tendon. Although plantar flexor muscle mechanics and Achilles tendon energy storage have been explored during rearfoot striking, they have not been fully characterized during forefoot striking. This study examines how plantar flexor muscle-tendon mechanics during running differ between rearfoot and forefoot striking. We used musculoskeletal simulations, driven by joint angles and electromyography recorded from runners using both rearfoot and forefoot striking running patterns, to characterize plantar flexor muscle-tendon mechanics. The simulations revealed that foot strike pattern affected the soleus and gastrocnemius differently. For the soleus, forefoot striking resulted in decreased tendon energy storage and decreased positive fiber work compared to rearfoot striking. For the gastrocnemius, forefoot striking resulted in greater activation and increased negative fiber work compared to rearfoot striking. The increased activation and negative fiber work in the gastrocnemius during forefoot striking suggest that runners planning to convert to forefoot striking would benefit from a progressive eccentric gastrocnemius strengthening program to avoid injury.

bioengineering↗

bioRxiv2018

Comparative genomics of Pseudomonas syringae reveals convergent gene gain and loss associated with specialisation onto cherry (Prunus avium)

O_LIGenome-wide analyses of the effector- and toxin-encoding genes were used to examine the phylogenetics and evolution of pathogenicity amongst diverse strains of Pseudomonas syringae causing bacterial canker of cherry (Prunus avium) including pathovars P.s pv. morsprunorum (Psm) races 1 and 2, P.s pv. syringae (Pss) and P.s pv. avii.\nC_LIO_LIGenome-based phylogenetic analyses revealed Psm races and P.s pv. avii clades were distinct and were each monophyletic, whereas cherry-pathogenic strains of Pss were interspersed amongst strains from other host species.\nC_LIO_LIA maximum likelihood approach was used to predict effectors associated with host specialisation on cherry. Pss possesses a smaller repertoire of type III effectors but has more toxin biosynthesis clusters compared with Psm and P.s pv. avii. Evolution of cherry pathogenicity was correlated with gain of genes such as hopAR1 and hopBB1 through putative phage transfer and horizontal transfer, respectively. By contrast, loss of the avrPto/hopAB redundant effector group was observed in cherry-pathogenic clades. Ectopic expression of hopAB and hopC1 triggered the hypersensitive reaction in cherry leaves, confirming computational predictions.\nC_LIO_LICherry canker provides a fascinating example of convergent evolution of pathogenicity that is explained by the mix of effector and toxin repertoires acting on a common host.\nC_LI

microbiology↗

bioRxiv2017

Characterisation of the pathogenicity of strains of Pseudomonas syringae towards cherry and plum

Bacterial canker is a major disease of cherry and other stone fruits caused by several pathovars of Pseudomonas syringae. These are P.s pv. morsprunorum race 1 (Psm R1), P.s pv. morsprunorum race 2 (Psm R2) and P.s pv. syringae (Pss). Psm R1 and R2 were originally designated as races of the same pathovar, however phylogenetic analysis has revealed them to be distantly related. This study characterised the pathogenicity of P. syringae on cherry and plum, in the field and the laboratory. The field experiment identified variation in host cultivar susceptibility to the different pathogen clades. The cherry cultivar Merton Glory exhibited a broad resistance to all clades, whilst cultivar Van showed race-specific resistance. Psm R1 may be divided into a race structure with some strains pathogenic to both cherry and plum and others only pathogenic to plum. The results of laboratory-based pathogenicity tests were compared to results obtained on whole-trees. Only cut shoot inoculations were found to be sensitive enough to detect cultivar variation in susceptibility. Measuring population growth of bacteria in detached leaves reliably discriminated pathogens from non-pathogens. In addition, symptom appearance discriminated Psm races from non-pathogens which triggered a rapid hypersensitive response (HR). The pathogen Pss rapidly induced disease lesions and therefore may exhibit a more necrotrophic lifestyle than hemi-biotrophic Psm races. This in-depth study of pathogenic interactions, identification of host resistance and optimisation of laboratory assays, will provide a framework for future genetic dissection of virulence and host resistance mechanisms.

plant biology↗