Biology subjects

Irvine, J.

Publications and source records attributed to Irvine, J..

4 recordsLinked to original sources

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

Generating functional plasmid origins with OriGen

While generative artificial intelligence (AI) has shown promise for biological design, no computational system has yet created and validated sequences capable of autonomous replication. Focusing on plasmids, one of the smallest types of replicating elements, we develop OriGen, a sequence model that generates new plasmid origins of replication while maintaining key elements essential for their replication. We experimentally validate OriGens ability to create functional origins that diverge from existing wild types, demonstrating the models capacity to capture the complex and often cryptic mechanisms of biological replication.

synthetic biology↗

bioRxiv2024

Arctic greening drives changes in the diet and gut microbiome of a resident herbivore with consequences for fitness

Rapid climate warming is "greening" the tundra due to higher plant productivity, particularly of deciduous shrubs and grasses, potentially changing the nutritional base for herbivores. However, the consequences for herbivores are unclear. Although the gut microbiome is an essential factor, mediating the capacity to adapt to dietary change, few studies have investigated the effect of annual changes in the diet-gut microbiome nexus on fitness traits. In a model system, the Svalbard reindeer, a species experiencing the greatest rate of climate warming on Earth, we investigate how climate-induced changes in diet and the gut microbiome impact reindeer body mass. Using high-resolution DNA metabarcoding, we quantified diet and microbiome composition in rumen samples from 97 animals culled in October from 1998 to 2004 in four different valleys. Overall diet diversity and grass consumption were significantly higher following warmer summers, while intake of the dwarf shrub Salix polaris increased with the maximum normalised difference vegetation index (NDVI). The proportion of Salix had a significant positive effect on autumn body mass, which in turn increases ovulation rates and overwinter survival. There was a significant positive effect of Salix on the microbiome diversity, while between-year variation in Bacteroidota, the most common bacteria phylum, was also significantly, positively related to maximum NDVI. However, a structural equation model revealed that the direct "path" effect of the proportion of Salix in the diet on reindeer body mass was stronger than the indirect path effect, mediated through the gut microbiome. Our results suggest a positive impact of climate-driven Arctic greening on Svalbard reindeer fitness, operating through a change in diet composition, partially mediated by the changes in the gut microbiome. These findings advance our understanding of the mechanistic underpinnings of Arctic warming on herbivore populations and contribute to the debate about the importance of the diet-gut microbiome nexus in facilitating species resilience in the face of climate change.

ecology↗

bioRxiv2021

The duration of antibiotic treatment is associated with carriage of toxigenic and atoxigenic strains of Clostridioides difficile in dogs.

Clostridioides difficile is a leading cause of human antibiotic-associated diarrhoeal disease globally. Zoonotic reservoirs of infection are increasingly suspected to play a role in the emergence of this disease in the community and dogs are considered as one potential source. Here we use a canine case-control study at a referral veterinary hospital in Scotland to assess: i) the risk factors associated with carriage of C. difficile by dogs, ii) whether carriage of C. difficile is associated with clinical disease in dogs and iii) the similarity of strains isolated from dogs with local human clinical surveillance. The overall prevalence of C. difficile carriage in dogs was 18.7% (95% CI 14.8-23.2%, n=61/327) of which 36% (n=22/61) were toxigenic strains. We found risk factors related to prior antibiotic treatment were significantly associated with C. difficile carriage by dogs. However, the presence of toxigenic strains of C. difficile in a canine faecal sample was not associated with diarrhoeal disease in dogs. Active toxin was infrequently detected in canine faecal samples carrying toxigenic strains (2/11 samples). Both dogs in which active toxin was detected had no clinical evidence of gastrointestinal disease. Among the ten toxigenic ribotypes of C. difficile detected in dogs in this study, six of these (012, 014, 020, 026, 078, 106) were ribotypes commonly associated with human clinical disease in Scotland, while atoxigenic isolates largely belonged to 010 and 039 ribotypes. Whilst C. difficile does not appear commonly associated with diarrhoeal disease in dogs, antibiotic treatment increases carriage of this bacteria including toxigenic strains commonly found in human clinical disease.

microbiology↗