Balancing the scales: assessing the impact of irrigation and pathogen burden on potato blackleg disease and soil microbial communities

Keating, Ciara; Kilbride, Elizabeth; Stalham, Mark A.; Nellist, Charlotte; Milner, Joel; Humphris, Sonia; Toth, Ian; Mable, Barbara K.; Ijaz, Umer Zeeshan

Abstract

Background: Understanding the interaction between environmental conditions, crop yields, and soil health is crucial for sustainable agriculture in a changing climate. Management practices to limit disease are a balancing act. For example, in potato production, dry conditions favour common scab (Streptomyces spp.) and wet conditions favour blackleg disease (Pectobacterium spp.). The exact mechanisms involved and how these link to changes in the soil microbiome are unclear. Our objectives were to test how irrigation management and bacterial pathogen load in potato seed stocks impact: (i) crop yields; (ii) disease development (blackleg or common scab); and (iii) soil microbial community dynamics. Methods: We used stocks of seed potatoes with varying natural levels of Pectobacterium (Jelly [high load], Jelly [low load] and Estima [Zero – no Pectobacterium]). Stocks were grown under four irrigation regimes that differed in the timing and level of watering. The soil microbial communities were profiled using amplicon sequencing at 50% plant emergence and at harvest. Generalised linear latent variable models and an annotation-free mathematical framework approach (ensemble quotient analysis) were then used to show the interacting microbes with irrigation regime and Pectobacterium pathogen levels. Results: Irrigation increased blackleg symptoms in the plots planted with stocks with low and high levels of Pectobacterium (22–34%) but not in the zero stock (2–6%). However, withholding irrigation increased common scab symptoms (2–5%) and reduced crop yields. Irrigation did not impact the composition of the soil microbiome, but planting stock with a high Pectobacterium burden resulted in an increased abundance of Planctomycetota, Anaerolinea and Acidobacteria species within the microbiome. Ensemble quotient analysis highlighted the Anaerolinea taxa were highly associated with high levels of Pectobacterium in the seed stock and blackleg symptoms in the field. Conclusions: We conclude that planting seed stocks with a high Pectobacterium burden alters the abundance of specific microbial species within the soil microbiome and suggest that managing pathogen load in seed stocks could substantially affect soil communities, affecting crop health and productivity. BWvw4eepooU5poSUC2MUy8Video Abstract

Citation

Keating, C., Kilbride, E., Stalham, M. A., Nellist, C., Milner, J., Humphris, S., Toth, I., Mable, B. K., & Ijaz, U. Z. (2024). Balancing the scales: assessing the impact of irrigation and pathogen burden on potato blackleg disease and soil microbial communities. Microbiome, 12(1), Article 210. https://doi.org/10.1186/s40168-024-01918-6

• Journal Article Type: Article
• Acceptance Date: Aug 26, 2024
• Online Publication Date: Oct 21, 2024
• Publication Date: Oct 21, 2024
• Deposit Date: Oct 28, 2024
• Publicly Available Date: Oct 28, 2024
• Journal: Microbiome
• Electronic ISSN: 2049-2618
• Publisher: BioMed Central
• Peer Reviewed: Peer Reviewed
• Volume: 12
• Issue: 1
• Article Number: 210
• DOI: https://doi.org/10.1186/s40168-024-01918-6
• Keywords: Soil microbial communities, Common scab disease, Bioinformatics, Pectobacterium, Potato blackleg, Potato crop health
• Public URL: https://durham-repository.worktribe.com/output/2989575