Genetic diversity and structure of the coffee leaf rust fungus Hemileia vastatrix across different coffee management systems in Ethiopia / Diversidad genética y estructura del hongo de la roya del café Hemileia vastatrix en diferentes sistemas de manejo del café en Etiopía

Although coffee leaf rust (CLR), caused by Hemileia vastatrix, poses an increasing threat to coffee production in Ethiopia, little is known regarding its genetic diversity and structure and how these are affected by coffee management. Here, we used genetic fingerprinting based on sequence-related amplified polymorphism (SRAP) markers to genotype H. vastatrix samples from different coffee shrubs, across 40 sites, covering four coffee production systems (forest coffee, semi plantation coffee, home garden coffee, and plantation coffee) and different altitudes in Ethiopia. In total, 96 H. vastatrix samples were successfully genotyped with three primer combinations, producing a total of 79 scorable bands. We found 35.44% of amplified bands to be polymorphic, and the polymorphic information content (PIC) was 0.45, suggesting high genetic diversity among our CLR isolates. We also found significant isolation-by-distance across the samples investigated and detected significant differences in fungal genetic composition among plantation coffee and home garden coffee and a marginally significant difference among plantation coffee and forest coffee. Furthermore, we found a significant effect of altitude on CLR genetic composition in the forest coffee and plantation systems. Our results suggest that both spore dispersal and different selection pressures in the different coffee management systems are likely responsible for the observed high genetic diversity and genetic structure of CLR isolates in Ethiopia. When selecting Ethiopian coffee genotypes for crop improvement, it is important that these genotypes carry some resistance against CLR. Because our study shows large variation in genetic composition across relatively short geographical distances, a broad selection of rust isolates must be used for coffee resistance screening.(AU)

Genetic diversity and structure of the coffee leaf rust fungus Hemileia vastatrix across different coffee management systems in Ethiopia.

Although coffee leaf rust (CLR), caused by Hemileia vastatrix, poses an increasing threat to coffee production in Ethiopia, little is known regarding its genetic diversity and structure and how these are affected by coffee management. Here, we used genetic fingerprinting based on sequence-related amplified polymorphism (SRAP) markers to genotype H. vastatrix samples from different coffee shrubs, across 40 sites, covering four coffee production systems (forest coffee, semi plantation coffee, home garden coffee, and plantation coffee) and different altitudes in Ethiopia. In total, 96 H. vastatrix samples were successfully genotyped with three primer combinations, producing a total of 79 scorable bands. We found 35.44% of amplified bands to be polymorphic, and the polymorphic information content (PIC) was 0.45, suggesting high genetic diversity among our CLR isolates. We also found significant isolation-by-distance across the samples investigated and detected significant differences in fungal genetic composition among plantation coffee and home garden coffee and a marginally significant difference among plantation coffee and forest coffee. Furthermore, we found a significant effect of altitude on CLR genetic composition in the forest coffee and plantation systems. Our results suggest that both spore dispersal and different selection pressures in the different coffee management systems are likely responsible for the observed high genetic diversity and genetic structure of CLR isolates in Ethiopia. When selecting Ethiopian coffee genotypes for crop improvement, it is important that these genotypes carry some resistance against CLR. Because our study shows large variation in genetic composition across relatively short geographical distances, a broad selection of rust isolates must be used for coffee resistance screening.

Impact of environmental nitrogen pollution on pollen allergy: A scoping review.

The current rise in the prevalence of allergies to aeroallergens is incompletely understood and attributed to interactions with environmental changes and lifestyle changes. Environmental nitrogen pollution might be a potential driver of this increasing prevalence. While the ecological impact of excessive nitrogen pollution has been widely studied and is relatively well understood, its indirect effect on human allergies is not well documented. Nitrogen pollution can affect the environment in various ways, including air, soil, and water. We aim to provide a literature overview of the nitrogen-driven impact on plant communities, plant productivity, and pollen properties and how they lead to changes in allergy burden. We included original articles investigating the associations between nitrogen pollution, pollen, and allergy, published in international peer-reviewed journals between 2001 and 2022. Our scoping review found that the majority of studies focus on atmospheric nitrogen pollution and its impact on pollen and pollen allergens, causing allergy symptoms. These studies often examine the impact of multiple atmospheric pollutants and not just nitrogen, making it difficult to determine the specific impact of nitrogen pollution. There is some evidence that atmospheric nitrogen pollution affects pollen allergy by increasing atmospheric pollen levels, altering pollen structure, altering allergen structure and release, and causing increased allergenic reactivity. Limited research has been conducted on the impact of soil and aqueous nitrogen pollution on pollen allergenic reactivity. Further research is needed to fill the current knowledge gap about the impact of nitrogen pollution on pollen and their related allergic disease burden.

Both organic and integrated pest management of apple orchards maintain soil health as compared to a semi-natural reference system.

Growing concerns about the negative environmental impacts of agriculture have resulted in the increasing adoption of farming systems that try to reconcile crop production with environmental sustainability, such as organic farming. As organic farming refrains from using synthetic inputs, it heavenly relies on maintaining soil health. However, it is still poorly understood how organic management performs in terms of maintaining soil health in real commercial and heterogeneous farm settings as compared to conventional management, and especially as compared to a natural reference system. Here, we compared a set of soil health indicators among 24 commercial apple orchards that were either managed organically or conventionally using Integrated Pest Management (IPM) practices. In addition, we quantified the same indicators in 12 semi-natural grasslands as a benchmark to assess to what extent soil processes and functions have been degraded due to agricultural practices. As soil heath indicators, we quantified soil bulk density, organic matter content, organic carbon content, organic carbon stock, total nitrogen (N), potential heterotrophic respiration, potential net N mineralization, litter decomposition and litter stabilization, and we added the diversity of the herbaceous vegetation and the soil microbiome as covariates in our models. We found no differences between organic and IPM orchards, and neither of the farming systems showed evidence of impaired soil health compared to the semi-natural benchmark, with the exception of higher decomposition rates measured in both orchard types. We observed, however, high spatial variation in soil health between drive and crop rows within the orchards. Especially in the IPM orchards, crop rows showed impaired soil health compared to the adjacent drive rows, indicating that there is still opportunity to improve soil management in the IPM system. In addition, our results show that a considerable part of the variation in soil characteristics can be attributed to the study site, suggesting that both natural heterogeneity and personal management preferences by individual farmers are more important than the management system. Overall, and at least in terms of the soil variables measured in this study, our results suggest that perennial crop systems can be managed in a sustainable way, without jeopardizing soil health.