Niche differentiation within a cryptic pathogen complex: climatic drivers and hyperparasitism at multiple spatial scales

Pathogens are embedded in multi-trophic food webs, which often include co-occurring cryptic species within the same pathogen complex. Nonetheless, we still lack an understanding of what dimensions of the ecological niche might allow these cryptic species to coexist. We explored the role of climate, host characteristics (tree autumn phenology) and attack by the fungal hyperparasite Ampelomyces (a group of fungi attacking plant pathogens) in defining the niches of three powdery mildew species (Erysiphe alphitoides, E. hypophylla and E. quercicola) within a cryptic pathogen complex on the pedunculate oak Quercus robur at the continental (Europe), national (Sweden and France) and landscape scales (a 5 km(2) island in southwestern Finland). Previous studies have shown that climate separated the niches of three powdery mildew species (E. alphitoides, E. hypophylla and E. quercicola) in Europe and two species (E. alphitoides and E. quercicola) in France. In our study, we did not detect a significant relationship between temperature or precipitation and the distribution of E. alphitoides and E. hypophylla present in Sweden, while at the landscape scale, temperature, but not relative humidity, negatively affected disease incidence of E. alphitoides in an exceptionally warm year. Tree variation in autumn phenology did not influence disease incidence of powdery mildew species, and hyperparasite presence did not differ among powdery mildew species at the continental, national and landscape scale. Climate did not affect the distribution of the hyperparasite at the continental scale and at the national scale in Sweden. However, climate affected the hyperparasite distribution in France, with a negative relationship between non-growing season temperature and presence of the hyperparasite. Overall, our findings, in combination with earlier evidence, suggest that climatic factors are more important than species interactions in defining the niches of cryptic species within a pathogen complex on oak

Fungal Metabarcoding Data for Two Grapevine Varieties (Regent and <i>Vitis vinifera</i> ‘Cabernet-Sauvignon’) Inoculated with Powdery Mildew (<i>Erysiphe necator</i>) Under Drought Conditions

The increasing needs of humanity for food supply, the need to reduce fertilizer and pesticide use to protect human and environmental health, and the threats of climate change and disease emergence all provide incentives to use microorganisms to promote crop growth and health (Busby et al. 2017; D'Hondt et al. 2021; Toju et al. 2018). One of the challenges currently facing us is discovering and identifying microbial strains or consortia capable of alleviating biotic and abiotic stresses, and integrating them into crop management (Berg et al. 2017; Poudel et al. 2016). Addressing this challenge is crucial in the case of European cultivated grapevine (Vitis vinifera L.) because this emblematic crop is a very heavy user of phytosanitary products (mainly copper, sulfur and synthetic chemical fungicides targeting leaf diseases). Strengthening microbial biocontrol of grapevine leaf diseases by stimulating the microbiota naturally present in vineyards or by inoculating new microorganisms (Bartoli et al. 2020) could reduce viticulture reliance on chemical fungicides. However, this nature-based solution (Maes and Jacobs 2017) will only be effective and sustainable if microbial antagonisms are resilient to microclimatic and climatic variations and associated changes in vine physiology. This is why vine-pathogen-microbiota interactions should be studied under a range of abiotic conditions. Powdery mildew is one of the grapevine leaf diseases for which the use of chemical fungicides must be reduced. It is caused by the ascomycete fungus Erysiphe necatorCultivating the grapevine without pesticides : towards agroecological wine-producing socio-ecosystem

Niche differentiation within a cryptic pathogen complex: climatic drivers and hyperparasitism at multiple spatial scales

Pathogens are embedded in multi-trophic food webs, which often include co-occurring cryptic species within the same pathogen complex. Nonetheless, we still lack an understanding of what dimensions of the ecological niche might allow these cryptic species to coexist. We explored the role of climate, host characteristics (tree autumn phenology) and attack by the fungal hyperparasite Ampelomyces (a group of fungi attacking plant pathogens) in defining the niches of three powdery mildew species (Erysiphe alphitoides, E. hypophylla and E. quercicola) within a cryptic pathogen complex on the pedunculate oak Quercus robur at the continental (Europe), national (Sweden and France) and landscape scales (a 5 km 2 island in southwestern Finland). Previous studies have shown that climate separated the niches of three powdery mildew species (E. alphitoides, E. hypophylla and E. quercicola) in Europe and two species (E. alphitoides and E. quercicola) in France. In our study, we did not detect a significant relationship between temperature or precipitation and the distribution of E. alphitoides and E. hypophylla present in Sweden, while at the landscape scale, temperature, but not relative humidity, negatively affected disease incidence of E. alphitoides in an exceptionally warm year. Tree variation in autumn phenology did not influence disease incidence of powdery mildew species, and hyperparasite presence did not differ among powdery mildew species at the continental, national and landscape scale. Climate did not affect the distribution of the hyperparasite at the continental scale and at the national scale in Sweden. However, climate affected the hyperparasite distribution in France, with a negative relationship between non-growing season temperature and presence of the hyperparasite. Overall, our findings, in combination with earlier evidence, suggest that climatic factors are more important than species interactions in defining the niches of cryptic species within a pathogen complex on oak

Leaf microbiome data for European cultivated grapevine (Vitis vinifera L.) during downy mildew (Plasmopara viticola) epidemics in three wine-producing regions in France

International audienceGrapevine downy mildew (Plasmopara viticola) is a major disease of European cultivatedgrapevine (Vitis vinifera L.) against which a large amount of synthetic pesticides are used. Developing microbial biocontrol of P. viticola could reduce the use of pesticides in viticulture and preserve human and environmental health. To achieve this goal, the ecological interactions that develop during infection between P. viticola and the vine foliar microbiome need to be explored. Here, we present metabarcoding datasets describing the bacterial and fungal communities of pairs of symptomatic and asymptomatic leaf samples collected during downy mildew epidemics in three major wine-producing regions of France. Fungal and bacterial communities were sequenced on a MiSeq Illumina platform, and the abundance of the oomycete P. viticola was quantified using qPCR. We provide the raw metabarcoding datasets, the amplicon sequence variant tables obtained after bioinformatic processing, the metadatadescribing sampling sites and tissue health conditions, and the code used for bioinformatic analysis. These datasets will enable microbiome comparison within pairs of symptomatic and asymptomatic samples collected at the same time on the same leaf. Such a comparison could help describe the ecological interactions between P. viticola and the grapevine foliar microbiome

Metagenomic next⁃generation sequencing (mNGS) data reveals the phyllosphere microbiome of wheat plants infected by the fungal pathogen Zymoseptoria tritici

The fungal pathogen Zymoseptoria tritici is the causal agent of Septoria tritici blotch (STB), a major wheat disease in Western Europe. Microorganisms inhabiting wheat leaves might act as beneficial, biocontrol or facilitating agents that could limit or stimulate the development of Z. tritici. Improving our understanding of microbial communities in the wheat phyllosphere would lead to new insights into STB management. This resource announcement provides fungal and bacterial metabarcoding datasets obtained by sampling wheat leaves with and without symptoms caused by Z. tritici. Tissues were sampled from three commercial wheat varieties on three sampling dates during a cropping season. Weeds around wheat fields were sampled as well. In total, more than 450 leaf samples were collected. The pathogen Z. tritici was quantified using qPCR. We provide the raw metabarcoding datasets, the Amplicon Sequence Variant (ASV) tables obtained after bioinformatic processing, the metadata associated to each sample (sampling date, wheat variety and tissue health condition), a preliminary descriptive analysis of the data, and the code used for bioinformatic and descriptive statistical analysis

Metagenomic next⁃generation sequencing (mNGS) data reveals the phyllosphere microbiome of wheat plants infected by the fungal pathogen Zymoseptoria tritici

International audienceThe fungal pathogen Zymoseptoria tritici is the causal agent of Septoria tritici blotch (STB), a major wheat disease in Western Europe. Microorganisms inhabiting wheat leaves might act as beneficial, biocontrol or facilitating agents that could limit or stimulate the development of Z. tritici. Improving our understanding of microbial communities in the wheat phyllosphere would lead to new insights into STB management. This resource announcement provides fungal and bacterial metabarcoding datasets obtained by sampling wheat leaves with and without symptoms caused by Z. tritici. Tissues were sampled from three commercial wheat varieties on three sampling dates during a cropping season. Weeds around wheat fields were sampled as well. In total, more than 450 leaf samples were collected. The pathogen Z. tritici was quantified using qPCR. We provide the raw metabarcoding datasets, the Amplicon Sequence Variant (ASV) tables obtained after bioinformatic processing, the metadata associated to each sample (sampling date, wheat variety and tissue health condition), a preliminary descriptive analysis of the data, and the code used for bioinformatic and descriptive statistical analysis