Seasonality and the evolutionary divergence of plant parasites

The coexistence of closely related plant parasites is widespread. Yet, understanding the ecological determinants of evolutionary divergence in plant parasites remains an issue. Niche differentiation through resource specialization has been widely researched, but it hardly explains the coexistence of parasites exploiting the same host plant. Time-partitioning has so far received less attention, although in temperate climates, parasites may specialize either in the early or in the late season. Accordingly we investigated whether seasonality can also promote phenotypic divergence. For plant parasites, seasonality generally engenders periodic host absence. To account for abrupt seasonal events, we made use of an epidemic model that combines continuous and discrete dynamics. Based on the assumption there is a trade-off between in-season transmission and inter-season survival, we found out through an 'evolutionary invasion analysis' that evolutionary divergence of the parasite phenotype can occur. Since such a trade-off has been reported, this study provides further ecological bases for the coexistence of closely related plant parasites. Moreover, this study provides original insights into the coexistence of sibling plant pathogens which perform either a single or several infection cycles within a season (mono- and poly-cyclic diseases, or uni- and multi-voltine life cycles)

Alteration of pathogenicity-linked life-history traits by resistance of its host Solanum tuberosum impacts sexual reproduction of the plant pathogenic oomycete Phytophthora infestans.

International audienceAlthough sexual reproduction implies a cost, it represents an evolutionary advantage for the adaptation and survival of facultative sexual pathogens. Understanding the maintenance of sex in pathogens requires to analyse how host resistance will impact their sexual reproduction through the alteration of their life-history traits. We explored this experimentally using potato (Solanum tuberosum) and one of its pathogens, the heterothallic oomycete Phytophthora infestans. Sexual reproduction was highest on hosts favouring asexual multiplication of the pathogen, suggesting similar nutritional requirements for both sexual and asexual sporulation. Sexual reproduction was also highest on hosts decreasing the latent period, probably because of a trade-off between growth and reproduction. Distinguishing host effects on each pathogenic trait remains however uneasy, as most life-history traits linked to pathogenicity were not independent of each other. We argue that sexual reproduction of P. infestans is an adaptation to survive when the host is susceptible and rapidly destroyed

Current use and legal status of crop protection inputs

This deliverable presents the results of the survey carried out in the frame of Tasks 3.1. and Task 5.1 in the Horizon 2020 Project Organic PLUS. A common table/questionnaire for both tasks was used in order to map the use of contentious inputs linked to plant protection (mainly Cu, S and mineral oils), and the use of peat, plastic and fertilisers used in growing, in 10 countries participating in Organic-PLUS (Denmark, France, Germany, Greece, Italy, Norway, Poland, Spain, Turkey and UK). The survey was carried out mainly by interviewing one to three experienced advisors per crop, asking them to fill in a table describing a typical organic production of the relevant crop, emphasising the use of various inputs. In some cases the survey was based on already available data of the Organic-PLUS partner while an online questionnaire was also developed and used (e.g. CUT for Poland). The collected raw material is presented in a separeate report, the D3.1 Annex I. Statistical data concerning the organic farming in the countries under study are also presented. The deliverable includes also documentation of current policies and legal status of the use of contentious plant protection products in organic farming with emphasis on potato, tomato, citrus and olive crops. Copper-based products are used in plant protection as bactericides and fungicides. Copper is the only active ingredient with a strong antimicrobial effect and a wide range of action that is approved for use in organic farming particularly for grape, potato and apple crops. Recently, the demonstrated adverse effects on the environment (on soil organisms and auxiliary species) have led to a reduction in its use in several European countries. The current regulation in EU related to the use of copper in organic production sets the limit of up to 6 kg copper per ha per year. For perennial crops, Member States may, by derogation, provide that the 6 kg copper limit can be exceeded in a given year provided that the average quantity actually used over a 5-year period consisting of that year and of the four preceding years does not exceed 6 kg. Among the investigated crops (mainly citrus, olive, tomato, potato, strawberry), large amounts of copper are used mainly by Mediterranean growers in citrus, olive and potato. For crops like citrus and olives the limit of 6 kg per ha and per year may not be always respected. Tomato producers apply high amounts of copper in winter crops (greenhouses). In the case of Norway, the use of copper and mineral oil were not permitted for organic growing until March 2017, when the EC regulations were implemented. However, the national limit for copper in Norway is 4 kg per ha and year, thus it is easier for these growers to comply with lower limits of copper use than those in EU. In Denmark, copper is not used in organic agriculture at all because national authorities have not (yet) been asked to approve any commercial product containing copper, or they have not approved it. Many alternatives to copper are under development, but few are already available on the market, and fewer still are currently used by growers to a substantial extent. Alternatives with a low concentration of copper ion are demonstrating good levels of efficacy. Possibly, a reduction of the concentration of copper, together with more efficient formulations, could reduce the presence of copper in the crops (and soils). Nevertheless, abandoning copper cannot be easily achieved through a simple substitution strategy (for instance, replacing copper by biocontrol products); it requires a more or less profound reconstruction of the crop production system, including changing cultivars (in favour of resistant ones), developing prophylaxis and sanitation measures, adjusting fertilisation, etc. This requires an integrative approach, which is still under-developed. Regarding sulphur, this substance is very common for organic vegetable growers, especially for greenhouse growers. The uses of sulphur can move from 10 to 100 kg/ha/year depending on the production system and the incidence of pests. However, it is seldom considered that the use of sulphur is problematic, except as a main component of sulphites in wine production. It is a sort of universal phytosanitary product: repellent to pests, killer of mites, and effective against powdery mildews. However, it is not selective, and it has harmful effects on beneficial arthropods. So, the use of sulphur can limit biological control. Alternatives to sulphur are not currently applied mainly for economic reasons since sulphur is cheap compared to other compounds. Moreover, since sulphur can be an alternative to mineral oil, its use is not easily reduced. Mineral oils are applied to exclusively control insects and mites in citrus and olive orchards and occasionally in tomato. There are not many data available for the use of mineral oils but from the data presented it was found that in some cases (e.g. in citrus) they are considered as the main contentious input. The wide spectrum of this substance makes it more versatile than other alternatives. In other cases, mineral oils are of minor use, and can easily be replaced by organic oils

Specific detection and quantification of virulent/avirulent Phytophthora infestans isolates using a real-time PCR assay that targets polymorphisms of the Avr3a gene.

Equipe 6International audienceMolecular tools that allow intraspecific quantification and discrimination of pathogen isolates are useful to assess fitness of competitors during mixed infections. However, methods that were developed for quantifying Phytophthora infestans are only specific at the species level. Here, we reported a TaqMan-based real-time PCR assay allowing, according to the specificity of the used probes, an accurate quantification of different proportions of two genetically distinct clones of P. infestans in mixed fractions. Indeed, in addition to a primer specific to P. infestans, two primers and two TaqMan(®) probes that target single-nucleotide polymorphisms located in the Avr3a/avr3a virulence gene sequence were designed. The reliability of the method was tested on serially diluted fractions containing plasmid DNA with either the Avr3a or the avr3a sequences at concentrations ranging from 10(2) to 10(8) copies per μl. Based on its specificity, sensitivity and repeatability, the proposed assay allowed a quantification of the targeted DNA sequence in fractions with a Avr3a/avr3a ratio in the range 1/99 to 99/1. The reliability of the test was also checked for counting zoospores. Applications for future research in P. infestans/host quantitative interactions were also discussed

Diversifikationsstrategien für das Management der Kraut-und Knollenfäule der Kartoffel

Fazit: Die bisherigen Ergebnisse deuten auf eine extreme Sortenabhängigkeit in den epidemiologischen Effekten von Diversifikationsstrategien hin. Außerdem spielt die Variabilität des Befallsdruckes selbst innerhalb eines Feldes eine kritische Rolle. Für die Auswertung von Daten muß deshalb die räumliche Verteilung des Befalles viel stärker mit entsprechenden statistischen Modellen in Betracht gezogen werden. Die Ergebnisse aus den Streifenexperimenten sind analog den Ergebnissen aus den Sortenmischungen und deuten darauf hin, daß Kartoffeln extrem empfindlich auf Konkurrenz sowohl verschiedener Sorten als auch Arten reagieren. Um Diversifikationsstrategien sinnvoll einsetzen zu können, sollten als erstes die Reaktionen von Sorten auf andere Sorten und Arten quantifiziert werden, um geeignete Sorten zu identifizieren. Es könnte auch ein Zuchtziel für die ökologische Landwirtschaft werden, die Konkurrenzfähigkeit mehr in den Vordergrund zu stellen. Dies wäre auch in Bezug auf Unkrautunterdrückung unter Umständen von Interesse. Um ein Streifenexperiment sinnvoll auszuwerten, muß der Ertrag und Befall der Außen- und Innenreihen von Parzellen getrennt erfaßt werden. Für die Beurteilung des Gesamtergebnisses kann dann nicht einfach auf Hektarerträge hochgerechnet werden sondern es muß das Gesamtsystem in Betracht gezogen werden. Insgesamt können Diversifikationsstrategien den Krankheitsdruck reduzieren. Dies belegen auch Beobachtungen aus China, wo der Streifenanbau von Kartoffeln und Mais zu bis zu 40% Reduktion im Befall mit P. infestans und damit zu einer Reduktion im Fungizideinsatz geführt hat (Z. Youyong, 2002, pers. Mitteilung)

Current use of copper, mineral oils and sulphur for plant protection in organic horticultural crops across 10 European countries

The use of several plant protection inputs of mineral origin, such as copper, sulphur or mineral oils is seen as contentious by many consumers and stakeholders within the organic sector. Although the use of these inputs is legal in organic systems and also applied in non-organic agriculture, their use by organic growers raises questions for organic practice, which aspires to be free from toxic, non-renewable chemicals. Data on the current use of permitted plant protection inputs is currently scarce, especially in horticulture where chemical inputs deserve special attention since horticultural products are often readily edible. A mapping of the use of copper, sulphur and mineral oils was conducted by collecting expert knowledge across 10 European countries during May–October 2018, i.e. before the limitation of copper use to 4 kg ha−1 year−1 from February 1, 2019. Results show that copper is widely used by Mediterranean organic growers in citrus, olive, tomato and potato production. The annual limit of 6 kg ha−1 year−1 was not always respected. We also found that tomato producers apply high amounts of copper in winter crops in greenhouses. Mineral oils are applied to control scales, mites and whiteflies. Sulphur is also commonly used by organic vegetable growers, especially in greenhouses. We conclude that the high usage found in various different crops (especially Mediterranean crops) confirms the need for researching alternatives

A Trade-Off Between Sporangia Size and Number Exists in the Potato Late Blight Pathogen Phytophthora infestans, and Is Not Altered by Biotic and Abiotic Factors

The negative relationship between offspring size and number is a classic example of trade-off between life-history traits, reported many times in animal and plant species. Here, we wanted to ascertain whether such a trade-off occurred in the oomycete Phytophthora infestans, and whether it was impacted by biotic and abiotic factors. We thus conducted three infection experiments under controlled conditions and measured the number and the size of sporangia (asexual propagules) produced on potato by different P. infestans isolates. In all experiments, we observed a negative relationship between sporangia size and number, demonstrating the existence of a trade-off. Moreover, although the potato host cultivar, temperature and host of origin (tomato or potato) all affected sporangia number, sporangia size or both, none of these biotic and abiotic factors did change the trade-off. Therefore, the trade-off between sporangia size and number could maintain the polyphenism for these traits in P. infestans populations, and favors the coexistence of distinct reproductive strategies within this species. Our results emphasize the relevance to focus on the relationship between offspring size and number in other fungal plant pathogens, as well as to study the impact of offspring size on fitness-linked traits (virulence and disease lesion development) in these organisms

CO-FREE Alternative Test Products for Copper Reduction in Agriculture

The project CO-FREE (2012-2016) aimed to develop strategies to replace/reduce copper use in organic, integrated and conventional farming. CO-FREE alternative test products (CTPs) were tested and integrated together with decision support systems, disease-tolerant varieties, and innovative breeding goals (ideotypes) into improved management strategies. CO-FREE focused on apple/apple scab (Venturia inaequalis), grape/downy mildew (Plasmopara viticola), and tomato and potato/late blight (Phytophthora infestans). Starting point of the project were ten CTPs with direct or indirect modes of action including Trichoderma atroviride SC1 and protein extract SCNB, Lysobacter spp., yeast-based derivatives, Cladosporium cladosporioides H39, the oligosaccharidic complex COS-OGA, Aneurinibacillus migulanus and Xenorhabdus bovienii, sage (Salvia officinalis) extract, liquorice (Glycyrrhiza glabra) extract, PLEX- and seaweed plant extracts. As the project progressed, further promising CTPs were included by the partners. Field trials were performed in different European countries in 2012-2015 following EPPO standards. In the first years, stand-alone applications of CTPs were tested. In the following years these were integrated into complete strategies. Effects on main and further diseases, on yield and on non-target organisms were assessed. Here, field trial results with CTPs are summarized

Genetic and Pathogenicity Diversity of Aphanomyces euteiches Populations From Pea-Growing Regions in France

Aphanomyces euteiches is an oomycete pathogen with a broad host-range on legumes that causes devastating root rot disease in many pea-growing countries and especially in France. Genetic resistance is a promising way to manage the disease since consistent QTL controlling partial resistance have been identified in near isogenic lines of pea. However, there are still no resistant pea varieties cultivated in France. This study aimed to evaluate the phenotypic and genetic diversity of A. euteiches populations from the major pea-growing regions in France. A collection of 205 isolates, from soil samples collected in infested pea fields located in five French regions, was established and genotyped using 20 SSR markers. Thirteen multilocus genotypes were found among the 205 isolates which displayed a low genotypic richness (ranged from 0 to 0.333). Two main clusters of isolates were identified using PCoA and STRUCTURE, including a predominant group comprising 88% of isolates and another group representing 12% of isolates mainly from the Bourgogne region. A subset of 34 isolates, representative of the fields sampled, was phenotyped for aggressiveness on a set of resistant and susceptible varieties of four legume hosts (pea, faba bean, vetch, alfalfa). Significant differences in disease severity were found among isolates and three groups of aggressiveness comprising 16, 17, and 2 isolates, respectively, were identified using HCA analysis. A higher diversity in pathogen aggressiveness was observed among isolates from Bourgogne, which included different legumes in its crop history. Little relationship was observed between genetic clusters and pathogenicity in the subset of 34 isolates, as expected using neutral markers. This study provides useful knowledge on the current state of low to moderate diversity among A. euteiches populations before resistant pea varieties are grown in France. New insights and hypotheses about the major factors shaping the diversity and evolution of A. euteiches are also discussed