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European ash, Fraxinus excelsior is facing the double threat of ongoing devastation by the invasive fungal pathogen, Hymenoscyphus fraxineus and the imminent arrival of the non-native emerald ash borer (EAB), Agrilus planipennis. The spread of EAB which is currently moving westwards from European Russia and Ukraine into central Europe, poses an additional substantial threat to European ash, F. excelsior. While the molecular basis for resistance or variation in resistance among European ash genotypes is heavily investigated, comparatively little is known about the molecular ash traits involved in resistance against EAB. In this study we have gathered transcriptomic data from EAB inoculated genotypes of F. excelsior that have previously shown different levels of susceptibility to EAB. Resultant datasets show differential gene expression in susceptible and resistant genotypes in response to EAB infestation. This data will provide important information on the molecular basis of resistance to the EAB and allow the development of management plans to combat a pending threat of a culturally and ecologically important European tree species.

The infection biology of Bipolaris oryzae and the defence responses of its host rice were studied using the rice cv. MTL 189 inoculated with two isolates of B5 (highly compatible with MTL 189) and K2 (less compatible). In the former interaction, the hyphal progress was accompanied by tissue degradation and extensive sporulation after 8 days, whereas in the latter interaction, only very limited tissue degradation and sporulation was observed. Quantitative microscopy of the infection showed that the percentages of conidia and appressoria causing penetration and fluorescent epidermal cells (FEC) were lower for isolate K2 than for isolate B5 at 12 and 24 hours after inoculation (hai). Fluorescent papillae (FP) were only seen in the less compatible interaction and the percentage of conidia causing single FEC was highest in the less compatible interaction at 12 hai, but not at 24 hai. Qualitative examination of other defence responses showed that H2O2 started to accumulate at 4 hai in the less compatible interaction, whereas it appeared in the compatible interaction only at 12 hai. The level of H2O2 was generally higher in the less compatible than in the compatible interaction. Cross sections of leaves showed that H2O2 accumulated in the outer walls of epidermal cells. Likewise, accumulation of callose and polyphenolic substances was most pronounced in the less compatible interaction and occurred at the same places as H2O2. To our knowledge, this is the first report implicating H2O2 as an early defence response against the hemibiotrophic pathogen B. oryzae during early infection stages in rice. Understanding defence reactions may aid in resistance breeding.

Damage to a host plant caused by insect herbivory and pathogens induces defence responses in the plant. Defence responses induced by hemipterans are often distinct from those elicited by chewing herbivores. Furthermore, hemipterans and pathogens induce a similar set of specific responses, which cannot only affect different species of insect herbivores, but also reduce the severity and symptoms of pathogen attack. Moreover, hemipteran predators can also induce plant resistance against insect herbivory, e.g. by probing/feeding attempts or via ovipositing into plant tissue. The aim of this review was to review only studies that involved direct induced resistance, induced by insects, such as hemipterans and predators, on subsequent attack by insect pests and pathogens. The criterion applied was that a reduced activity of the aggressors was measured, accompanied by direct defence responses. Studies on herbivore-induced plant volatiles (HIPVs) were excluded as our focus is on induced resistance that would also have effect on pathogens that cannot themselves respond to HIPVs. Out of a total of 375 studies generated by a systematic search, 24 studies fulfilled the criteria. The review shows that the release of hemipteran predators for biological control in greenhouses may also lead to induced resistance against subsequent attackers. Monitoring of hemipterans and plant diseases are used to inform early warning systems for pest management. Accordingly, a thorough understanding of the responses induced by hemipterans can facilitate further progress in crop protection strategies in both greenhouse facilities and in open field productions.

Antibiosis is a key feature widely exploited to develop biofungicides based on the ability of biological control agents (BCAs) to produce fungitoxic compounds. A less recognised attribute of plant-associated beneficial microorganisms is their ability to stimulate the plant immune system, which may provide long-term, systemic self-protection against different types of pathogens. By using conventional antifungal in vitro screening coupled with in planta assays, we found antifungal and non-antifungal Bacillus strains that protected the ornamental plant Kalanchoe against the soil-borne pathogen Fusarium oxysporum in experimental and commercial production settings. Further examination of one antifungal and one non-antifungal strain indicated that high protection efficacy in planta did not correlate with antifungal activity in vitro. Whole-genome sequencing showed that the non-antifungal strain EC9 lacked the biosynthetic gene clusters associated with typical antimi-crobial compounds. Instead, this bacterium triggers the expression of marker genes for the jasmonic and salicylic acid defence pathways, but only after pathogen challenge, indicating that this strain may protect Kalanchoe plants by priming immunity. We suggest that the stimulation of the plant immune system is a promising mode of action of BCAs for the development of novel biological crop protection products.

BACKGROUND: Silicon (Si) application to miniature potted roses can decrease severity of powdery mildew (Podosphaera pannosa) and this is associated with increased accumulation of callose and hydrogen peroxide (H2O2) as well as hypersensitive (HR) cells. We used microscopy, gene expression and specific inhibitors of callose and H2O2 to determine how effective these plant responses are in stopping infection. RESULTS: Pathogen arrest in Si-treated (Si+) plants was accompanied by increased accumulation of callose and H2O2 in papillae and HR cells, respectively. These responses were reduced by application of specific inhibitors (2-deoxy-d-glucose for callose and catalase for H2O2), which increased disease severity in Si+, but not in Si− plants. As markers for HR and callose, expression of the HR-specific gene hsr203J and the wound-related callose synthase GSL5, respectively, was studied. An up-regulation of expression was only seen after isolation of HR cells with laser capture microdissection. The up-regulation was higher in Si+ than in Si− plants and occurred concomitantly with more efficient photosynthesis in Si+ plants at high disease severity as compared to Si− plants. CONCLUSION: Silicon-mediated activation of callose and H2O2 are decisive factors in the defence of rose against P. pannosa and these responses were accompanied with more efficient photosynthesis to strengthen the plant. Only by isolation of HR cells using laser capture microdissection as compared to analysis of whole leaf tissues allowed detection of elevated transcript levels of hsr203J and GSL5 at infection sites as markers for HR.

Fungi living inside plants affect many aspects of plant health, but little is known about how plant genotype influences the fungal endophytic microbiome. However, a deeper understanding of interactions between plant genotype and biotic and abiotic environment in shaping the plant microbiome is of significance for modern agriculture, with implications for disease management, breeding and the development of biocontrol agents. For this purpose, we analysed the fungal wheat microbiome from seed to plant to seeds and studied how different potential sources of inoculum contributed to shaping of the microbiome. We conducted a large-scale pot experiment with related wheat cultivars over one growth-season in two environments (indoors and outdoors) to disentangle the effects of host genotype, abiotic environment (temperature, humidity, precipitation) and fungi present in the seed stock, air and soil on the succession of the endophytic fungal communities in roots, flag leaves and seeds at harvest. The communities were studied with ITS1 metabarcoding and environmental climate factors were monitored during the experimental period. Host genotype, tissue type and abiotic factors influenced fungal communities significantly. The effect of host genotype was mostly limited to leaves and roots, and was location-independent. While there was a clear effect of plant genotype, the relatedness between cultivars was not reflected in the microbiome. For the phyllosphere microbiome, location-dependent weather conditions factors largely explained differences in abundance, diversity, and presence of genera containing pathogens, whereas the root communities were less affected by abiotic factors. Our findings suggest that airborne fungi are the primary inoculum source for fungal communities in aerial plant parts whereas vertical transmission is likely to be insignificant. In summary, our study demonstrates that host genotype, environment and presence of fungi in the environment shape the endoph

The organisms described in this chapter are eukaryotic and they belong to two different kingdoms, Chromista and Protozoa. They are often incorrectly referred to as 'fungi' because they have some morphological traits in common with true fungi. Most of them are microscopic, but some can make structures visible to the naked eye. The major group of plant pathogens described in this chapter is the oomycetes, which belong to kingdom Chromista. An overview of the characteristics and classification of the kingdoms are presented, and species causing important plant diseases are described.

Greenhouse cultivation of ornamentals is subjected to a high incidence of soil-borne fungal pathogens. In Kalanchoe, these pathogens are responsible for root and stem rot, and for infection of the vascular tissue. Well-known soil-borne pathogens are believed to cause these diseases. Yet, a systematized survey of these pathogens is lacking for Kalanchoe produced commercially. Here, we studied the occurrence of soil-borne fungal pathogens associated with cultivation of Kalanchoe in Denmark and production of cuttings and stock plants in greenhouse facilities located in Turkey and Vietnam. Molecular identification of pathogens complemented mycological identification and pathogenicity testing of the soil-borne fungal pathogens. This study revealed that the fungi Corynespora cassiicola, Thielaviopsis basicola, Fusarium solani, and F. oxysporum are the most prevalent pathogens associated with root and stem rotting and wilt of Kalanchoe under the conditions studied. Furthermore, the study showed that some of the pathogens are part of an infection complex comprising both primary and opportunistic fungal species. The fact that some of the pathogens were present in some regions, while absent in others, suggests how they move between greenhouse facilities on infected plant material. This study generated important information about the soil-borne fungal complex affecting Kalanchoe, which is useful for a better understanding of the biology of the disease and for designing control strategies.

Coffee leaf rust (CLR), caused by the fungal pathogen Hemileia vastatrix, has plagued coffee production worldwide for over 150 years. Hemileia vastatrix produces urediniospores, teliospores, and the sexual basidiospores. Infection of coffee by basidiospores of H. vastatrix has never been reported and thus far, no alternate host, capable of supporting an aecial stage in the disease cycle, has been found. Due to this, some argue that an alternate host of H. vastatrix does not exist. Yet, to date, the plant pathology community has been puzzled by the ability of H. vastatrix to overcome resistance in coffee cultivars despite the apparent lack of sexual reproduction and an aecidial stage. The purpose of this study was to introduce a new method to search for the alternate host(s) of H. vastatrix. To do this, we present the novel hypothetical alternate host ranking (HAHR) method and an automated text mining (ATM) procedure, utilizing comprehensive biogeographical botanical data from the designated sites of interests (Ethiopia, Kenya and Sri Lanka) and plant pathology insights. With the HAHR/ATM methods, we produced prioritized lists of potential alternate hosts plant of coffee leaf rust. This is a first attempt to seek out an alternate plant host of a pathogenic fungus in this manner. The HAHR method showed the highest‐ranking probable alternate host as Psychotria mahonii, Rubus apetalus, and Rhamnus prinoides. The cross‐referenced results by the two methods suggest that plant genera of interest are Croton, Euphorbia, and Rubus. The HAHR and ATM methods may also be applied to other plant–rust interactions that include an unknown alternate host or any other biological system, which rely on data mining of published data.

Endophytes are microbes capable of colonizing the inner part of plants without causing disease. In some cases, they improve host plant resilience to biotic and abiotic stresses and promote plant growth. The plant-endophyte interaction involves complex mechanisms ranging from the recruitment of the microorganisms to the colonization of internal plant tissue, with the need to escape the plant immune system. These processes are regulated by different plant and endophyte signalling molecules. Phytohormones are among these signalling compounds, but little is known about the specific ways by which they influence recruitment and colonization. The current project aims to obtain a deeper knowledge of the role of signalling compounds in plant-endophyte interactions. To understand how phytohormones influence the composition of endophytic communities, a microbiome analysis (isolation and amplicon sequencing) of endophytic fungi was conducted on roots of tomato mutants impaired in synthesis of ethylene and jasmonic acid. The amplicon sequencing analysis showed a significant effect of the phytohormones, but only the relative abundance of a few taxa was affected (e.g. Fusarium and Pseudogymnoascus). In contrast, there was a stronger effect of plant genotype (comparison of the two wild-types) where the abundance of e.g. Thielaviopsis, Apiotrichum, Fusarium, Saitozyma and Pyrenochaeta differed significantly. The community analysis also revealed high abundance of potential pathogens (e.g. Thielaviopsis basicola and Pyrenochaeta lycopersici) and isolated strains of these species were pathogenic when tested in planta. To understand why healthy plants can harbour such a high amount of pathogenic fungi, experiments with synthetic communities holding both endophytic and pathogenic isolates are currently conducted in order to elucidate possible “natural biocontrol effects” by the endophytic fungi present in the microbiome. “This project has received funding from the European Union’

Black Sigatoka is a major disease of East African highland cooking bananas in Uganda. Aqueous extracts of Azadirachta indica, Cinnamomum zeylanicum and Capsicum annuum have shown the potential to reduce Black Sigatoka in banana plantlets. The mechanisms by which plant extracts confer protection against plant pathogens has previously been reported to involve activation of defence and direct antimicrobial activity. In the current study, both antimicrobial activities of selected extracts were studied as well as expression of three defence-related genes using quantitative real-time PCR. Gene expression was compared in susceptible (cv. Musakala, genomic group AAA-EA) and resistant (cv. Kayinja, genomic group ABB) banana cultivars. Additionally, Musakala treated with A indica extract at 1 day before inoculation (DBI) was tested for induction of defence-related genes at 0, 10 and 20 days after inoculation (DAI). Pathogenesis-related genes (PR-1 and PR-3) and non-expressor of PR-genes (NPR1B) were up-regulated in the resistant cultivar. The genes analysed responded at late time points to M. fijiensis inoculation in both extract-treated and control plants in the susceptible cv. Musakala. On the other hand, A. indica and C. annuum completely inhibited mycelial growth of M. fijiensis at 30% (w/v). These findings suggest that the effect of plant extracts on Black Sigatoka is strongly associated with the direct antimicrobial effects.