Background: Fungal endophytes occur ubiquitously in plants and are being increasingly studied for their ability to support plant health and protect the host from diseases. Using endophytes in disease control provides potential advantages compared to other bio-control agents since they colonise the plant internally. A thorough understanding of their mechanisms is required in their mutualistic association with plants; both to optimise their efficacy and for registration as plant protection products. Aims: To provide a critical review on the mechanisms employed by endophytic fungi in biological disease control. Furthermore, we draw attention to gaps in our knowledge of the complex interactions between plant, pathogen and endophyte and discuss implications for future research. Methods: Review of literature where endophytic colonisation during the specific interaction has been confirmed. Results: Known disease-reducing mechanisms include direct inhibition of pathogen activity by competition, antibiosis and mycoparasitism and indirect inhibition by induced resistance, where the plant's own defence system is activated to combat the diseases. Relying on in vitro studies of alone can result in misleading conclusions. Conclusions: We need to investigate nature and requirements for establishment of successful plantendophyte interactions, for development of efficient bio-control agents.

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HighlightsWe establish the sdi1 of Z. tritici locus for targeted integration of constructs as single copies.Integration of constructs conveys carboxin resistance.We provide a vector for integration of eGFP-expressing construct into the sdi1 locus.Integration into sdi1 locus is not affecting virulence of Z. tritici.

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HighlightsWe establish Z. tritici polarity markers ZtSec4, ZtMlc1, ZtRab11, ZtExo70 and ZtSpa2.All markers localize correctly, labeling the Spitzenkörper and sites of polar exocytosis.We provide 5 carboxin-resistance conveying vectors for integration of all markers into the sdi1 locus.We provide 5 hygromycin B-resistance conveying vectors for random integration of all markers.

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There are increasing efforts aiming to utilise endophytes as biological control agents (BCAs) to improve crop production. However, reliability remains a major practical constraint for the development of novel BCAs. Many organisms are adapted to their specific habitat; it is optimistic to expect that a new organism added can find a niche or even out-compete those adapted and already present. Our approach for isolating novel BCAs for specific plant diseases is therefore to look in healthy plants in a habitat where disease is a problem, since we predict that it is more likely to find competitive strains among those present and adapted. In vitro inhibitory activities often do not correlate with in planta efficacy, especially since endophytes rely on intimate plant contact. They can, however, be useful to indicate modes of action. We therefore screen for in planta biological activity as early as possible in the process in order to minimise the risk of discarding valuable strains. Finally, some fungi are endophytic in one situation and pathogenic in another (the mutualism-parasitism continuum). This depends on their biology, environmental conditions, the formulation of inoculum, the health, developmental stage and cultivar of the host plant, and the structure of the plant microbiome .

HighlightsWe establish Z. tritici fimbrin (ZtFim1) and small GTPases (ZtRab5, ZtRab7) as endocytic markers.All markers localize correctly, proven by live cell imaging and co-staining and pharmaceutical studies.We provide 3 carboxin-resistance conveying vectors for integration of all markers into the sdi1 locus.We provide 3 hygromycin B-resistance conveying vectors for random integration of all markers.