Pathogens 2021, 10, 1288. https://doi.org/10.3390/pathogens10101288 www.mdpi.com/journal/pathogens Review Fungi Inhabiting the Wheat Endosphere Błaszczyk Lidia *, Salamon Sylwia and Mikołajczak Katarzyna Department of Plant Microbiomics, Institute of Plant Genetics, Polish Academy of Sciences, 34 Strzeszyńska Street, 60-479 Poznań, Poland; ssal@igr.poznan.pl (S.S.); kmiko@igr.poznan.pl (M.K.) * Correspondence: lbla@igr.poznan.pl Abstract: Wheat production is influenced by changing environmental conditions, including climatic conditions, which results in the changing composition of microorganisms interacting with this ce- real. The group of these microorganisms includes not only endophytic fungi associated with the wheat endosphere, both pathogenic and symbiotic, but also those with yet unrecognized functions and consequences for wheat. This paper reviews the literature in the context of the general charac- teristics of endophytic fungi inhabiting the internal tissues of wheat. In addition, the importance of epigenetic regulation in wheat–fungus interactions is recognized and the current state of knowledge is demonstrated. The possibilities of using symbiotic endophytic fungi in modern agronomy and wheat cultivation are also proposed. The fact that the current understanding of fungal endophytes in wheat is based on a rather small set of experimental conditions, including wheat genotypes, plant organs, plant tissues, plant development stage, or environmental conditions, is recognized. In addi- tion, most of the research to date has been based on culture-dependent methods that exclude bio- trophic and slow-growing species and favor the detection of fast-growing fungi. Additionally, only a few reports of studies on the entire wheat microbiome using high-throughput sequencing tech- niques exist. Conducting comprehensive research on the mycobiome of the endosphere of wheat, mainly in the context of the possibility of using this knowledge to improve the methods of wheat management, mainly the productivity and health of this cereal, is needed. Keywords: Triticaceae; endophytes; mycobiome; wheat–fungal endophyte interaction; epigenetic regulation; endophytic fungi-based bio-substances 1. Introduction Fungi play an essential role in natural ecosystems and in modern agriculture because of their nutritional versatility, miscellaneous lifestyle, and multifarious interactions with plants. Fungi are important decomposers and recyclers of organic materials [1]. They in- teract with plant roots in the rhizosphere or with aboveground plant components; while living in close association with plants, they are located either outside or within plant tis- sues [1]. Fungi that periodically or constantly colonize the internal parts of plant tissues without disease manifestation in their host are defined as fungal endophytes [2–4]. Fungal endophytes requiring plant tissues to complete their life cycle are classified as “obligate” endophytes. Well-documented examples of obligate endophytes are found among my- corrhizal fungi and members of the fungal genera Balansia, Epichloë, and Neotyphodium from the family Clavicipitaceae (Ascomycota) [5,6]. However, fungal endophytes that mainly thrive outside plant tissues and sporadically enter the plant endosphere are called “opportunistic” endophytes [7,8]. Between these two groups is an intermediate group, which includes the vast majority of endophytic fungi, the so-called “facultative” endo- phytes [9,10]. Fungi that remain endophytic throughout the entire life cycle of the host are catego- rized as clavicipitaceus endophytes (C-endophytes) and represent class I fungal endo- phytes [8,11]. Species of clavicipitaceus endophytes, including Balansia spp., Epichloë spp., Citation: Błaszczyk , L.; Salamon, S.; Mikołajczak, K. Fungi Inhabiting the Wheat Endosphere. Pathogens 2021, 10, 1288. https://doi.org/10.3390/ pathogens10101288 Academic Editors: Paul L. Guy and Nemat O. Keyhani Received: 31 August 2021 Accepted: 4 October 2021 Published: 7 October 2021 Publisher’s Note: MDPI stays neu- tral with regard to jurisdictional claims in published maps and insti- tutional affiliations. Copyright: © 2021 by the author. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses /by/4.0/).