Coffee is grown in more than 80 countries as a cash crop and consumed worldwide as a beverage and food additive. It is susceptible to fungal infection during growth, processing and storage. Fungal infections, in particular, can seriously affect the quality of coffee and threaten human health. The data for this comprehensive review were collected from the United States Department of Agriculture, Agricultural Research Service (USDA ARS) website and published papers. This review lists the fungal species reported on coffee based on taxonomy, life mode, host, affected plant part and region. Five major fungal diseases and mycotoxin-producing species (post-harvest diseases of coffee) are also discussed. Furthermore, we address why coffee yield and quality are affected by fungi and propose methods to control fungal infections to increase coffee yield and improve quality. Endophytic fungi and their potential as biological control agents of coffee disease are also discussed.

In Yunnan Province, the coffee-growing regions are mainly distributed in Pu’er and Xishuangbanna. During the surveys of microfungi associated with coffee in Yunnan Province, seven taxa were isolated from coffee samples. Based on molecular phylogenetic analyses of combined ITS, LSU, SSU, rpb2, and tef1-α sequence data and morphological characteristics, four new species viz. Deniquelata yunnanensis, Paraconiothyrium yunnanensis, Pseudocoleophoma puerensis, and Pse. yunnanensis, and three new records viz. Austropleospora keteleeriae, Montagnula thailandica, and Xenocamarosporium acaciae in Pleosporales are introduced. In addition, Paracamarosporium fungicola was transferred back to Paraconiothyrium based on taxonomy and DNA sequences. Full descriptions, illustrations, and phylogenetic trees to show the placement of new and known taxa are provided. In addition, the morphological comparisons of new taxa with closely related taxa are given.

Coffee endophytes have been studied for almost 74 years, and several studies have demonstrated coffee-endophytic fungi with antibacterial and antifungal potential for human and plant pathogens. In this study, we isolated and identified a total of 235 strains of endophytic fungi from coffee leaf tissues collected in four coffee plantations in Pu’er city, Yunnan province, China. Molecular identification was carried out using maximum likelihood phylogenetic analysis of nuclear ribosomal internal transcribed spacer (ITS1-5.8S rDNA-ITS2) sequences, while the colonization rate and the isolation frequency were also calculated. Two pathogenic fungi (Alternaria alternata and Penicillium digitatum) and two pathogenic bacteria (Pseudomonas syringae and Salmonella enterica subsp. enterica) were used for screening the antagonistic activities of 61 strains of coffee-endophytic fungi by a dual-culture test assay while maximum likelihood phylogenetic analysis confirmed their natural classification. This is the first study of coffee-leaf-endophytic fungal diversity in China, and the results revealed that coffee-endophytic fungi from this study belong to the Ascomycota, distributed among two classes, 10 orders, and 17 families. Concurrently, endophytic fungi isolates distributed in Arthrinium, Biscogniauxia, Daldinia, Diaporthe, and Nigrospora showed strong antagonistic activities against the pathogens. For the pathogens Alternaria alternata and Pseudomonas syringae, Nigrospora XCE-7 showed the best inhibitory effects with inhibition rates of 71.76% and 61.11%, respectively. For the pathogen Penicillium digitatum, Daldinia ME-9 showed the best inhibitory effect with a 74.67% inhibition rate, while Biscogniauxia PTE-7 and Daldinia T5E-1-3 showed the best inhibitory effect with a rate of 60.42% against the pathogen Salmonella enterica subsp. enterica. Overall, our study shows the diversity of coffee endophytes in four coffee-growing areas in Pu’er city, Yunnan province, China, and their potential use as biological control agents against two fungal and two bacterial pathogens.

There has been renewed interest in the application of endophytic fungi to control phytopathogenic fungi, which cause significant damage to crop health, ultimately leading to losses in agricultural productivity. Endophytic fungi inhibit pathogens via different modes of action—mycoparasitism, competition (for nutrients and ecological niches), antibiosis, and induction of plant defense—thus demonstrating the ability to control a wide range of phytopathogenic fungi in different growth phases and habitats. However, many studies have been conducted under laboratory conditions, and there is a huge lack of studies in which real field testing was performed. Aspergillus, Clonostachys, Coniothyrium, Trichoderma, and Verticillium have been proven to be the most effective fungal biocontrol agents. Trichoderma is regarded as the most promising group in commercial formulations. In this study, we attempted to emphasize the significance of fungal endophytes in controlling phytopathogenic fungi, while reporting recent advances in endophytic biology and application.

Endophytic microbes are a ubiquitous group of plant-associated communities that colonize the intercellular or intracellular host tissues while providing numerous beneficial effects to the plants. All the plant species are thought to be associated with endophytes, majorly constituted with bacteria and fungi. During the last two decades, there has been a considerable movement toward the study of endophytes associated with coffee plants. In this review, the main consideration is given to address the coffee-associated endophytic bacteria and fungi, particularly their action on plant growth promotion and the biocontrol of pests. In addition, we sought to identify and analyze the gaps in the available research. Additionally, the potential of endophytes to improve the quality of coffee seeds is briefly discussed. Even though there are limited studies on the subject, the potentiality of coffee endophytes in plant growth promotion through enhancing nitrogen fixation, availability of minerals, nutrient absorption, secretion of phytohormones, and other bioactive metabolites has been well recognized. Further, the antagonistic effect against various coffee pathogenic bacteria, fungi, nematodes, and also insect pests leads to the protection of the crop. Furthermore, it is recognized that endophytes enhance the sensory characteristics of coffee as a new field of study.

In this study, twelve terrestrial hysteriaceous saprobic fungi growing on different pieces of dead wood were collected from Yunnan Province, China. All hysteriaceous strains isolated in this study tallied with the general characteristics associated with Rhytidhysteron. Detailed morphological characteristics and combined multigene phylogeny of LSU, ITS, SSU, and TEF showed that the twelve hysteriaceous fungi strains represent four distinct new species, and seven new host or geographical records of Rhytidhysteron. Based on morphological and phylogenetic evidence, the four new species (Rhytidhysteron bannaense sp. nov., R. coffeae sp. nov., R. mengziense sp. nov., and R. yunnanense sp. nov.) expand the number of species of Rhytidhysteron from thirty-three to thirty-seven, while seven new geographical records expand the records of Rhytidhysteron in China from six to thirteen. In addition, 10 new Rhytidhysteron host records are reported for the first time, thus expanding the known hosts for Rhytidhysteron from 52 to 62. Full descriptions, images of the morphology, and phylogenetic analyses to show the position of the Rhytidhysteron taxa are provided. In addition, the present study summarizes the main morphological characteristics, host associations, and locations of this genus.