Endophytic fungi (EF) are increasingly gaining attention due to the numerous benefits many species can offer to the plant host, while reducing the application of chemicals in agriculture, thus providing advantages to human health and the environment. The growing demand for safer agrifood products and the challenge of increasing food production with a lower use of pesticides and fertilizers stimulates investigations on the use and understanding of EF. Other than direct consequences on the plant damaging agents, these microorganisms can also deliver bioactive metabolites with antimicrobial, insecticidal, or plant biostimulant activities. In tomato, EF are artificially introduced as biological control agents or naturally acquired from the surrounding environment. To date, the applications of EF to tomato has been generally limited to a restricted group of beneficial fungi. In this work, considerations are made to the effects and methods of introduction and detection of EF on tomato plants, consolidating in a review the main findings that regard pest and pathogen control, and improvement of plant performance. Moreover, a survey was undertaken of the naturally occurring constitutive endophytes present in this horticultural crop, with the aim to evaluate the potential role in the selection of new beneficial EF useful for tomato crop improvement.

An extensive literature search was performed to review current knowledge about endophytic fungi isolated from plants included in the European Food Safety Authority (EFSA) dossier. The selected genera of plants were Acacia, Albizia, Bauhinia, Berberis, Caesalpinia, Cassia, Cornus, Hamamelis, Jasminus, Ligustrum, Lonicera, Nerium, and Robinia. A total of 120 fungal genera have been found in plant tissues originating from several countries. Bauhinia and Cornus showed the highest diversity of endophytes, whereas Hamamelis, Jasminus, Lonicera, and Robinia exhibited the lowest. The most frequently detected fungi were Aspergillus, Colletotrichum, Fusarium, Penicillium, Phyllosticta, and Alternaria. Plants and plant products represent an inoculum source of several mutualistic or pathogenic fungi, including quarantine pathogens. Thus, the movement of living organisms across continents during international trade represents a serious threat to ecosystems and biosecurity measures should be taken at a global level.