Endophytic fungi constitute a rich source of secondary metabolites that can be manipulated to produce desirable novel analogs for combating current agricultural challenges for crop production, especially controlling plant disease. The endophytic fungus Daldinia eschscholtzii MFLUCC 19-0629, was newly isolated from tropical ancient plants, Oncosperma sp., and displays a broad-spectrum of antifungal and antibacterial activities against several plant pathogens including Ralstonia solanacearum, Fusarium oxysporum, Colletotrichum gloeosporioides, Colletotrichum acutatum, Stagonosporopsis cucurbitacearum, Corynespora cassiicola and Stemphylium spp. A high-quality genome sequence was obtained using Oxford nanopore technology, the accuracy and length of reads resulting in no need for Illumina or other sequencing techniques, for D. eschscholtzii MFLUCC 19-0629, resulting in a genome size of 37.56 Mb assembled over 11 contigs of significant size, likely to be at the chromosomal level. Bioinformatics analysis revealed that this strain is biosynthetically talented encoding 67 predicted biosynthetic gene clusters (BGCs). Only eight of the 67 BGCs matched or demonstrated high similarity to previously characterized BGCs linked to the production of known secondary metabolites. The high number of predicted unknown BGCs makes this strain a promising source of novel natural products. The discovery that D. eschscholtzii MFLUCC 19-0629 has a broad spectrum of antimicrobial activity against seven major plant pathogenic microorganisms relevant to crop production and its complete genome sequence carries immense importance in the advancement of novel microbial biocontrol agents (MBCAs). This also unveils the prospect of uncovering new compounds that could be utilized for sustainable agriculture and pharmaceutical purposes.

Bacterial fruit blotch (BFB) is a bacterial disease that devastates Cucurbitaceae crops worldwide, causing significant economic losses. Currently, there is no means to treat or control the disease. This study focused on exploring the antibacterial properties of endophytic fungi against Acidovorax citrulli (Aac), the causative agent of BFB. Based on disc diffusion, time kill and MIC microdilution broth assays, four endophytes showed promise in controlling Aac. Nonetheless, only one strain, Neocosmospora sp. MFLUCC 17-0253, reduced the severity of disease on watermelon and melon seedlings up to 80%. Structure analysis revealed production of several compounds by the fungus. Three of these secondary metabolites, including mixture of 2-methoxy-6-methyl-7-acetonyl-8-hydroxy-1,4-maphthalenedione and 5,8-dihydroxy-7-acetonyl-1,4-naphthalenedione, anhydrojavanicin, and fusarnaphthoquinones B exhibited antagonistic activity against Aac. The chemical profile data in planta experiment analyzed by LC-Q/TOF-MS suggested successful colonization of endophytic fungi in their host plant and different metabolic profiles between treated and untreated seedling. Biofilm assay also demonstrated that secondary metabolites of Neocosmospora sp. MFLUCC 17-0253 significantly inhibited biofilm development of Aac. To the best of our knowledge, secondary metabolites that provide significant growth inhibition of Aac are reported for the first time. Thus, Neocosmospora sp. MFLUCC 17-0253 possesses high potential as a biocontrol agent for BFB disease.

Sordariomycetes, Dothideomycetes, and Eurotioycetes are three classes of endophytes that colocalize with tea (Camellia sinensis). Overall, the diversity indexes in this study indicated a greater abundance of fungal endophytes in roots and stems. Taking the production system into account, conventional tea plantations exhibit lower diversity compared to organic tea plantations. Notably, the influence of agrochemicals had the largest impact on the fungal endophyte communities within roots and young leaves. Despite the limited fungal diversity in conventional plantations, three fungal endophytes were isolated from tea in this culture system: Diaporthe sp., YI-005; Diaporthe sp., SI-007; and Eurotium sp., RI-008. These isolated endophytes exhibited high antagonistic activity (93.00–97.00% inhibition of hypha growth) against Stagonosporopsis cucurbitacearum, the causal agent of gummy stem blight disease. On the other hand, endophytic fungi isolated from tea in an organic system—Pleosporales sp., SO-006 and Pleosporales sp., RO-013—established the ability to produce indole-3-acetic acid (IAA; 0.65 ± 0.06 µg/mL) and assist the solubilizing phosphorus (5.17 ± 1.03 µg/mL) from the soil, respectively. This suggested that the level of diversity, whether at the tissue level or within the farming system, did not directly correlate with the discovery of beneficial fungi. More importantly, these beneficial fungi showed the potential to develop into biological agents to control the devastating diseases in the cucurbit family and the potential for use as biofertilizers with a wide range of applications in plants. Therefore, it can be concluded that there are no restrictions limiting the use of fungal endophytes solely to the plant host from which they were originally isolated.