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Plant-Associated Fungi
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Plant-Associated Fungi

A special issue of Journal of Fungi (ISSN 2309-608X). This special issue belongs to the section "Fungi in Agriculture and Biotechnology".

Deadline for manuscript submissions: closed (31 July 2023) | Viewed by 8669

Special Issue Editor

Prof. Dr. Xiaohui Pang

E-Mail Website
Guest Editor
Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
Interests: fungal detection and diversity in medicinal herbs

Special Issue Information

Dear Colleagues,

Plants are associated with a diverse range of fungi. Plant-associated fungi can be beneficial, neutral, or harmful. Beneficial fungi confer fitness advantages on the host, including nutrient acquisition, growth promotion, pathogen resistance, and stress tolerance. For example, some endophytic fungi colonizing within plant tissues can produce bioactive chemicals that promote host growth and resistance to environmental stress. Rhizosphere fungi colonizing soil can increase nutrient availability and combat pathogens. There are also some harmful species, for instance, toxigenic fungi, which can produce toxic metabolites called mycotoxins. Studies on microbiomes are essential to improving plant productivity and health as well as the quality and safety of medicinal herbs. For this Special Issue, we invite submissions advancing the current knowledge on fungi affecting plants. Research and review papers on fungal occurrence, detection and diversity, plant–microbiome interactions, and the prevention of toxigenic fungi are welcome.

Prof. Dr. Xiaohui Pang
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Journal of Fungi is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • microbiome
  • fungal occurrence
  • fungal detection
  • fungal diversity
  • plant-microbiome interactions
  • prevention of toxigenic fungi

Published Papers (6 papers)

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Research

16 pages, 7428 KiB  
Article
A Relationship Prediction Method for Magnaporthe oryzae–Rice Multi-Omics Data Based on WGCNA and Graph Autoencoder
by Enshuang Zhao, Liyan Dong, Hengyi Zhao, Hao Zhang, Tianyue Zhang, Shuai Yuan, Jiao Jiao, Kang Chen, Jianhua Sheng, Hongbo Yang, Pengyu Wang, Guihua Li and Qingming Qin
J. Fungi 2023, 9(10), 1007; https://doi.org/10.3390/jof9101007 - 12 Oct 2023
Viewed by 1144
Abstract
Magnaporthe oryzae Oryzae (MoO) pathotype is a devastating fungal pathogen of rice; however, its pathogenic mechanism remains poorly understood. The current research is primarily focused on single-omics data, which is insufficient to capture the complex cross-kingdom regulatory interactions between MoO and rice. To address [...] Read more.
Magnaporthe oryzae Oryzae (MoO) pathotype is a devastating fungal pathogen of rice; however, its pathogenic mechanism remains poorly understood. The current research is primarily focused on single-omics data, which is insufficient to capture the complex cross-kingdom regulatory interactions between MoO and rice. To address this limitation, we proposed a novel method called Weighted Gene Autoencoder Multi-Omics Relationship Prediction (WGAEMRP), which combines weighted gene co-expression network analysis (WGCNA) and graph autoencoder to predict the relationship between MoO–rice multi-omics data. We applied WGAEMRP to construct a MoO–rice multi-omics heterogeneous interaction network, which identified 18 MoO small RNAs (sRNAs), 17 rice genes, 26 rice mRNAs, and 28 rice proteins among the key biomolecules. Most of the mined functional modules and enriched pathways were related to gene expression, protein composition, transportation, and metabolic processes, reflecting the infection mechanism of MoO. Compared to previous studies, WGAEMRP significantly improves the efficiency and accuracy of multi-omics data integration and analysis. This approach lays out a solid data foundation for studying the biological process of MoO infecting rice, refining the regulatory network of pathogenic markers, and providing new insights for developing disease-resistant rice varieties. Full article
(This article belongs to the Special Issue Plant-Associated Fungi)
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17 pages, 2123 KiB  
Article
The Fungal, Nutritional, and Metabolomic Diagnostics of the Oil Palm Elaeis guineensis Affected by Bud Rot Disease in Esmeraldas, Ecuador
by Raluca A. Mihai, Erly J. Melo Heras, Pablo A. Landazuri Abarca and Rodica D. Catana
J. Fungi 2023, 9(9), 952; https://doi.org/10.3390/jof9090952 - 21 Sep 2023
Viewed by 1093
Abstract
The oil palm Elaeis guineensis represents one of the most important crops in Ecuador. Considering that bud rot disease is deadly in Ecuador, more attention has been given to identifying possible causes for palm debility from this disease. We studied the involvement of [...] Read more.
The oil palm Elaeis guineensis represents one of the most important crops in Ecuador. Considering that bud rot disease is deadly in Ecuador, more attention has been given to identifying possible causes for palm debility from this disease. We studied the involvement of fungi and nutrients in triggering bud rot disease in E. guineensis. Special emphasis was given to the molecules synthesized by the plant to protect against this devastating disease. Techniques like Diagnosis and Recommendation Integrated System (DRIS) and metagenomic analysis were used to understand the possible implications of biotic and abiotic factors in the development of bud rot disease in oil palm in Ecuador. Liquid chromatography-mass spectrometry (LC-MS) analysis was used to identify the phenolic protection barrier of the palm facing the disease. Our results indicate that fungi from Ascomyceta phylum were found in the tested samples. The species directly involved are different in soil compared with plants. The results indicate a deficiency of chemical elements, such as Ca, Mn, Mg, and Fe, which are responsible for palm debility from bud rot disease. More than 30 compounds with protective roles were identified in the leaves of symptomatic plants from the first stage of the infection. Full article
(This article belongs to the Special Issue Plant-Associated Fungi)
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24 pages, 4596 KiB  
Article
Unveiling Cryptic Species Diversity and Genetic Variation of Lasiodiplodia (Botryosphaeriaceae, Botryosphaeriales) Infecting Fruit Crops in Taiwan
by Ya-Zhu Ko, Wasantha Kumara Liyanage, Huei-Chuan Shih, Min-Nan Tseng, Meng-Shin Shiao and Yu-Chung Chiang
J. Fungi 2023, 9(9), 950; https://doi.org/10.3390/jof9090950 - 20 Sep 2023
Viewed by 933
Abstract
The genus Lasiodiplodia, a member of the family Botryosphaeriaceae, is an important fungal disease genus in agriculture. However, the Lasiodiplodia species survey and genetic diversity in Taiwan remain unclear. This study aimed to investigate the Lasiodiplodia species associated with various fruit species [...] Read more.
The genus Lasiodiplodia, a member of the family Botryosphaeriaceae, is an important fungal disease genus in agriculture. However, the Lasiodiplodia species survey and genetic diversity in Taiwan remain unclear. This study aimed to investigate the Lasiodiplodia species associated with various fruit species to explore the cryptic Lasiodiplodia species diversity, validate species delimitation, and unveil cryptic genetic diversity. Overall, six Lasiodiplodia species were identified, with several new records of infection identified. Additionally, phylogenetic analyses indicated that the relations of all isolates of L. theobromae might be paraphyletic. They were grouped with L. brasiliense based on Automatic Barcode Gap Discovery (ABGD), Automatic Partitioning (ASAP) and structure-based clustering analyses. These analyses did not provide conclusive evidence for L. brasiliensis as a stable species. It may be necessary to gather more information to clarify the species delineation. The multiple new records of Lasiodiplodia species with high genetic diversity and differentiation revealed that the diversity of Lasiodiplodia in Taiwan was underestimated in the past. We found that L. theobromae has the highest number of haplotypes but the lowest number of haplotype and nucleotide diversities, indicating a recent population expansion. This was supported by the significant negative Tajima’s D and Fu and Li’s D* tests. The high genetic diversity, low gene flow, and host-associated differentiation of Lasiodiplodia species indicate that they might harbour powerful evolutionary potential in Taiwan. This study provided critical insights into genetic variation, host-associated differentiation, and demography of Lasiodiplodia species, which would be helpful for disease management of related pathogens. Full article
(This article belongs to the Special Issue Plant-Associated Fungi)
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19 pages, 2987 KiB  
Article
Comparison of Fungal Genera Isolated from Cucumber Plants and Rhizosphere Soil by Using Various Cultural Media
by Chong-Yang Cheng, Ming-Yuan Zhang, Yong-Chun Niu, Meng Zhang, Yue-Hua Geng and Hui Deng
J. Fungi 2023, 9(9), 934; https://doi.org/10.3390/jof9090934 - 15 Sep 2023
Viewed by 1022
Abstract
Plant endophytic fungi and rhizosphere soil fungi are often reported as biocontrol agents against plant pathogens or with plant growth promotion potential. Four treatments were performed in field and greenhouse experiments where cucumber plants were inoculated with Trichoderma harzianum and Fusarium oxysporum in [...] Read more.
Plant endophytic fungi and rhizosphere soil fungi are often reported as biocontrol agents against plant pathogens or with plant growth promotion potential. Four treatments were performed in field and greenhouse experiments where cucumber plants were inoculated with Trichoderma harzianum and Fusarium oxysporum in 2022. The roots, stems and leaves of cucumber plants and their rhizosphere soil were collected twice individually from the field and greenhouse for isolation of cucumber endophytic and rhizosphere soil fungi. All fungal strains were identified through sequence similarity of the ITS1-5.8s-ITS2 rDNA region. The potato dextrose agar (PDA) media yielded the highest number of genera isolated from cucumber plants, rhizosphere soil and both compared to other media. There were no significant differences among the four media for the isolation of all cucumber endophytic fungi. However, in the roots, the number of endophytic fungi isolated by MRBA was significantly higher than that isolated on malt extract agar (MEA), while in the stems, the number of fungi isolated with PDA was significantly higher than that isolated with Martin’s rose bengal agar medium (MRBA). PDA had significantly higher isolation efficiency for the rhizosphere soil fungi than MRBA. The 28 fungal genera had high isolation efficiency, and the endophytic Trichoderma strains were significantly more isolated by MEA than those of MRBA. It is suggested that PDA can be used as a basic medium, and different cultural media can be considered for specific fungal genera. Full article
(This article belongs to the Special Issue Plant-Associated Fungi)
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12 pages, 3757 KiB  
Article
A Novel Effector FlSp1 Inhibits the Colonization of Endophytic Fusarium lateritium and Increases the Resistance to Ralstonia solanacearum in Tobacco
by Jianming Huang, Zhangjiang He, Jiankang Wang, Xingping Zha, Qing Xiao, Guihua Liu, Yongjie Li and Jichuan Kang
J. Fungi 2023, 9(5), 519; https://doi.org/10.3390/jof9050519 - 27 Apr 2023
Cited by 3 | Viewed by 1171
Abstract
Effectors are crucial for the interaction between endophytes and their host plants. However, limited attention has been paid to endophyte effectors, with only a few reports published. This work focuses on an effector of Fusarium lateritium, namely FlSp1 (Fusarium-lateritium-Secreted-Protein), a typical unknown secreted [...] Read more.
Effectors are crucial for the interaction between endophytes and their host plants. However, limited attention has been paid to endophyte effectors, with only a few reports published. This work focuses on an effector of Fusarium lateritium, namely FlSp1 (Fusarium-lateritium-Secreted-Protein), a typical unknown secreted protein. The transcription of FlSp1 was up-regulated after 48 h following fungal inoculation in the host plant, i.e., tobacco. The inactivation of FlSp1 with the inhibition rate decreasing by 18% (p < 0.01) resulted in a remarkable increase in the tolerance of F. lateritium to oxidative stress. The transient expression of FlSp1 stimulated the accumulation of reactive oxygen species (ROS) without causing plant necrosis. In comparison with the wild type of F. lateritium (WT), the FlSp1 mutant of the F. lateritium plant (ΔFlSp1) reduced the ROS accumulation and weakened the plant immune response, which resulted in significantly higher colonization in the host plants. Meanwhile, the resistance of the ΔFlSp1 plant to the pathogenic Ralstonia solanacearum, which causes bacterial wilt, was increased. These results suggest that the novel secreted protein FlSp1 might act as an immune-triggering effector to limit fungal proliferation by stimulating the plant immune system through ROS accumulation and thus balance the interaction between the endophytic fungi and their host plants. Full article
(This article belongs to the Special Issue Plant-Associated Fungi)
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15 pages, 1517 KiB  
Article
Assessing the Importance of Native Mycorrhizal Fungi to Improve Tree Establishment after Wildfires
by Cristian Atala, Sebastián A. Reyes and Marco A. Molina-Montenegro
J. Fungi 2023, 9(4), 421; https://doi.org/10.3390/jof9040421 - 29 Mar 2023
Cited by 1 | Viewed by 2770
Abstract
The Chilean matorral is a heavily threatened Mediterranean-type ecosystem due to human-related activities such as anthropogenic fires. Mycorrhizal fungi may be the key microorganisms to help plants cope with environmental stress and improve the restoration of degraded ecosystems. However, the application of mycorrhizal [...] Read more.
The Chilean matorral is a heavily threatened Mediterranean-type ecosystem due to human-related activities such as anthropogenic fires. Mycorrhizal fungi may be the key microorganisms to help plants cope with environmental stress and improve the restoration of degraded ecosystems. However, the application of mycorrhizal fungi in the restoration of the Chilean matorral is limited because of insufficient local information. Consequently, we assessed the effect of mycorrhizal inoculation on the survival and photosynthesis at set intervals for two years after a fire event in four native woody plant species, namely: Peumus boldus, Quillaja saponaria, Cryptocarya alba, and Kageneckia oblonga, all dominant species of the matorral. Additionally, we assessed the enzymatic activity of three enzymes and macronutrient in the soil in mycorrhizal and non-mycorrhizal plants. The results showed that mycorrhizal inoculation increased survival in all studied species after a fire and increased photosynthesis in all, but not in P. boldus. Additionally, the soil associated with mycorrhizal plants had higher enzymatic activity and macronutrient levels in all species except in Q. saponaria, in which there was no significant mycorrhization effect. The results suggest that mycorrhizal fungi could increase the fitness of plants used in restoration initiatives after severe disturbances such as fires and, consequently, should be considered for restoration programs of native species in threatened Mediterranean ecosystems. Full article
(This article belongs to the Special Issue Plant-Associated Fungi)
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