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Current Research in Soil Borne Plant Pathogens
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Current Research in Soil Borne Plant Pathogens

A special issue of Journal of Fungi (ISSN 2309-608X).

Deadline for manuscript submissions: 31 July 2025 | Viewed by 6290

Special Issue Editors

Dr. Andrew Chen

E-Mail Website1 Website2
Guest Editor
School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, QLD 4072, Australia
Interests: Fusarium oxysporum; Fusarium wilt in banana; banana—Fusarium interactions; Verticillium dahliae; host plant resistance to Fusarium oxysporum
Prof. Dr. Elizabeth Aitken

E-Mail Website1 Website2
Guest Editor
School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, QLD 4072, Australia
Interests: diseases of tropical crops; the genetics of plant—pathogen interactions; molecular aspects of pathogenicity and disease diagnostics; Fusarium oxysporum; Fusarium wilt in banana; Verticillium dahliae

Special Issue Information

Dear Colleagues,

Soilborne diseases cause major reductions in crop production every year. With a changing climate, pathogens are believed to be adapting and evolving under different geographical conditions conducive for diseases. Crops of all size and shapes, including vegetables, fruits, cereals, ornamentals, and high-value crops are vulnerable to a wide range of soilborne pathogens including but not limited to fungi, oomycetes, nematodes, and viruses. Some of the common soilborne pathogens include Fusarium ssp., Phytophthora spp., Pythium spp., Sclerotinia spp., Verticillium spp., Rhizoctonia spp., and Thielaviopsis spp. In this Special Issue, we welcome original research, short communications, reviews, and reports on all aspects of soilborne pathogens, including advances in pathogen population genetics; pathogen diagnostics to aid early detection of pathogens in the field; forward or reverse genetics in understanding the fungal effectors that are important in plant pathogenesis; epidemiology of the infection process; biological control systems in the effective management of soilborne diseases; soil fertility, health, and studies on pathogen-suppressive soils; integrated systems for disease management; studies at the gene expression and protein level to understand plant–pathogen interactions; host plant resistance mechanisms; large genomic and transcriptomic datasets to understand genome structure and diversity, as well as the pathogenicity of plant soilborne pathogens and the corresponding host defence pathways; proof-of-function knockout mutants; and identification, isolation, and cultivation of these pathogens.

Given the prevalence of these pathogens in agriculture, the difficulties in the long-term control of these pathogens, and their economic significance, we hope that this Special Issue will provide a platform for current research in soilborne plant pathogens to be disseminated and thereby addressing the knowledge gaps to improve our understanding of these pathogens and their management in the field.

Dr. Andrew Chen
Prof. Dr. Elizabeth Aitken
Guest Editors

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

  • soilborne pathogens
  • Fusarium spp.
  • Phytophthora spp.
  • Pythium spp.
  • Sclerotinia spp.
  • Verticillium spp.
  • Rhizoctonia spp.
  • Thielaviopsis spp.
  • pathogen population genetics
  • pathogen diagnostics
  • biological control of soilborne diseases
  • plant-pathogen interactions
  • host resistance to soilborne pathogens
  • characterization of pathogen effectors
  • genomic and transcriptomic characterisation of these pathogens

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Published Papers (5 papers)

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Research

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18 pages, 7007 KiB  
Article
Autophagy-Related Proteins (ATGs) Are Differentially Required for Development and Virulence of Sclerotinia sclerotiorum
by Thilini Weerasinghe, Josh Li, Xuanye Chen, Jiayang Gao, Lei Tian, Yan Xu, Yihan Gong, Weijie Huang, Yuelin Zhang, Liwen Jiang and Xin Li
J. Fungi 2025, 11(5), 391; https://doi.org/10.3390/jof11050391 - 19 May 2025
Viewed by 209
Abstract
Sclerotinia sclerotiorum is a devastating fungal pathogen that can colonize numerous crops. Despite its economic importance, the regulation of its development and pathogenicity remains poorly understood. From a forward genetic screen in S. sclerotiorum, six UV mutants were identified with loss-of-function mutations [...] Read more.
Sclerotinia sclerotiorum is a devastating fungal pathogen that can colonize numerous crops. Despite its economic importance, the regulation of its development and pathogenicity remains poorly understood. From a forward genetic screen in S. sclerotiorum, six UV mutants were identified with loss-of-function mutations in SsATG1, SsATG2, SsATG4, SsATG5, SsATG9, and SsATG26. Functional validation through gene knockouts revealed that each ATG is essential for sclerotia formation, although the morphology of appressoria was not significantly altered in the mutants. Different levels of virulence attenuation were observed among these mutants. Autophagy, monitored using GFP-ATG8, showed dynamic activities during sclerotia development. These findings suggest that macroautophagy and pexophagy contribute to sclerotia maturation and virulence processes. Future work will reveal how autophagy controls target organelle or protein turnover to regulate these processes. Full article
(This article belongs to the Special Issue Current Research in Soil Borne Plant Pathogens)
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12 pages, 4781 KiB  
Article
Response of the Endophytic Microbiome in Cotinus coggygria Roots to Verticillium Wilt Infection
by Yanli Cheng, Juan Zhao, Yayong Liu, Taotao Zhang, Tom Hsiang, Zhihe Yu and Wentao Qin
J. Fungi 2024, 10(11), 792; https://doi.org/10.3390/jof10110792 - 15 Nov 2024
Viewed by 1071
Abstract
Verticillium wilt caused by Verticillium dahliae Kleb. is a lethal soil-borne fungal disease of Cotinus coggygria. The plant endophytic microbiome plays an important role in maintaining plant health and disease resistance, but it is unclear how the endophytic microbiome of C. coggygria [...] Read more.
Verticillium wilt caused by Verticillium dahliae Kleb. is a lethal soil-borne fungal disease of Cotinus coggygria. The plant endophytic microbiome plays an important role in maintaining plant health and disease resistance, but it is unclear how the endophytic microbiome of C. coggygria roots varies in response to Verticillium wilt occurrence. In this study, the endophytic microbial diversity, community composition, dominant species, and co-occurrence network of C. coggygria under Verticillium wilt-affected and healthy conditions were assessed using Illumina sequencing. Compared with healthy plants, the bacterial alpha diversity indices of Verticillium wilt-affected plants decreased significantly, while the fungal alpha diversity indices showed obvious increases. The relative abundance of dominant taxa including Proteobacteria, Actinobacteriota, Ascomycota, and Basidiomycota at the phylum level, as well as Gammaproteobacteria, Thermoleophilia, Dothideomycetes, and Agaricomycetes at the class level, differed significantly between Verticillium wilt-affected and healthy plants. Co-occurrence networks revealed that the fungal network of Verticillium wilt-affected roots was denser with more negative interactions, which may be relevant to functional changes from reciprocity to competition in the microbial community, in response to V. dahliae infection. The results enhanced our understanding on the relationships between the endophytic microbiome and Verticillium wilt, which could provide information for the management of this disease in C. coggygria. Full article
(This article belongs to the Special Issue Current Research in Soil Borne Plant Pathogens)
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15 pages, 6319 KiB  
Article
Biocontrol Agents Inhibit Banana Fusarium Wilt and Alter the Rooted Soil Bacterial Community in the Field
by Chanjuan Du, Di Yang, Shangbo Jiang, Jin Zhang, Yunfeng Ye, Lianfu Pan and Gang Fu
J. Fungi 2024, 10(11), 771; https://doi.org/10.3390/jof10110771 - 6 Nov 2024
Cited by 1 | Viewed by 1659
Abstract
Banana is an important fruit and food crop in tropical and subtropical regions worldwide. Banana production is seriously threatened by Fusarium wilt of banana (FWB), a disease caused by Fusarium oxysporum f. sp. cubense, and biological control is an important means of [...] Read more.
Banana is an important fruit and food crop in tropical and subtropical regions worldwide. Banana production is seriously threatened by Fusarium wilt of banana (FWB), a disease caused by Fusarium oxysporum f. sp. cubense, and biological control is an important means of curbing this soil-borne disease. To reveal the effects of biocontrol agents on inhibiting FWB and altering the soil bacterial community under natural ecosystems, we conducted experiments at a banana plantation. The control efficiency of a compound microbial agent (CM), Paenibacillus polymyxa (PP), Trichoderma harzianum (TH), and carbendazim (CA) on this disease were compared in the field. Meanwhile, the alterations in structure and function of the rooted soil bacterial community in different treatments during the vigorous growth and fruit development stages of banana were analyzed by microbiomics method. The results confirmed that the different biocontrol agents could effectively control FWB. In particular, CM significantly reduced the incidence of the disease and showed a field control efficiency of 60.53%. In terms of bacterial community, there were no significant differences in the richness and diversity of banana rooted soil bacteria among the different treatments at either growth stage, but their relative abundances differed substantially. CM treatment significantly increased the ratios of Bacillus, Bryobacter, Pseudomonas, Jatrophihabitans, Hathewaya, and Chujaibacter in the vigorous growth stage and Jatrophihabitans, Occallatibacter, Cupriavidus, and 1921-3 in the fruit development stage. Furthermore, bacterial community function in the banana rooted soil was affected differently by the various biocontrol agents. CM application increased the relative abundance of multiple soil bacterial functions, including carbohydrate metabolism, xenobiotic biodegradation and metabolism, terpenoid and polyketide metabolism, lipid metabolism, and metabolism of other amino acids. In summary, our results suggest that the tested biocontrol agents can effectively inhibit the occurrence of banana Fusarium wilt and alter the soil bacterial community in the field. They mainly modified the relative abundance of bacterial taxa and the metabolic functions rather than the richness and diversity. These findings provide a scientific basis for the use of biocontrol agents to control banana Fusarium wilt under field conditions, which serves as a reference for the study of the soil microbiological mechanisms of other biocontrol agents. Full article
(This article belongs to the Special Issue Current Research in Soil Borne Plant Pathogens)
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21 pages, 15596 KiB  
Article
Assessing the Pathogenicity of Berkeleyomyces rouxiae and Fusarium oxysporum f. sp. vasinfectum on Cotton (Gossypium hirsutum) Using a Rapid and Robust Seedling Screening Method
by Andrew Chen, Duy P. Le, Linda J. Smith, Dinesh Kafle, Elizabeth A. B. Aitken and Donald M. Gardiner
J. Fungi 2024, 10(10), 715; https://doi.org/10.3390/jof10100715 - 15 Oct 2024
Cited by 2 | Viewed by 1412
Abstract
Cotton (Gossypium spp.) is the most important fibre crop worldwide. Black root rot and Fusarium wilt are two major diseases of cotton caused by soil-borne Berkeleyomyces rouxiae and Fusarium oxysporum f. sp. vasinfectum (Fov), respectively. Phenotyping plant symptoms caused by [...] Read more.
Cotton (Gossypium spp.) is the most important fibre crop worldwide. Black root rot and Fusarium wilt are two major diseases of cotton caused by soil-borne Berkeleyomyces rouxiae and Fusarium oxysporum f. sp. vasinfectum (Fov), respectively. Phenotyping plant symptoms caused by soil-borne pathogens has always been a challenge. To increase the uniformity of infection, we adapted a seedling screening method that directly uses liquid cultures to inoculate the plant roots and the soil. Four isolates, each of B. rouxiae and Fov, were collected from cotton fields in Australia and were characterised for virulence on cotton under controlled plant growth conditions. While the identities of all four B. rouxiae isolates were confirmed by multilocus sequencing, only two of them were found to be pathogenic on cotton, suggesting variability in the ability of isolates of this species to cause disease. The four Fov isolates were phylogenetically clustered together with the other Australian Fov isolates and displayed both external and internal symptoms characteristic of Fusarium wilt on cotton plants. Furthermore, the isolates appeared to induce varied levels of plant disease severity indicating differences in their virulence on cotton. To contrast the virulence of the Fov isolates, four putatively non-pathogenic Fusarium oxysporum (Fo) isolates collected from cotton seedlings exhibiting atypical wilt symptoms were assessed for their ability to colonise cotton host. Despite the absence of Secreted in Xylem genes (SIX6, SIX11, SIX13 and SIX14) characteristic of Fov, all four Fo isolates retained the ability to colonise cotton and induce wilt symptoms. This suggests that slightly virulent strains of Fo may contribute to the overall occurrence of Fusarium wilt in cotton fields. Findings from this study will allow better distinction to be made between plant pathogens and endophytes and allow fungal effectors underpinning pathogenicity to be explored. Full article
(This article belongs to the Special Issue Current Research in Soil Borne Plant Pathogens)
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12 pages, 1248 KiB  
Brief Report
Poly ADP-Ribosylation in a Plant Pathogenic Oomycete Phytophthora infestans: A Key Controller of Growth and Host Plant Colonisation
by Viktoriya O. Samarskaya, Sofya Koblova, Tatiana Suprunova, Eugene A. Rogozhin, Nadezhda Spechenkova, Sofiya Yakunina, Andrew J. Love, Natalia O. Kalinina and Michael Taliansky
J. Fungi 2025, 11(1), 29; https://doi.org/10.3390/jof11010029 - 3 Jan 2025
Viewed by 947
Abstract
ADP-ribosylation is a reversible modification of proteins and nucleic acids, which controls major cellular processes, including DNA damage repair, cell proliferation and differentiation, metabolism, stress, and immunity in plants and animals. The involvement of ADP-ribosylation in the life cycle of Dictyostelium and some [...] Read more.
ADP-ribosylation is a reversible modification of proteins and nucleic acids, which controls major cellular processes, including DNA damage repair, cell proliferation and differentiation, metabolism, stress, and immunity in plants and animals. The involvement of ADP-ribosylation in the life cycle of Dictyostelium and some filamentous fungi has also been demonstrated. However, the role of this process in pathogenic oomycetes has never been addressed. Here, we show that the Phytophthora infestans genome contains two PARP-like protein genes (PiPARP1 and PiPARP2), and provide evidence of PARylation activity for one of them (PiPARP2). Using dsRNA-mediated RNA silencing of the PiPARP2 gene and chemical (pharmacological) inhibition of PARP activity by 3-aminobenzamide (3AB) PARP inhibitor, we demonstrate the critical functional role of ADP-ribosylation in Phytophthora mycelium growth. Virulence test on detached leaves also suggests an important role of ADP-ribosylation in Phytophthora host plant colonisation and pathogenesis. On a practical level, our data suggest that targeting the PARylation system may constitute a novel powerful approach for the management of Phytophthora diseases. Full article
(This article belongs to the Special Issue Current Research in Soil Borne Plant Pathogens)
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