This study evaluated the red clover (Trifolium pratense) root associated microbiota to clarify the presence of pathogenic and beneficial microorganisms in 89 Swedish field sites. 16S rRNA and ITS amplicon sequencing analysis were performed on DNA extracted from the red clover root samples collected to determine the composition of the prokaryotic and eukaryotic root-associated microbe communities. Alpha and beta diversities were calculated and relative abundance of various microbial taxa and their co-occurrence analyzed. Rhizobium was the most prevalent bacterial genus, followed by Sphingomonas, Mucilaginibacter, Flavobacterium and the unclassified Chloroflexi group KD4-96. The Leptodontidium, Cladosporium, Clonostachys and Tetracladium fungal genera known for endophytic, saprotrophic and mycoparasitic lifestyles were also frequently observed in all samples. Sixty-two potential pathogenic fungi were identified with a bias toward grass pathogens and a higher abundance in samples from conventional farms. We showed that the microbial community was mainly shaped by geographic location and management procedures. Co-occurrence networks revealed that the R. leguminosarum bv. trifolii was negatively associated with all fungal pathogenic taxa recognized in this study.

Red clover (Trifolium pratense) is an important forage legume crop that suffers like most perennial crops from attacks by soil‐borne pathogens. Fusarium root rot is one of the most serious diseases and at the same time problematic to identify resistance because of its hidden life in the soil. Current screening methods are laborious and hampered by limited reproducibility. To remedy this situation, we aimed to establish a simple and reliable hydroponics‐based screening system to facilitate studies of red clover–Fusarium avenaceum interactions. First, the fungal spore concentrations were balanced toward the development of red clover plants grown hydroponically. We found that the optimum concentration was 30,000 spores in 2 L of hydroponic medium to ensure infection during the plant growth period in this system. The procedure was scaled‐up to screen plants from 25 populations to identify red clover individuals with the improved resistance to F. avenaceum. Susceptible plants had approximately two‐fold higher amounts of fungal DNA than resistant plants, demonstrating a correlation between the disease readings of the plants and pathogen DNA. We foresee this screening procedure meeting the needs of both applied breeding work and in‐depth molecular studies of responses between this pathogen and its host plant. This method could be applied for the screening of other plant species for resistance to Fusarium spp. or to other root microbes.

The fungal pathogen Magnaporthe oryzae poses a major threat to the global production of cereals such as rice, wheat, and millets. Similar to other fungal pathogens, it secretes effector proteins to manipulate host immune responses, enabling successful colonization and infection. In this study, M. oryzae strains were collected from diseased finger millet plants and wild grasses in Uganda. A candidate effector gene— Mo2928Fm—was identified from a highly virulent finger millet strain and found to be strongly induced at 2 days postinoculation, suggesting a role in the early infection process. In silico analysis indicated that Mo2928Fm is present only in a subset of M. oryzae genomes and encodes a protein with two domains connected by a serine-rich linker. Confocal microscopy confirmed its nuclear localization in host cells, and gene deletion significantly reduced fungal virulence. Transient expression of Mo2928Fm suppressed the transcription of key plant immune response genes. Further analyses also revealed a potential interaction between Mo2928Fm and the plant mitogen-activated protein kinase 3 (MAPK3) protein. Based on these findings, we propose that the Mo2928Fm–MAPK3 complex interferes with basal plant immune signaling and promotes susceptibility to blast disease. [ ] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Background Red clover (Trifolium pratense) is an important forage legume crop that suffers like most perennial crops from attacks by soilborne pathogens. Fusarium root rot is one of the most serious diseases and at the same time problematic to identify resistance to due to its hidden life in the soil. Current screening methods are laborious and hampered by limited reproducibility. To remedy this situation, we aimed to establish a more undemanding and reliable system to facilitate studies of red clover-Fusarium avenaceum interactions.Results First, the fungal spore concentrations were balanced toward the development of red clover plants grown hydroponically. We found that the optimum concentration was 30,000 spores in 2 L of hydroponic medium to ensure infection during the plant growth period in this system. The procedure was scaled-up to screen twenty-five populations to identify red clover genotypes with the most contrasting responses to F. avenaceum. Susceptible plants had approximately 2-fold higher amounts of fungal DNA than resistant plants, demonstrating a correlation between the disease readings of the plants and pathogen DNA.Conclusions A hydroponics-based screening system was established to facilitate reproducible and rapid screening of Fusarium root rot disease in red clover. We foresee this screening procedure meeting the needs of both applied breeding work and in-depth molecular studies of responses between this pathogen and its host plant. This method could be applied for the screening of other plant species for resistance to Fusarium spp. or to other root microbes.