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Sequence data from the 18S nrDNA (SSU) and 28S nrDNA (LSU) regions of isolates of Phoma section Paraphoma were compared with those of representative isolates of the morphologically similar anamorph genera Pleurophoma and Pyrenochaeta and of the type species of Phoma sections Phoma, Pilosa and Plenodomus. Phoma section Paraphoma was found to be highly polyphyletic within the Pleosporales and only distantly related to Phoma section Phoma. The genus Paraphoma, which is based on Paraphoma radicina, is reintroduced in the Phaeosphaeriaceae with two additional taxa. The new genera Setophoma and Neosetophoma, type species Setophoma terrestris comb. nov. and Neosetophoma samarorum comb. nov., are introduced and represent species that are closely related to Paraphoma but differ based on morphological characters and molecular phylogeny. Phoma coonsii is transferred to genus Chaetosphaeronema that also belongs to the Phaeosphaeriaceae. Pyrenochaetopsis gen. nov. is introduced to accommodate the type species Pyrenochaetopsis leptospora comb. nov., as well as several other species formerly accommodated in Phoma and Pyrenochaeta. Pyrenochaetopsis is closely related to Pyrenochaeta and classified in the Cucurbitariaceae. Pleurophoma cava is transferred to genus Pyrenochaeta. The new genera elucidate the confusing taxonomy of species in genera Phoma, Pyrenochaeta and Pleurophoma and recognize monophyletic genera with distinct teleomorph affinities.

The soil-borne fungi, Setophoma terrestris and Fusarium spp., are often associated with pink root, although the etiology of the disease remains doubtful. While recognized as the primary inoculum, studies show conflicting views on the formation of chlamydospores and microsclerotia in Setophoma. Therefore, this study aims to clarify the etiology of the pink root of garlic and onion and the formation of chlamydospores and microsclerotia in Setophoma. The isolates were obtained from symptomatic tissues of garlic, leeks, brachiaria, onions, chives, and maize collected from seven different states in Brazil. Representative isolates were selected for pathogenicity tests. Sequence comparison of the tubulin gene showed Setophoma (n = 50) and Fusarium clades (n = 25). Garlic and onion plants inoculated with Setophoma showed pink root symptoms, while plants inoculated with different Fusarium isolates remained asymptomatic. Multigene analysis of pathogenic isolates confirms that only Setophoma terrestris causes pink root in garlic and onion. In addition, brachiaria, chives, and leeks are newly identified hosts of this pathogen in Brazil. To our knowledge, the main sources of primary inoculum of the disease are chlamydospores, pycnidia, colonized roots of garlic, onion, and plant debris of susceptible crops. The new information obtained in this study will be fundamental for researchers in the development of genotypes that are resistant to pink root and will help the efficient management of the disease.

Background Peanut root rot is a common disease worldwide, which can cause serious economic losses to the peanut industry. In 2021, symptoms of peanut root rot were observed in five cities of Henan province, China, i.e., Xinxiang, Puyang, Pingdingshan, Zhumadian, and Nanyang. Results A total of 22 isolates of Setophoma sp. were obtained from 120 diseased peanut root samples. Based on the morphological characteristics and multilocus phylogenetic analyses with the sequences of ITS, LSU, TUB2 , TEF-1a , and RPB2 , these fungal isolates were identified as a new species of Setophoma spp., and named as Setophoma henanensis . Through Koch’s postulates, we demonstrated that S. henanensis could cause root rot disease in peanuts. Pathogenicity test revealed that S. henanensis could cause root rot symptoms in four different hosts, including corn, wheat, pepper, and Welsh onion, indicating that this species may have a wide host range. Furthermore, S. henanensis was sensitive to all tested fungicides, including difenoconazole, tetramycin, pyraclostrobin, and carboxin. Conclusions This is the first report of S. henanensis as a new pathogen of peanut root rot in the world. Furthermore, our findings will also provide a basis for further epidemiological research and the development of control strategies.

Plants with certain medicinal values are a good source for isolating function-specific endophytes. Rosa roxburghii Tratt. has been reported to be a botanical source of antimicrobial compounds, which may represent a promising candidate for screening endophytic fungi with antimicrobial potential. In this study, 54 endophytes were isolated and molecularly identified from R. roxburghii . The preliminary screening using the plate confrontation method resulted in 15 different endophytic strains showing at least one strong inhibition or three or more moderate inhibition against the 12 tested strains. Further re-screening experiments based on the disc diffusion method demonstrated that Epicoccum latusicollum HGUP191049 and Setophoma terrestris HGUP190028 had excellent antagonistic activity. The minimum inhibitory concentration (MIC) test for extracellular metabolites finally indicated that HGUP191049 had lower MIC values and a broader antimicrobial spectrum, compared to HGUP190028. Genomic, non-target metabolomic, and comparative genomic studies were performed to understand the biosynthetic capacity of the screened-out endophytic fungus. Genome sequencing and annotation of HGUP191049 revealed a size of 33.24 megabase pairs (Mbp), with 24 biosynthetic gene clusters (BGCs), where the putative antimicrobial compounds, oxyjavanicin, patulin and squalestatin S1 were encoded by three different BGCs, respectively. In addition, the non-targeted metabolic results demonstrated that the strain contained approximately 120 antimicrobial secondary metabolites and was structurally diverse. Finally, comparative genomics revealed differences in pathogenicity, virulence, and carbohydrate-active enzymes in the genome of Epicoccum spp. Moreover, the results of the comparative analyses presumed that Epicoccum is a promising source of antimicrobial terpenes, while oxyjavanicin and squalestatin S1 are antimicrobial compounds shared by the genus. In conclusion, R. roxburghii and the endophytic HGUP191049 isolated from it are promising sources of broad-spectrum antimicrobial agents.

Background Healthy soil is crucial for maintaining the sustainability of soil ecosystem services and ensuring food security. The soil microbiome serves as a key indicator of soil health. However, long-term continuous monoculture significantly adversely affects the diversity and functioning of soil microbial communities, posing a serious threat to sustainable agricultural development. Therefore, making it crucial to understand the microbial mechanisms underlying these challenges. Methods In this study, tobacco was subjected to different planting durations: 1 year (CR), 5 years (CC5), 10 years (CC10), and 15 years (CC15). The rhizosphere microbial community assembly process, composition, keystone taxa, and their relationship to continuous cropping challenges were analyzed. Results The rhizosphere bacterial community structure of tobacco after 5 years of continuous cropping was significantly separated from other treatments, while no significant separation was observed in the fungal community. Further investigation into the assembly processes of microbial communities under different continuous cropping durations revealed that bacterial community assembly processes exhibited differences, whereas no significant differences were observed in fungal community assembly processes. Specifically, the rhizosphere bacterial community in CC5 was predominantly shaped by deterministic assembly processes, explaining its structural distinctiveness from other treatments. Co-occurrence network analysis revealed that the number of nodes and edges in bacterial-fungal interactions decreased by 22.70% and 79.86%, respectively, in CC5 compared with CR. Differential microbial abundance identified a significant decline in key microbes ( Rhodanobacter , Ellin6067 , Frankiales , and Setophoma ) alongside a marked increase in the abundance of genus Verticillium in CC5 relative to CR. RDA indicated these bacterial genera correlated negatively with pathogen accumulation and disease incidence but postively with yield These relationships potentially constituted the primary driver for exacerbated continuous cropping obstacles in CC5. In CC10, bacterial community assembly was primarily dominated by stochastic processes. Although the number of network nodes and edges increased by 21.96% and 204.73%, respectively, compared to CC5, they remained lower than those in CR. By extending the continuous cropping to 15 years, the bacterial community assembly was shaped by stochastic processes. Compared with CC5, the number of network nodes and edges in CC15 increased by 34.39% and 405.44%, respectively, with beneficial microbes ( Rhodanobacter , Ellin6067 , Frankiales , and Setophoma ) showing remarkable abundance recovery and pathogenic fungi like Verticillium declining, ultimately resulting in microbial community characteristics approximating those observed in the CR. Conclusions The bacterial community in CC5 was driven by deterministic assembly processes, resulting in a distinct structure. The complexity and stability of the co-occurrence network significantly decreased, accompanied by a higher abundance of harmful microbes and a lower abundance of beneficial microbes, which exacerbated the continuous cropping obstacles. In contrast, after 15 years of continuous cropping, the bacterial community assembly shifted to stochastic processes and trans-kingdom co-occurrence network complexity and stability strengthened, beneficial microbes increased, and continuous cropping challenges alleviated.

Seed health is an indispensable prerequisite of food security. While the toolkit of plant protection products is currently limited, evidence suggests that the seed microbiome could protect seeds from pathogens. Thus, given their possible disease suppressive potential, we tested 11 different pathosystems to achieve the following proof-of-concept: seed microbiomes can be beneficial for seed health through conferring disease suppression. This study focused on beetroot, onion, spinach, pepper, coriander, red fescue and perennial ryegrass seeds, with each crop being challenged with one or two from a total of six pathogens, namely Pythium ultimum (or a Pythium sp.), Setophoma terrestris, Fusarium oxysporum, Phytophthora capsici, Laetisaria fuciformis and a mix of Puccinia sp. isolates. Each seed lot of each crop was tested with and without treatment with a disinfectant as a proxy for comparing intact seed microbiomes with seed microbiomes after partial elimination by disinfection. We found disease suppression in two pathosystems. Beetroot and spinach seed lots were able to suppress disease caused by P. ultimum when their microbiomes were intact but not after seed disinfection. We speculate that this relates to the microorganisms residing on and in the seed. Yet, seed microbiome disease suppression was not found in all pathosystems, highlighting the variation in seed morphology, plant cultivars, pathogens and seed disinfection treatments. A holistic understanding of the characteristics of seeds that harbour suppressive microbiomes as well as the pathogens that are sensitive to suppression could lead to more targeted and informed seed processing and treatment and, consequently, to the sustainable management of seedling diseases.

The soil-borne pathogen Setophoma terrestris is the causal agent of pink root of onion, one of the most challenging diseases in onion production. Conventional approaches for managing the disease like solarization, soil fumigation and crop rotation have not been proven effective enough. In this work, we evaluated the biocontrol capacity of Bacillus subtilis ALBA01 (BsA01) against S. terrestris, in a highly susceptible onion cultivar, both under greenhouse and field conditions. Disease incidence and severity were evaluated together with growth, photosynthesis among other physiological variables, and yield parameters. When compared with plants infected with the pathogen, those plants co-inoculated with BsA01 showed significantly less damage and levels of biocontrol above 50%. With regard to physiological parameters, plants challenged with S. terrestris and inoculated with BsA01 performed as well as the control non-infected plants revealing a growth promotion effect of BsA01 on onion plants.

Trichoderma is a rhizosphere fungus widely used in agriculture due to the variety of mechanisms of biological control. It can establish a direct relationship with the plant root cells, modifying the morphology and physiological processes, conferring a better defensive capacity against the attack of pathogens in the soil. This research aimed to study the interaction of T. asperellum, T. harzianum, T. virens, Setophoma terrestris and Sclerotium cepivorum on onion roots (Allium cepa), both in vitro and in field trials, to evaluate the histological modifications and the effect on in vitro growth promotion, and to test the effect of Trichoderma in the field, over the incidence of these pathogens and the crops harvest. In vitro plant promotion assay was made using T. asperellum, T. harzianum, and T. virens to test their effect on the development of onion seedlings from disinfected seeds. Roots of these plants were subjected to histological analysis using Transmission Electronic Microscopy (TEM) to examine changes in cell structure. This analysis also included the pathogens S. cepivorum and S. terrestris, the major soilborne pathogens of onion worldwide. To verify the effect of the Trichoderma species used in the study, a field experiments were performed where the fresh and dry weight of onion bulbs and the incidence of pathogens were measured. Histological modifications were observed in the root cells in the different treatments and were related to the effects caused for Trichoderma. It was shown that although T. asperellum did not stimulate in vitro root growth it can have an important effect in the field by reducing the incidence of S. cepivorum and S. terrestris while improving the onion’s harvest. On the contrary, species that have a root promoting effect do not necessarily improved yield. Besides, rather than this study, there are no other histological studies published in the onion- S. terrestris pathosystem.

To investigate the effects of the endophytic fungus Setophoma terrestris (isolated from Panax notoginseng roots) on the growth and rhizosphere microbiota of understory-cultivated P. notoginseng, we prepared liquid and solid fermentates of the fungus and applied them separately via irrigation. Rhizosphere soil of P. notoginseng was subjected to non-targeted metabolomics and microbiome sequencing for detection and analysis. Relative to the control, P. notoginseng treated with liquid and solid fermentates exhibited increases in plant height (3.5% and 0.7%), chlorophyll content (23.4% and 20.4%), and total saponin content (14.6% and 17.0%), respectively. Non-targeted metabolomics identified 3855 metabolites across 23 classes, with amino acids and their derivatives (21.54%) and benzene derivatives (14.21%) as the primary components. The significantly altered metabolic pathways shared by the two treatment groups included ABC transporters, purine metabolism, and the biosynthesis of various other secondary metabolites. Exogenous addition of S. terrestris significantly affected the composition of the rhizosphere soil microbial community of P. notoginseng and increased the relative abundance of genera such as Bradyrhizobium. In conclusion, the endophytic fungus S. terrestris enhances P. notoginseng growth and modulates both rhizosphere soil metabolites and microbial abundance. This study can provide certain data support for research on endophytic fungi of P. notoginseng.

Setophoma terrestris is an important phytopathogenic fungus listed by China as a harmful fungus subject to phytosanitary import control. This pathogen is a threat to a wide range of plants, particularly as the causal agent of onion pink root rot, one of the most severe diseases of onions. In order to provide rapid identification and early warning of S. terrestris and prevent its spread, we have developed a rapid, accurate, and visually intuitive diagnostic assay for this pathogen, by utilizing recombinase polymerase amplification (RPA), coupled with CRISPR/Cas12a cleavage and fluorescence-based detection systems or paper-based lateral flow strips. The developed RPA-CRISPR/Cas12a assay exhibited remarkable specificity for the detection of S. terrestris. Moreover, this protocol can detect the pathogen at a sensitivity level of 0.01 pg/μL, which significantly outperforms the 1 pg/μL sensitivity achieved by the existing qPCR-based detection method. The entire diagnostic procedure, including DNA extraction, the RPA reaction, the Cas12a cleavage, and the result interpretation, can be accomplished in 40 min. Furthermore, the successful application of the assay in infected plant samples highlighted its potential for rapid and accurate pathogen detection in agricultural settings. In summary, this RPA-CRISPR/Cas12a diagnostic method offers a potentially valuable technological solution for quarantine and disease management.