Plant Pathogenic Fungi Research Articles

Sir2-mediated cytoplasmic deacetylation facilitates pathogenic fungi infection in host plants.

Lysine acetylation is an evolutionarily conserved and widespread post-translational modification implicated in the regulation of multiple metabolic processes, but its function remains largely unknown in plant pathogenic fungi. A comprehensive analysis combined with proteomic, molecular and cellular approaches was presented to explore the roles of cytoplasmic acetylation in Fusarium oxsysporum f.sp. lycopersici (Fol). The divergent cytoplasmic deacetylase FolSir2 was biochemically characterized, which is contributing to fungal virulence. Based on this, a total of 1752 acetylated sites in 897 proteins were identified in Fol via LC-MS/MS analysis. Further analyses of the quantitative acetylome revealed that 115 proteins representing two major pathways, translational and ribosome biogenesis, were hyperacetylated in the ∆Folsir2 strain. We experimentally examined the regulatory roles of FolSir2 on K271 deacetylation of FolGsk3, a serine/tyrosine kinase implicated in a variety of cellular functions, which was found to be crucial for the activation of FolGsk3 and thus modulated Fol pathogenicity. Cytoplasmic deacetylation by FolSir2 homologues has a similar function in Botrytis cinerea and likely other fungal pathogens. These findings reveal a conserved mechanism of silent information regulator 2-mediated cytoplasmic deacetylation that is involved in plant-fungal pathogenicity, providing a candidate target for designing broad-spectrum fungicides to control plant diseases.

Invitro analysis of antifungal effects of botanicals on sclerotinia sclerotiorum causing white mold disease

White mold, Sclerotinia sclerotiorum, is a devastating fungal plant pathogen that has affected many crop species worldwide. Using chemicals to control the disease has been practiced over the years, whose prolonged application has negatively impacted the environment, thus finding an organic solution is crucial. The analysis quantifies the effect of 5 different local plants that have been proven to have fungicidal properties; Artemisia vulgaris L., Azadirachta indica L., Zingiber officinale Roscoe, Allium sativum L., and Lantana camara L. Poisoned food technique was used to study the inhibition effect, carried out by inoculating and growing the fungus on PDA media infused with botanical extracts. The data of mycelial mat diameter was recorded till the control plates were fully occupied. The growth-inhibiting capacity was found as 100% by Allium sativum, 28% & 43% by Azadirachta indica, 22.44% & 44% by Zingiber officinale, and 16.33% & 8.55% by Lantana camara at 10% and 20% concentrations respectively. Only a slight difference between the overall inhibition effect of the two concentrations was found with 37.22% inhibition by 20% concentration and 33.38% inhibition by 10% concentration. No inhibition effect was observed from Artemisia vulgaris which could be due to heat neutralization of the active constituent during sterilization. Further research needs to be conducted using the botanical with different sterilization techniques. This in-vitro study identified garlic as a critical antifungal alternative to conventional fungicides. Field experiments need to be done to prove its effectiveness.

Discovery and Development of 4-Hydroxyphenylpyruvate Dioxygenase as a Novel Crop Fungicide Target.

Plant pathogenic fungi pose a significant threat to crop yields and quality, and the emergence of fungicide resistance has further exacerbated the problem in agriculture. Therefore, there is an urgent need for efficient and environmentally friendly fungicides. In this study, we investigated the antifungal activity of (+)-Usnic acid and its inhibitory effect on crop pathogenic fungal 4-hydroxyphenylpyruvate dioxygenases (HPPDs) and determined the structure of Zymoseptoria tritici HPPD (ZtHPPD)-(+)-Usnic acid complex. Thus, the antifungal target of (+)-Usnic acid and its inhibitory basis toward HPPD were uncovered. Additionally, we discovered a potential lead fungicide possessing a novel scaffold that displayed remarkable antifungal activities. Furthermore, our molecular docking analysis revealed the unique binding mode of this compound with ZtHPPD, explaining its high inhibitory effect. We concluded that HPPD represents a promising target for the control of phytopathogenic fungi, and the new compound serves as a novel starting point for the development of fungicides and dual-purpose pesticides.

Bioinspired total synthesis and biological activity of Pegaharine A.

Phytopathogens cause various diseases by parasitizing crops, reducing crop yield and resulting in substantial economic losses in agricultural production. A novel type isolated from the perennial herbaceous Peganum harmala L. seeds, β-carboline alkaloids pegaharine A (PA), has become a hot topic in developing plant-originated green pesticides owing to their significant physiological activities. A scalable bioinspired total synthesis of PA is accomplished in the present work. The systematical biological assay study showed that PA exhibited moderate inhibitory activity against nine tested plant pathogenic fungi and showed significant inhibitory activity in vitro against the three tested plant pathogenic bacteria. Most noteworthy is the inhibitory rates of PA on Xanthomonas oryzae pv. oryzae (Xoo), X. oryzae pv. oryzicola (Xoc) and X. axonopodis pv. citri (Xac) of 93.6%, 92.1% and 86.1%, respectively, which are better than the control drug, bismerthiazol (63.4%, 61.2% and 53.7% at 100 μg mL-1 concentration). Furthermore, the EC50 value of PA against Xoo, Xoc and Xac was 52.2, 60.0 and 65.1 μg mL-1 , respectively, superior to 72.9, 64.2 and 70.1 μg mL-1 of the control drug. Moreover, the anti-Xoo mechanistic studies revealed that PA exerted its antibacterial effects by increasing the permeability of the bacterial membrane, reducing the extracellular polysaccharide content and inducing morphological changes in bacterial cells. A novel β-carboline alkaloid, PA, was prepared by biomimetic total synthesis. Its significant antibacterial activity was closely related to the permeation of bacterial cell membranes, which was confirmed by anti-Xoo mechanistic studies. More importantly, the structure could be regarded as a model for developing novel bactericides. © 2023 Society of Chemical Industry.

Discrimination of plant pathogenic fungi using attenuated total reflectance Fourier transform infrared spectroscopy and chemometrics

Discrimination of plant pathogenic fungi using attenuated total reflectance Fourier transform infrared spectroscopy and chemometrics

An efficient targeted gene deletion approach for Cochliobolus heterostrophus using Agrobacterium tumefaciens-mediated transformation

Cochliobolus heterostrophus is a plant pathogenic fungus of southern corn leaf blight, which has been regarded as a model necrotrophic plant pathogen. Many methods have been developed to knock out targeted genes in C. heterostrophus, of which the most widely-used one is protoplast-mediated transformation. However, there are several problems of this method associated with protoplast preparation, DNA product, time consumption, or high cost. In this study, a highly efficient target gene deletion approach in C. heterostrophus was established and optimized, based on Agrobacterium tumefaciens-mediated transformation (ATMT); the transformation efficiency of this approach was 85–88 transformants per 105 conidia, and the homologous recombination efficiency was approximately 68.3%. Furthermore, six gene knockout mutants of C. heterostrophus were obtained using this ATMT method. The phenotypes of this fungus altered in the mutant strains, and the virulence of the mutants significantly reduced compared to of the wild type strain. Taken together, this ATMT system established in this study can be used as a genetic manipulation tool for C. heterostrophus, to better understand the functions of genes and its relation to virulence.

Impacts of prothioconazole and prothioconazole-desthio on bile acid and glucolipid metabolism: Upregulation of CYP7A1 expression in HepG2 cells

As an efficient triazole fungicide, prothioconazole (PTC) is widely used for the prevention and control of plant fungal pathogens. It was reported that the residues of PTC and prothioconazole-desthio (PTC-d) have been detected in the environment and crops, and the effects of PTC-d may be higher than that of PTC. Currently, PTC and PTC-d have been proven to induce hepatic metabolic disorders. However, their toxic effects on cellular bile acid (BA) and glucolipid metabolism remain unknown. In this study, HepG2 cells were exposed to 1–500 μM of PTC or PTC-d. High concentrations of PTC and PTC-d were found to induce cytotoxicity; thus, subsequent experimental exposure was conducted at concentrations of 10–50 μM. The expression levels of CYP7A1 and TG synthesis-related genes and levels of TG and total BA were observed to increase in HepG2 cells. Molecular docking analysis revealed direct interactions between PTC or PTC-d and CYP7A1 protein. To further investigate the underlying mechanisms, PTC and PTC-d were treated to HepG2 cells in which CYP7A1 expression was knocked down using siCYP7A1. It was observed that PTC and PTC-d affected the BA metabolism process and regulated the glycolipid metabolism process by promoting the expression of CYP7A1. In summary, we comprehensively analyzed the effects and mechanisms of PTC and PTC-d on cellular metabolism in HepG2 cells, providing theoretical data for evaluating the safety and potential risks associated with these substances.

Whole genome sequencing provides evidence for Bacillus velezensis SH-1471 as a beneficial rhizosphere bacterium in plants

Bacillus is widely used in agriculture due to its diverse biological activities. We isolated a Bacillus velezensis SH-1471 from the rhizosphere soil of healthy tobacco, which has broad-spectrum antagonistic activity against a variety of plant pathogenic fungi such as Fusarium oxysporum, and can be colonized in the rhizosphere of a variety of plants. This study will further explore its mechanism by combining biological and molecular biology methods. SH-1471 contains a ring chromosome of 4,181,346 bp with a mean G + C content of 46.18%. We identified 14 homologous genes related to biosynthesis of resistant secondary metabolite, and three clusters encoded potential new antibacterial substances. It also contains a large number of genes from colonizing bacteria and genes related to plant bacterial interactions. It also contains genes related to environmental stress, as well as genes related to drug resistance. We also found that there are many metabolites in the strain that can inhibit the growth of pathogens. In addition, our indoor pot test found that SH-1471 has a good control effect on tomato wilt, and could significantly improve plant height, stem circumference, root length, root weight, and fresh weight and dry weight of the aboveground part of tomato seedlings. Therefore, SH-1471 is a potential biological control strain with important application value. The results of this study will help to further study the mechanism of SH-1471 in biological control of plant diseases and promote its application.

Bacillus subtilis and Bacillus amyloliquefaciens Mix Suppresses Rhizoctonia Disease and Improves Rhizosphere Microbiome, Growth and Yield of Potato (Solanum tuberosum L.).

Black scurf and stem canker caused by Rhizoctonia solani is a significant disease problem of potatoes. Currently, chemical methods are the primary means of controlling this pathogen. This study sought to explore an alternative approach by harnessing the biocontrol potential of a bacterial mix of Bacillus subtilis and Bacillus amyloliquefaciens against black scurf, and to determine their effect on rhizosphere microorganisms of soil microbiota. This study showed that these bacteria demonstrate antagonistic activity against Rhizoctonia solani. Reduced damage to potato plants during the growing season in Siberia was observed. The index of disease development decreased from 40.9% to 12.0%. The treatment of tubers with this mix of bacteria also led to a change in the composition of the rhizosphere microbiota (according to CFU, 16S and ITS sequencing). This effect was accompanied by a positive change in plant physiological parameters (spectrophotometric analysis). The concentration of chlorophyll in potatoes with the bacterial mix treatment increased by 1.3 fold (p ≤ 0.001), and of carotenoids by 1.2 fold (p ≤ 0.01) compared with the control. After bacterial mix treatment, the length of the aerial parts of plants was 1.3 fold higher (p ≤ 0.001), and the number of stems 1.4 fold higher (p ≤ 0.05). The yield of potatoes was increased by 8.2 t/ha, while the large tuber fraction was increased by 16% (p ≤ 0.05). The bacteria mix of Bacillus subtilis and Bacillus amyloliquefaciens suppressed the plant pathogenic fungus Rhizoctonia solani, and simultaneously enhanced the physiological parameters of potato plants. This treatment can be used to enhance the yield/quality of potato tubers under field conditions.

The application of entomopathogenic nematode modified microbial communities within nesting mounds of the red imported fire ants, Solenopsis invicta

Entomopathogenic microorganisms (e.g., fungi, bacteria, nematodes) have been widely used in biological control of soil-dwelling pests, including the red imported fire ant (RIFA), Solenopsis invicta, a notorious invasive pest worldwide. The application of large amounts of entomopathogenic microorganisms to soil may affect the indigenous soil microbial communities. However, reports about the effect of entomopathogenic nematodes (EPN) on soil microbial communities are very few. In this study, the effects of EPN on RIFA populations and microbial communities in mounds were investigated. Our results showed that the application of the EPN Steinernema carpocapsae. All strain on mounds efficaciously suppressed RIFA worker populations, without forming significantly more satellite mounds compared with the control treatment. The application of EPN did not impact the bacterial and fungal diversity in soils derived from the RIFA mounds. However, it slightly altered the taxonomic make-up of the bacterial communities, but significantly altered the taxonomic composition of fungal communities at the phylum, family, and genus levels. The abundances of some beneficial bacteria and fungi, such as Streptomyces, decreased, while those of plant and animal pathogenic bacteria and fungi, dramatically increased, after EPN treatment. On the other hand, the abundances of some entomopathogenic fungi, such as Fusicolla, Clonostachys, and Mortierella, increased. Redundancy analysis or canonical correspondence analysis revealed a positive correlation between the efficacious EPN control and the presence of the insect-resistant bacteria, Sinomonas, as well as entomopathogenic fungi Fusicolla and Mortierella. This suggests that the interactions between EPN and entomopathogenic fungi may play a role in the biological control of RIFA. Our discoveries shed light on the interactions among EPN, RIFA, and soil microbial communities, and emphasize a possible mutualistic relationship between EPN and entomopathogenic fungi in the biological control of RIFA.

Polyacrylamide quaternary ammonium salts based on stable adsorption in soil and its application on the control of soil-borne fungal disease

Currently, soil-borne fungal disease (SBFD) have caused a huge damage in agriculture, and small molecule soil disinfectants have been widely used for the prevention and control of SBFD, which could not only kill the chlamydospore of pathogenic fungi, but also completely destroy the microbial community and its functional diversity in the soil, and is not conducive to subsequent plant planting. Therefore, how to effectively inhibit plant pathogenic fungi while maintaining the general balance of microbial population in the soil to facilitate subsequent plant planting come to be critical problem in the prevention and control of SBFD. In this work, a series of polyacrylamide containing quaternary ammonium salts (PAM-X) were synthesized based on the radical copolymerization of acrylamide (AM) and acrylamide containing different quaternary ammonium salts groups (AMX). Owing to the entanglement between polymer chains and soil, PAM-X could be stably absorbed in the soil, thus effectively delaying the free migration of PAM-X chains in soil, and reducing the probability of being leached from soil, which might be the key to obtain novel polymeric quaternary ammonium salts that have less impact on the environment. Banana Fusarium wilt, also known as “banana cancer”, caused by Fusarium oxysporum f. sp. cubense (Foc), was chosen as a typical soil-borne pathogen disease to verify the rationality of the above thoughts. The results showed PAM-X had well anti-Foc4 activities in soil, and could maintain the general balance of microbial population in the soil, which are almost non-toxic to earthworms in soil and fish, thus provides a new prevention and control method for SBFD.

A potential antifungal agent: Insight into the antifungal mechanism against Phomopsis sp

19 myricetin derivatives containing thiazole were designed and synthesized. Their fungicidal activities in vitro against ten species of plant pathogenic fungi were evaluated. Bioassay results indicated that some of compounds exhibited remarkable antifungal activities. Among them, Z17 showed the strongest antifungal activity against Phomopsis sp, with in vitro EC50 of 12.3 µg/mL, which was superior to those of the control drug azoxystrobin (32.2 µg/mL) and fluopyram (77.7 µg/mL). In addition, Z18 also had the inhibitory activity against the Alternaria brassicae, with an EC50 value of 32.5 µg/mL, which was much higher than azoxystrobin (49.3 µg/mL). Z17 exhibited good protective activity (62.5 %) against Phomopsis sp on kiwifruit in vivo at 200 µg/mL. The results of in vivo experiments revealed that Z18 could effectively defend against the infestation of cabbage by Alternaria brassicae, and improve the protection ability of the crop. Scanning electron microscopy (SEM) and fluorescence microscopy (FM) demonstrated that Z17 could destroy the integrity of cell membrane of pathogen Phomopsis sp, thus affecting the normal growth of mycelia. The results of the mechanism research further confirmed that the action of Z17 changed the mycelial morphology of Phomopsis sp, affected the permeability of cells, increased the leakage of cytoplasm and MDA contents. Molecular docking simulation results revealed that compound Z17 could readily bind with the active site of SDH and could be a potential SDH inhibitor. In summary, this study provides new ideas for effectively controlling plant fungal diseases and developing new green chemical pesticide products.

Leaf, root, and soil microbiomes of an invasive plant, Ardisia crenata, differ between its native and exotic ranges

IntroductionEcological underpinnings of the invasion success of exotic plants may be found in their interactions with microbes, either through the enemy release hypothesis and the enhanced mutualism hypothesis. Whereas recent high-throughput sequencing techniques have significantly expanded our understanding of plant-associated microbiomes and their functional guilds, few studies to date have used these techniques to compare the microbiome associated with invasive plants between their native and exotic ranges.MethodsWe extracted fungal and bacterial DNA within leaf endosphere, root endosphere and soil of an invasive plant, Ardisia crenata, sampled from their native range Japan and exotic range Florida, USA. Using Illumina sequencing data, we compared microbial community compositions and diversity between the native and exotic ranges, and tested whether abundance of pathogenic or mutualistic microbes differ between the native or exotic ranges in accordance to the enemy release hypothesis or the enhanced mutualism hypothesis.ResultsFungal and bacterial community compositions differed among leaves, roots and soil, and between the native and exotic ranges. Despite a higher microbial diversity in the soil in the exotic range than in the native range, the microbial diversity within leaf and root was lower in the exotic range compared to the native range. In addition, leaves in the native range harbored a greater number of plant pathogenic fungi compared to those in the exotic range.DiscussionThese patterns suggest plant controls over what microbes become associated with leaves and roots. The higher abundance of leaf pathogenic fungi, including the pathogen which is known to cause specific disease in A. crenata in the exotic range than in the native range, support the enemy release hypothesis and highlighted potential importance of examining microbial communities both above- and below-ground.

Towards unlocking the biocontrol potential of Pichia kudriavzevii for plant fungal diseases: in vitro and in vivo assessments with candidate secreted protein prediction

BackgroundPlant fungal pathogens cause substantial economic losses through crop yield reduction and post-harvest storage losses. The utilization of biocontrol agents presents a sustainable strategy to manage plant diseases, reducing the reliance on hazardous chemical. Recently, Pichia kudriavzevii has emerged as a promising biocontrol agent because of its capacity to inhibit fungal growth, offering a potential solution for plant disease management.ResultsTwo novel Pichia kudriavzevii strains, Pk_EgyACGEB_O1 and Pk_EgyACGEB_O2, were isolated from olive brine samples. The microscopic characterization of the strains revealed similar structures. However, there were noticeable differences in their visual morphology. Based on their internal transcribed spacer (ITS) DNA sequences, Pk_EgyACGEB_O1 and Pk_EgyACGEB_O2 strains assigned by GenBank IDs MZ507552.1 and MZ507554.1 shared high sequence similarity (~ 99.8% and 99.5%) with P. kudriavzevii, respectively. Both strains were evaluated in vitro against plant pathogenic fungi. The strains revealed the ability to consistently inhibit fungal growth, with Pk_EgyACGEB_O2 showing higher effectiveness. In addition, both P. kudriavzevii strains effectively controlled grey mold disease caused by B. cinerea in golden delicious apples, suggesting their potential as sustainable and eco-friendly biocontrol agents for post-harvest diseases. Based on a comprehensive bioinformatics pipeline, candidate-secreted proteins responsible for the potent antifungal activity of P. kudriavzevii were identified. A total of 59 proteins were identified as common among the P. kudriavzevii CBS573, SD108, and SD129 strains. Approximately 23% of the secreted proteins in the P. kudriavzevii predicted secretome are hydrolases with various activities, including proteases, lipases, glycosidases, phosphatases, esterases, carboxypeptidases, or peptidases. In addition, a set of cell-wall-related proteins was identified, which might enhance the biocontrol activity of P. kudriavzevii by preserving the structure and integrity of the cell wall. A papain inhibitor was also identified and could potentially offer a supplementary defense against plant pathogens.ConclusionOur results revealed the biocontrol capabilities of P. kudriavzevii against plant pathogenic fungi. The research focused on screening novel strains for their ability to inhibit the growth of common pathogens, both in vitro and in vivo. This study shed light on how P. kudriavzevii interacts with fungal pathogens. The findings can help develop effective strategies for managing plant diseases.

Intraspecific Variation of Transposable Elements Reveals Differences in the Evolutionary History of Fungal Phytopathogen Pathotypes.

Transposable elements (TEs) contribute to intraspecific variation and play important roles in the evolution of fungal genomes. However, our understanding of the processes that shape TE landscapes is limited, as is our understanding of the relationship between TE content, population structure, and evolutionary history of fungal species. Fungal plant pathogens, which often have host-specific populations, are useful systems in which to study intraspecific TE content diversity. Here, we describe TE dynamics in five lineages of Magnaporthe oryzae, the fungus that causes blast disease of rice, wheat, and many other grasses. We identified differences in TE content across these lineages and showed that recent lineage-specific expansions of certain TEs have contributed to overall greater TE content in rice-infecting and Setaria-infecting lineages. We reconstructed the evolutionary histories of long terminal repeat-retrotransposon expansions and found that in some cases they were caused by complex proliferation dynamics of one element and in others by multiple elements from an older population of TEs multiplying in parallel. Additionally, we found evidence suggesting the recent transfer of a DNA transposon between rice- and wheat-infecting M. oryzae lineages and a region showing evidence of homologous recombination between those lineages, which could have facilitated such a transfer. By investigating intraspecific TE content variation, we uncovered key differences in the proliferation dynamics of TEs in various pathotypes of a fungal plant pathogen, giving us a better understanding of the evolutionary history of the pathogen itself.

Disentangling the genetic diversity and population structure of Magnaporthe oryzae from Telangana State of Southren Peninsular India

Magnaporthe oryzae is a plant pathogenic fungus and model organism due to its agricultural impact and tractability that causes severe blast disease affecting rice. Due to its complex cryptic species, VNTRs and complex polyphyletic lineage due to the presence of many transposable elements. In the present study the internal transcribed spacers (ITS) of the ribosomal DNA sequences were used to characterize the 40 monoconidial M. oryzae strains from blast disease samples of the Telangana. Using DNAsp, performed a population genetics study on the sequencing data and discovered that rDNA sequence variation was highly polymorphic, with 0.01521 nucleotide diversity. In the present investigation 8 haplotype groups with Haplotype 2 (Hap_2) were reported to have with a broader genetic base. With a D value of −2.660 and a P 0.05 Tajima's neutrality test, the haplotype diversity is 0.52317, implying that there are variations in the pathogen isolates' sequences. The pathogen's apparent clonal reproductive behaviour was in contrast to the observed population structure, which suggested that genetic recombination may still be occurring within the pathogen population. The total number of variable sites (S) and mutations (Eta) were 63 and 73 respectively. Further, a haplotype network was constructed for the comparison of genealogical relationship's among (ITS) allele's using Population analysis with reticulate trees (PopArt software) a population genetics software to visualize the broader genetic base and genetic drift among the samples collected from the various locations of Telangana.

The Monothiol Glutaredoxin Grx4 Influences Iron Homeostasis and Virulence in Ustilago maydis.

The corn smut fungus, Ustilago maydis, is an excellent model for studying biotrophic plant-pathogen interactions, including nutritional adaptation to the host environment. Iron acquisition during host colonization is a key aspect of microbial pathogenesis yet less is known about this process for fungal pathogens of plants. Monothiol glutaredoxins are central regulators of key cellular functions in fungi, including iron homeostasis, cell wall integrity, and redox status via interactions with transcription factors, iron-sulfur clusters, and glutathione. In this study, the roles of the monothiol glutaredoxin Grx4 in the biology of U. maydis were investigated by constructing strains expressing a conditional allele of grx4 under the control of the arabinose-inducible, glucose-repressible promoter Pcrg1. The use of conditional expression was necessary because Grx4 appeared to be essential for U. maydis. Transcriptome and genetic analyses with strains depleted in Grx4 revealed that the protein participates in the regulation of iron acquisition functions and is necessary for the ability of U. maydis to cause disease on maize seedlings. Taken together, this study supports the growing appreciation of monothiol glutaredoxins as key regulators of virulence-related phenotypes in pathogenic fungi.

Plant–soil feedbacks among boreal forest species

Abstract Plant–microbial interactions in soils are considered to play a central role in regulating biodiversity in many global ecosystems. However, studies on plant–soil feedbacks (PSFs) and how these affect forest stand patterns in boreal regions are rare. We conducted a fully reciprocal PSF glasshouse experiment using four boreal tree species. Alnus glutinosa, Betula pendula, Picea abies and Pinus sylvestris seedlings were grown under controlled conditions in sterilised soil with or without soil inoculum collected under mature trees of each of the four species. Bacterial, fungal and oomycete communities in the rhizosphere were investigated using metabarcoding and correlated with differences in plant biomass. Alder grew best in conspecific soil, whereas birch grew equally well in all soil types. Pine and spruce grew best in heterospecific soil, particularly in soil from their successional predecessor. Ectomycorrhizal fungi (EMF) enhanced the growth of most seedlings, and Actinomycetota supported alder and birch growth and fungal plant pathogens hampered pine growth. Increased growth was linked to the ability of trees to recruit specific EMF and root‐associated fungi in heterospecific soils. Synthesis. This study experimentally examines the influence of root‐associated microbiota on the growth of boreal tree species. The observed plant–soil feedbacks mirror the successional patterns found in boreal forests, suggesting a possible contribution of soil microbiota to the successional progression. Species‐specific ectomycorrhizal fungi and a few bacteria rather than fungal plant pathogens or oomycetes seem to drive the feedbacks by promoting seedling growth in heterospecific soils.

Combined reference-free and multi-reference based GWAS uncover cryptic variation underlying rapid adaptation in a fungal plant pathogen.

Microbial pathogens often harbor substantial functional diversity driven by structural genetic variation. Rapid adaptation from such standing variation threatens global food security and human health. Genome-wide association studies (GWAS) provide a powerful approach to identify genetic variants underlying recent pathogen adaptation. However, the reliance on single reference genomes and single nucleotide polymorphisms (SNPs) obscures the true extent of adaptive genetic variation. Here, we show quantitatively how a combination of multiple reference genomes and reference-free approaches captures substantially more relevant genetic variation compared to single reference mapping. We performed reference-genome based association mapping across 19 reference-quality genomes covering the diversity of the species. We contrasted the results with a reference-free (i.e., k-mer) approach using raw whole-genome sequencing data in a panel of 145 strains collected across the global distribution range of the fungal wheat pathogen Zymoseptoria tritici. We mapped the genetic architecture of 49 life history traits including virulence, reproduction and growth in multiple stressful environments. The inclusion of additional reference genome SNP datasets provides a nearly linear increase in additional loci mapped through GWAS. Variants detected through the k-mer approach explained a higher proportion of phenotypic variation than a reference genome-based approach and revealed functionally confirmed loci that classic GWAS approaches failed to map. The power of GWAS in microbial pathogens can be significantly enhanced by comprehensively capturing structural genetic variation. Our approach is generalizable to a large number of species and will uncover novel mechanisms driving rapid adaptation of pathogens.

Design, Synthesis, Structure-Activity Relationship, and Three-Dimensional Quantitative Structure-Activity Relationship of Fusarium Acid Derivatives and Analogues as Potential Fungicides.

In research related to fungicides, the development of compounds from natural products with high antifungal activity has attracted considerable attention. Fusaric acid (FA), an alkaloid isolated from the metabolites of Fusarium oxysporum, is an important precursor for developing pharmacologically active herbicides. In our previous work, we reported that FA has a wide range of inhibitory activities against 14 plant pathogenic fungi. In particular, it exhibited excellent antifugal effects on Colletotrichum higginsianum (EC50 = 31.7 μg/mL). Herein, to explore the practical application in the agricultural field, the design and synthesis of three series of FA derivatives and their inhibitory activities against plant pathogenic fungi were examined. Results demonstrated that the optimized FA derivatives had excellent inhibitory activities against C. higginsianum, Helminthosporium (Harpophora maydis), and Pyricularia grisea. In particular, the inhibitory activities were considerably improved when the 5-butyl groups of FA were substituted. The EC50 of C. higginsianum and P. grisea was only 1.2 and 12.0 μg/mL when 5-butylalkyl groups were substituted with 5-([1,1'-biphenyl]-4-yl) and 5-phenyl, respectively. Moreover, the safety index of target compounds, which was obtained from the treatment index of medicines, on rice seeds was evaluated. Finally, 16 leading compounds (H4, H22-H24, H27, H29, H30-H34, H37, H45, H50, H52, and H53) were obtained; they had considerable potential for additional modification and optimization as agricultural fungicides. Moreover, three-dimensional quantitative structure-activity relationship models were developed for obtaining a systematic structure-activity relationship profile to explore the possibility of more potent FA derivatives as novel fungicides.