A new dollar spot disease of turfgrass caused by Clarireedia paspali

Unveiling Dominant Fungal Pathogens Associated with Root Rot of Hybrid Bermudagrass Based on Culture Dependent and Independent Methods

Hybrid bermudagrass (Cynodon dactylon × C. transvaalensis) is widely used as turf in southern and transition zones of China. From June to September in 2022, an unknown disease was consistently observed on hybrid bermudagrass in different regions of Nanjing, China, that exhibited distinct symptoms of leaf necrosis, severe root rot, and circular or irregular necrotic patches with 20- to 300-cm diameters. In this study, culture-independent and -dependent methods were used to elucidate the dominant fungal pathogens associated with the disease. Basidiomycota and Marasmiellus were shown to be the dominant phyla (51.96 to 70.60%) and genera (50.09 to 69.84%) in the symptomatic samples. A total of 128 fungal strains were isolated from symptomatic root tissues, and 40 strains representing the largest proportion (31.25%) were identified as Marasmiellus mesosporus based on the morphological characteristics, phylogenetic analysis of the ITS and LSU rDNA region, and pathogenicity testing. Temperature sensitivity tests revealed that M. mesosporus grew well at high temperatures (growth rate of 13.74 mm/day at 36°C). To our knowledge, this is the first report of M. mesosporus causing root rot disease on hybrid bermudagrass during hot summer months. The study will have important implications for the management of the disease.

Activity of the Succinate Dehydrogenase Inhibitor Fungicide Benzovindiflupyr Against Clarireedia spp

Dollar spot (DS), caused by Clarireedia spp. (formerly Sclerotinia homoeocarpa), is one of the most important diseases of turfgrasses worldwide. Benzovindiflupyr, a pyrazole carboxamide fungicide belonging to succinate dehydrogenase inhibitors, was recently registered for DS control. In this study, baseline sensitivity, toxicity, and control efficacy of benzovindiflupyr against Clarireedia spp. were evaluated. The frequency of sensitivities had a unimodal distribution (Kolmogorov-Smirnov, P > 0.10). The mean EC50 value was 1.109 ± 0.555 μg/ml, with individual values ranging from 0.160 to 2.548 μg/ml. Benzovindiflupyr increased the number of hyphal offshoots and cell membrane permeability and inhibited oxalic acid production. Positive cross-resistance was observed between benzovindiflupyr and boscalid, but not between benzovindiflupyr and thiophanate-methyl, propiconazole, or iprodione. Benzovindiflupyr showed high protective and curative control efficacies in vivo and in field applications. Both protective and curative control efficacies of benzovindiflupyr were significantly better than propiconazole, and equivalent to boscalid, over 2 years of field research. The results have important implications for managing DS and fungicide resistance problems in Clarireedia spp.

Genome-wide transcriptional analyses of Clarireedia jacksonii isolates associated with multi-drug resistance

Emerging multidrug resistance (MDR) in Clarireedia spp. is a huge challenge to the management of dollar spot (DS) disease on turfgrass. Insight into the molecular basis of resistance mechanisms may help identify key molecular targets for developing novel effective chemicals. Previously, a MDR isolate (LT586) of C. jacksonii with significantly reduced sensitivities to propiconazole, boscalid, and iprodione, and a fungicide-sensitive isolate (LT15) of the same species were isolated from creeping bentgrass (Agrostis stolonifera L.). The present study aimed to further explore the molecular mechanisms of resistance by using genome-wide transcriptional analyses of the two isolates. A total of 619 and 475 differentially expressed genes (DEGs) were significantly down and upregulated in the MDR isolate LT586, compared with the sensitive isolate LT15 without fungicide treatment. Three hundreds and six and 153 DEGs showed significantly lower and higher expression in the MDR isolate LT586 than those in the sensitive isolate LT15, which were commonly induced by the three fungicides. Most of the 153 upregulated DEGs were xenobiotic detoxification-related genes and genes with transcriptional functions. Fifty and 17 upregulated DEGs were also commonly observed in HRI11 (a MDR isolate of the C. jacksonii) compared with the HRS10 (a fungicide-sensitive isolate of same species) from a previous study without and with the treatment of propiconazole, respectively. The reliability of RNA-seq data was further verified by qRT-PCR method using a few select potentially MDR-related genes. Results of this study indicated that there were multiple uncharacterized genes, possibly responsible for MDR phenotypes in Clarireedia spp., which may have important implications in understanding the molecular mechanisms underlying MDR resistance.

Sensitivity of Clarireedia spp. to benzimidazoles and dimethyl inhibitors fungicides and efficacy of biofungicides on dollar spot of warm season turfgrass

Dollar spot caused by Clarireedia spp. (formerly Sclerotinia homoeocarpa) is an economically destructive fungal disease of turfgrass that can significantly compromise turf quality, playability, and aesthetic value. Fungicides are frequently used to manage the disease but are costly and potentially unfavorable to the environment. Repeated use of some active ingredients has resulted in reduced efficacy on C. jacksonii causing dollar spot in cool-season turfgrasses in the US. Experiments were conducted to study fungicide sensitivity of Clarireedia spp. as well as to develop alternatives to fungicides against dollar spot on warm-season turfgrass in Georgia. First, 79 isolates of Clarireedia spp. collected across the state were tested on fungicide-amended agar plates for their sensitivity to thiophanate-methyl (benzimidazole) and propiconazole (dimethyl inhibitor). Seventy-seven isolates (97.5%) were sensitive (0.001 to 0.654 μg/mL) and two isolates (2.5%) were found resistant (>1000 μg/mL) to thiophanate-methyl. However, in the case of propiconazole, 27 isolates (34.2%) were sensitive (0.005 to 0.098 μg/mL) while 52 isolates (65.8%) were resistant (0.101 to 3.820 μg/mL). Next, the efficacy of three bio- and six synthetic fungicides and ten different combinations were tested in vitro against C. monteithiana. Seven bio- and synthetic fungicide spray programs comprising Bacillus subtilis QST713 and propiconazole were further tested, either alone or in a tank mix in a reduced rate, on dollar spot infected bermudagrass 'TifTuf' in growth chamber and field environments. These fungicides were selected as they were found to significantly reduce pathogen growth up to 100% on in vitro assays. The most effective spray program in growth chamber assays was 100% B. subtilis QST713 in rotation with 75% B. subtilis QST713 + 25% propiconazole tank mix applied every 14 days. However, the stand-alone application of the biofungicide B. subtilis QST713 every seven days was an effective alternative and equally efficacious as propiconazole, suppressing dollar spot severity and AUDPC up to 75%, while resulting in acceptable turf quality (>7.0) in field experiments. Our study suggests that increased resistance of Clarireedia spp. to benzimidazoles and dimethyl inhibitors warrants continuous surveillance and that biofungicides hold promise to complement synthetic fungicides in an efficacious and environmentally friendly disease management program.

Comparative physiological and transcriptome analysis provide insights into the inhibitory effect of 6-pentyl-2H-pyran-2-one on Clarireedia jacksonii

Clarireedia spp. is a destructive phytopathogenic fungus that causes turf dollar spot of bent-grass, leading to widespread lawn death. In this study, we explored the antifungal capability of 6-pentyl-2H-pyran-2-one (6PP), a natural metabolite volatilized by microorganisms, which plays an important role in the biological control of turfgrass dollar spot. However, the mechanisms by which 6PP inhibits Clarireedia jacksonii remain unknown. In the present study, C. jacksonii mycelial growth was inhibited by the 6PP treatment and the 6PP treatment damaged cell membrane integrity, causing an increase in relative conduc-tivity. Furthermore, physiological and biochemistry assay showed that 6PP treatment can enhance reactive oxygen species (ROS) levels, malondialdehyde (MDA) content obviously increased with 6PP exposure, increased alchohol dehydrogenase (ADH) and depleted acetalde-hyde dehydrogenase (ALDH), and activated the activities of many antioxidant enzymes in C. jacksonii. Gen Ontology and Kyoto Encyclopedia of Genes and Genomes analysis revealed that some genes in C. jacksonii after 6PP treatment related to integrity of the cell wall and membrane, and oxidative stress were significantly downregulated. It is worth mentioning that the fatty acid degradation pathway is significantly upregulated, with an increase in ATP content and ATP synthase activity, which may promote fungal cell apoptosis. Moreover, we found that the expression of ABC transporters, and glutathione metabolism encoding genes were increased to respond to external stimuli. Taken together, these findings revealed the potential antifungal mechanism of 6PP against Clarireedia spp., which also provides a theoretical basis for the commercial utilization of 6PP as a green pesticide in the future.

Bryorutstroemia (Rutstroemiaceae, Helotiales), a New Genus to Accommodate the Neglected Sclerotiniaceous Bryoparasitic Discomycete Helotium fulvum

The new genus Bryorutstroemia is established for the red-brown, stipitate, bryoparasitic discomycete Helotium fulvum Boud. Combined phylogenetic analysis of ITS and LSU rDNA and EF1α revealed that Bryorutstroemia fulva belongs to the sclerotiniaceous clade, which comprises the paraphyletic families Rutstroemiaceae and Sclerotiniaceae. Bryorutstroemia formed with Clarireedia a supported clade (Rutstroemiaceae s.l.), though with high distance. Bryorutstroemia closely resembles other Rutstroemiaceae in having uninucleate ascospores with high lipid content and an ectal excipulum of textura porrecta, but is unique because of its bryophilous lifestyle and is extraordinary with its thick-walled inamyloid ascus apex. Although B. fulva was described in 1897, very few records came to our notice. The present study summarizes the known distribution of the species, including 25 personal collections from the years 2001-2022. Bryorutstroemia fulva was most often encountered on Dicranella heteromalla, and rarely on other members of Dicranales or Grimmiales, while inducing necrobiosis of the leaves. A detailed description based on mainly fresh apothecia is provided together with a rich photographic documentation. Six new combinations are proposed based on our phylogenetic results and unpublished personal morphological studies: Clarireedia asphodeli, C. calopus, C. gladioli, C. henningsiana, C. maritima, and C. narcissi.

A one-step multiplex PCR assay for the detection and differentiation of four species of Clarireedia causing dollar spot on turfgrass

BACKGROUND

Dollar spot (DS) is one of the most destructive and economically important diseases of cool- and warm-season turfgrasses worldwide. A total of six species causing DS disease in the genus Clarireedia have been described, and four of them have been reported to be distributed countrywide in China. Identification of different species of Clarireedia is a prerequisite for the effective management of DS disease.

RESULTS

Here we report a novel polymerase chain reaction (PCR)-based method for the detection and differentiation of the four species of Clarireedia associated with DS on turfgrass in China: C. jacksonii, C. paspali, C. monteithiana and C. hainanense. Species-specific genes were identified for each species by comparative genomics analysis. Four primer pairs were designed and mixed to amplify species-specific PCR fragments with differential sizes for the four species of Clarireedia in a single multiplex PCR assay. No PCR products were generated from the DNA templates of other common fungal pathogens associated with multiple turfgrass diseases. The multiplex PCR method developed can be used for the rapid and accurate detection and differentiation of the four species of Clarireedia from pure cultures as well as from infected turfgrass blades with DS symptoms.

CONCLUSION

The study developed a one-step multiplex PCR assay for the detection and differentiation of four species of Clarireedia causing DS on turfgrass in China, which will have important implications for DS management in China and worldwide. © 2022 Society of Chemical Industry.

Genome Resources for Four Clarireedia Species Causing Dollar Spot on Diverse Turfgrasses

Dollar spot (DS) is a destructive fungal disease impacting almost all warm- and cool-season turfgrasses worldwide. Multiple fungal species in the genus Clarireedia are causal agents of DS. Here, we present whole-genome assemblies of nine fungal isolates in the genus Clarireedia, including four species (C. paspali, C. hainanense, C. jacksonii, and C. monteithiana) causing DS on seashore paspalum (Paspalum vaginatum Sw.), creeping bentgrass (Agrostis stolonifera L.), and Kentucky bluegrass (Poa pratensis L.) in China. This work provides valuable baseline genomic data to support further research and management of DS pathogens on turfgrasses.

Whole genome sequencing of Clarireedia aff. paspali reveals potential pathogenesis factors in Clarireedia species, causal agents of dollar spot in turfgrass

Dollar spot is one of the most damaging diseases in turfgrass, reducing its quality and playability. Two species, Clarireedia monteithiana and C. jacksonii (formerly Sclerotinia homoeocarpa) have been reported so far in the United States To study the Clarireedia genome, two isolates H2 and H3, sampled from seashore paspalum in Hawaii in 2019 were sequenced via Illumina paired-end sequencing by synthesis technology and PacBio SMRT sequencing. Both isolates were identified as C. aff. paspali, a novel species in the United States Using short and long reads, C. aff. paspali H3 contained 193 contigs with 48.6 Mbp and presented the most completed assembly and annotation among Clarireedia species. Out of the 13,428 protein models from AUGUSTUS, 349 cytoplasmic effectors and 13 apoplastic effectors were identified by EffectorP. To further decipher Clarireedia pathogenicity, C. aff. paspali genomes (H2 and H3), as well as available C. jacksonii (LWC-10 and HRI11), C. monteithiana (DRR09 and RB-19) genomes were screened for fifty-four pathogenesis determinants, previously identified in S. sclerotiorum. Seventeen orthologs of pathogenicity genes have been identified in Clarireedia species involved in oxalic acid production (pac1, nox1), mitogen-activated protein kinase cascade (pka1, smk3, ste12), appressorium formation (caf1, pks13, ams2, rgb1, rhs1) and glycolytic pathway (gpd). Within these genes, 366 species-specific SNPs were recorded between Clarireedia species; twenty-eight were non-synonymous and non-conservative. The predicted protein structure of six of these genes showed superimposition of the models among Clarireedia spp. The genomic variations revealed here could potentially lead to differences in pathogenesis and other physiological functions among Clarireedia species.

Diversity Patterns of Macrofungi in Xerothermic Grasslands from the Nida Basin (Małopolska Upland, Southern Poland): A Case Study

Simple Summary

Southern Poland exhibits a diverse array of habitats for fungi; however, little is known about the richness and diversity of macrofungi occurring in xerothermic grasslands known as dry grasslands. Xerothermic grasslands with their unique flora and fauna are among the most valuable and, at the same time, most severely threatened habitats of Europe’s natural environment. Studies on such habitats were conducted in southern Poland during the period of 2010 to 2013.

Abstract

Macrofungal communities were investigated in seven plant associations of xerothermic grasslands in the Nida Basin located in the Małopolska Upland of southern Poland. Designation of associations at selected study sites was based on phytosociological relevés using the Braun-Blanquet method. During the years 2010–2013, we studied the diversity and distribution of macrofungi in dry grasslands, where 164 species of basidio- and ascomycetes were recovered. We determined the properties of the studied fungal communities and habitat preferences of individual species found in the analyzed xerothermic plant associations using ecological indicators for macrofungi according to Ellenberg indicator values. Diversity patterns of fungal communities in xerothermic grasslands are strongly influenced by various environmental factors. In our study, we focused on recording the fruiting bodies of all macrofungi and the proportion of each species in the study communities, as well as possible identification of the most likely indicator species for particular habitats. We found significant differences for two of the seven associations analyzed, namely Thalictro-Salvietum pratensis and Inuletum ensifoliae. However, based on Ellenberg indicator values for fungi, it is not possible to clearly define fungi as indicator species.

Clarireedia hainanense: A New Species Is Associated with Dollar Spot of Turfgrass in Hainan, China

The genus Clarireedia contains multiple species causing dollar spot (DS) on turfgrass worldwide. In November 2020, 119 Clarireedia isolates were obtained from symptomatic seashore paspalum at golf courses in Hainan province and identified to species level based on partial sequence of the internal transcribed spacer (ITS) region. A total of 45 and 22 isolates were identified as C. paspali and C. monteithiana, respectively; the remaining 52 isolates defined a new clade. Isolates from this clade were further selected for phylogenetic, morphological, and biological analyses. Maximum likelihood and Bayesian methods were implemented to obtain phylogenetic trees for partial sequences of the ITS, EF-1α, and McM7 genes. The selected isolates consistently fell into a distinct, well-supported clade within Clarireedia. Morphological and biological characteristics were observed among the different species in Clarireedia. Altogether, this study described a new species, Clarireedia hainanense, which has widespread distribution in Hainan, China. These findings may have important implications for the management of DS disease.

New Approaches to an Old Problem: Dollar Spot of Turfgrass

Dollar spot, caused by fungal pathogens Clarireedia spp. (formerly Sclerotinia homoeocarpa), is the most common and widely distributed disease of turfgrass worldwide. It can drastically reduce the quality of turfgrass species and affect their aesthetic value and playability. Management of dollar spot typically includes a costly program of multiple application of fungicides within a growing season. Consequently, there have been reported cases of fungicide resistance in populations of Clarireedia spp. Host resistance could be an important component of dollar spot management; however, this approach has been hampered by the lack of sources of resistance because nearly all known warm- and cool-season turfgrass species are susceptible. With the recent advancement in genome sequencing technologies, studies on pathogen genomics and host-pathogen interactions are emerging with the hope of revealing candidate resistance genes in turfgrass and genes for virulence and pathogenicity in Clarireedia spp. Large-scale screening of turfgrass germplasm and quantitative trait locus (QTL) analysis for dollar spot resistance are important for resistance breeding, but only a handful of such studies have been conducted to date. This review summarizes currently available information on the dollar spot pathosystem, taxonomy, pathogen genomics, host-pathogen interaction, genetics of resistance, and QTL mapping and also provides some thoughts for future research prospects to better manage this disease.

Development of a Co-Dominant Cleaved Amplified Polymorphic Sequences Assay for the Rapid Detection and Differentiation of Two Pathogenic Clarireedia spp. Associated with Dollar Spot in Turfgrass

Dollar spot is one of the most destructive diseases in turfgrass. The causal agents belong to the genus Clarireedia, which are known for causing necrotic, sunken spots in turfgrass that coalesce into large damaged areas. In low tolerance settings like turfgrass, it is of vital importance to rapidly detect and identify the pathogens. There are a few methods available to identify the genus Clarireedia, but none of those are rapid enough and characterize down to the species level. This study produced a co-dominant cleaved amplified polymorphic sequences (CAPS) test that differentiates between C. jacksonii and C. monteithiana, the two species that cause dollar spot disease within the United States. The calmodulin gene (CaM) was targeted to generate Clarireedia spp. specific PCR primers. The CAPS assay was optimized and tested for specificity and sensitivity using DNA extracted from pure cultures of two Clarireedia spp. and other closely related fungal species. The results showed that the newly developed primer set could amplify both species and was highly sensitive as it detected DNA concentrations as low as 0.005 ng/µL. The assay was further validated using direct PCR to speed up the diagnosis process. This drastically reduces the time needed to identify the dollar spot pathogens. The resulting assay could be used throughout turfgrass settings for a rapid and precise identification method in the US.

A Rapid Molecular Detection System for SdhB and SdhC Point Mutations Conferring Differential Succinate Dehydrogenase Inhibitor Resistance in Clarireedia Populations

Dollar spot, caused by the ascomycete fungus Clarireedia (formerly Sclerotinia), is one of the most resource-demanding diseases on amenity turfgrasses in North America. Differential resistance to the succinate dehydrogenase inhibitor (SDHI) fungicide class, conferred by singular point mutations on the SdhB, SdhC, and SdhD subunits of the succinate dehydrogenase enzyme (SDH), has been reported in dollar spot as well as many other plant-pathogenic fungal diseases. Four unique mutations were previously reported from Clarireedia field isolates collected from two different cool-season golf courses in Japan and Rhode Island: an amino acid substitution H267Y and a silent mutation (CTT to CTC) at codon 181 on the SdhB subunit gene, and amino acid substitutions G91R and G150R on the SdhC subunit gene. To properly diagnose and monitor SDHI resistance in the field, a rapid detection system for known mutations is crucial. As part of this study, additional SDHI-resistant Clarireedia isolates were collected from Rutgers University research plots and in vitro sensitivity to four SDHI active ingredients was assessed. SdhB, SdhC, and SdhD subunits of these isolates were sequenced to reveal an additional mutation on the SdhB subunit gene, H267R, not previously observed in Clarireedia. Cleaved amplified polymorphic sequence (CAPS) and derived CAPS molecular markers were developed to detect five mutations conferring SDHI resistance in Clarireedia isolates and validated using samples from two additional golf courses in Connecticut and Wisconsin experiencing SDHI field failure. This PCR-based molecular detection system will be useful for continued monitoring, assessment, and delay of SDHI resistance in the field.

Genome Resources for Seven Fungal Isolates That Cause Dollar Spot Disease in Turfgrass, Including Clarireedia jacksonii and C. monteithiana

Fungi in the genus Clarireedia are widespread and destructive pathogens of grasses worldwide, and are best known as the causal agents of dollar spot disease in turfgrass. Here, we report genome assemblies of seven Clarireedia isolates, including ex-types of the two most widespread species, Clarireedia jacksonii and C. monteithiana. These datasets provide a valuable resource for ongoing studies of the dollar spot pathogens that include population diversity, host-pathogen interactions, marker development, and disease control.

Real-Time PCR Detection of Clarireedia spp., the Causal Agents of Dollar Spot in Turfgrasses

Dollar spot is one of the most economically important diseases of turfgrasses. Recent taxonomic revisions have placed the dollar spot fungal pathogens in the new genus Clarireedia, with five species described. The main goal of this study was to develop a quantitative real-time PCR (qPCR) molecular detection assay based on the internal transcribed spacer (ITS) of the ribosomal RNA genes to quantify the abundance of Clarireedia spp. from environmental (field) samples. The qPCR assay was able to detect isolates of the four tested Clarireedia spp. but did not cross react with nontarget fungi, including closely related taxa, other turfgrass pathogens, or other fungal species commonly isolated from turfgrass. The assay is capable of detecting as little as 38.0 fg (3.8 × 10^-14 g) of Clarireedia genomic DNA in 3 h. The qPCR assay detected Clarireedia spp. in both symptomatic and asymptomatic creeping bentgrass (Agrostis stolonifera) foliar tissue. Clarireedia spp. were rarely detected in the thatch or soil, indicating that these pathogens are not widely distributed in these areas of the environment. The fact that the pathogen was detected in asymptomatic tissue suggests that creeping bentgrass may be able to tolerate a certain quantity of the pathogens in leaves before disease symptoms appear; however, further research is needed to validate this hypothesis.