Sclerotinia homoeocarpa overwinters in turfgrass and is present in commercial seed

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.

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.

Cold Plasma Affects Germination and Fungal Community Structure of Buckwheat Seeds

Crop seeds are frequently colonised by fungi from the field or storage places. Some fungi can cause plant diseases or produce mycotoxins, compromising the use of seeds as seeding material, food or feed. We have investigated the effects of cold plasma (CP) on seed germination and diversity of seed-borne fungi in common and Tartary buckwheat. The seeds were treated with CP for 15, 30, 45, 60, 90, and 120 s in a low-pressure radiofrequency system using oxygen as the feed gas. The fungi from the seed surface and fungal endophytes were isolated using potato dextrose agar plates. After identification by molecular methods, the frequency and diversity of fungal strains were compared between CP treated and chemically surface-sterilised (30% of H2O2) seeds. CP treatments above 60 s negatively affected the germination of both buckwheat species. A significant reduction in fungal frequency and diversity was observed after 90 s and 120 s in common and Tartary buckwheat, respectively. The filamentous fungi of genera Alternaria and Epicoccum proved to be the most resistant to CP. The results of our study indicate that CP treatment used in our study may be applicable in postharvest and food production, but not for further seed sowing.

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.

Brachypodium: A Potential Model Host for Fungal Pathogens of Turfgrasses

Brachypodium distachyon is a C3 grass that is an attractive model host system for studying pathogenicity of major turfgrass pathogens due to its genetic similarity to many cool-season turfgrasses. Infection assays with two or more isolates of the casual agents of dollar spot, brown patch, and Microdochium patch resulted in compatible interactions with B. distachyon inbred line Bd21-3. The symptoms produced by these pathogens on Bd21-3 closely resembled those observed on the natural turfgrass host (creeping bentgrass), demonstrating that B. distachyon is susceptible to the fungal pathogens that cause dollar spot, brown patch, and Microdochium patch on turfgrasses. The interaction between Sclerotinia homoeocarpa isolates and Brachypodium ecotypes was also investigated. Interestingly, differential responses of these ecotypes to S. homoeocarpa isolates was found, particularly when comparing B. distachyon to B. hybridum ecotypes. Taken together, these findings demonstrate that B. distachyon can be used as a model host system for these turfgrass diseases and leveraged for studies of molecular mechanisms contributing to host resistance.

Genes Required for the Anti-fungal Activity of a Bacterial Endophyte Isolated from a Corn Landrace Grown Continuously by Subsistence Farmers Since 1000 BC

Endophytes are microbes that inhabit internal plant tissues without causing disease. Some endophytes are known to combat pathogens. The corn (maize) landrace Chapalote has been grown continuously by subsistence farmers in the Americas since 1000 BC, without the use of fungicides, and the crop remains highly valued by farmers, in part for its natural tolerance to pests. We hypothesized that the pathogen tolerance of Chapalote may, in part, be due to assistance from its endophytes. We previously identified a bacterial endophyte from Chapalote seeds, Burkholderia gladioli strain 3A12, for its ability to combat a diversity of crop pathogens, including Sclerotinia homoeocarpa, the most important fungal disease of creeping bentgrass, a relative of maize used here as a model system. Strain 3A12 represents a unique opportunity to understand the anti-fungal activities of an endophyte associated with a crop variety grown by subsistence farmers since ancient times. Here, microscopy combined with Tn5-mutagenesis demonstrates that the anti-fungal mode of action of 3A12 involves flagella-dependent swarming toward its pathogen target, attachment and biofilm-mediated microcolony formation. The mutant screen revealed that YajQ, a receptor for the secondary messenger c-di-GMP, is a critical signaling system that mediates this endophytic mobility-based defense for its host. Microbes from the traditional seeds of farmers may represent a new frontier in elucidating host-microbe mutualistic interactions.

Temporal changes in fungal communities from buckwheat seeds and their effects on seed germination and seedling secondary metabolism

Seed-associated fungal communities affect multiple parameters of seed quality at all stages of production, from seed development to post-harvest storage and germination. We therefore investigated the diversity and dynamics of fungal communities in the seeds of common buckwheat (Fagopyrum esculentum) and Tartary buckwheat (F. tataricum) from harvest to 1 y of storage. Fungal populations in seeds were relatively stable, comprised mainly of field fungi. Incidence of fungi was most likely determined by fungal interspecies direct interactions, as well as by their synthesis of volatile organic compounds. Most prominent antagonistic interactions were seen for two plant pathogens, Alternaria alternata on Botrytis cinerea. Detrimental effects of the fungi on seed germination and seedling development were related to fungal extracellular enzyme activity, and in particular to amylase, cellulase and, polyphenol oxidase. Polyphenol and tannin concentrations in buckwheat seedlings were related to fungal growth rate and intensity of fungal cellulase activity, respectively, which suggests that physical penetration of the fungi through the host tissues is probably the stimulus for the activation of plant defence reactions in these seedlings.

Relevance of in vitro agar based screens to characterize the anti-fungal activities of bacterial endophyte communities

BACKGROUND

Endophytes are microbes that inhabit internal plant tissues without causing disease. Plant microbial communities consist of large numbers of endophyte species. Understanding the functions of these endophytes is a major challenge. An important function of some endophytes is to suppress fungal pathogens. Typically, plant associated microbes are screened for anti-fungal activities in vitro using the high-throughput dual culture screen, but it is not clear whether this method correlates with the activities of these microbes in planta. Furthermore, it is not clear whether in vitro screening captures all of the microbes that show this activity inside plants. The objective of this study was to evaluate the relevance of the in vitro dual culture method for screening endophytes with anti-fungal activity.

RESULTS

In parallel, 190 bacterial endophytes from the corn grass family (Zea) were screened for suppression of two fungal pathogens (Sclerotinia homoeocarpa and Rhizoctonia solani) using the in vitro dual culture method, and in planta using the model plant, creeping bentgrass. All endophytes that showed anti-fungal activity in planta against Sclerotinia homoeocarpa and Rhizoctonia solani (3 or 4 strains, respectively, out of 190), were captured in vitro. The in vitro and in planta screening results strongly correlated (r = 0.81 and r = 0.94 for the two pathogens, respectively).

CONCLUSIONS

Evidence was gained here that the in vitro dual culture method is a relevant method for high throughput screening of plant endophyte communities for anti-fungal activity. In our study, the method captured all of the microbes that suppressed the corresponding pathogens in planta.