Synchrospora gen. nov., a New Peronosporaceae Genus with Aerial Lifestyle from a Natural Cloud Forest in Panama

During a survey of Phytophthora diversity in Panama, fast-growing oomycete isolates were obtained from naturally fallen leaves of an unidentified tree species in a tropical cloud forest. Phylogenetic analyses of sequences from the nuclear ITS, LSU and ßtub loci and the mitochondrial cox1 and cox2 genes revealed that they belong to a new species of a new genus, officially described here as Synchrospora gen. nov., which resided as a basal genus within the Peronosporaceae. The type species S. medusiformis has unique morphological characteristics. The sporangiophores show determinate growth, multifurcating at the end, forming a stunted, candelabra-like apex from which multiple (8 to >100) long, curved pedicels are growing simultaneously in a medusa-like way. The caducous papillate sporangia mature and are shed synchronously. The breeding system is homothallic, hence more inbreeding than outcrossing, with smooth-walled oogonia, plerotic oospores and paragynous antheridia. Optimum and maximum temperatures for growth are 22.5 and 25-27.5 °C, consistent with its natural cloud forest habitat. It is concluded that S. medusiformis as adapted to a lifestyle as a canopy-dwelling leaf pathogen in tropical cloud forests. More oomycete explorations in the canopies of tropical rainforests and cloud forests are needed to elucidate the diversity, host associations and ecological roles of oomycetes and, in particular, S. medusiformis and possibly other Synchrospora taxa in this as yet under-explored habitat.

Host-generalist fungal pathogens of seedlings may maintain forest diversity via host-specific impacts and differential susceptibility among tree species

Host-specialized pathogens are credited with the maintenance of tropical forest diversity under the Janzen-Connell hypothesis. Yet, in diverse forests, selection may favor pathogens with broad host ranges, given their passive dispersal and the relative rarity of tree species. We surveyed the host associations of potential pathogens isolated from symptomatic seedlings in forests in Panama and used inoculations to assess the pathogenicity and host ranges of 27 fungal isolates, and differences among tree species in susceptibility. Thirty-one of the 33 nonsingleton operational taxonomic units (OTUs) isolated from seedlings are multi-host. All 31 multi-host OTUs exhibit low to moderate specialization, and we observed phylogenetically overdispersed host use for 19 OTUs. The pathogenicity of 10 isolates was experimentally confirmed; nine caused disease in seedlings in multiple families. However, the outcome of infection differs among tree species susceptible to a given multi-host pathogen. Furthermore, some tree species were seemingly resistant to all fungi tested, while others were susceptible to multiple fungi. Tree species adapted to environments with lower disease pressure were most likely to exhibit disease. Our results suggest that generalist pathogens contribute to the maintenance of local and regional forest diversity via host-specific impacts and the exclusion of disease-sensitive trees from disease-prone habitats.

Whole-Genome Comparisons of Ergot Fungi Reveals the Divergence and Evolution of Species within the Genus Claviceps Are the Result of Varying Mechanisms Driving Genome Evolution and Host Range Expansion

The genus Claviceps has been known for centuries as an economically important fungal genus for pharmacology and agricultural research. Only recently have researchers begun to unravel the evolutionary history of the genus, with origins in South America and classification of four distinct sections through ecological, morphological, and metabolic features (Claviceps sects. Citrinae, Paspalorum, Pusillae, and Claviceps). The first three sections are additionally characterized by narrow host range, whereas section Claviceps is considered evolutionarily more successful and adaptable as it has the largest host range and biogeographical distribution. However, the reasons for this success and adaptability remain unclear. Our study elucidates factors influencing adaptability by sequencing and annotating 50 Claviceps genomes, representing 21 species, for a comprehensive comparison of genome architecture and plasticity in relation to host range potential. Our results show the trajectory from specialized genomes (sects. Citrinae and Paspalorum) toward adaptive genomes (sects. Pusillae and Claviceps) through colocalization of transposable elements around predicted effectors and a putative loss of repeat-induced point mutation resulting in unconstrained tandem gene duplication coinciding with increased host range potential and speciation. Alterations of genomic architecture and plasticity can substantially influence and shape the evolutionary trajectory of fungal pathogens and their adaptability. Furthermore, our study provides a large increase in available genomic resources to propel future studies of Claviceps in pharmacology and agricultural research, as well as, research into deeper understanding of the evolution of adaptable plant pathogens.

Sympatric divergence of the ergot fungus, Claviceps purpurea, populations infecting agricultural and nonagricultural grasses in North America

The ergot diseases of agricultural and nonagricultural grasses are caused by the infection of Claviceps spp. (Hypocreales, Ascomycota) on florets, producing dark spur-like sclerotia on spikes that are toxic to humans and animals, leading to detrimental impacts on agriculture and economy due to the downgrading of cereal grains, import-export barriers, reduced yield, and ecological concerns. At least seven phylogenetic lineages (phylogenetic species) were identified within the premolecular concept of C. purpurea s.l. (sensu lato) in agricultural areas and vicinities in Canada and the Western United States. Claviceps purpurea s.s (sensu stricto) remained as the most prevalent species with a wide host range, including cereal crops, native, invasive, and weedy grasses. The knowledge on genetic diversity and distribution of C. purpurea s.s. in North America is lacking. The objective of the present study was to shed light on genetic differentiation and evolution of the natural populations of C. purpurea s.s. Multilocus DNA sequences of samples from Canada and the Western USA were analyzed using a phylogenetic network approach, and population demographic parameters were investigated. Results showed that three distinct genetically subdivided populations exist, and the subdivision is not correlated with geographic or host differentiations. Potential intrinsic mechanisms that might play roles in leading to the cessation of gene flows among the subpopulations, that is, mating and/or vegetative incompatibility, genomic adaptation, were discussed. The neutrality of two house-keeping genes that are widely used for DNA barcoding, that is, translation elongation factor 1-α (TEF1-α) and RNA polymerase II second largest subunit (RPB2), was challenged and discussed.

Occurrence in Seeds and Potential Seed Transmission of Xanthomonas vasicola pv. vasculorum in Maize in the United States

This paper reports original evidence regarding the potential role of seed transmission of Xanthomonas vasicola pv. vasculorum in the epidemiology of bacterial leaf streak (BLS) in maize. We evaluated the occurrence of the pathogen on seeds from diseased fields and its subsequent transmission to seedlings. In 2016 and 2017, X. vasicola pv. vasculorum was detected by TaqMan PCR from 22 of 41 maize seed lots harvested from naturally infected fields in Colorado, Nebraska, and Iowa. However, many of the PCR-positive samples did not yield culturable X. vasicola pv. vasculorum colonies. The highest levels of seed contamination were detected in dent maize and popcorn from NE and CO. Seed transmission was evaluated in greenhouse grow-outs from eight seed lots, totaling more than 14,000 plants. Putative seed transmission events from naturally contaminated seed lots, estimated from PCR results, occurred at a frequency between 0.1 and 0.5% in 10-seedling pooled samples and at a frequency of 2.7% from individual plant assays. However, no seedling symptoms were observed during these assays and live X. vasicola pv. vasculorum colonies were not recovered from PCR-positive seedlings. In contrast, seed transmission was readily demonstrated from artificially contaminated seed lots, including typical symptoms and recovery of live bacteria. Seed transmission consistently occurred from seeds soaked in bacterial suspensions with concentrations of ≥10⁶ CFU/ml, suggesting that a threshold population of the bacterium is necessary for the development of BLS symptoms and recovery of live bacteria. The low bacterial populations on naturally contaminated seeds apparently were not sufficient to result in diseased seedlings.

Effect of Climatic Variables on Abundance and Dispersal of Lecanosticta acicola Spores and Their Impact on Defoliation on Eastern White Pine

The disease complex white pine needle damage (WPND), first reported in 2006, has now escalated to an epidemic state across the northeastern United States. Although this complex is composed of several fungal species, Lecanosticta acicola is considered to be the primary causal agent. Knowledge regarding the epidemiology, specific climatic factors that affect the spread of L. acicola on eastern white pine (Pinus strobus) in natural forest settings, and potential risks repeated defoliation may have on tree health is limited. Therefore, this study examined how climatic variables affect the abundance and distance of spore dispersal of L. acicola and compared litterfall caused by defoliation versus natural needle abscission. Conidia were observed on spore traps from May through August, with a peak in abundance occurring in June, corresponding to the defoliation of second- and third-year foliage measured in litter traps. During peak spore production, relative humidity and the occurrence of rainfall was found to have the greatest influence on spore abundance. Our results will aid managers in determining how far from infected trees natural regeneration will likely be affected and predicting future disease severity based on climatic conditions.

Phylogenetic Diversity of Rhizoctonia solani Associated with Canola and Wheat in Alberta, Manitoba, and Saskatchewan

Rhizoctonia solani is a damaging soilborne pathogen, which affects most field crops in the Canadian provinces of Alberta, Manitoba, and Saskatchewan. The objective of this study was to conduct a phylogenetic comparison of isolates of R. solani collected from a previous survey in the major canola- and wheat-growing regions of western Canada. A total of 128 multinucleate isolates from a previous survey were identified by internal transcribed spacer (ITS) sequence and compared to anastomosis group (AG) results. The multinucleate isolates of R. solani were grouped into eight distinct clades. Each clade corresponded to a specific AG with the exception of two distinct clades that were observed for isolates classified as AG 2-1 by anastomosis testing. While most isolates of AG 5 clustered together according to ITS sequences, three isolates classified by anastomosis grouping as AG 5 grouped with AG 2-1, AG 4, and a binucleate Rhizoctonia sp. in the phylogenetic analysis. In most instances, the results from AG tests were consistent with ITS sequence, but there were still several cases where isolates were inconsistently classified or failed to undergo anastomosis with any of the tester strains used in this study. This provides support for the use of the ITS region as a valuable tool for rapid identification of R. solani isolates to their respective AGs.

Population structure of the butternut canker fungus, Ophiognomonia clavigignenti-juglandacearum, in North American forests

The occurrence of multiple introduction events, or sudden emergence from a host jump, of forest pathogens may be an important factor in successful establishment in a novel environment or on a new host; however, few studies have focused on the introduction and emergence of fungal pathogens in forest ecosystems. While Ophiognomonia clavigignenti-juglandacearum (Oc-j), the butternut canker fungus, has caused range-wide mortality of butternut trees in North America since its first observation in 1967, the history of its emergence and spread across the United States and Canada remains unresolved. Using 17 single nucleotide polymorphic loci, we investigated the genetic population structure of 101 isolates of Oc-j from across North America. Clustering analysis revealed that the Oc-j population in North America is made up of three differentiated genetic clusters of isolates, and these genetic clusters were found to have a strong clonal structure. These results, in combination with the geographic distribution of the populations, suggest that Oc-j was introduced or has emerged in North America on more than one occasion, and these clonal lineages have since proliferated across much of the range of butternut. No evidence of genetic recombination was observed in the linkage analysis, and conservation of the distinct genetic clusters in regions where isolates from two or more genetic clusters are present, would indicate a very minimal or non-existent role of sexual recombination in populations of Oc-j in North America.

Two new species of Pythium, P. schmitthenneri and P. selbyi pathogens of corn and soybean in Ohio

Two new species of Pythium, pathogens of corn and soybean in Ohio, are described. Pythium schmitthenneri sp. nov. and Pythium selbyi sp. nov. both have morphological and sequence characteristics that place them in clade E1 of the genus Pythium. Morphology and sequence analysis of the ITS1-5.8S-ITS2 regions of these species were different from previously described species. The ITS region of Pythium schmitthenneri was 99.9% similar to P. acrogynum and 99.8% similar to P. hypogynum. All three species are characterized by globose to limoniform sporangia and plerotic oospores. Pythium schmitthenneri has mostly diclinous antheridia, compared to the strictly hypogynous antheridia of P. acrogynum and P. hypogynum. The temperature for growth of P. schmitthenneri is below 4 C to 32 C, and optimum growth is 18-25 C compared to 31-34 C for P. hypogynum. The ITS region of P. selbyi was 97.1% similar to P. longandrum and 97.5% similar to P. longisporangium. All three species are characterized by globose sporangia, mostly plerotic oospores, with one to two oospores per oogonium, and hypogynous or monoclinous antheridia. The temperature for growth of P. selbyi is below 4 to 32 C, with an optimum 18-25 C. These new species were widely dispersed throughout the soybean- and corn-producing regions in Ohio, making their characterization critical for managing the Pythium complex that causes seedling and root-rot disease in Ohio soybean and corn fields.

Infection of Soybean Seed by Fusarium graminearum and Effect of Seed Treatments on Disease Under Controlled Conditions

Fusarium graminearum causes seed decay and damping-off of soybean. This study evaluated the effect of inoculum density of F. graminearum, temperature, and fungicide seed treatments on disease development. To determine the optimum conditions for disease development, individual soybean seed was inoculated with 100 μl of a suspension of 2.5 × 10², 2.5 × 10³, 2.5 × 10⁴, or 2.5 × 10⁵ macroconidia/ml in a rolled-towel assay at temperatures of 18, 22, and 25°C. Inoculum concentrations of 2.5 × 10⁴ macroconidia/ml or higher were necessary for optimum disease development at all temperatures. The efficacy of captan, fludioxonil, mefenoxam + fludioxonil, azoxystrobin, trifloxystrobin, and pyraclostrobin as seed treatments was then evaluated with the same assay at 2.5 × 10⁴ and 2.5 × 10⁵ macroconidia/ml. Seed treated with captan at 61.9 g a.i. or fludioxonil at 2.5 or 5.0 g a.i. per 100 kg developed smaller lesions than other seed treatments and the nontreated control. Based on these results, there are limited choices in fungicide seed treatments for managing this seedling disease, and it is possible that shifts in seed treatment products may have played a role in the recent emergence of this soybean pathogen.

Discovery of single-nucleotide polymorphisms (SNPs) in the uncharacterized genome of the ascomycete Ophiognomonia clavigignenti-juglandacearum from 454 sequence data

The benefits from recent improvement in sequencing technologies, such as the Roche GS FLX (454) pyrosequencing, may be even more valuable in non-model organisms, such as many plant pathogenic fungi of economic importance. One application of this new sequencing technology is the rapid generation of genomic information to identify putative single-nucleotide polymorphisms (SNPs) to be used for population genetic, evolutionary, and phylogeographic studies on non-model organisms. The focus of this research was to sequence, assemble, discover and validate SNPs in a fungal genome using 454 pyrosequencing when no reference sequence is available. Genomic DNA from eight isolates of Ophiognomonia clavigignenti-juglandacearum was pooled in one region of a four-region sequencing run on a Roche 454 GS FLX. This yielded 71 million total bases comprising 217,000 reads, 80% of which collapsed into 16,125,754 bases in 30,339 contigs upon assembly. By aligning reads from multiple isolates, we detected 298 SNPs using Roche's GS Mapper. With no reference sequence available, however, it was difficult to distinguish true polymorphisms from sequencing error. Eagleview software was used to manually examine each contig that contained one or more putative SNPs, enabling us to discard all but 45 of the original 298 putative SNPs. Of those 45 SNPs, 13 were validated using standard Sanger sequencing. This research provides a valuable genetic resource for research into the genus Ophiognomonia, demonstrates a framework for the rapid and cost-effective discovery of SNP markers in non-model organisms and should prove especially useful in the case of asexual or clonal fungi with limited genetic variability.

Molecular Diagnostic Assay for Detection of the Butternut Canker Pathogen Sirococcus clavigignenti-juglandacearum

Butternut canker, caused by the fungal pathogen Sirococcus clavigignenti-juglandacearum, is present throughout the range of butternut (Juglans cinerea) and is the primary cause for its decline. A quick and reliable method for identification of S. clavigignenti-juglandacearum would provide a valuable tool for the detection of the pathogen on propagative material to avoid spread, as well as assist studies targeted at the epidemiology of this pathogen, in particular the dissemination of the pathogen by seeds of the butternut. The objective of this study was to develop a diagnostic assay to detect S. clavigignenti-juglandacearum in butternut plant tissue. The primers were developed using an alignment of internal transcribed spacer (ITS) sequences from isolates of S. clavigignenti-juglandacearum and several closely related species. These primers were tested on J. cinerea, 48 isolates of S. clavigignenti-juglandacearum recovered from diseased trees, and 26 species of other fungi recovered from butternut tissue. The primers amplified a product from the DNA of all isolates of S. clavigignenti-juglandacearum, detected its DNA at a concentration as low as 1 pg/μl, and detected the pathogen at a concentration of 1 × 10³ spore/ml. The primers developed in this study will be a valuable tool for the detection of S. clavigignenti-juglandacearum present on butternut seeds, and as a rapid diagnostic tool for early detection of the pathogen on butternut trees.

Association of soil chemical and physical properties with Pythium species diversity, community composition, and disease incidence

A high-throughput baiting and identification process identified more than 7,000 isolates of Pythium from 88 locations in Ohio. Isolates were identified using direct-colony polymerase chain reaction followed by single-strand conformational polymorphism, and communities were assembled using the Jaccard similarity coefficient and cluster analysis. Both univariate and multivariate statistics were used to evaluate differences in soil properties between communities, and canonical discriminant analysis (CDA) was used to assess the strength of the association of soil variables within communities from 83 of the locations. In all, 21 species of Pythium were identified but only 6 were recovered from >40% of the locations. Five communities were formed using the cluster analysis, and significant differences were observed in disease incidence, as well as soil pH, calcium, magnesium, and cation exchange capacity between communities. Stepwise multiple discriminant analysis and CDA identified pH, calcium, magnesium, and field capacity as contributing the most to the separation of the five Pythium communities. There was a strong association between abiotic soil components and the structure of Pythium communities, as well as diversity of Pythium spp. collected from agronomic production fields in Ohio.

Pythium delawarii--a new species isolated from soybean in Ohio

A new species of Pythium isolated from soybean in Ohio is described. Pythium delawarii sp. nov. is characterized by globose internally proliferating sporangia, aplerotic oospores and diclinous antheridia that make broad lengthwise contact. Sporangia produce conspicuous papilla and germinate indirectly by producing zoospores via a vesicle and proliferate internally or the sporangia germinate directly with either one or more germ tubes. Pythium delawarii is pathogenic on soybean causing damping-off of seedlings. This oomycete can grow at 10-34 C with an optimum of 28 C. The sequence of the ITS1, 5.8S and ITS2 region of the rDNA did not match the sequence of any known Pythium species but was similar to P. citrinum, P. litorale and P. sterilum. P. delawarii can be distinguished from these three species based on the presence of aplerotic oospores and diclinous antheridia and the absence of hypogynous antheridia. Therefore biological, morphological and molecular data support the recognition of a new species.

Evaluation of Fusarium graminearum Associated with Corn and Soybean Seed and Seedling Disease in Ohio

Fusarium graminearum is an important pathogen of cereal crops in Ohio causing primarily head blight in wheat and stalk and ear rot of corn. During the springs of 2004 and 2005, 112 isolates of F. graminearum were recovered from diseased corn and soybean seedlings from 30 locations in 13 Ohio counties. These isolates were evaluated in an in vitro pathogenicity assay on both corn and soybean seed, and 28 isolates were tested for sensitivity to the seed treatment fungicides azoxystrobin, trifloxystrobin, fludioxonil, and captan. All of the isolates were highly pathogenic on corn seed and moderately to highly pathogenic on soybean seed. Fludioxonil was the only fungicide that provided sufficient inhibition of mycelial growth; however, several fludioxonil-resistant mutants were identified during the sensitivity experiments. These results indicate that F. graminearum is an important pathogen of both corn and soybean seed and seedlings in Ohio, and that continued use of fludioxonil potentially may select for less sensitive isolates of F. graminearum.

Characterization of Pythium spp. Associated with Corn and Soybean Seed and Seedling Disease in Ohio

Cool, moist conditions in combination with minimum tillage, earlier planting, and recent shifts in commercial fungicide seed-treatment active ingredients have led to an increase in corn (Zea mays) and soybean (Glycine max) seedling establishment problems. This situation resulted in an investigation of Pythium spp. associated with seed and seedling diseases. Samples of diseased corn and soybean seedlings were collected from 42 production fields in Ohio. All isolates of Pythium recovered were identified to species using morphological and molecular techniques and evaluated in an in vitro pathogenicity assay on both corn and soybean seed, and a subset of the isolates was tested for sensitivity to fungicides currently used as seed treatments. Eleven species and two distinct morphological groups of Pythium were identified, of which six species were moderately to highly pathogenic on corn seed and nine species were highly pathogenic on soybean seed. There was significant variation (P < 0.05) in sensitivity to mefenoxam, azoxystrobin, trifloxystrobin, and captan both across and within species. Multiple species of Pythium had the capacity to reduce germination of both corn and soybean seed. Results indicated that mefenoxam, azoxystrobin, trifloxystrobin, or captan, when used individually, may not inhibit all pathogenic species of Pythium found in Ohio soils.