Detection of Race-Specific Resistance Against Puccinia coronata f. sp. avenae in Brachypodium Species

Aecial and Telial Host Specificity of Puccinia coronata var. coronata, a Eurasian Crown Rust Fungus of Two Highly Invasive Wetland Species in North America

The Eurasian crown rust fungus Puccinia coronata var. coronata (Pcc) was recently reported in North America and is widespread across the Midwest and Northeast United States. Pcc is a close relative of major pathogens of oats, barley, and turfgrasses. It infects two highly invasive wetland plants, glossy buckthorn (Frangula alnus) and reed canarygrass (Phalaris arundinacea), and could be useful as an augmentative biological control agent. We conducted large greenhouse trials to assess the host specificity of Pcc and determine any threat to cultivated cereals, turfgrasses, or native North American species. A total of 1,830 accessions of cereal crop species and 783 accessions of 110 other gramineous species were evaluated. Young plants were first inoculated with a composite uredinial inoculum derived from aecia. Accessions showing sporulation were further tested with pure urediniospore isolates. Sixteen potential aecial hosts in the families Rhamnaceae and Elaeagnaceae were tested for susceptibility through inoculation with germinating teliospores. Thirteen grass species within five genera in the tribe Poeae (Apera, Calamagrostis, Lamarckia, Phalaris, and Puccinellia) and four species in Rhamnaceae (Frangula alnus, F. californica, F. caroliniana, and Rhamnus lanceolata) were found to be susceptible to Pcc, with some species native to North America. All assessed crop species and turfgrasses were resistant. Limited sporulation, however, was observed on some resistant species within Poeae and four other tribes: Brachypodieae, Bromeae, Meliceae, and Triticeae. Among these species are oats, barley, and Brachypodium distachyon, suggesting the possible use of Pcc in studies of nonhost resistance.

The microbiome of an outpatient rehabilitation clinic and predictors of contamination: A pilot study

BACKGROUND

Understanding sources of microbial contamination in outpatient rehabilitation (REHAB) clinics is important to patients and healthcare providers.

PURPOSE

The purpose of this study was to characterize the microbiome of an outpatient REHAB clinic and examine relationships between clinic factors and contamination.

METHODS

Forty commonly contacted surfaces in an outpatient REHAB clinic were observed for frequency of contact and swiped using environmental sample collection kits. Surfaces were categorized based on frequency of contact and cleaning and surface type. Total bacterial and fungal load was assessed using primer sets specific for the 16S rRNA and ITS genes, respectively. Bacterial samples were sequenced using the Illumina system and analyzed using Illumina-utils, Minimum Entropy Decomposition, QIIME2 (for alpha and beta diversity), LEfSe and ANCOM-BC for taxonomic differential abundance and ADONIS to test for differences in beta diversity (p<0.05).

RESULTS

Porous surfaces had more bacterial DNA compared to non-porous surfaces (median non-porous = 0.0016ng/μL, 95%CI = 0.0077-0.00024ng/μL, N = 15; porous = 0.0084 ng/μL, 95%CI = 0.0046-0.019 ng/μL, N = 18. p = 0.0066,DNA. Samples clustered by type of surface with non-porous surfaces further differentiated by those contacted by hand versus foot. ADONIS two-way ANOVA showed that the interaction of porosity and contact frequency (but neither alone) had a significant effect on 16S communities (F = 1.7234, R2 = 0.0609, p = 0.032).

DISCUSSION

Porosity of surfaces and the way they are contacted may play an underestimated, but important role in microbial contamination. Additional research involving a broader range of clinics is required to confirm results. Results suggest that surface and contact-specific cleaning and hygiene measures may be needed for optimal sanitization in outpatient REHAB clinics.

A chromosome-level, fully phased genome assembly of the oat crown rust fungus Puccinia coronata f. sp. avenae: a resource to enable comparative genomics in the cereal rusts

Advances in sequencing technologies as well as development of algorithms and workflows have made it possible to generate fully phased genome references for organisms with nonhaploid genomes such as dikaryotic rust fungi. To enable discovery of pathogen effectors and further our understanding of virulence evolution, we generated a chromosome-scale assembly for each of the 2 nuclear genomes of the oat crown rust pathogen, Puccinia coronata f. sp. avenae (Pca). This resource complements 2 previously released partially phased genome references of Pca, which display virulence traits absent in the isolate of historic race 203 (isolate Pca203) which was selected for this genome project. A fully phased, chromosome-level reference for Pca203 was generated using PacBio reads and Hi-C data and a recently developed pipeline named NuclearPhaser for phase assignment of contigs and phase switch correction. With 18 chromosomes in each haplotype and a total size of 208.10 Mbp, Pca203 has the same number of chromosomes as other cereal rust fungi such as Puccinia graminis f. sp. tritici and Puccinia triticina, the causal agents of wheat stem rust and wheat leaf rust, respectively. The Pca203 reference marks the third fully phased chromosome-level assembly of a cereal rust to date. Here, we demonstrate that the chromosomes of these 3 Puccinia species are syntenous and that chromosomal size variations are primarily due to differences in repeat element content.

A Homolog of the Arabidopsis TIME FOR COFFEE Gene Is Involved in Nonhost Resistance to Wheat Stem Rust in Brachypodium distachyon

Plants resist infection by pathogens using both preexisting barriers and inducible defense responses. Inducible responses are governed in a complex manner by various hormone signaling pathways. The relative contribution of hormone signaling pathways to nonhost resistance to pathogens is not well understood. In this study, we examined the molecular basis of disrupted nonhost resistance to the fungal species Puccinia graminis, which causes stem rust of wheat, in an induced mutant of the model grass Brachypodium distachyon. Through bioinformatic analysis, a 1-bp deletion in the mutant genotype was identified that introduces a premature stop codon in the gene Bradi1g24100, which is a homolog of the Arabidopsis thaliana gene TIME FOR COFFEE (TIC). In Arabidopsis, TIC is central to the regulation of the circadian clock and plays a crucial role in jasmonate signaling by attenuating levels of the transcription factor protein MYC2, and its mutational disruption results in enhanced susceptibility to the hemibiotroph Pseudomonas syringae. Our similar finding for an obligate biotroph suggests that the biochemical role of TIC in mediating disease resistance to biotrophs is conserved in grasses, and that the correct modulation of jasmonate signaling during infection by Puccinia graminis may be essential for nonhost resistance to wheat stem rust in B. distachyon.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Identification of Candidate Susceptibility Genes to Puccinia graminis f. sp. tritici in Wheat

Wheat stem rust disease caused by Puccinia graminis f. sp. tritici (Pgt) is a global threat to wheat production. Fast evolving populations of Pgt limit the efficacy of plant genetic resistance and constrain disease management strategies. Understanding molecular mechanisms that lead to rust infection and disease susceptibility could deliver novel strategies to deploy crop resistance through genetic loss of disease susceptibility. We used comparative transcriptome-based and orthology-guided approaches to characterize gene expression changes associated with Pgt infection in susceptible and resistant Triticum aestivum genotypes as well as the non-host Brachypodium distachyon. We targeted our analysis to genes with differential expression in T. aestivum and genes suppressed or not affected in B. distachyon and report several processes potentially linked to susceptibility to Pgt, such as cell death suppression and impairment of photosynthesis. We complemented our approach with a gene co-expression network analysis to identify wheat targets to deliver resistance to Pgt through removal or modification of putative susceptibility genes.

Isolate-Specific Responses of the Nonhost Grass Brachypodium distachyon to the Fungal Pathogen Zymoseptoria tritici Compared with Wheat

Septoria tritici blotch (STB) is an important foliar disease of wheat that is caused by the fungal pathogen Zymoseptoria tritici. The grass Brachypodium distachyon has been used previously as a model system for cereal-pathogen interactions. In this study, we examined the nonhost resistance (NHR) response of B. distachyon to two different Z. tritici isolates in comparison with wheat. These isolates vary in aggressiveness on wheat cultivar Remus, displaying significant differences in disease and pycnidia coverage. Using microscopy, we found that similar isolate-specific responses were observed for hydrogen peroxide accumulation and cell death in both wheat and B. distachyon. Despite this, induction of isolate-specific patterns of defense gene expression by Z. tritici did differ between B. distachyon and wheat. Our results suggest that expression of the phenylalanine ammonia lyase PAL gene may be important for NHR in B. distachyon, while pathogenesis-related PR genes and expression of genes regulating reactive oxygen species may be important to limit disease in wheat. Future studies of the B. distachyon-Z. tritici interaction may allow identification of conserved plant immunity targets that are responsible for the isolate-specific responses observed in both plant species.