First report of rust caused by Gymnosporangium in Iceland.

Sorbus is a genus of trees and shrubs in the Rosaceae commonly known as rowan and mountain-ash. They are usually found in temperate regions of the Northern Hemisphere and cultivated as ornamental trees for parks and gardens. In September 2023, infection by a rust was observed on a single Sorbus aucuparia tree in Sólbrekkuskógur, Reykjanesbær (64.046645, -22.707276; ~13 m) in Iceland. Infected leaves were collected from this single cultivated tree at an outdoor recreation area in a natural wooded location, with a 2% disease severity. Sori were infrequent, scattered, embedded within circular yellow lesions on leaf margins. On average, one sorus was observed per leaf and only 2% of leaves were infected. Spermogonia epiphyllous, punctate and aggregated, pale yellow to black. Hypophyllous aecia roestelioid with cornute peridium rupturing at apex with peridial cells rhomboidal, aeciospores yellowish brown globoid 17.67-25.17 x 17.20-21.94 µm, walls 1.22-2.28 µm thick (n = 20). The features of this rust and dimensions of spores are consistent with descriptions of Gymnosporangium cornutum (Arthur 1909, Kern 1911). To confirm the identity (specimen MCA9732), a ~620 bp region of the 28S subunit of the ribosomal DNA repeat was sequenced using primers Rust2inv and LR6 following published protocols (Aime 2006). The sequence (GenBank PP413765) shared 100% (649/649 bp) identity with a sequence deposited as Gymnosporangium cornutum (KY764066, BPI910184; J. E. Demers, M. K. Romberg, and L. A. Castlebury, unpublished data) from S. americana and 100% (620/620 bp) identity with G. cornutum (PURN11049) on Sorbus sp. from Canada when blasted against the RustHUBB database (Kaishian et al. 2024). The specimen has been deposited in the Arthur Fungarium at Purdue University as PURN24233. Disease on Sorbus sp. caused by G. cornutum has been reported in various countries in Africa, Asia, North America, and Europe (Kern 1911). To our knowledge, this is the first report of the occurrence of this genus in Iceland from any host. Gymnosporangium cornutum alternates on Juniperus species. In Iceland, J. communis (sect. Oxycedrus) seems to be the only naturally occurring Juniperus species but it is an alternate host for G. cornutum. The presence of the primary and alternative hosts in Iceland and the ability of Gymnosporangium spp. to produce systemic infections in Juniperus spp., represents the potential for reinfection of Sorbus every year, resulting in potential impacts on both host species. With J. communis being the only Juniperus spp. in natural habitats in Iceland, the presence of this rust represents a potential ecological disruption, as repeated infections may reduce host vitality and predispose the host to winter injury and attack from opportunistic pathogens or insects.

DNA Sequence-Based Identification of Fusarium: A Work in Progress.

Accurate species-level identification of an etiological agent is crucial for disease diagnosis and management because knowing the agent's identity connects it with what is known about its host range, geographic distribution, and toxin production potential. This is particularly true in publishing peer-reviewed disease reports, where imprecise and/or incorrect identifications weaken the public knowledge base. This can be a daunting task for phytopathologists and other applied biologists that need to identify Fusarium in particular, because published and ongoing multilocus molecular systematic studies have highlighted several confounding issues. Paramount among these are: (i) this agriculturally and clinically important genus is currently estimated to comprise more than 400 phylogenetically distinct species (i.e., phylospecies), with more than 80% of these discovered within the past 25 years; (ii) approximately one-third of the phylospecies have not been formally described; (iii) morphology alone is inadequate to distinguish most of these species from one another; and (iv) the current rapid discovery of novel fusaria from pathogen surveys and accompanying impact on the taxonomic landscape is expected to continue well into the foreseeable future. To address the critical need for accurate pathogen identification, our research groups are focused on populating two web-accessible databases (FUSARIUM-ID v.3.0 and the nonredundant National Center for Biotechnology Information nucleotide collection that includes GenBank) with portions of three phylogenetically informative genes (i.e., TEF1, RPB1, and RPB2) that resolve at or near the species level in every Fusarium species. The objectives of this Special Report, and its companion in this issue (Torres-Cruz et al. 2022), are to provide a progress report on our efforts to populate these databases and to outline a set of best practices for DNA sequence-based identification of fusaria.

FUSARIUM-ID v.3.0: An Updated, Downloadable Resource for Fusarium Species Identification.

Species within Fusarium are of global agricultural, medical, and food/feed safety concern and have been extensively characterized. However, accurate identification of species is challenging and usually requires DNA sequence data. FUSARIUM-ID (http://isolate.fusariumdb.org/blast.php) is a publicly available database designed to support the identification of Fusarium species using sequences of multiple phylogenetically informative loci, especially the highly informative ∼680-bp 5' portion of the translation elongation factor 1-alpha (TEF1) gene that has been adopted as the primary barcoding locus in the genus. However, FUSARIUM-ID v.1.0 and 2.0 had several limitations, including inconsistent metadata annotation for the archived sequences and poor representation of some species complexes and marker loci. Here, we present FUSARIUM-ID v.3.0, which provides the following improvements: (i) additional and updated annotation of metadata for isolates associated with each sequence, (ii) expanded taxon representation in the TEF1 sequence database, (iii) availability of the sequence database as a downloadable file to enable local BLAST queries, and (iv) a tutorial file for users to perform local BLAST searches using either freely available software, such as SequenceServer, BLAST+ executable in the command line, and Galaxy, or the proprietary Geneious software. FUSARIUM-ID will be updated on a regular basis by archiving sequences of TEF1 and other loci from newly identified species and greater in-depth sampling of currently recognized species.

Microscopic characterization of orchid mycorrhizal fungi: Scleroderma as a putative novel orchid mycorrhizal fungus of Vanilla in different crop systems.

Vanilla is an orchid of economic importance widely cultivated in tropical regions and native to Mexico. We sampled three species of Vanilla (V. planifolia, V. pompona, and V. insignis) in different crop systems. We studied the effect of crop system on the abundance, type of fungi, and quality of pelotons found in the roots using light and electron microscopy and direct sequencing of mycorrhizal structures. Fungi were identified directly from pelotons obtained from terrestrial roots of vanilla plants in the flowering stage. Root samples were collected from plants in crop systems located in the Totonacapan area in Mexico (states of Puebla and Veracruz). DNA was extracted directly from 40 pelotons and amplified using ITS rRNA sequencing. Peloton-like structures were observed, presenting a combination of active pelotons characterized by abundant hyphal coils and pelotons in various stages of degradation. The most active pelotons were observed in crop systems throughout living tutors (host tree) in comparison with roots collected from dead or artificial tutors. Fungi identified directly from pelotons included Scleroderma areolatum, a common ectomycorrhizal fungus that has not been reported as a mycorrhizal symbiont in orchids. Direct amplification of pelotons also yielded common plant pathogens, including Fusarium and Pyrenophora seminiperda, especially in those sites with low colonization rates, and where large numbers of degraded pelotons were observed. This research reports for the first time the potential colonization of Vanilla by Scleroderma, as a putative orchid mycorrhizal symbiont in four sites in Mexico and the influence of crop system on mycorrhizal colonization on this orchid.

Bifiguratus adelaidae, gen. et sp. nov., a new member of Mucoromycotina in endophytic and soil-dwelling habitats.

Illumina amplicon sequencing of soil in a temperate pine forest in the southeastern United States detected an abundant, nitrogen (N)-responsive fungal genotype of unknown phylogenetic affiliation. Two isolates with ribosomal sequences consistent with that genotype were subsequently obtained. Examination of records in GenBank revealed that a genetically similar fungus had been isolated previously as an endophyte of moss in a pine forest in the southwestern United States. The three isolates were characterized using morphological, genomic, and multilocus molecular data (18S, internal transcribed spacer [ITS], and 28S rRNA sequences). Phylogenetic and maximum likelihood phylogenomic reconstructions revealed that the taxon represents a novel lineage in Mucoromycotina, only preceded by Calcarisporiella, the earliest diverging lineage in the subphylum. Sequences for the novel taxon are frequently detected in environmental sequencing studies, and it is currently part of UNITE's dynamic list of most wanted fungi. The fungus is dimorphic, grows best at room temperature, and is associated with a wide variety of bacteria. Here, a new monotypic genus, Bifiguratus, is proposed, typified by Bifiguratus adelaidae.

Ribosomal RNA gene detection and targeted culture of novel nitrogen-responsive fungal taxa from temperate pine forest soil.

Soil fungal communities are responsible for carbon and nitrogen (N) cycling. The high complexity of the soil fungal community and the high proportion of taxonomically unidentifiable sequences confound ecological interpretations in field studies because physiological information is lacking for many organisms known only by their rRNA sequences. This situation forces experimental comparisons to be made at broader taxonomic racks where functions become difficult to infer. The objective of this study was to determine OTU (operational taxonomic units) level responses of the soil fungal community to N enrichment in a temperate pine forest experiment and to use the sequencing data to guide culture efforts of novel N-responsive fungal taxa. Replicate samples from four soil horizons (up to 10 cm depth) were obtained from ambient, enriched CO2 and N-fertilization plots. Through a fungal large subunit rRNA gene (LSU) sequencing survey, we identified two novel fungal clades that were abundant in our soil sampling (representing up to 27% of the sequences in some samples) and responsive to changes in soil N. The two N-responsive taxa with no predicted taxonomic association were targeted for isolation and culturing from specific soil samples where their sequences were abundant. Representatives of both OTUs were successfully cultured using a filtration approach. One taxon (OTU6) was most closely related to Saccharomycotina; the second taxon (OTU69) was most closely related to Mucoromycotina. Both taxa likely represent novel species. This study shows how observation of specific OTUs level responses to altered N status in a large rRNA gene field survey provided the impetus to design targeted culture approaches for isolation of novel N-responsive fungal taxa.