The genera Cephalotrichum and Microascus contain ecologically, morphologically and lifestyle diverse fungi in Microascaceae (Microascales, Sordariomycetes) with a world-wide distribution. Despite previous studies having elucidated that Cephalotrichum and Microascus are highly polyphyletic, the DNA phylogeny of many traditionally morphology-defined species is still poorly resolved, and a comprehensive taxonomic overview of the two genera is lacking. To resolve this issue, we integrate broad taxon sampling strategies and the most comprehensive multi-gene (ITS, LSU, tef1 and tub2) datasets to date, with fossil calibrations to address the phylogenetic relationships and divergence times among major lineages of Microascaceae. Two previously recognised main clades, Cephalotrichum (24 species) and Microascus (49 species), were re-affirmed based on our phylogenetic analyses, as well as the phylogenetic position of 15 genera within Microascaceae. In this study, we provide an up-to-date overview on the taxonomy and phylogeny of species belonging to Cephalotrichum and Microascus, as well as detailed descriptions and illustrations of 21 species of which eight are newly described. Furthermore, the divergence time estimates indicate that the crown age of Microascaceae was around 210.37 Mya (95 % HPD: 177.18-246.96 Mya) in the Late Triassic, and that Cephalotrichum and Microascus began to diversify approximately 27.07 Mya (95 % HPD: 20.47-34.37 Mya) and 70.46 Mya (95 % HPD: 56.96-86.24 Mya), respectively. Our results also demonstrate that multigene sequence data coupled with broad taxon sampling can help elucidate previously unresolved clade relationships. Citation: Wei TP, Wu YM, Zhang X, et al. 2024. A comprehensive molecular phylogeny of Cephalotrichum and Microascus provides novel insights into their systematics and evolutionary history. Persoonia 52: 119-160. https://doi.org/10.3767/persoonia.2024.52.05 .

The genus Peronospora is the largest genus of the oomycetes, fungus-like members of the kingdom Straminipila that also contains amoeboid (e.g., Leukarachnion) and plant-like (e.g., Laminaria) lifeforms. Peronospora species are obligate biotrophic plant pathogens, causing high economic losses in various crops and ornamentals, including Plantago species. Several species of Plantago are used as speciality crops and medicinal plants. In this study, Peronospora species parasitic on Plantago were investigated based on morphology and phylogenetic analyses using two nuclear (ITS, nrLSU) loci and one mitochondrial (cox2) locus. As a result of these investigations, 10 new species are added to the already known Peronospora species on Plantago. Interestingly, it was found that four independent species are parasitic to Plantago major, highlighting that the reliance on the host plant for pathogen determination can be misleading in Peronospora. Taking this into account, morphological and phylogenetic analyses should be conducted as a prerequisite for effective quarantine regulations and phytosanitary measures. Citation: Mu M, Choi Y-J, Kruse J, et al. 2024. Single host plant species may harbour more than one species of Peronospora - a case study on Peronospora infecting Plantago. Persoonia 52: 94-118. https://doi.org/10.3767/persoonia.2024.52.04 .

Candida is a polyphyletic genus of asexually reproducing yeasts in the Saccharomycotina with more than 400 species that occur in almost all families of the subclass and its name is strongly connected with the infectious disease candidiasis. During the last two decades, approximately half of the Candida species have been reassigned into more than 36 already existing genera and 14 newly proposed genera, but the polyphyletic feature of the genus largely remained. Candida auris is an important, globally emerging opportunistic pathogen that has caused life-threatening outbreaks in healthcare facilities worldwide. This species belongs to the Candida auris-Candida haemuli (CAH) clade in the Metschnikowiaceae, a clade that contains multidrug-resistant clinically relevant species, but also species isolated from natural environments. The clade is phylogenetically positioned remotely from the type species of the genus Candida that is Candida vulgaris (currently interpreted as a synonym of Candida tropicalis) and belongs to the family Debaryomycetaceae. Although previous phylogenetic and phylogenomic studies confirmed the position of C. auris in the Metschnikowiaceae, these analyses failed to resolve the position of the CAH clade within the family and its delimitation from the genera Clavispora and Metschnikowia. To resolve the position of the CAH clade, phylogenomic and comparative genomics analyses were carried out to address the phylogenetic position of C. auris and related species in the Metschnikowiaceae using several metrics, such as the average amino acid identity (AAI) values, the percentage of conserved proteins (POCP) and the presence-absence patterns of orthologs (PAPO). Based on those approaches, 13 new genera are proposed for various Candida and Hyphopichia species, including members of the CAH clade in the Metschnikowiaceae. As a result, C. auris and related species are reassigned to the genus Candidozyma. Fifty-five new combinations and nine new species are introduced and this will reduce the polyphyly of the genus Candida. Citation: Liu F, Hu Z-D, Zhao X-M, et al. 2024. Phylogenomic analysis of the Candida auris-Candida haemuli clade and related taxa in the Metschnikowiaceae, and proposal of thirteen new genera, fifty-five new combinations and nine new species. Persoonia 52: 22-43. https://doi.org/10.3767/persoonia.2024.52.02 .

A correct classification of fungi, including yeasts, is of prime importance to understand fungal biodiversity and to communicate about this diversity. Fungal genera are mainly defined based on phenotypic characteristics and the results of single or multigene-based phylogenetic analyses. However, because yeasts often have less phenotypic characters, their classification experienced a strong move towards DNA-based data, from short ribosomal sequences to multigene phylogenies and more recently to phylogenomics. Here, we explore the usefulness of various genomics-based parameters to circumscribe fungal genera more correctly taking the yeast domain as an example. Therefore, we compared the results of a phylogenomic analysis, average amino acid identity (AAI) values, the presence of conserved signature indels (CSIs), the percentage of conserved proteins (POCP) and the presence-absence patterns of orthologs (PAPO). These genome-based metrics were used to investigate their usefulness in demarcating 13 hitherto relatively well accepted genera in Saccharomycetaceae, namely Eremothecium, Grigorovia, Kazachstania, Kluyveromyces, Lachancea, Nakaseomyces, Naumovozyma, Saccharomyces, Tetrapisispora, Torulaspora, Vanderwaltozyma, Zygosaccharomyces and Zygotorulaspora. As a result, most of these genera are supported by the genomics-based metrics, but the genera Kazachstania, Nakaseomyces and Tetrapisispora were shown to be genetically highly diverse based on the above listed analyses. Considering the results obtained for the presently recognized genera, a range of 80-92 % POCP values and a range of 60-70 % AAI values might be valuable thresholds to discriminate genera in Saccharomycetaceae. Furthermore, the genus-specific genes identified in the PAPO analysis and the CSIs were found to be useful as synapomorphies to characterize and define genera in Saccharomycetaceae. Our results indicate that the combined monophyly-based phylogenomic analysis together with genomic relatedness indices and synapomorphies provide promising approaches to delineating yeast genera and likely those of filamentous fungi as well. The genera Kazachstania, Nakaseomyces and Tetrapisispora are revised and we propose eight new genera and 41 new combinations. Citation: Liu F, Hu Z-D, Yurkov A, et al. 2024. Saccharomycetaceae: delinaeation of fungal genera based on phylogenomic analyses, genomic relatedness indices and genomics-based synapomorphies. Persoonia 52: 1-21. https://doi.org/10.3767/persoonia.2024.52.01.

Oceanic islands have been recognized as natural laboratories in which to study a great variety of evolutionary processes. One such process is evolutionary radiations, the diversification of a single ancestor into a number of species that inhabit different environments and differ in the traits that allow them to exploit those environments. The factors that drive evolutionary radiations have been studied for decades in charismatic organisms such as birds or lizards, but are lacking in lichen-forming fungi, despite recent reports of some lineages showing diversification patterns congruent with radiation. Here we propose the Ramalina decipiens group as a model system in which to carry out such studies. This group is currently thought to be comprised of five saxicolous species, all of them endemic to the Macaronesian region (the Azores, Madeira, Selvagens, Canary and Cape Verde islands). Three species are single-island endemics (a rare geographic distribution pattern in lichens), whereas two are widespread and show extreme morphological variation. The latter are suspected to harbor unrecognized species-level lineages. In order to use the Ramalina decipiens group as a model system it is necessary to resolve the group\'s phylogeny and to clarify its species boundaries. In this study we attempt to do so following an integrative taxonomy approach. We constructed a phylogenetic tree based on six molecular markers, four of which are newly developed and generated competing species hypotheses based on molecular (species discovery strategies based on both single locus and multilocus datasets) and phenotypic data (unsupervised clustering algorithms based on morphology, secondary chemistry and geographic origin). We found that taxonomic diversity in the Ramalina decipiens group has been highly underestimated in previous studies. In consequence, we describe six new species, most of them single-island endemics and provide a key to the group. Phylogenetic relationships among species have been reconstructed with almost full support which, coupled with the endemic character of the group, makes it an excellent system for the study of island radiations in lichen-forming fungi. Citation: Blázquez M, Pérez-Vargas I, Garrido-Benavent I, et al. 2024. Endless forms most frustrating: disentangling species boundaries in the Ramalina decipiens group (Lecanoromycetes, Ascomycota), with the description of six new species and a key to the group. Persoonia 52: 44-93. https://doi.org/10.3767/persoonia.2024.52.03 .

Two Gram-negative, obligately aerobic, rod-shaped bacteria, strains G1-22T and G1-23T, were isolated from the phycosphere of a marine brown alga. Both strains exhibited catalase- and oxidase-positive activities. Strain G1-22T displayed optimal growth at 25 °C, pH 8.0, and 2.0-3.0% (w/v) NaCl, while strain G1-23T exhibited optimal growth at 25 °C, pH 8.0, and 4.0% NaCl. Ubiquinone-8 was identified as the sole isoprenoid quinone in both strains. As major fatty acids (> 5%), strain G1-22T contained C16 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C12 : 1 3-OH, and C10 : 0 3-OH, while strain G1-23T contained C16 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), and C14 : 0. Phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol were major polar lipids in both strains. Strains G1-22T and G1-23T had DNA G+C contents of 40.2 and 38.9 mol%, respectively. Phylogenetic analyses based on 16S rRNA and genome sequences revealed that strains G1-22T and G1-23T formed distinct phylogenetic lineages within the genera Psychrosphaera and Paraglaciecola, respectively. Strain G1-22T showed closest relatedness to Psychrosphaera ytuae MTZ26T with 97.8% 16S rRNA gene sequence similarity, 70.2% average nucleotide identity (ANI), and a 21.5% digital DNA-DNA hybridization (dDDH) value, while strain G1-23T was most closely related to Paraglaciecola aquimarina KCTC 32108T with 95.6% 16S rRNA gene sequence similarity, 74.6% ANI, and a 20.1% dDDH value. Based on phenotypic and molecular characteristics, strains G1-22T and G1-23T are proposed to represent two novel species, namely Psychrosphaera algicola sp. nov. (type strain G1-22T=KACC 22486T=JCM 34971T) and Paraglaciecola algarum sp. nov. (type strain G1-23T=KACC 22490T=JCM 34972T), respectively. Additionally, based on the comparison of whole genome sequences, it is proposed that Pseudoalteromonas elyakovii, Pseudoalteromonas flavipulchra, and Pseudoalteromonas profundi are reclassified as later heterotypic synonyms of Pseudoalteromonas distincta, Pseudoalteromonas maricaloris, and Pseudoalteromonas gelatinilytica, respectively.

During a survey of culturable microfungi from the bark of sugar maple (Acer saccharum), Atrocalyx glutinosus and Nigrograna rubescens, two novel species of Pleosporales (Dothideomycetes) were isolated from several locations in eastern Ontario, Canada. Formal species descriptions are presented based on unique colony phenotypes and micromorphological characteristics and supported using multi-locus molecular phylogenetic comparisons with similar species. Both A. glutinosus and N. rubescens produce pycnidial asexual morphs in culture. As their names imply, under specific culture conditions, A. glutinosus excretes large amounts of the glutinous polysaccharide pullulan and N. rubescens produces a dark red naphthoquinone pigment that diffuses in the culture medium. Citation: Mack JN, Sproule A, Shields SW, Seifert KA, Smith M, Overy DP (2024). Two novel Pleosporales species isolated from the bark of Acer saccharum . Fungal Systematics and Evolution 13: 1-14. doi: 10.3114/fuse.2024.13.01.

A Gram-stain-positive, strictly aerobic, creamy-white colored, endospore-forming and non-motile rods strain, designated as strain 2205SS18-9T, was isolated from a marine sponge, Axinella sp. collected from Seopseom Island, Republic of Korea. Optimal growth of strain 2205SS18-9T was observed at 25-30 °C, pH 6.5-7.0, and in the presence of 3.0% (w/v) NaCl. Cells were oxidase-positive and catalase-negative. Negative for nitrate reduction and indole production. Phylogenetic analyses based on the 16S rRNA gene and whole-genome sequences revealed that strain 2205SS18-9T formed a distinct phyletic lineage in the genus Chengkuizengella, and it was most closely related to Chengkuizengella marina YPA3-1-1T and Chengkuizengella sediminis J15A17T with 97.1 and 96.6% 16S rRNA gene sequence similarities, respectively. The average nucleotide identity and digital DNA-DNA hybridization values between strain 2205SS18-9T and Chengkuizengella marina YPA3-1-1T were 79.0 and 21.6%, respectively. The genomic DNA G + C content was 34.1%. The genome harbors a number of host-adhesion and transporter genes, suggested that strain 2205SS18-9T may interact with its sponge host as a symbiont. Menaquinone-7 was the sole isoprenoid quinone and antieiso-C15:0 (28.5%), iso-C16:0 (25.8%), C16:1 ω7c alcohol (15.0%), and iso-C15:0 (11.2%) were detected as the major fatty acids. Polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified aminophospholipids, and an unidentified lipid. The cell-wall peptidoglycan contained lysine, alanine, glutamate, and aspartate. Based on these analyses, strain 2205SS18-9T represents a novel species of the genus Chengkuizengella, for which the name Chengkuizengella axinellae sp. nov. is proposed. The type strain is 2205SS18-9T (= KACC 23238T = LMG 33063T).

Two new Keratinophyton species, K. kautmanovae sp. nov. and K. keniense sp. nov., isolated from soil samples originating from two different geographical and environmental locations (Africa and Europe) are described and illustrated. Phylogenetically informative sequences obtained from the internal transcribed spacer (ITS) region and the nuclear large subunit (LSU) rDNA, as well as their unique phenotype, fully support novelty of these two fungi for this genus. Based on ITS and LSU combined phylogeny, both taxa are resolved in a cluster with eight accepted species, including K. alvearium, K. chongqingense, K. hubeiense, K. durum, K. lemmensii, K. siglerae, K. submersum, and K. sichuanense. The new taxon, K. kautmanovae, is characterized by clavate, smooth to coarsely verrucose conidia, absence of arthroconidia, slow growth at 25 °C, and no growth at 30 °C, while K. keniense is morphologically unique with a high diversity of conidial shapes (clavate, filiform, globose, cymbiform and rhomboid). Both species are described based on their asexual, a chrysosporium-like morph. While the majority of hitherto described Keratinophyton taxa came from Europe, India and China, the new species K. keniense represents the first reported taxonomic novelty for this genus from Africa.

Two new Cortinarius species in subgenus Leprocybe, Cortinarius hengduanensis and C. yadingensis, are proposed based on a combination of morphological and molecular evidence. Cortinarius hengduanensis has distinct olive tinged basidiomata, a squamulose pileus, and small, subglobose to broadly ellipsoid basidiospores, the ITS sequence differs from that of C. flavifolium by at least 28 substitutions and independent positions. Cortinarius yadingensis has a squamulose pileus and subglobose to broadly ellipsoid coarsely verrucose basidiospores, the ITS sequence has at least 11 substitutions and index position deviations from the other members of the Leprocybe section. Both new species were found in mixed forests of southwest China.