A fungi hotspot deep in the ocean: explaining the presence of Gjaerumia minor in equatorial Pacific bathypelagic waters.

A plant parasite associated with the white haze disease in apples, the Basidiomycota Gjaerumia minor, has been found in most samples of the global bathypelagic ocean. An analysis of environmental 18S rDNA sequences on 12 vertical profiles of the Malaspina 2010 expedition shows that the relative abundance of this cultured species increases with depth while its distribution is remarkably different between the deep waters of the Pacific and Atlantic oceans, being present in higher concentrations in the former. This is evident from sequence analysis and a microscopic survey with a species-specific newly designed TSA-FISH probe. Several hints point to the hypothesis that G. minor is transported to the deep ocean attached to particles, and the absence of G. minor in bathypelagic Atlantic waters could then be explained by the absence of this organism in surface waters of the equatorial Atlantic. The good correlation of G. minor biomass with Apparent Oxygen Utilization, recalcitrant carbon and free-living prokaryotic biomass in South Pacific waters, together with the identification of the observed cells as yeasts and not as resting spores (teliospores), point to the possibility that once arrived at deep layers this species keeps on growing and thriving.

Mrakia polaris sp. nov. and Mrakia amundsenii sp. nov. (Mrakiaceae, Cystofilobasidiales), two novel psychrophilic yeast species isolated from Arctic habitats.

Four yeast strains belonging to the basidiomycetous yeast genus Mrakia were isolated from diverse habitats in the Ny-Ålesund region (Svalbard, High Arctic): two from vascular plants, one from seawater and one from freshwater. Phylogenetic analysis, based on the ITS region and the D1/D2 domain of the 28S rRNA gene, identified these four strains as representing two novel species within the genus Mrakia. The names Mrakia polaris sp. nov. (MycoBank number: MB 852063) and Mrakia amundsenii sp. nov. (MycoBank number: MB 852064) are proposed. These two new species show distinct psychrophilic adaptations, as they exhibit optimal growth at temperatures between 10 and 15°C, while being unable to grow at 25°C. The holotype of M. polaris sp. nov. is CPCC 300345T, and the holotype of M. amundsenii sp. nov. is CPCC 300572T.

How do phytophagous insects affect phyllosphere fungi? Tracking fungi from milkweed to monarch caterpillar frass reveals communities dominated by fungal yeast.

Since a significant proportion of plant matter is consumed by herbivores, a necessary adaptation for many phyllosphere microbes could be to survive through the guts of herbivores. While many studies explore the gut microbiome of herbivores by surveying the microbiome in their frass, few studies compare the phyllosphere microbiome to the gut microbiome of herbivores. High-throughput metabarcode sequencing was used to track the fungal community from milkweed (Asclepias spp.) leaves to monarch caterpillar frass. The most commonly identified fungal taxa that dominated the caterpillar frass after the consumption of leaves were yeasts, mostly belonging to the Basidiomycota phylum. While most fungal communities underwent significant bottlenecks and some yeast taxa increased in relative abundance, a consistent directional change in community structure was not identified from leaf to caterpillar frass. These results suggest that some phyllosphere fungi, especially diverse yeasts, can survive herbivory, but whether herbivory is a key stage of their life cycle remains uncertain. For exploring phyllosphere fungi and the potential coprophilous lifestyles of endophytic and epiphytic fungi, methods that target yeast and Basidiomycota fungi are recommended.

Austropuccinia licaniae, first congeneric with the myrtle rust pathogen A. psidii.

In 1895 and 2001, rust fungi affecting Licania trees (Chrysobalanchaceae) in Brazil were described as Uredo licaniae by Hennings in the state of Goiás and as Phakopsora tomentosae by Ferreira et al. in the state of Amazonas, respectively. Recently, a Licania rust fungus collected close to the Amazonian type location sharing symptoms with the former two species was subjected to morphological examinations and molecular phylogenetic analyses using 28S nuc rDNA (ITS2-28S) and cytochrome c oxidase subunit III (CO3) gene sequences. Since the original type specimen of Ph. tomentosae is considered lost, we carefully reviewed the type description and questioned the identity of the telium, which justified the description of the fungus as a Phakopsora species. Furthermore, the additional revision of the type material described by Hennings revealed that Ph. tomentosae is a synonym of U. licaniae. Based on the morphological examinations, disease symptoms, and shared hosts, we concluded that the newly collected material is conspecific with U. licaniae. However, the phylogenetic analyses rejected allocation in Phakopsora and instead assigned the Licania rust fungus in a sister relationship with Austropuccinia psidii (Sphaerophragmiaceae), the causal agent of the globally invasive myrtle rust pathogen. We therefore favored a recombination of U. licaniae (syn. Ph. tomentosae) into Austropuccinia and proposed the new name Austropuccina licaniae for the second species now identified for this genus. The fungus shares conspicuous symptoms with A. psidii, causing often severe infections of growing leaves and shoots that lead to leaf necrosis, leaf shedding, and eventually to the dieback of entire shoots. In view of the very similar symptoms of its aggressively invasive sister species, we briefly discuss the current state of knowledge about A. licaniae and the potential risks, and the opportunity of its identification.

Screening of White-Rot Fungi Isolates for Decolorization of Pulp and Paper Mill Effluent and Assessment of Biodegradation and Biosorption Processes.

Ten white-rot fungal isolates were evaluated for the decolorization potential of pulp and paper mill effluent. Trametes elegans PP17-06, Pseudolagarobasidium sp. PP17-33, and Microporus sp.2 PP17-20 showed the highest decolorization efficiencies between 42 and 54% in 5 d. To reveal the mechanisms involved in decolorization and assess the long-term performance, PP17-06, which showed the highest decolorization efficiency, was further investigated. It could reduce the ADMI color scale by 63.6% in 10 d. However, extending the treatment period for more than 10 d did not significantly enhance the decolorization efficiencies. The maximum MnP activity of 3.27 U L-1 was observed on the 6 d during the biodegradation. In comparison, laccase activities were low with the maximum activity of 0.38 U L-1 (24 d). No significant LiP activities were monitored during the experiment. Dead fungal biomass showed an optimum decolorization efficiency of 44.18% in 8 d employing the biosorption mechanism. No significant changes in the decolorization efficiency were observed after that, suggesting the equilibrium status was reached. These results revealed that PP17-06 has the potential to decolorize pulp and paper mill effluent by employing both biodegradation and biosorption processes.

Spencerozyma pingqiaoensis sp. nov., a yeast species isolated from the external surface of rice leaves in China.

Four strains (NYNU 178247, NYNU 178251, DMKU-PAL160 and DMKU-PAL137) representing a novel yeast species were isolated from the external surfaces of rice and pineapple leaves collected in China and Thailand. Phylogenetic analysis based on the concatenated sequences of the internal transcribed spacer (ITS) regions and the D1/D2 domains of the large subunit rRNA gene revealed that the novel species belonged to the genus Spencerozyma. The D1/D2 sequence of the novel species differed from its closest relative, Spencerozyma acididurans SYSU-17T, by 3.2 % sequence divergence. The species also differed from Spencerozyma crocea CBS 2029T and Spencerozyma siamensis DMKU13-2T, by 3.0-6.9 % sequence divergence in the D1/D2 sequences out of 592 bp. In the ITS regions, the novel species displayed 19.8-29.2% sequence divergence from S. acididurans SYSU-17T, S. crocea CBS 2029T and S. siamensis DMKU13-2T out of 655 bp. Furthermore, the novel species could also be differentiated from the closely related species by some physiological characteristics. The species name of Spencerozyma pingqiaoensis sp. nov. (Holotype CBS 15238, Mycobank MB 844734) is proposed to accommodate these four strains.

Begerowomyces aurantius sp. nov., a novel yeast isolated from koalas' habitat in a Japanese zoological park.

Koalas are iconic mammals indigenous to Australia. These rare animals and their habitats are occasionally associated with pathogenic fungi, including species of Cryptococcus, and consequently, monitoring the mycobiota of areas inhabited by koalas is of considerable importance. In this report, we describe a novel basidiomycetous yeast isolated from a site in Kanazawa Zoo, Japan, associated with captive koalas. Swab samples were collected from koala breeding environments, from which we isolated a novel unencapsulated yeast characterized by ovoid to ellipsoidal cells (3.2-4.9 × 3.5-5 µm). These cells were observed to undergo polar budding and grow as parent bud pairs, with an optimal growth temperature of 28°C. Colonies grown on yeast extract peptone dextrose agar at 28°C have a characteristic coral pink color. On the basis of physiological, morphological, and molecular characters, the new species was placed in the genus Begerowomyces, and the name Begerowomyces aurantius JCM33898T(LSEM1333T=CBS16241T) is proposed.

Tremella ananatis sp. nov. and Tremella lamprococci sp. nov., two yeast species associated with bromeliads.

Eight yeast isolates with an affinity to the genus Tremella were obtained from bromeliads from different locations in Brazil. Although the formation of basidia and basidiocarp were not observed, on the basis of the results of sequence analysis of the D1/D2 domain of the large subunit (LSU) rRNA gene and internal transcribed spacer (ITS) region, we suggest that these isolates represent two novel species of the genus Tremella. These yeasts are phylogenetically related to Tremella saccharicola and Tremella globispora. Therefore, we propose Tremella ananatis sp. nov. and Tremella lamprococci sp. nov. as novel yeast species of the order Tremellales (Agaricomycotina, Basidiomycota). Sequence analysis revealed that Tremella ananatis sp. nov. differs by 11 and 28 nucleotide substitutions from Tremella saccharicola in the D1/D2 sequence and ITS region, respectively. Moreover, Tremella lamprococci sp. nov. differs by 15 and 29 nucleotide substitutions from Tremella globispora in the D1/D2 sequence and ITS region, respectively. The holotypes of Tremella ananatis sp. nov. and Tremella lamprococci sp. nov. are CBS 14568T and CBS 14567T, and the MycoBank numbers are MB840480 and MB840481, respectively.

qPCR Assays for Sensitive and Rapid Detection of Quambalaria Species from Plant Tissues.

Several species from the genus Quambalaria (order Microstromatales) cause diseases on eucalypts (Eucalyptus and related genera) both in plantations and natural ecosystems. We developed real-time quantitative PCR (qPCR) assays to rapidly detect and distinguish five Quambalaria species. The design of the species-specific qPCR assay for each species, Q. pitereka (PIT), Q. coyrecup (COR), Q. cyanescens (CYN), Q. pusilla (PUS), and Q. eucalypti (EUC), was based on the ITS region and was evaluated for specificity and sensitivity. The PIT, COR, and CYN qPCR assays could amplify as little as 10 fg µl-1 from pure cultures, whereas PUS and EUC qPCR assays could amplify 100 fg µl-1 of their target species. The PIT, COR, and CYN qPCR assays were further validated using naturally and artificially infected samples of their plant host Corymbia calophylla. These assays will be used for rapid diagnostics and future experiments on the infection process.

Omnipresence of Partitiviruses in Rice Aggregate Sheath Spot Symptom-Associated Fungal Isolates from Paddies in Thailand.

Partitiviruses are one of the most prevalent double-stranded RNA viruses that have been identified mostly in filamentous fungi and plants. Partitiviruses generally infect host fungi asymptomatically but infrequently exert significant effect(s) on morphology and virulence, thus being considered a potential source of biological control agents against pathogenic fungi. In this study, we performed a screening for mycoviruses of a collection of Thai isolates of rice fungal pathogen Rhizoctonia oryzae-sativae, a causal agent of rice aggregated sheath spot disease. As a result, 36% of tested isolates carried potentially viral double-stranded RNAs with sizes ranging from 2 to 3 kbp. By conventional cDNA library construction and RNA-seq, we determined six new alphapartitiviruses that infected three isolates: tentatively named Rhizoctonia oryzae-sativae partitivirus 1 to 6 (RosPV1-6). Furthermore, RT-PCR detection of each virus revealed their omnipresent nature in different R. oryzae-sativae isolates. Although virus-curing of basidiomycetous fungi is generally difficult, our repeated attempts successfully obtained virus-free (for RosPV1, RosPV2, and uncharacterized partitiviruses), isogenic strain of R. oryzae-sativae TSS190442. The virus-cured strain showed slightly faster colony growth on the synthetic media and severe symptom development on the rice sheath compared to its virus-infected counterpart. Overall, this study shed light on the distribution of partitiviruses in R. oryzae-sativae in a paddy environment and exemplified a virus-curing protocol that may be applicable for other basidiomycetous fungi.

Phaffia brasiliana sp. nov., a yeast species isolated from soil in a Cerrado-Atlantic Rain Forest ecotone site in Brazil.

During studies of yeasts associated with soil in a Cerrado-Atlantic Rain Forest ecotone site in Brazil, three orange-pigmented yeast strains were isolated from samples collected in Minas Gerais state, Brazil. Molecular analyses combining the 26S rRNA gene (D1/D2 domains) and the internal transcribed spacer (ITS) sequences as well as whole-genome sequence data showed that these strains could not be ascribed to any known species in the basidiomycetous genus Phaffia, and thus they are considered to represent a novel species for which the name Phaffia brasiliana sp. nov. is proposed. The holotype is CBS 16121T and the MycoBank number is MB 839315. The occurrence of P. brasiliana in a tropical region is unique for the genus, since all other species occur in temperate regions. Two factors appear to contribute to the distribution of the novel taxon: first, the region where it was found has relatively moderate temperature ranges and, second, an adaptation to grow or withstand temperatures higher than those of the other species in the genus seems to be in place.

Cryptococcus liquefaciens isolated from the hand of a healthcare professional in a neonatal intensive care unit.

Fungal infections are responsible for high morbidity and mortality in neonatal patients, especially in premature newborns. Infections in neonates caused by Cryptococcus spp. are rare, but it has occurred in an immunocompromised population. This study aims to describe the isolation of Cryptococcus liquefaciens from the hands of a health professional in a neonatal intensive care unit, and to evaluate the production of biofilm and virulence factors and susceptibility to antifungals. Antifungal susceptibility tests were performed according to Clinical and Laboratory Standard Institute document M27-A3. Thermotolerance virulence factors and DNase, phospholipase, proteinase, and hemolytic activities were verified through phenotypic tests; biofilm was evaluated by determining the metabolic activity and biomass. The isolate did not produce any of the tested enzymes and was susceptible to all antifungals (amphotericin B, fluconazole, and micafungin). The growth at 37 °C was very weak; however, the isolate showed a strong biomass production and low metabolic activity. This is the first report of C. liquefaciens isolated from the hands of a health professional. The isolate did not express any of the studied virulence factors in vitro, except for the low growth at 37 °C in the first 48 h, and the strong production of biofilm biomass. Cryptococcus liquefaciens can remain in the environment for a long time and is a human pathogen because it tolerates temperature variations. This report draws attention to the circulation of rare species in critical locations, information that may help in a fast and correct diagnosis and, consequently, implementation of an appropriate treatment.

Bilateral Trichosporon asahii keratitis after ptosis correction: A case report.

RATIONALE: Fungal keratitis (FK) is a severe vision-threatening disease that can lead to corneal perforation or endophthalmitis despite proper treatment. It is important to diagnose the disease promptly due to its indolent nature and disproportionate disease symptoms. Trichosporon asahii is reported rarely as the causative organism of FK. We report a case of highly unusual bilateral T asahii keratitis following ptosis surgery. PATIENT CONCERNS: An 86-year-old female underwent bilateral levator resection surgery for ptosis. Postoperatively, the patient complained of gradually worsening bilateral ocular pain and a decrease in visual acuity associated with a chronic non-healing epithelial defect. DIAGNOSES: Both eyes of the patient were evaluated using best-corrected visual acuity, intraocular pressure, slit-lamp examination, fundus examination, and corneal culture. Multifocal deep stromal infiltrates were found in both corneas. Cultures from both corneal ulcers revealed growth of T asahii. Optical coherence tomographic examination showed bilateral macular edema. INTERVENTIONS: The patient was treated with revisional ptosis surgery, an antifungal agent for the corneal ulcer, and intravitreal injection of steroid for macular edema. OUTCOMES: Both eyes recovered well. Her best-corrected visual acuity improved from 20/200 to 20/40 in the right eye and from 20/100 to 20/40 in the left eye. LESSONS: FK can develop in the cornea when certain risk factors are present, including recent lid surgery, chronic keratitis, and steroid eye drop use. Identification and correction of risk factors can be beneficial in the treatment of FK.

Inopinatum lactosum gen. & comb. nov., the first yeast-like fungus in Leotiomycetes.

Sporobolomyces lactosus is a pink yeast-like fungus that is not congeneric with other members of Sporobolomyces (Basidiomycota, Microbotryomycetes, Sporidiobolales). During our ongoing studies of pink yeasts we determined that S. lactosus was most closely related to Pseudeurotium zonatum (Ascomycota, Leotiomycetes, Thelebolales). A molecular phylogenetic analysis using sequences of the ITS region and the small and large subunit (SSU, LSU) rRNA genes, indicated that four isolates of S. lactosus, including three ex-type isolates, were placed in Thelebolales with maximum support. A new genus is proposed to accommodate S. lactosus, Inopinatum. This is the first pink yeast reported in Leotiomycetes.

The Enigmatic Snow Microorganism, Chionaster nivalis, Is Closely Related to Bartheletia paradoxa (Agaricomycotina, Basidiomycota).

Chionaster nivalis is frequently detected in thawing snowpacks and glaciers. However, the taxonomic position of this species above the genus level remains unclear. We herein conducted molecular analyses of C. nivalis using the ribosomal RNA operon sequences obtained from more than 200 cells of this species isolated from a field-collected material. Our molecular phylogenetic analyses revealed that C. nivalis is a sister to Bartheletia paradoxa, which is an orphan basal lineage of Agaricomycotina. We also showed that C. nivalis sequences were contained in several previously examined meta-amplicon sequence datasets from snowpacks and glaciers in the Northern Hemisphere and Antarctica.

Development of a loop-mediated isothermal amplification assay for the detection of Tilletia controversa based on genome comparison.

Tilletia controversa causing dwarf bunt of wheat is a quarantine pathogen in several countries. Therefore, its specific detection is of great phytosanitary importance. Genomic regions routinely used for phylogenetic inferences lack suitable polymorphisms for the development of species-specific markers. We therefore compared 21 genomes of six Tilletia species to identify DNA regions that were unique and conserved in all T. controversa isolates and had no or limited homology to other Tilletia species. A loop-mediated isothermal amplification (LAMP) assay for T. controversa was developed based on one of these DNA regions. The specificity of the assay was verified using 223 fungal samples comprising 43 fungal species including 11 Tilletia species, in particular 39 specimens of T. controversa, 92 of T. caries and 40 of T. laevis, respectively. The assay specifically amplified genomic DNA of T. controversa from pure cultures and teliospores. Only Tilletia trabutii generated false positive signals. The detection limit of the LAMP assay was 5 pg of genomic DNA per reaction. A test performance study that included five laboratories in Germany resulted in 100% sensitivity and 97.7% specificity of the assay. Genomic regions, specific to common bunt (Tilletia caries and Tilletia laevis together) are also provided.

Trichosporon asahii superinfections in critically ill COVID-19 patients overexposed to antimicrobials and corticosteroids.

OBJECTIVES: To investigate the occurrence of Trichosporon asahii fungemia among critically ill COVID-19 patients. METHODS: From 1 July to 30 September 2020, cases of T asahii fungemia (TAF) in a Brazilian COVID-19 referral centre were investigated. The epidemiology and clinical courses were detailed, along with a mycological investigation that included molecular species identification, haplotype diversity analysis and antifungal susceptibility testing. RESULTS: Five critically ill COVID-19 patients developed TAF in the period. All five patients had common risk conditions for TAF: central venous catheter at fungemia, previous exposure to broad-spectrum antibiotics, prior echinocandin therapy and previous prolonged corticosteroid therapy. The average time of intensive care unit hospitalisation previous to the TAF episode was 23 days. All but one patient had voriconazole therapy, and TAF 30-day mortality was 80%. The five T asahii strains from the COVID-19 patients belonged to 4 different haplotypes, mitigating the possibility of skin origin and cross-transmission linking the 5 reported episodes. The antifungal susceptibility testing revealed low minimal inhibitory concentrations for azole derivatives. CONCLUSIONS: Judicious prescription of antibiotics, corticosteroids and antifungals needs to be discussed in critically ill COVID-19 patients to prevent infections by hard-to-treat fungi like T asahii.

Native yeast and non-yeast fungal communities of Cabernet Sauvignon berries from two Washington State vineyards, and persistence in spontaneous fermentation.

To address a knowledge gap about the grape berry mycobiome from Washington State vineyards, next-generation sequencing of the internal transcribed spacer region (ITS1) was used to identify native yeast and fungal species on berries of cultivar 'Cabernet Sauvignon' from two vineyards at veraison and harvest in 2015 and 2016. Four hundred fifty-six different yeast amplicon sequence variants (ASV), representing 184 distinct taxa, and 2467 non-yeast fungal ASV (791 distinct taxa) were identified in this study. A set of 50 recurrent yeast taxa, including Phaeococcomyces, Vishniacozyma and Metschnikowia, were found at both locations and sampling years. These yeast species were monitored from the vineyard into laboratory-scale spontaneous fermentations. Taxa assignable to Metschnikowia and Saccharomyces persisted during fermentation, whereas Curvibasidium, which also has possible impact on biocontrol and wine quality, did not. Sulfite generally reduced yeast diversity and richness, but its effect on the abundance of specific yeasts during fermentation was negligible. Among the 106 recurring non-yeast fungal taxa, Alternaria, Cladosporium and Ulocladium were especially abundant in the vineyard. Vineyard location was the primary factor that accounted for the variation among both communities, followed by year and berry developmental stage. The Washington mycobiomes were compared to those from other parts of the world. Sixteen recurrent yeast species appeared to be unique to Washington State vineyards. This subset also contained a higher proportion of species associated with cold and extreme environments, relative to other localities. Certain yeast and non-yeast fungal species known to suppress diseases or modify wine sensory properties were present in Washington vineyards, and likely have consequences to vineyard health and wine quality.

Greenland and Svalbard glaciers host unknown basidiomycetes: the yeast Camptobasidium arcticum sp. nov. and the dimorphic Psychromyces glacialis gen. and sp. nov.

Sampling campaigns in Greenland and Svalbard were executed to explore fungal diversity in cold habitats. Three very abundant groups of strains were discovered, consisting either of recently described or of yet-undescribed psychrophilic and oligotrophic yeasts and dimorphic fungi, accounting for around 50 % of the total cultivable diversity of basidiomycetes in our studies. The occurrence of these taxa has also been demonstrated by culture-independent methods. Based on phylogenetic analyses of ribosomal gene cluster sequences (D1/D2 domains of 28S (LSU), 18S (SSU), ITS with 5.8S rDNA) and sequences of protein-coding genes for elongation factor one alpha (TEF), cytochrome b (CYTB) and two subunits of the RNA polymerase II (RPB1 and RPB2) obtained from pure cultures, the isolated taxa presented in this study belong to Basidiomycota, subphylum Pucciniomycotina, class Microbotryomycetes, family Camptobasidiaceae. The dataset of the sequences supported the recognition of three species: Camptobasidium gelus, Camptobasidium arcticum sp. nov. (ex-type strain EXF-12713) and Psychromyces glacialis gen. and sp. nov. (ex-type strain EXF-13111). Camptobasidium gelus was found in the Svalbard and Greenland samples, while representatives of the here proposed new species, C. arcticum, were found only in the Greenland Ice Sheet. Psychromyces gen. nov. was erected for the dimorphic/filamentous isolates found in Svalbard and Greenland glacial environments. The taxon, for which the invalid name 'Rhodotorula svalbardensis' has been used, belongs to this genus. Based on ribosomal genes, Camptobasidium arcticum and Psychromyces glacialis are related, phylogenetically most closely related to the genera Glaciozyma and Cryolevonia. Seven genes phylogeny restricted to taxa with available sequences, supported the placement of Psychromyces to Camptobasidiaceae.