A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina

Funding Information: We want to thank Barbara Roberts from the NCBI Taxonomy Team for providing the update of the current fungal names in NCBI Taxonomic database. Masako Takashima is supported by the Institution for Fermentation, Osaka (IFO). Heide-Marie Daniel is supported by the Belgian Science Policy Office grant C5/00/BCCM. Chris Todd Hittinger is supported by the National Science Foundation under Grant Nos. DEB-1442148 and DEB-2110403, the USDA National Institute of Food and Agriculture (Hatch Project 1020204), in part by the DOE Great Lakes Bioenergy Research Center (DOE BER Office of Science DE–SC0018409, and an H.I. Romnes Faculty Fellowship, supported by the Office of the Vice Chancellor for Research and Graduate Education with funding from the Wisconsin Alumni Research Foundation. Research in Antonis Rokas’s lab is supported by grants from the National Science Foundation (DEB-1442113 and DEB-2110404), the National Institutes of Health/National Institute of Allergy and Infectious Diseases (R01 AI153356), and the Burroughs Wellcome Fund. Antonis Rokas acknowledges support from a Klaus Tschira Guest Professorship from the Heidelberg Institute for Theoretical Studies and from a Visiting Research Fellowship from Merton College of the University of Oxford. Marc-André Lachance acknowledges lifelong financial support from the Natural Sciences and Engineering Research Council of Canada. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Carlos A. Rosa is supported by the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq – Brazil, process numbers 408733/2021-7 and 406564/2022-1); Fundação do Amparo a Pesquisa do Estado de Minas Gerais (FAPEMIG, process numberAPQ-01525-14). Teun Boekhout is supported by the Distinguished Scientist Fellow Program of King Saud University, Ryadh, Saudi Arabia. Publisher Copyright: © 2023 Westerdijk Fungal Biodiversity Institute.The subphylum Saccharomycotina is a lineage in the fungal phylum Ascomycota that exhibits levels of genomic diversity similar to those of plants and animals. The Saccharomycotina consist of more than 1 200 known species currently divided into 16 families, one order, and one class. Species in this subphylum are ecologically and metabolically diverse and include important opportunistic human pathogens, as well as species important in biotechnological applications. Many traits of biotechnological interest are found in closely related species and often restricted to single phylogenetic clades. However, the biotechnological potential of most yeast species remains unexplored. Although the subphylum Saccharomycotina has much higher rates of genome sequence evolution than its sister subphylum, Pezizomycotina, it contains only one class compared to the 16 classes in Pezizomycotina. The third subphylum of Ascomycota, the Taphrinomycotina, consists of six classes and has approximately 10 times fewer species than the Saccharomycotina. These data indicate that the current classification of all these yeasts into a single class and a single order is an underappreciation of their diversity. Our previous genome-scale phylogenetic analyses showed that the Saccharomycotina contains 12 major and robustly supported phylogenetic clades; seven of these are current families (Lipomycetaceae, Trigonopsidaceae, Alloascoideaceae, Pichiaceae, Phaffomycetaceae, Saccharomycodaceae, and Saccharomycetaceae), one comprises two current families (Dipodascaceae and Trichomonascaceae), one represents the genus Sporopachydermia, and three represent lineages that differ in their translation of the CUG codon (CUG-Ala, CUG-Ser1, and CUG-Ser2). Using these analyses in combination with relative evolutionary divergence and genome content analyses, we propose an updated classification for the Saccharomycotina, including seven classes and 12 orders that can be diagnosed by genome content. This updated classification is consistent with the high levels of genomic diversity within this subphylum and is necessary to make the higher rank classification of the Saccharomycotina more comparable to that of other fungi, as well as to communicate efficiently on lineages that are not yet formally named.publishersversionpublishe

Nomenclatural issues concerning cultured yeasts and other fungi: why it is important to avoid unneeded name changes

The unambiguous application of fungal names is important to communicate scientific findings. Names are critical for (clinical) diagnostics, legal compliance, and regulatory controls, such as biosafety, food security, quarantine regulations, and industrial applications. Consequently, the stability of the taxonomic system and the traceability of nomenclatural changes is crucial for a broad range of users and taxonomists. The unambiguous application of names is assured by the preservation of nomenclatural history and the physical organisms representing a name. Fungi are extremely diverse in terms of ecology, lifestyle, and methods of study. Predominantly unicellular fungi known as yeasts are usually investigated as living cultures. Methods to characterize yeasts include physiological (growth) tests and experiments to induce a sexual morph; both methods require viable cultures. Thus, the preservation and availability of viable reference cultures are important, and cultures representing reference material are cited in species descriptions. Historical surveys revealed drawbacks and inconsistencies between past practices and modern requirements as stated in the International Code of Nomenclature for Algae, Fungi, and Plants (ICNafp). Improper typification of yeasts is a common problem, resulting in a large number invalid yeast species names. With this opinion letter, we address the problem that culturable microorganisms, notably some fungi and algae, require specific provisions under the ICNafp. We use yeasts as a prominent example of fungi known from cultures. But viable type material is important not only for yeasts, but also for other cultivable Fungi that are characterized by particular morphological structures (a specific type of spores), growth properties, and secondary metabolites. We summarize potential proposals which, in our opinion, will improve the stability of fungal names, in particular by protecting those names for which the reference material can be traced back to the original isolate

Fluid release from the subducted Cocos plate and partial melting of the crust deduced from magnetotelluric studies in southern Mexico: implications for the generation of volcanism and subduction dynamics

In order to study electrical conductivity phenomena that are associated with subduction related fluid release and melt production, magnetotelluric (MT) measurements were carried out in southern Mexico along two coast to coast profiles. The conductivity-depth distribution was obtained by simultaneous two-dimensional inversion of the transverse magnetic and transverse electric modes of the magnetotelluric transfer functions. The MT models demonstrate that the plate southern profile shows enhanced conductivity in the deep crust. The northern profile is dominated by an elongated conductive zone extending >250 km below the Trans-Mexican Volcanic Belt (TMVB). The isolated conductivity anomalies in the southern profile are interpreted as slab fluids stored in the overlying deep continental crust. These fluids were released by progressive metamorphic dehydration of the basaltic oceanic crust. The conductivity anomalies may be related to the main dehydration reactions at the zeolite → blueschist → eclogite facies transitions and the breakdown of chlorite. This relation allows the estimation of a geothermal gradient of ∼8.5°C/km for the top of the subducting plate. The same dehydration reactions may be recognized along the northern profile at the same position relative to the depth of the plate, but more inland due to a shallower dip, and merge near the volcanic front due to steep downbending of the plate. When the oceanic crust reaches a depth of 80–90 km, ascending fluids produce basaltic melts in the intervening hot subcontinental mantle wedge that give rise to the volcanic belt. Water-rich basalts may intrude into the lower continental crust leading to partial melting. The elongated highly conductive zone below the TMVB may therefore be caused by partial melts and fluids of various origins, ongoing migmatization, ascending basaltic and granitic melts, growing plutons as well as residual metamorphic fluids. Zones of extremely high conductance (>8000 S) in the continental crust on either MT profile might indicate extinct magmatism

Species Accumulation Curves and Incidence-Based Species Richness Estimators to Appraise the Diversity of Cultivable Yeasts from Beech Forest Soils

Background: Yeast-like fungi inhabit soils throughout all climatic zones in a great abundance. While recent estimations predicted a plethora of prokaryotic taxa in one gram of soil, similar data are lacking for fungi, especially yeasts. Methodology/Principal Findings: We assessed the diversity of soil yeasts in different forests of central Germany using cultivation-based techniques with subsequent identification based on rDNA sequence data. Based on experiments using various pre-cultivation sample treatment and different cultivation media we obtained the highest number of yeasts by analysing mixed soil samples with a single nutrient-rich medium. Additionally, several species richness estimators were applied to incidence-based data of 165 samples. All of them predicted a similar range of yeast diversity, namely 14 to 16 species. Randomized species richness curves reached saturation in all applied estimators, thus indicating that the majority of species is detected after approximately 30 to 50 samples analysed. Conclusions/Significance: In this study we demonstrate that robust species identification as well as mathematical approaches are essential to reliably estimate the sampling effort needed to describe soil yeast communities. This approach has great potential for optimisation of cultivation techniques and allows high throughput analysis in the future

Relapse patterns in NMOSD: evidence for earlier occurrence of optic neuritis and possible seasonal variation

Neuromyelitis optica spectrum disorders (NMOSD) and multiple sclerosis (MS) show overlap in their clinical features. We performed an analysis of relapses with the aim of determining differences between the two conditions. Cases of NMOSD and age- and sex-matched MS controls were collected from across Australia and New Zealand. Demographic and clinical information, including relapse histories, were recorded using a standard questionnaire. There were 75 cases of NMOSD and 101 MS controls. There were 328 relapses in the NMOSD cases and 375 in MS controls. Spinal cord and optic neuritis attacks were the most common relapses in both NMOSD and MS. Optic neuritis (p P = 0.002) were more common in NMOSD and other brainstem attacks were more common in MS (p P = 0.065). Optic neuritis and transverse myelitis are the most common types of relapse in NMOSD and MS. Optic neuritis tends to occur more frequently in NMOSD prior to the age of 30, with transverse myelitis being more common thereafter. Relapses in NMOSD were more severe. A seasonal bias for relapses in spring-summer may exist in NMOSD

Striatal Proteomic Analysis Suggests that First L-Dopa Dose Equates to Chronic Exposure

L-3,4-dihydroxypheylalanine (L-dopa)-induced dyskinesia represent a debilitating complication of therapy for Parkinson's disease (PD) that result from a progressive sensitization through repeated L-dopa exposures. The MPTP macaque model was used to study the proteome in dopamine-depleted striatum with and without subsequent acute and chronic L-dopa treatment using two-dimensional difference in-gel electrophoresis (2D-DIGE) and mass spectrometry. The present data suggest that the dopamine-depleted striatum is so sensitive to de novo L-dopa treatment that the first ever administration alone would be able (i) to induce rapid post-translational modification-based proteomic changes that are specific to this first exposure and (ii), possibly, lead to irreversible protein level changes that would be not further modified by chronic L-dopa treatment. The apparent equivalence between first and chronic L-dopa administration suggests that priming would be the direct consequence of dopamine loss, the first L-dopa administrations only exacerbating the sensitization process but not inducing it

Grain lupin cultivation in Victoria : some agronomic aspects

The results of five field experiments and one laboratory experiment, have been included in the chapters of this thesis. They describe the adaptation of lupins to the environment of North-East Victoria in terms of seed germination, establishment, growth and grain yield. Chapters 2, 3 and 4 have been submitted as scientific papers and published (or are to be published) in the Australian Journal of Experimental Agriculture and Animal Husbandry. I was actively involved in field work at the Rutherglen Research Institute and at the regional sites during these investigations. Mr. T. G. Reeves was my supervisor during the time when the experiments reported in Chapters 2 and 3 were being conducted. I carried out the field work and analysed and reported the data under the supervision of Mr. Reeves. We shared senior authorship of the two scientific papers resulting from this work. For the experiment reported in Chapter 4, Dr. C. M. Piggin assisted me with experimental design and facilities, however, I conducted measurements and analyses and solely prepared these for publication. I was responsible for the lupin research and development programme at Rutherglen Research Institute from 1976 to 1981