Pioneering studies performed in the nineteenth century demonstrated that yeasts are present in below‐ground sources. Soils were regarded more as a reservoir for yeasts that reside in habitats above ...it. Later studies showed that yeast communities in soils are taxonomically diverse and different from those above‐ground. Soil yeasts possess extraordinary adaptations that allow them to survive in a wide range of environmental conditions. A few species are promising sources of yeast oils and have been used in agriculture as potential antagonists of soil‐borne plant pathogens or as plant growth promoters. Yeasts have been studied mainly in managed soils such as vineyards, orchards and agricultural fields, and to a lesser extent under forests and grasslands. Our knowledge of soil yeasts is further biased towards temperate and boreal forests, whereas data from Africa, the Americas and Asia are scarce. Although soil yeast communities are often species‐poor in a single sample, they are more diverse on the biotope level. Soil yeasts display pronounced endemism along with a surprisingly high proportion of currently unidentified species. However, like other soil inhabitants, yeasts are threatened by habitat alterations owing to anthropogenic activities such as agriculture, deforestation and urbanization. In view of the rapid decline of many natural habitats, the study of soil yeasts in undisturbed or low‐managed biotopes is extremely valuable. The purpose of this review is to encourage researchers, both biologists and soil scientists, to include soil yeasts in future studies.
Soils are regarded as an important reservoir for yeasts, although data from Africa, the Americas and Asia are scarce. In view of the rapid decline of many natural habitats, the study of soil yeasts in undisturbed or low‐managed biotopes is extremely valuable. Yeasts interact with plants and animals above and below ground; they contribute to nutrient transformation in soils and improve soil aggregate stability.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. ...Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.
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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.
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.
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.
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It is now a decade since The International Commission on the Taxonomy of Fungi (ICTF) produced an overview of requirements and best practices for describing a new fungal species. In the meantime the ...International Code of Nomenclature for algae, fungi, and plants (ICNafp) has changed from its former name (the International Code of Botanical Nomenclature) and introduced new formal requirements for valid publication of species scientific names, including the separation of provisions specific to Fungi and organisms treated as fungi in a new Chapter F. Equally transformative have been changes in the data collection, data dissemination, and analytical tools available to mycologists. This paper provides an updated and expanded discussion of current publication requirements along with best practices for the description of new fungal species and publication of new names and for improving accessibility of their associated metadata that have developed over the last 10 years. Additionally, we provide: (1) model papers for different fungal groups and circumstances; (2) a checklist to simplify meeting (i) the requirements of the ICNafp to ensure the effective, valid and legitimate publication of names of new taxa, and (ii) minimally accepted standards for description; and, (3) templates for preparing standardized species descriptions.
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In exploring the evolutionary trajectories of both pathogenesis and karyotype dynamics in fungi, we conducted a large-scale comparative genomic analysis spanning the Cryptococcus genus, encompassing ...both global human fungal pathogens and nonpathogenic species, and related species from the sister genus Kwoniella . Chromosome-level genome assemblies were generated for multiple species, covering virtually all known diversity within these genera. Although Cryptococcus and Kwoniella have comparable genome sizes (about 19.2 and 22.9 Mb) and similar gene content, hinting at preadaptive pathogenic potential, our analysis found evidence of gene gain (via horizontal gene transfer) and gene loss in pathogenic Cryptococcus species, which might represent evolutionary signatures of pathogenic development. Genome analysis also revealed a significant variation in chromosome number and structure between the 2 genera. By combining synteny analysis and experimental centromere validation, we found that most Cryptococcus species have 14 chromosomes, whereas most Kwoniella species have fewer (11, 8, 5, or even as few as 3). Reduced chromosome number in Kwoniella is associated with formation of giant chromosomes (up to 18 Mb) through repeated chromosome fusion events, each marked by a pericentric inversion and centromere loss. While similar chromosome inversion–fusion patterns were observed in all Kwoniella species with fewer than 14 chromosomes, no such pattern was detected in Cryptococcus . Instead, Cryptococcus species with less than 14 chromosomes showed reductions primarily through rearrangements associated with the loss of repeat-rich centromeres. Additionally, Cryptococcus genomes exhibited frequent interchromosomal translocations, including intercentromeric recombination facilitated by transposons shared between centromeres. Overall, our findings advance our understanding of genetic changes possibly associated with pathogenicity in Cryptococcus and provide a foundation to elucidate mechanisms of centromere loss and chromosome fusion driving distinct karyotypes in closely related fungal species, including prominent global human pathogens.
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In 2006 several yeast-like fungi were isolated from apples that showed a postharvest disorder named "white haze." These strains were morphologically and molecularly assigned to the genus
. Following ...the recent reclassification of yeasts in Ustilaginomycotina and the genus
in particular, species that caused "white haze" disorder were re-identified based on the phylogenetic analysis of five DNA-loci (ITS, LSU, SSU,
, and
) and analysis of D1/D2 domains of the 26S/28S rRNA (LSU). Six novel species belonging to three orders in the Exobasidiomycetes, namely
(holotype: CBS 111600; ex-type: DSM 29114) MB 823155,
(holotype: CBS 111604; ex-type: DSM 100135) MB 823154,
(holotype: CBS 111593; ex-type: DSM 29113) MB 823153,
(holotype: CBS 111606; ex-type: DSM 100136) MB 823156,
(holotype: CBS 111625; ex-type: DSM 29121) MB 823151 and
(holotype: CBS 111610; ex-type: DSM 100176) MB 823152 are proposed to accommodate these strains. In addition, sequences representing phylogenetically related but yet undescribed fungi were obtained from GenBank in order to show the diversity of
-like yeast states in Exobasidiomycetes.
Six conspecific yeast strains, representing an undescribed species, were isolated from rotten wood collected in different locations in Hungary and Germany and an additional one from fungal fruiting ...body in Taiwan. The seven strains share identical nucleotide sequences in the D1/D2 domain of the nuclear large subunit (LSU) rRNA gene. The Hungarian and Taiwanese isolates share identical internal transcribed spacer (ITS) sequences as well, while the two German isolates differ from them merely by three substitutions and four indels in this region. The investigated strains are very closely related to
. Along their LSU D1/D2 domain they differ only by one substitution from the type strain of
. However, in the ITS region of Hungarian and Taiwanese strains we detected 3.5 % divergence (nine substitutions and nine indels) between the undescribed species and
, while the German strains differed by 13 substitutions and nine indels from
. This ITS sequence divergence has raised the possibility that the strains investigated in this study may represent a different species from
. This hypothesis was supported by comparisons of partial translation elongation factor 1-α (EF-1α) and cytochrome oxidase II (COX II) gene sequences. While no difference and 1-2 substitutions among the partial EF-1α and COX II gene sequences of the strains of the undescribed species, respectively, were detected; the undescribed species differ by about 4 % (36 substitutions) and 10 % (50-51 substitutions) from
in these regions. Parsimony network analysis of the partial COX II gene sequences also separated the investigated strains from the type strain of
. In this paper we propose
f.a., sp. nov. (holotype: NCAIM Y.02121; isotypes: CBS 17819, DSM 114156) to accommodate the above-noted strains.
The fungal mycelium represents the essence of the fungal lifestyle, and understanding how a mycelium is constructed is of fundamental importance in fungal biology and ecology. Previous studies have ...examined initial developmental patterns or focused on a few strains, often mutants of model species, and frequently grown under non-harmonized growth conditions; these factors currently collectively hamper systematic insights into rules of mycelium architecture. To address this, we here use a broader suite of fungi (31 species including members of the Ascomycota, Basidiomycota and Mucoromycota), all isolated from the same soil, and tested for ten architectural traits under standardized laboratory conditions. We find great variability in traits among the saprobic fungal species, and detect several clear tradeoffs in mycelial architecture, for example between internodal length and hyphal diameter. Within the constraints so identified, we document otherwise great versatility in mycelium architecture in this set of fungi, and there was no evidence of trait 'syndromes' as might be expected. Our results point to an important dimension of fungal properties with likely consequences for coexistence within local communities, as well as for functional complementarity (e.g. decomposition, soil aggregation).
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The present work studied novel basidiomycetous yeasts from maize and northern wild rice plants. From comparisons of ribosomal internal transcribed spacer region (ITS) and large subunit (LSU) (D1 and ...D2 domains), and subsequent phylogenetic analyses, the following species were resolved and described: Papiliotrema zeae Yurkov & Kurtzman sp. nov. (ex-type cultures DSM 104035, NRRL Y-63980, MB 827356, GenBank MH718306), Solicoccozyma zizaniae Yurkov & Kurtzman sp. nov. (ex-type cultures DSM 104031, NRRL Y-7649, MB 827354, GenBank MH718302) and Vishniacozyma kurtzmanii Yurkov sp. nov. (ex-type cultures DSM 104032, NRRL Y-63981, MB 827355, GenBank MH718303). A search among environmental sequences showed that all three yeasts were previously detected, but not reliably assigned to a genus or clade. Papiliotrema zeae from maize and S. zizaniae from northern wild rice were previously found in agricultural soils under maize and rice, respectively.
Two novel yeast species were isolated from the guts of two different termite species. A new member of the genus Sugiyamaella was isolated from the hindgut and nest material of the lower Australian ...termite Mastotermes darwiniensis. The second novel yeast species, isolated from the higher termite Odontotermes obesus, was identified as a member of the genus Papiliotrema. Both yeast species were able to hydrolyse xylan, methylumbelliferyl β-xylobiose and methylumbelliferyl β-xylotriose. The ability to debranch different hemicellulose side chains and growth without the addition of external vitamins was observed. A symbiotic role of the novel yeast species is indicated, especially in respect to xylan degradation and the production of vitamins. Here, we describe these species as Sugiyamaella mastotermitis sp. nov., MycoBank 816574 (type strain MD39VT=DSM 100793T=CBS 14182T), and Papiliotrema odontotermitis f.a., sp. nov., MycoBank 816575 (type strain OO5T=DSM 100791T=CBS 14181T). Additionally, we transfer Candida qingdaonensis to the genus Sugiyamaella and propose the following combination: Sugiyamaella qingdaonensis f.a., comb. nov., MycoBank 816576.
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