Studies in the Phaeotremella foliacea group (Tremellomycetes, Basidiomycota)

A modified diatomite additive alleviates cadmium-induced oxidative stress in Bidens pilosa L. by altering soil microbial communities

In the present study, a modified silicon adsorbent (MDSA) was used as a passivator, and we explored the mechanism by which the MDSA helps B. pilosa L. alleviate Cd-induced oxidative stress and its effect on the rhizosphere microbial community. Therefore, a field study was conducted, and MDSA was applied at four levels (control (0 mg m^-2), A1 (100 mg m^-2), A2 (200 mg m^-2), and A3 (400 mg m^-2)). The application of MDSA significantly increased the soil pH and decreased the acid-soluble Cd content, which decreased by 30.3% with A3 addition. The addition of MDSA increased the relative abundance of Sordariomycetes due to the increased invertase activity and total nitrogen (TN) and total phosphorus (TP) contents, and the increased soil pH led to increased relative abundances of Alphaproteobacteria and Thermoleophilia. Meanwhile, MDSA addition significantly decreased the Cd concentrations in leaves and stems, which decreased by 19.7 to 39.5% in stems and 24.6 to 43.2% in leaves. All MDSA additions significantly decreased the translocation factor (TF) values of Cd, which decreased by 30.5% (A1), 50.9% (A2), and 52.7% (A3). Moreover, peroxidase (POD) from the antioxidant enzyme system and glutathione (GSH) from the nonenzymatic system played vital roles in scavenging reactive oxygen intermediates (ROIs) such as H₂O₂ and ⋅O₂^- in leaves, thereby helping B. pilosa L. alleviate Cd-induced oxidative stress and promote plant growth. Hence, our study indicated that MDSA application improved the rhizosphere soil environment, reconstructed the soil microbial community, helped B. pilosa L. alleviate Cd-induced oxidative stress, and promoted plant growth.

Fungal sporocarps house diverse and host-specific communities of fungicolous fungi

Sporocarps (fruit bodies) are the sexual reproductive stage in the life cycle of many fungi. They are highly nutritious and consequently vulnerable to grazing by birds and small mammals, and invertebrates, and can be infected by microbial and fungal parasites and pathogens. The complexity of communities thriving inside sporocarps is largely unknown. In this study, we revealed the diversity, taxonomic composition and host preference of fungicolous fungi (i.e., fungi that feed on other fungi) in sporocarps. We carried out DNA metabarcoding of the ITS2 region from 176 sporocarps of 11 wood-decay fungal host species, all collected within a forest in northeast Finland. We assessed the influence of sporocarp traits, such as lifespan, morphology and size, on the fungicolous fungal community. The level of colonisation by fungicolous fungi, measured as the proportion of non-host ITS2 reads, varied between 2.8-39.8% across the 11 host species and was largely dominated by Ascomycota. Host species was the major determinant of the community composition and diversity of fungicolous fungi, suggesting that host adaptation is important for many fungicolous fungi. Furthermore, the alpha diversity was consistently higher in short-lived and resupinate sporocarps compared to long-lived and pileate ones, perhaps due to a more hostile environment for fungal growth in the latter too. The fungicolous fungi represented numerous lineages in the fungal tree of life, among which a significant portion was poorly represented with reference sequences in databases.

Phaeotremella camelliae sp. nov. (Phaeotremellaceae, Tremellales), A Novel Yeasts Isolated from Tea-Oil Fruits in Jiangxi Province, China

Sixty-two isolates among the 65 yeast strains isolated from Jiangxi province, China, were identified into 15 known species based on the sequence analysis of the D1/D2 domains of the LSU rRNA and ITS region. The other three strains, GaoanZ14, GaoanC57, and GaoanC191, isolated from tea-oil fruits, were identified as two undescribed species of Phaeotremella based on the multiple gene sequence analysis, physiological, and biochemical comparisons. Strains GaoanC57 and GaoanC191 had one substitution difference both in the D1/D2 domains of the LSU rRNA and ITS region. They formed a separate branch from the other Phaeotremella species in the D1/D2 and multiple genes trees, and differed from the known species by at least 10 nucleotide substitutions in the D1/D2 domains and more than 6% mismatches in the ITS region. The phylogenetic analysis indicated that those two strains represent a novel species of Phaeotremella, for which the names Phaeotremella camelliae sp. nov. (Holotype CGMCC 2.6141, Mycobank MB832699) is proposed. Only one strain, GaoanZ14, represents the other undescribed species of Phaeotremella, so it will be described in latter when more strains are found.

A complete digitization of German herbaria is possible, sensible and should be started now

Plants, fungi and algae are important components of global biodiversity and are fundamental to all ecosystems. They are the basis for human well-being, providing food, materials and medicines. Specimens of all three groups of organisms are accommodated in herbaria, where they are commonly referred to as botanical specimens.

The large number of specimens in herbaria provides an ample, permanent and continuously improving knowledge base on these organisms and an indispensable source for the analysis of the distribution of species in space and time critical for current and future research relating to global biodiversity. In order to make full use of this resource, a research infrastructure has to be built that grants comprehensive and free access to the information in herbaria and botanical collections in general. This can be achieved through digitization of the botanical objects and associated data.

The botanical research community can count on a long-standing tradition of collaboration among institutions and individuals. It agreed on data standards and standard services even before the advent of computerization and information networking, an example being the Index Herbariorum as a global registry of herbaria helping towards the unique identification of specimens cited in the literature.

In the spirit of this collaborative history, 51 representatives from 30 institutions advocate to start the digitization of botanical collections with the overall wall-to-wall digitization of the flat objects stored in German herbaria. Germany has 70 herbaria holding almost 23 million specimens according to a national survey carried out in 2019. 87% of these specimens are not yet digitized. Experiences from other countries like France, the Netherlands, Finland, the US and Australia show that herbaria can be comprehensively and cost-efficiently digitized in a relatively short time due to established workflows and protocols for the high-throughput digitization of flat objects.

Most of the herbaria are part of a university (34), fewer belong to municipal museums (10) or state museums (8), six herbaria belong to institutions also supported by federal funds such as Leibniz institutes, and four belong to non-governmental organizations. A common data infrastructure must therefore integrate different kinds of institutions.

Making full use of the data gained by digitization requires the set-up of a digital infrastructure for storage, archiving, content indexing and networking as well as standardized access for the scientific use of digital objects. A standards-based portfolio of technical components has already been developed and successfully tested by the Biodiversity Informatics Community over the last two decades, comprising among others access protocols, collection databases, portals, tools for semantic enrichment and annotation, international networking, storage and archiving in accordance with international standards. This was achieved through the funding by national and international programs and initiatives, which also paved the road for the German contribution to the Global Biodiversity Information Facility (GBIF).

Herbaria constitute a large part of the German botanical collections that also comprise living collections in botanical gardens and seed banks, DNA- and tissue samples, specimens preserved in fluids or on microscope slides and more. Once the herbaria are digitized, these resources can be integrated, adding to the value of the overall research infrastructure. The community has agreed on tasks that are shared between the herbaria, as the German GBIF model already successfully demonstrates.

We have compiled nine scientific use cases of immediate societal relevance for an integrated infrastructure of botanical collections. They address accelerated biodiversity discovery and research, biomonitoring and conservation planning, biodiversity modelling, the generation of trait information, automated image recognition by artificial intelligence, automated pathogen detection, contextualization by interlinking objects, enabling provenance research, as well as education, outreach and citizen science.

We propose to start this initiative now in order to valorize German botanical collections as a vital part of a worldwide biodiversity data pool.

Diversity and phylogeny of basidiomycetous yeasts from plant leaves and soil: Proposal of two new orders, three new families, eight new genera and one hundred and seven new species

Nearly 500 basidiomycetous yeast species were accepted in the latest edition of The Yeasts: A Taxonomic Study published in 2011. However, this number presents only the tip of the iceberg of yeast species diversity in nature. Possibly more than 99 % of yeast species, as is true for many groups of fungi, are yet unknown and await discovery. Over the past two decades nearly 200 unidentified isolates were obtained during a series of environmental surveys of yeasts in phyllosphere and soils, mainly from China. Among these isolates, 107 new species were identified based on the phylogenetic analyses of nuclear ribosomal DNA (rDNA) [D1/D2 domains of the large subunit (LSU), the small subunit (SSU), and the internal transcribed spacer region including the 5.8S rDNA (ITS)] and protein-coding genes [both subunits of DNA polymerase II (RPB1 and RPB2), the translation elongation factor 1-α (TEF1) and the mitochondrial gene cytochrome b (CYTB)], and physiological comparisons. Forty-six of these belong to 16 genera in the Tremellomycetes (Agaricomycotina). The other 61 are distributed in 26 genera in the Pucciniomycotina. Here we circumscribe eight new genera, three new families and two new orders based on the multi-locus phylogenetic analyses combined with the clustering optimisation analysis and the predicted similarity thresholds for yeasts and filamentous fungal delimitation at genus and higher ranks. Additionally, as a result of these analyses, three new combinations are proposed and 66 taxa are validated.

Heterocephalacria sinensis sp. nov., Phaeotremella lacus sp. nov. and Solicoccozyma aquatica sp. nov., three novel basidiomycetous yeast species isolated from crater lakes

The Arxan-Chaihe volcanic field of the Da Hinggan mountains in north-East PR China hosts various typical crater lakes. In this study we performed a yeast diversity survey using water sampled from five crater lakes and a total of 122 yeast strains belonging to 33 species of 25 genera were isolated. Three strains, TFL1-L, TFL2B and ATC4C, were identified as three novel species belonging to the Tremellomycetes based on a multiple gene phylogeny and on the comparison of physiological data. A phylogenetic study employing the sequences of seven genes indicated that the new species were more related to three separated phylogenetic lineages of the Tremellomycetes and their closest relatives were Heterocephalacria arrabidensis, Phaeotremella skinneri and Solicoccozyma keelungensis. The divergence values of the D1/D2 domain of LSU sequences of strains TFL1-L, TFL2B and ATC4C from H. arrabidensis CBS 8678^T, P. skinneri CBS 5029^T and S. keelungensisSN-82^T were 4.8，3.4，2.1 %， respectively. The divergence values of the sequences of ITS regions between strains TFL1-L, TFL2B and ATC4C and their close relatives (H. arrabidensis, P. skinneri and S. keelungensis) were 16.1, 5.9 and 8.1  %, respectively. Moreover, the three strains differed from their phylogenetic neighbours by the ability to grow on distinct carbon and nitrogen sources. On the basis of these findings, it is suggested that these strains represent three novel species for which the names Heterocephalacria sinensis sp. nov. (holotype CGMCC 2.5595), Phaeotremella lacus sp. nov. (holotype CGMCC 2.5580) and Solicoccozyma aquatica sp. nov. (holotype CGMCC 2.5574) are proposed.

Notes, outline and divergence times of Basidiomycota

The Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names, with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information. Furthermore, three phylogenetic analyses with combined LSU, SSU, 5.8s, rpb1, rpb2, and ef1 datasets for the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina are conducted, respectively. Divergence time estimates are provided to the family level with 632 species from 62 orders, 168 families and 605 genera. Our study indicates that the divergence times of the subphyla in Basidiomycota are 406–430 Mya, classes are 211–383 Mya, and orders are 99–323 Mya, which are largely consistent with previous studies. In this study, all phylogenetically supported families were dated, with the families of Agaricomycotina diverging from 27–178 Mya, Pucciniomycotina from 85–222 Mya, and Ustilaginomycotina from 79–177 Mya. Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of their phylogeny and evolution.

Mrakia fibulata sp. nov., a psychrotolerant yeast from temperate and cold habitats

Tree fluxes are sugar-rich, sometimes ephemeral, substrates occurring on sites where tree sap (xylem or phloem) is leaking through damages of tree bark. Tree sap infested with microorganisms has been the source of isolation of many species, including the biotechnologically relevant carotenoid yeast Phaffia rhodozyma. Tree fluxes recently sampled in Germany yielded 19 species, including several psychrophilic yeasts of the genus Mrakia. Four strains from tree fluxes represented a potential novel Mrakia species previously known from two isolates from superficial glacial melting water of Calderone Glacier (Italy). The Italian isolates, originally identified as Mrakia aquatica, and two strains from Germany did not show any sexual structures. But another culture collected in Germany produced clamped hyphae with teliospores. A detailed examination of the five isolates (three from Germany and two from Italy) proved them to be a novel yeast species, which is described in this manuscript as Mrakia fibulata sp. nov. (MB 830398), holotype DSM 103931 and isotype DBVPG 8059. In contrast to other sexually reproducing Mrakia species, M. fibulata produces true hyphae with clamp connections. Also, this is the first psychrotolerant Mrakia species which grows above 20 °C. Spring tree fluxes are widespread and can be recognized and sampled by amateurs in a Citizen Science project. This substrate is a prominent source of yeasts, and may harbor unknown species, as demonstrated in the present work. The description of Mrakia fibulata is dedicated to our volunteer helpers and amateurs, like Anna Yurkova (9-years-old daughter of Andrey Yurkov), who collected the sample which yielded the type strain of this species.

Four new species of Tremella (Tremellales, Basidiomycota) based on morphology and DNA sequence data

In the present study, a total of 33 Tremella specimens in China were collected and examined using molecular phylogenetic analysis based on a combined sequence dataset of the nuc rDNA internal transcribed spacer (ITS) region and nuc 28S rDNA D1/D2 domain in conjunction with the morphological characters. Four new species, namely Tremellabasidiomaticola, T.cheejenii, T.erythrina, and T.salmonea, are newly described based on their distinct phylogenetic relationships and the comparison of morphological characters with known Tremella species. Our results indicate a high species diversity of Tremella waiting to be discovered.