Multilocus DNA sequencing of the whiskey fungus reveals a continental-scale speciation pattern

Sunken Riches: Ascomycete Diversity in the Western Mediterranean Coast through Direct Plating and Flocculation, and Description of Four New Taxa

The Mediterranean Sea stands out as a hotspot of biodiversity, whose fungal composition remains underexplored. Marine sediments represent the most diverse substrate; however, the challenge of recovering fungi in culture hinders the precise identification of this diversity. Concentration techniques like skimmed milk flocculation (SMF) could represent a suitable solution. Here, we compare the effectiveness in recovering filamentous ascomycetes of direct plating and SMF in combination with three culture media and two incubation temperatures, and we describe the fungal diversity detected in marine sediments. Sediments were collected at different depths on two beaches (Miracle and Arrabassada) on the Spanish western Mediterranean coast between 2021 and 2022. We recovered 362 strains, and after a morphological selection, 188 were identified primarily with the LSU and ITS barcodes, representing 54 genera and 94 species. Aspergillus, Penicillium, and Scedosporium were the most common genera, with different percentages of abundance between both beaches. Arrabassada Beach was more heterogeneous, with 42 genera representing 60 species (Miracle Beach, 28 genera and 54 species). Although most species were recovered with direct plating (70 species), 20 species were exclusively obtained using SMF as a sample pre-treatment, improving our ability to detect fungi in culture. In addition, we propose three new species in the genera Exophiala, Nigrocephalum, and Queenslandipenidiella, and a fourth representing the novel genus Schizochlamydosporiella. We concluded that SMF is a useful technique that, in combination with direct plating, including different culture media and incubation temperatures, improves the chance of recovering marine fungal communities in culture-dependent studies.

Physiological, Genomic and Transcriptomic Analyses Reveal the Adaptation Mechanisms of Acidiella bohemica to Extreme Acid Mine Drainage Environments

Fungi in acid mine drainage (AMD) environments are of great concern due to their potentials of decomposing organic carbon, absorbing heavy metals and reducing AMD acidity. Based on morphological analysis and ITS/18S high-throughput sequencing technology, previous studies have provided deep insights into the diversity and community composition of fungi in AMD environments. However, knowledge about physiology, metabolic potential and transcriptome profiles of fungi inhabiting AMD environments is still scarce. Here, we reported the physiological, genomic, and transcriptomic characterization of Acidiella bohemica SYSU C17045 to improve our understanding of the physiological, genomic, and transcriptomic mechanisms underlying fungal adaptation to AMD environments. A. bohemica was isolated from an AMD environment, which has been proved to be an acidophilic fungus in this study. The surface of A. bohemica cultured in AMD solutions was covered with a large number of minerals such as jarosite. We thus inferred that the A. bohemica might have the potential of biologically induced mineralization. Taking advantage of PacBio single-molecule real-time sequencing, we obtained the high-quality genome sequences of A. bohemica (50 Mbp). To our knowledge, this was the first attempt to employ a third-generation sequencing technology to explore the genomic traits of fungi isolated from AMD environments. Moreover, our transcriptomic analysis revealed that a series of genes in the A. bohemica genome were related to its metabolic pathways of C, N, S, and Fe as well as its adaptation mechanisms, including the response to acid stress and the resistance to heavy metals. Overall, our physiological, genomic, and transcriptomic data provide a foundation for understanding the metabolic potential and adaptation mechanisms of fungi in AMD environments.

Transcriptomics of the Rooibos (Aspalathus linearis) Species Complex

Rooibos (Aspalathus linearis), widely known as a herbal tea, is endemic to the Cape Floristic Region of South Africa (SA). It produces a wide range of phenolic compounds that have been associated with diverse health promoting properties of the plant. The species comprises several growth forms that differ in their morphology and biochemical composition, only one of which is cultivated and used commercially. Here, we established methodologies for non-invasive transcriptome research of wild-growing South African plant species, including (1) harvesting and transport of plant material suitable for RNA sequencing; (2) inexpensive, high-throughput biochemical sample screening; (3) extraction of high-quality RNA from recalcitrant, polysaccharide- and polyphenol rich plant material; and (4) biocomputational analysis of Illumina sequencing data, together with the evaluation of programs for transcriptome assembly (Trinity, IDBA-Trans, SOAPdenovo-Trans, CLC), protein prediction, as well as functional and taxonomic transcript annotation. In the process, we established a biochemically characterized sample pool from 44 distinct rooibos ecotypes (1–5 harvests) and generated four in-depth annotated transcriptomes (each comprising on average ≈86,000 transcripts) from rooibos plants that represent distinct growth forms and differ in their biochemical profiles. These resources will serve future rooibos research and plant breeding endeavours.

Fungal Planet description sheets: 1042-1111

Novel species of fungi described in this study include those from various countries as follows: Antarctica, Cladosporium arenosum from marine sediment sand. Argentina, Kosmimatamyces alatophylus (incl. Kosmimatamyces gen. nov.) from soil. Australia, Aspergillus banksianus, Aspergillus kumbius, Aspergillus luteorubrus, Aspergillus malvicolor and Aspergillus nanangensis from soil, Erysiphe medicaginis from leaves of Medicago polymorpha, Hymenotorrendiella communis on leaf litter of Eucalyptus bicostata, Lactifluus albopicri and Lactifluus austropiperatus on soil, Macalpinomyces collinsiae on Eriachne benthamii, Marasmius vagus on soil, Microdochium dawsoniorum from leaves of Sporobolus natalensis, Neopestalotiopsis nebuloides from leaves of Sporobolus elongatus, Pestalotiopsis etonensis from leaves of Sporobolus jacquemontii, Phytophthora personensis from soil associated with dying Grevillea mccutcheonii.Brazil, Aspergillus oxumiae from soil, Calvatia baixaverdensis on soil, Geastrum calycicoriaceum on leaf litter, Greeneria kielmeyerae on leaf spots of Kielmeyera coriacea. Chile, Phytophthora aysenensis on collar rot and stem of Aristotelia chilensis.Croatia, Mollisia gibbospora on fallen branch of Fagus sylvatica.Czech Republic, Neosetophoma hnaniceana from Buxus sempervirens.Ecuador, Exophiala frigidotolerans from soil. Estonia, Elaphomyces bucholtzii in soil. France, Venturia paralias from leaves of Euphorbia paralias.India, Cortinarius balteatoindicus and Cortinarius ulkhagarhiensis on leaf litter. Indonesia, Hymenotorrendiella indonesiana on Eucalyptus urophylla leaf litter. Italy, Penicillium taurinense from indoor chestnut mill. Malaysia, Hemileucoglossum kelabitense on soil, Satchmopsis pini on dead needles of Pinus tecunumanii.Poland, Lecanicillium praecognitum on insects’ frass. Portugal, Neodevriesia aestuarina from saline water. Republic of Korea, Gongronella namwonensis from freshwater. Russia, Candida pellucida from Exomias pellucidus, Heterocephalacria septentrionalis as endophyte from Cladonia rangiferina, Vishniacozyma phoenicis from dates fruit, Volvariella paludosa from swamp. Slovenia, Mallocybe crassivelata on soil. South Africa, Beltraniella podocarpi, Hamatocanthoscypha podocarpi, Coleophoma podocarpi and Nothoseiridium podocarpi (incl. Nothoseiridium gen. nov.) from leaves of Podocarpus latifolius, Gyrothrix encephalarti from leaves of Encephalartos sp., Paraphyton cutaneum from skin of human patient, Phacidiella alsophilae from leaves of Alsophila capensis, and Satchmopsis metrosideri on leaf litter of Metrosideros excelsa.Spain, Cladophialophora cabanerensis from soil, Cortinarius paezii on soil, Cylindrium magnoliae from leaves of Magnolia grandiflora, Trichophoma cylindrospora (incl. Trichophoma gen. nov.) from plant debris, Tuber alcaracense in calcareus soil, Tuber buendiae in calcareus soil. Thailand, Annulohypoxylon spougei on corticated wood, Poaceascoma filiforme from leaves of unknown Poaceae.UK, Dendrostoma luteum on branch lesions of Castanea sativa, Ypsilina buttingtonensis from heartwood of Quercus sp. Ukraine, Myrmecridium phragmiticola from leaves of Phragmites australis.USA, Absidia pararepens from air, Juncomyces californiensis (incl. Juncomyces gen. nov.) from leaves of Juncus effusus, Montagnula cylindrospora from a human skin sample, Muriphila oklahomaensis (incl. Muriphila gen. nov.) on outside wall of alcohol distillery, Neofabraea eucalyptorum from leaves of Eucalyptus macrandra, Diabolocovidia claustri (incl. Diabolocovidia gen. nov.) from leaves of Serenoa repens, Paecilomyces penicilliformis from air, Pseudopezicula betulae from leaves of leaf spots of Populus tremuloides. Vietnam, Diaporthe durionigena on branches of Durio zibethinus and Roridomyces pseudoirritans on rotten wood. Morphological and culture characteristics are supported by DNA barcodes.