Has taxonomic vandalism gone too far? A case study, the rise of the pay-to-publish model and the pitfalls of Morchella systematics

Genome assembly of M. spongiola and comparative genomics of the genus Morchella provide initial insights into taxonomy and adaptive evolution

Morchella spongiola is a highly prized mushroom for its delicious flavor and medical value and is one of the most flourishing, representative, and dominant macrofungi in the Qilian Mountains of the Qinghai-Tibet Plateau subkingdoms (QTPs). However, the understanding of M. spongiola remains largely unknown, and its taxonomy is ambiguous. In this study, we redescribed a unique species of M. spongiola, i.e., micromorphology, molecular data, genomics, and comparative genomics, and the historical biogeography of M. spongiola were estimated for 182 single-copy homologous genes. A high-quality chromosome-level reference genome of M. spongiola M12-10 was obtained by combining PacBio HiFi data and Illumina sequencing technologies; it was approximately 57.1 Mb (contig N50 of 18.14 Mb) and contained 9775 protein-coding genes. Comparative genome analysis revealed considerable conservation and unique characteristics between M. spongiola M12-10 and 32 other Morchella species. Molecular phylogenetic analysis indicated that M. spongiola M12-10 is similar to the M. prava/Mes-7 present in sandy soil near rivers, differentiating from black morels ~ 43.06 Mya (million years ago), and diverged from M. parva/Mes-7 at approximately 12.85 Mya (in the Miocene epoch), which is closely related to the geological activities in the QTPs (in the Neogene). Therefore, M. spongiola is a unique species rather than a synonym of M. vulgaris/Mes-5, which has a distinctive grey-brown sponge-like ascomata. This genome of M. spongiola M12-10 is the first published genome sequence of the species in the genus Morchella from the QTPs, which could aid future studies on functional gene identification, germplasm resource management, and molecular breeding efforts, as well as evolutionary studies on the Morchella taxon in the QTPs.

Antimicrobial Activity of Three Italian Strains of Morchella esculenta (Ascomycota)

Three genetically identified and morphologically characterized strains (MesAQ2-C, MesAQ6-2 and MesFI2-3) of the culinary-medicinal ascomycete mushroom Morchella esculenta (L.) Pers. collected in central-north Italy have been studied for their antifungal and antibacterial activities. The obtained data showed that mycelium of M. esculenta possess variable antimicrobial activity against four test fungi (Chrysosporium keratinophilum, Microsporum gypseum, Trichophyton terrestre, Penicillium griseofulvum), as well as one Gram positive (Staphylococcus aureus) and three Gram negative (Escherichia coli, Salmonella typhimurium, Pseudomonas aeruginosa) test bacteria potentially pathogenic for humans and animals. Up to 20.4% of inhibition of the average mycelial growth rate (GRavr) of test fungi in dual culture experiment was detected. The samples of cultural liquid (CL) and mycelial extract (ME) obtained by static cultivation of M. esculenta strains showed up to 13.9 and 23.0% of GRavr inhibition of test fungi, respectively. Similarly, the inhibition of the bacterial colonies by CL and ME samples was 34.1 and 32.3%, respectively in comparison with the control with streptomycin indicating almost equal secretion of both intra- and extracellular antimicrobial compounds by M. esculenta mycelium. As a producer of antimicrobial compounds among tested M. esculenta strains, MesAQ2-C was the most effective. It may be considered for further myco-pharmacological research to develop mushroom-based antimicrobial biotech products with biomedical significance.

Associated bacterial communities, confrontation studies, and comparative genomics reveal important interactions between Morchella with Pseudomonas spp

Members of the fungal genus Morchella are widely known for their important ecological roles and significant economic value. In this study, we used amplicon and genome sequencing to characterize bacterial communities associated with sexual fruiting bodies from wild specimens, as well as vegetative mycelium and sclerotia obtained from Morchella isolates grown in vitro. These investigations included diverse representatives from both Elata and Esculenta Morchella clades. Unique bacterial community compositions were observed across the various structures examined, both within and across individual Morchella isolates or specimens. However, specific bacterial taxa were frequently detected in association with certain structures, providing support for an associated core bacterial community. Bacteria from the genus Pseudomonas and Ralstonia constituted the core bacterial associates of Morchella mycelia and sclerotia, while other genera (e.g., Pedobacter spp., Deviosa spp., and Bradyrhizobium spp.) constituted the core bacterial community of fruiting bodies. Furthermore, the importance of Pseudomonas as a key member of the bacteriome was supported by the isolation of several Pseudomonas strains from mycelia during in vitro cultivation. Four of the six mycelial-derived Pseudomonas isolates shared 16S rDNA sequence identity with amplicon sequences recovered directly from the examined fungal structures. Distinct interaction phenotypes (antagonistic or neutral) were observed in confrontation assays between these bacteria and various Morchella isolates. Genome sequences obtained from these Pseudomonas isolates revealed intriguing differences in gene content and annotated functions, specifically with respect to toxin-antitoxin systems, cell adhesion, chitinases, and insecticidal toxins. These genetic differences correlated with the interaction phenotypes. This study provides evidence that Pseudomonas spp. are frequently associated with Morchella and these associations may greatly impact fungal physiology.

Ten years and a million links: building a global taxonomic library connecting persistent identifiers for names, publications and people

A major gap in the biodiversity knowledge graph is a connection between taxonomic names and the taxonomic literature. While both names and publications often have persistent identifiers (PIDs), such as Life Science Identifiers (LSIDs) or Digital Object Identifiers (DOIs), LSIDs for names are rarely linked to DOIs for publications. This article describes efforts to make those connections across three large taxonomic databases: Index Fungorum, International Plant Names Index (IPNI) and the Index of Organism Names (ION). Over a million names have been matched to DOIs or other persistent identifiers for taxonomic publications. This represents approximately 36% of names for which publication data are available. The mappings between LSIDs and publication PIDs are made available through ChecklistBank. Applications of this mapping are discussed, including a web app to locate the citation of a taxonomic name and a knowledge graph that uses data on researcher ORCID ids to connect taxonomic names and publications to authors of those names.

Food and Antioxidant Supplements with Therapeutic Properties of Morchella esculenta (Ascomycetes): A Review

Morchella esculenta, commonly known as yellow morels, is an edible and medicinal mushroom popular worldwide for its unique flavor and culinary purposes. The traditional medical system effectively uses morels against infertility, fatigue, cancer, muscular pain, cough, and cold. The M. esculenta possesses many health-promoting nutritional components such as mono and polyunsaturated fatty acids, polyphenols, protein hydrolysates, vitamins, amino acids and minerals. The potential medicinal properties of morels is due to polysaccharides (galactomannan, chitin, β-glucans, and β-1,3-1,6-glucan) present that has high economic importance worldwide. Polysaccharides present possess a broad spectrum of biological activities such as anti-cancer, anti-inflammatory, anti-microbial, anti-diabetic, and antioxidant. However, the toxicity and clinical trials to prove its safety and efficacy for medicinal uses are yet to be evaluated. Moreover, the separation, purification, identification, and structural elucidation of active compounds responsible for the unique flavors and biological activities are still lacking in M. esculenta. The available information provides a new base for future perspectives. It highlights the need for further studies of this potent medicinal mushroom species as a source of beneficial therapeutic drugs and nutraceutical supplements.

Ten decadal advances in fungal biology leading towards human well-being

Fungi are an understudied resource possessing huge potential for developing products that can greatly improve human well-being. In the current paper, we highlight some important discoveries and developments in applied mycology and interdisciplinary Life Science research. These examples concern recently introduced drugs for the treatment of infections and neurological diseases; application of -OMICS techniques and genetic tools in medical mycology and the regulation of mycotoxin production; as well as some highlights of mushroom cultivaton in Asia. Examples for new diagnostic tools in medical mycology and the exploitation of new candidates for therapeutic drugs, are also given. In addition, two entries illustrating the latest developments in the use of fungi for biodegradation and fungal biomaterial production are provided. Some other areas where there have been and/or will be significant developments are also included. It is our hope that this paper will help realise the importance of fungi as a potential industrial resource and see the next two decades bring forward many new fungal and fungus-derived products.

Organization and Unconventional Integration of the Mating-Type Loci in Morchella Species

True morels (Morchella spp.) are a group of delicious fungi in high demand worldwide, and some species of morels have been successfully cultivated in recent years. To better understand the sexual reproductive mechanisms of these fungi, we characterized the structure of the mating-type loci from ten morel species, and seven of them were obtained using long-range PCR amplification. Among the studied species, eight were heterothallic, two were homothallic, and four types of composition were observed in the MAT loci. In three of the five black morel species, the MAT1-1-1, MAT1-1-10, and MAT1-1-11 genes were in the MAT1-1 idiomorph, and only the MAT1-2-1 gene was in the MAT1-2 idiomorph, while an integration event occurred in the other two species and resulted in the importation of the MAT1-1-11 gene into the MAT1-2 idiomorph and survival as a truncated fragment in the MAT1-1 idiomorph. However, the MAT1-1-11 gene was not available in the four yellow morels and one blushing morel species. M. rufobrunnea, a representative species of the earliest diverging branch of true morels, along with another yellow morel Mes-15, were confirmed to be homothallic, and the MAT1-1-1, MAT1-1-10, and MAT1-2-1 genes were arranged in a tandem array. Therefore, we hypothesized that homothallism should be the ancestral reproductive state in Morchella. RT-PCR analyses revealed that four mating genes could be constitutively expressed, while the MAT1-1-10 gene underwent alternative splicing to produce different splice variants.