Draft Genome Sequence of Xylaria hypoxylon DSM 108379, a Ubiquitous Fungus on Hardwood

Enzymatic machinery of wood-inhabiting fungi that degrade temperate tree species

Deadwood provides habitat for fungi and serves diverse ecological functions in forests. We already have profound knowledge of fungal assembly processes, physiological and enzymatic activities, and resulting physico-chemical changes during deadwood decay. However, in situ detection and identification methods, fungal origins, and a mechanistic understanding of the main lignocellulolytic enzymes are lacking. This study used metaproteomics to detect the main extracellular lignocellulolytic enzymes in 12 tree species in a temperate forest that have decomposed for 8 ½ years. Mainly white-rot (and few brown-rot) Basidiomycota were identified as the main wood decomposers, with Armillaria as the dominant genus; additionally, several soft-rot xylariaceous Ascomycota were identified. The key enzymes involved in lignocellulolysis included manganese peroxidase, peroxide-producing alcohol oxidases, laccase, diverse glycoside hydrolases (cellulase, glucosidase, xylanase), esterases, and lytic polysaccharide monooxygenases. The fungal community and enzyme composition differed among the 12 tree species. Ascomycota species were more prevalent in angiosperm logs than in gymnosperm logs. Regarding lignocellulolysis as a function, the extracellular enzyme toolbox acted simultaneously and was interrelated (e.g. peroxidases and peroxide-producing enzymes were strongly correlated), highly functionally redundant, and present in all logs. In summary, our in situ study provides comprehensive and detailed insight into the enzymatic machinery of wood-inhabiting fungi in temperate tree species. These findings will allow us to relate changes in environmental factors to lignocellulolysis as an ecosystem function in the future.

Mushrooms as Potential Sources of Active Metabolites and Medicines

Background

Mushrooms exist as an integral and vital component of the ecosystem and are very precious fungi. Mushrooms have been traditionally used in herbal medicines for many centuries.

Scope and Approach

There are a variety of medicinal mushrooms mentioned in the current work such as Agaricus, Amanita, Calocybe, Cantharellus, Cordyceps, Coprinus, Cortinarius, Ganoderma, Grifola, Huitlacoche, Hydnum, Lentinus, Morchella, Pleurotus, Rigidoporus, Tremella, Trametes sp., etc., which play a vital role in various diseases because of several metabolic components and nutritional values. Medicinal mushrooms can be identified morphologically on the basis of their size, color (white, black, yellow, brown, cream, pink and purple-brown, etc.), chemical reactions, consistency of the stalk and cap, mode of attachment of the gills to the stalk, and spore color and mass, and further identified at a molecular level by Internal Transcribed Spacer (ITS) regions of gene sequencing. There are also other methods that have recently begun to be used for the identification of mushrooms such as high-pressure liquid chromatography (HPLC), nuclear magnetic resonance spectroscopy (NMR), microscopy, thin-layer chromatography (TLC), DNA sequencing, gas chromatography-mass spectrometry (GC-MS), chemical finger printing, ultra-performance liquid chromatography (UPLC), fourier transform infrared spectroscopy (FTIR), liquid chromatography quadrupole time-of-flight mass spectrometry (LCMS-TOF) and high-performance thin-layer chromatography (HPTLC). Lately, the matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) technique is also used for the identification of fungi.

Key Finding and Conclusion

Medicinal mushrooms possess various biological activities like anti-oxidant, anti-cancer, anti-inflammatory, anti-aging, anti-tumor, anti-viral, anti-parasitic, anti-microbial, hepatoprotective, anti-HIV, anti-diabetic, and many others that will be mentioned in this article. This manuscript will provide future direction, action mechanisms, applications, and the recent collective information of medicinal mushrooms. In addition to many unknown metabolites and patented active metabolites are also included.

High quality genome sequences of thirteen Hypoxylaceae (Ascomycota) strengthen the phylogenetic family backbone and enable the discovery of new taxa

The Hypoxylaceae (Xylariales, Ascomycota) is a diverse family of mainly saprotrophic fungi, which commonly occur in angiosperm-dominated forests around the world. Despite their importance in forest and plant ecology as well as a prolific source of secondary metabolites and enzymes, genome sequences of related taxa are scarce and usually derived from environmental isolates. To address this lack of knowledge thirteen taxonomically well-defined representatives of the family and one member of the closely related Xylariaceae were genome sequenced using combinations of Illumina and Oxford nanopore technologies or PacBio sequencing. The workflow leads to high quality draft genome sequences with an average N50 of 3.0 Mbp. A backbone phylogenomic tree was calculated based on the amino acid sequences of 4912 core genes reflecting the current accepted taxonomic concept of the Hypoxylaceae. A Percentage of Conserved Proteins (POCP) analysis revealed that 70% of the proteins are conserved within the family, a value with potential application for the definition of family boundaries within the order Xylariales. Also, Hypomontagnella spongiphila is proposed as a new marine derived lineage of Hypom. monticulosa based on in-depth genomic comparison and morphological differences of the cultures. The results showed that both species share 95% of their genes corresponding to more than 700 strain-specific proteins. This difference is not reflected by standard taxonomic assessments (morphology of sexual and asexual morph, chemotaxonomy, phylogeny), preventing species delimitation based on traditional concepts. Genetic changes are likely to be the result of environmental adaptations and selective pressure, the driving force of speciation. These data provide an important starting point for the establishment of a stable phylogeny of the Xylariales; they enable studies on evolution, ecological behavior and biosynthesis of natural products; and they significantly advance the taxonomy of fungi.