Modified recipe to inhibit fruiting body formation for living fungal biomaterial manufacture

Snowball: a novel gene family required for developmental patterning of fruiting bodies of mushroom-forming fungi (Agaricomycetes)

The morphogenesis of sexual fruiting bodies of fungi is a complex process determined by a genetically encoded program. Fruiting bodies reached the highest complexity levels in the Agaricomycetes; yet, the underlying genetics is currently poorly known. In this work, we functionally characterized a highly conserved gene termed snb1, whose expression level increases rapidly during fruiting body initiation. According to phylogenetic analyses, orthologs of snb1 are present in almost all agaricomycetes and may represent a novel conserved gene family that plays a substantial role in fruiting body development. We disrupted snb1 using CRISPR/Cas9 in the agaricomycete model organism Coprinopsis cinerea. snb1 deletion mutants formed unique, snowball-shaped, rudimentary fruiting bodies that could not differentiate caps, stipes, and lamellae. We took advantage of this phenotype to study fruiting body differentiation using RNA-Seq analyses. This revealed differentially regulated genes and gene families that, based on wild-type RNA-Seq data, were upregulated early during development and showed tissue-specific expression, suggesting a potential role in differentiation. Taken together, the novel gene family of snb1 and the differentially expressed genes in the snb1 mutants provide valuable insights into the complex mechanisms underlying developmental patterning in the Agaricomycetes.

IMPORTANCE

Fruiting bodies of mushroom-forming fungi (Agaricomycetes) are complex multicellular structures, with a spatially and temporally integrated developmental program that is, however, currently poorly known. In this study, we present a novel, conserved gene family, Snowball (snb), termed after the unique, differentiation-less fruiting body morphology of snb1 knockout strains in the model mushroom Coprinopsis cinerea. snb is a gene of unknown function that is highly conserved among agaricomycetes and encodes a protein of unknown function. A comparative transcriptomic analysis of the early developmental stages of differentiated wild-type and non-differentiated mutant fruiting bodies revealed conserved differentially expressed genes which may be related to tissue differentiation and developmental patterning fruiting body development.

Transcriptome Analysis Reveals Mycelial and Fruiting Responses to Lithium Chloride in Coprinopsis cinerea

Lithium chloride (LiCl) has been used in signalling and molecular studies of animals, plants, and yeast. However, information on its roles in basidiomycetous fungi is still limited. In this study, we used RNA-Seq to study the effects of LiCl on Coprinopsis cinerea. LiCl enhanced mycelial growth and inhibited fruiting body formation in C. cinerea. RNA-Seq of the LiCl-treated C. cinerea resulted in a total of 14,128 genes. There were 1199 differentially expressed genes (DEGs) between the LiCl-treated samples and control samples in the mycelium stage (the first time point), and 1391 DEGs were detected when the control samples were forming hyphal knots while the treated samples were still in the mycelium (the second time point). Pathway enrichment analysis of the DEGs revealed a significant association between enhanced mycelium growth in the LiCl-treated C. cinerea and metabolic pathways. In addition, the DEGs involved in cellular process pathways, including "cell cycle-yeast" and "meiosis-yeast", were identified in suppressed C. cinerea fruiting body formation by LiCl under favourable environmental conditions. As LiCl can predominantly inhibit the activity of glycogen synthase kinase3 (GSK3), our findings suggest that LiCl affects the expression of genes involved in fruiting body initiation and cellular processes by inhibiting GSK3 activity which is essential for fruiting body formation.

Exploring the Application and Prospects of Synthetic Biology in Engineered Living Materials

At the intersection of synthetic biology and materials science, engineered living materials (ELMs) exhibit unprecedented potential. Possessing unique "living" attributes, ELMs represent a significant paradigm shift in material design, showcasing self-organization, self-repair, adaptability, and evolvability, surpassing conventional synthetic materials. This review focuses on reviewing the applications of ELMs derived from bacteria, fungi, and plants in environmental remediation, eco-friendly architecture, and sustainable energy. The review provides a comprehensive overview of the latest research progress and emerging design strategies for ELMs in various application fields from the perspectives of synthetic biology and materials science. In addition, the review provides valuable references for the design of novel ELMs, extending the potential applications of future ELMs. The investigation into the synergistic application possibilities amongst different species of ELMs offers beneficial reference information for researchers and practitioners in this field. Finally, future trends and development challenges of synthetic biology for ELMs in the coming years are discussed in detail.

Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes

Fruiting bodies (sporocarps, sporophores or basidiomata) of mushroom-forming fungi (Agaricomycetes) are among the most complex structures produced by fungi. Unlike vegetative hyphae, fruiting bodies grow determinately and follow a genetically encoded developmental program that orchestrates their growth, tissue differentiation and sexual sporulation. In spite of more than a century of research, our understanding of the molecular details of fruiting body morphogenesis is still limited and a general synthesis on the genetics of this complex process is lacking. In this paper, we aim at a comprehensive identification of conserved genes related to fruiting body morphogenesis and distil novel functional hypotheses for functionally poorly characterised ones. As a result of this analysis, we report 921 conserved developmentally expressed gene families, only a few dozens of which have previously been reported to be involved in fruiting body development. Based on literature data, conserved expression patterns and functional annotations, we provide hypotheses on the potential role of these gene families in fruiting body development, yielding the most complete description of molecular processes in fruiting body morphogenesis to date. We discuss genes related to the initiation of fruiting, differentiation, growth, cell surface and cell wall, defence, transcriptional regulation as well as signal transduction. Based on these data we derive a general model of fruiting body development, which includes an early, proliferative phase that is mostly concerned with laying out the mushroom body plan (via cell division and differentiation), and a second phase of growth via cell expansion as well as meiotic events and sporulation. Altogether, our discussions cover 1 480 genes of Coprinopsis cinerea, and their orthologs in Agaricus bisporus, Cyclocybe aegerita, Armillaria ostoyae, Auriculariopsis ampla, Laccaria bicolor, Lentinula edodes, Lentinus tigrinus, Mycena kentingensis, Phanerochaete chrysosporium, Pleurotus ostreatus, and Schizophyllum commune, providing functional hypotheses for ~10 % of genes in the genomes of these species. Although experimental evidence for the role of these genes will need to be established in the future, our data provide a roadmap for guiding functional analyses of fruiting related genes in the Agaricomycetes. We anticipate that the gene compendium presented here, combined with developments in functional genomics approaches will contribute to uncovering the genetic bases of one of the most spectacular multicellular developmental processes in fungi. Citation: Nagy LG, Vonk PJ, Künzler M, Földi C, Virágh M, Ohm RA, Hennicke F, Bálint B, Csernetics Á, Hegedüs B, Hou Z, Liu XB, Nan S, M. Pareek M, Sahu N, Szathmári B, Varga T, Wu W, Yang X, Merényi Z (2023). Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes. Studies in Mycology 104: 1-85. doi: 10.3114/sim.2022.104.01.

Secrets of Flavonoid Synthesis in Mushroom Cells

Flavonoids are chemical compounds that occur widely across the plant kingdom. They are considered valuable food additives with pro-health properties, and their sources have also been identified in other kingdoms. Especially interesting is the ability of edible mushrooms to synthesize flavonoids. Mushrooms are usually defined as a group of fungal species capable of producing macroscopic fruiting bodies, and there are many articles considering the content of flavonoids in this group of fungi. Whereas the synthesis of flavonoids was revealed in mycelial cells, the ability of mushroom fruiting bodies to produce flavonoids does not seem to be clearly resolved. This article, as an overview of the latest key scientific findings on flavonoids in mushrooms, outlines and organizes the current state of knowledge on the ability of mushroom fruiting bodies to synthesize this important group of compounds for vital processes. Putting the puzzle of the current state of knowledge on flavonoid biosynthesis in mushroom cells together, we propose a universal scheme of studies to unambiguously decide whether the fruiting bodies of individual mushrooms are capable of synthesizing flavonoids.

Fungi in Mycelium-Based Composites: Usage and Recommendations

Mycelium-Based Composites (MBCs) are innovative engineering materials made from lignocellulosic by-products bonded with fungal mycelium. While some performance characteristics of MBCs are inferior to those of currently used engineering materials, these composites nevertheless prove to be superior in ecological aspects. Improving the properties of MBCs may be achieved using an adequate substrate type, fungus species, and manufacturing technology. This article presents scientifically verified guiding principles for choosing a fungus species to obtain the desired effect. This aim was realized based on analyses of scientific articles concerning MBCs, mycological literature, and patent documents. Based on these analyses, over 70 fungi species used to manufacture MBC have been identified and the most commonly used combinations of fungi species-substrate-manufacturing technology are presented. The main result of this review was to demonstrate the characteristics of the fungi considered optimal in terms of the resulting engineering material properties. Thus, a list of the 11 main fungus characteristics that increase the effectiveness in the engineering material formation include: rapid hyphae growth, high virulence, dimitic or trimitic hyphal system, white rot decay type, high versatility in nutrition, high tolerance to a substrate, environmental parameters, susceptibility to readily controlled factors, easy to deactivate, saprophytic, non-mycotoxic, and capability to biosynthesize natural active substances. An additional analysis result is a list of the names of fungus species, the types of substrates used, the applications of the material produced, and the main findings reported in the scientific literature.

Growth and Mechanical Characterization of Mycelium-Based Composites towards Future Bioremediation and Food Production in the Material Manufacturing Cycle

Today’s architectural and agricultural practices negatively impact the planet. Mycelium-based composites are widely researched with the aim of producing sustainable building materials by upcycling organic byproducts. To go further, this study analyzed the growth process and tested the mechanical behavior of composite materials grown from fungal species used in bioremediation. Agricultural waste containing high levels of fertilizers serves as the substrate for mycelium growth to reduce chemical dispersal in the environment. Compression and three-point bending tests were conducted to evaluate the effects of the following variables on the mechanical behavior of mycelium-based materials: substrate particle size (with or without micro-particles), fungal species (Pleurotus ostreatus and Coprinus comatus), and post-growth treatment (dried, baked, compacted then dried, and compacted then baked). Overall, the density of the material positively correlated with its Young’s and elastic moduli, showing higher moduli for composites made from substrate with micro-particles and for compacted composites. Compacted then baked composites grown on the substrate with micro-particles provided the highest elastic moduli in compression and flexural testing. In conclusion, this study provides valuable insight into the selection of substrate particle size, fungal species, and post-growth treatment for various applications with a focus on material manufacturing, food production, and bioremediation.

Risk assessment of fungal materials

Sustainable fungal materials have a high potential to replace non-sustainable materials such as those used for packaging or as an alternative for leather and textile. The properties of fungal materials depend on the type of fungus and substrate, the growth conditions and post-treatment of the material. So far, fungal materials are mainly made with species from the phylum Basidiomycota, selected for the mechanical and physical properties they provide. However, for mycelium materials to be implemented in society on a large scale, selection of fungal species should also be based on a risk assessment of the potential to be pathogenic, form mycotoxins, attract insects, or become an invasive species. Moreover, production processes should be standardized to ensure reproducibility and safety of the product.

Enabling community-based metrology for wood-degrading fungi

BACKGROUND

Lignocellulosic biomass could support a greatly-expanded bioeconomy. Current strategies for using biomass typically rely on single-cell organisms and extensive ancillary equipment to produce precursors for downstream manufacturing processes. Alternative forms of bioproduction based on solid-state fermentation and wood-degrading fungi could enable more direct means of manufacture. However, basic methods for cultivating wood-degrading fungi are often ad hoc and not readily reproducible. Here, we developed standard reference strains, substrates, measurements, and methods sufficient to begin to enable reliable reuse of mycological materials and products in simple laboratory settings.

RESULTS

We show that a widely-available and globally-regularized consumer product (Pringles™) can support the growth of wood-degrading fungi, and that growth on Pringles™-broth can be correlated with growth on media made from a fully-traceable and compositionally characterized substrate (National Institute of Standards and Technology Reference Material 8492 Eastern Cottonwood Whole Biomass Feedstock). We also establish a Relative Extension Unit (REU) framework that is designed to reduce variation in quantification of radial growth measurements. So enabled, we demonstrate that five laboratories were able to compare measurements of wood-fungus performance via a simple radial extension growth rate assay, and that our REU-based approach reduced variation in reported measurements by up to ~ 75%.

CONCLUSIONS

Reliable reuse of materials, measures, and methods is necessary to enable distributed bioproduction processes that can be adopted at all scales, from local to industrial. Our community-based measurement methods incentivize practitioners to coordinate the reuse of standard materials, methods, strains, and to share information supporting work with wood-degrading fungi.