Critical Factors Involved in Primordia Building in Agaricus bisporus: A Review

Nitrogen balance and supply in Australasian mushroom composts

Mushrooms are an important source of protein in the human diet. They are increasingly viewed as a sustainable meat replacement in an era of growing populations, with button mushrooms (Agaricus bisporus) the most popular and economically important mushroom in Europe, Australia and North America. Button mushrooms are cultivated on a defined, straw-derived compost, and the nitrogen (N) required to grow these high-protein foods is provided mainly by the addition of poultry manure and horse manure. Using the correct balance of carbon (C) and N sources to produce mushroom compost is critically important in achieving maximum mushroom yields. Changes in the amount and form of N added, the rate and timing of N addition and the other compost components used can dramatically change the proportion of added N recovered in the mushroom caps, the yield and quality of the mushrooms and the loss of N as ammonia and nitrogen oxide gases during composting. This review examines how N supply for mushroom production can be optimised by the use of a broad range of inorganic and organic N sources for mushroom composting, together with the use of recycled compost leachate, gypsum and protein-rich supplements. Integrating this knowledge into our current molecular understanding of mushroom compost biology will provide a pathway for the development of sustainable solutions in mushroom production that will contribute strongly to the circular economy. KEY POINTS: • Nitrogen for production of mushroom compost can be provided as a much wider range of organic feedstocks or inorganic compounds than currently used • Most of the nitrogen used in production of mushroom compost is not recovered as protein in the mushroom crop • The sustainability of mushroom cropping would be increased through alternative nitrogen management during composting and cropping.

Manipulating Agaricus bisporus developmental patterns by passaging microbial communities in complex substrates

IMPORTANCE

Agaricus bisporus is an economically important edible mushroom and manipulating its developmental patterns is crucial for maximizing yield and quality. One of the potential strategies for achieving such a goal is passaging microbial communities in compost or casing. The current study demonstrated that passaging substrates develop enriched microbial communities, and after a few passages, certain levels of changes in mushroom developmental patterns (the timing of fruiting bodies formation) were observed as well as shifts in the bacterial communities. Overall, a better understanding of the complex interactions between microorganisms present in the cultivation system may help farmers and researchers to develop more efficient and sustainable cultivation practices that can both benefit the environment and human health.

A journey with psychedelic mushrooms: From historical relevance to biology, cultivation, medicinal uses, biotechnology, and beyond

Psychedelic mushrooms containing psilocybin and related tryptamines have long been used for ethnomycological purposes, but emerging evidence points to the potential therapeutic value of these mushrooms to address modern neurological, psychiatric health, and related disorders. As a result, psilocybin containing mushrooms represent a re-emerging frontier for mycological, biochemical, neuroscience, and pharmacology research. This work presents crucial information related to traditional use of psychedelic mushrooms, as well as research trends and knowledge gaps related to their diversity and distribution, technologies for quantification of tryptamines and other tryptophan-derived metabolites, as well as biosynthetic mechanisms for their production within mushrooms. In addition, we explore the current state of knowledge for how psilocybin and related tryptamines are metabolized in humans and their pharmacological effects, including beneficial and hazardous human health implications. Finally, we describe opportunities and challenges for investigating the production of psychedelic mushrooms and metabolic engineering approaches to alter secondary metabolite profiles using biotechnology integrated with machine learning. Ultimately, this critical review of all aspects related to psychedelic mushrooms represents a roadmap for future research efforts that will pave the way to new applications and refined protocols.

Microbial succession during button mushroom (Agaricus bisporus) production evaluated via high-throughput sequencing

Button mushrooms (Agaricus bisporus), are one of the most widely consumed mushrooms in the world. However, changes within its microbial community as it relates to the use of different raw materials and cultivation methods, as well as potential points of microbial contamination throughout the production process have not been investigated extensively. In the present study, button mushroom cultivation was investigated in each of the four stages (raw materials, composting (phase I, Ⅱ, and Ⅲ), casing, and harvesting), and samples (n = 186) from mushrooms and their related environments were collected from four distinct mushroom-growing farms (A-D) in Korea. Shifts within the bacterial consortium during mushroom production were characterized with 16 S rRNA amplicon sequencing. The succession of bacterial communities on each farm was dependent on the raw material incorporated, aeration, and the farm environment. The dominant phyla of the compost stack at the four farms were Pseudomonadota (56.7%) in farm A, Pseudomonadota (43.3%) in farm B, Bacteroidota (46.0%) in farm C, and Bacillota (62.8%) in farm D. During the Phase Ⅰ, highly heat-resistant microbes, such as those from the phylum Deinococcota (0.6-65.5%) and the families Bacillaceae (1.7-36.3%), Thermaceae (0.1-65.5%), and Limnochordaceae (0.3-30.5%) greatly proliferated. The microbial diversity within compost samples exhibited a marked decline as a result of the proliferation of thermophilic bacteria. In the spawning step, there were considerable increases in Xanthomonadaceae in the pasteurized composts of farms C and D - both of which employed an aeration system. In the harvesting phase, beta diversity correlated strongly between the casing soil layer and pre-harvest mushrooms, as well as between gloves and packaged mushrooms. The results suggest that gloves may be a major source of cross-contamination for packaged mushrooms, highlighting the need for enhanced hygienic practices during the harvesting phase to ensure product safety. These findings contribute to the current understanding of the influence of environmental and adjacent microbiomes on mushroom products to benefit the mushroom industry and relevant stakeholders by ensuring quality production.

Fate of antibiotic resistance genes in cultivation substrate and its association with bacterial communities throughout commercial production of Agaricus bisporus

Animal manure is an important raw material for Agaricus bisporus production; however, it is also a reservoir for antibiotic residues, antibiotic resistance genes (ARGs), and antibiotic-resistant bacteria. Little is known about the influence of the commercial cultivation of A. bisporus on the dynamics of ARGs and the underlying mechanisms that cause their variations. In this study, we investigated the fate of 285 ARGs, 10 mobile genetic elements, and seven major categories of antibiotic residues in substrate and mushroom samples at different production phases. The results showed that commercial substrate preparation, particularly the pasteurization phase, was highly efficient in removing ARGs from the substrate. We further found that mycelium proliferation of A. bisporus contributed significantly to the removal of ARGs from the substrate and casing soil. The bacterial community is the key driver of changes in ARGs during the commercial cultivation of A. bisporus, which explained 46.67% of the variation in ARGs. Our results indicate that, despite the addition of animal manure, the risk of ARG dissemination to fruiting bodies and the environment is low. We propose that bioremediation by specific edible fungi might be a novel and promising method for scavenging antimicrobial resistance contamination from soil environment.

Metagenomics analysis of the effects of Agaricus bisporus mycelia on microbial diversity and CAZymes in compost

Agaricus bisporus growth alters the lignocellulosic composition and structure of compost. However, it is difficult to differentiate the enzyme activities of A. bisporus mycelia from the wider microbial community owing to the complication of completely speareting the mycelia from compost cultures. Macrogenomics analysis was employed in this study to examine the fermentation substrate of A. bisporus before and after mycelial growth, and the molecular mechanism of substrate utilization by A. bisporus mycelia was elucidated from the perspective of microbial communities and CAZymes in the substrate. The results showed that the relative abundance of A. bisporus mycelia increased by 77.57-fold after mycelial colonization, the laccase content was significantly increased and the lignin content was significantly decreased. Analysis of the CAZymes showed that AA10 family was extremely differentiated. Laccase-producing strains associated with AA10 family were mostly bacteria belonging to Thermobifida and Thermostaphylospora, suggesting that these bacteria may play a synergistic role in lignin decomposition along with A. bisporus mycelia. These findings provide preliminary evidence for the molecular mechanism of compost utilization by A. bisporus mycelia and offer a reference for the development and utilization of strains related to lignocellulose degradation.

Dynamics of microbial community and enzyme activities during preparation of Agaricus bisporus compost substrate

Button mushrooms (Agaricus bisporus) are grown commercially on a specialized substrate that is usually prepared from wheat straw and poultry manure in a microbially-mediated composting process. The quality and yield of the mushroom crop depends critically on the quality of this composted substrate, but details of the microbial community responsible for compost production have only emerged recently. Here we report a detailed study of microbial succession during mushroom compost production (wetting, thermophilic, pasteurization/conditioning, spawn run). The wetting and thermophilic phases were characterized by a rapid succession of bacterial and fungal communities, with maximum diversity at the high heat stage. Pasteurization/conditioning selected for a more stable community dominated by the thermophilic actinomycete Mycothermus thermophilus and a range of bacterial taxa including Pseudoxanthomonas taiwanensis and other Proteobacteria. These taxa decreased during spawn run and may be acting as a direct source of nutrition for the proliferating Agaricus mycelium, which has previously been shown to use microbial biomass in the compost for growth. Comparison of bacterial communities at five geographically separated composting yards in south-eastern Australia revealed similarities in microbial succession during composting, although the dominant bacterial taxa varied among sites. This suggests that specific microbial taxa or combinations of taxa may provide useful biomarkers of compost quality and may be applied as predictive markers of mushroom crop yield and quality.

Feeding growing button mushrooms: The role of substrate mycelium to feed the first two flushes

A number of experiments were done to further our understanding of the substrate utilization in button mushroom crops (Agaricus bisporus). An analysis of the degradation of dry matter of the substrate during a crop cycle revealed that for pin formation the upper 1/3rd layer is used, for the production of flush one all layers are involved and for flush two mainly the lower 1/3 layer is used. A reduction in substrate depth leads to a decrease in yield/m2 but an apparent increase in yield per tonne of substrate with a lower mushroom quality. A short daily interruption of the connection between the casing soil with the substrate results in a delay of the first flush. Interruptions with only part of the substrate did not lead to delay in production. Daily interruption of the connection with all or only part of the substrate leads to a shift in yield from flush one to flush two but the total yield remains unchanged. The mycelial biomass in the substrate increases from filling up to pinning, has a steeper increase during flush one, and is levelling off during flush two, indicating that in the period of venting and up to/including flush one, enzymes are secreted by growing hyphae generating nutrients to feed a fixed amount of mushroom biomass for two flushes. A sidewise extension of the substrate (without casing soil, thus not producing mushrooms) showed that the substrate at a distance more than somewhere between 20-50 cm away from the casing soil does not contribute to feeding mushrooms in the first two flushes. The observations are discussed with respect to relevant previous research.

Bacterial Community Patterns in the Agaricus bisporus Cultivation System, from Compost Raw Materials to Mushroom Caps

Different from other fungal species that can be largely cultivated in 'axenic conditions' using plant material (e.g., species of Lentinula and Pleurotus in 'sterile' straw-based substrate), the commercial Agaricus bisporus cultivation system relies heavily on ecological relationships with a broad range of microorganisms present in the system (compost and casing). Since the A. bisporus cultivation system consists of a microbial manipulation process, it is important to know the microbial community dynamics during the entire cultivation cycle to design further studies and/or crop management strategies to optimize this system. To capture the bacterial community 'flow' from compost raw materials to the casing to the formation and maturation of mushroom caps, community snapshots were generated by direct DNA recovery (amplicon sequencing). The 'bacterial community flow' revealed that compost, casing and mushrooms represent different niches for bacteria present in the cultivation system, but at the same time, a bacterial exchange between microenvironments can occur for a portion of the community. Within each microenvironment, compost showed intense bacterial populational dynamics, probably due to the environmental changes imposed by composting conditions. In casing, the colonization of A. bisporus appeared, to reshape the native bacterial community which later, with some other members present in compost, becomes the core community in mushroom caps. The current bacterial survey along with previous results provides more cues of specific bacteria groups that can be in association with A. bisporus development and health.

Impact of Cultivation Substrate and Microbial Community on Improving Mushroom Productivity: A Review

Simple Summary

Lignocellulosic material and substrate formulations affect mushroom productivity. The microbial community in cultivation substrates affects the quality of the substrates and the efficiency of mushroom production. The elucidation of the key microbes and their biochemical function can serve as a useful guide in the development of a more effective system for mushroom cultivation.

Abstract

Lignocellulosic materials commonly serve as base substrates for mushroom production. Cellulose, hemicellulose, and lignin are the major components of lignocellulose materials. The composition of these components depends upon the plant species. Currently, composted and non-composted lignocellulosic materials are used as substrates in mushroom cultivation depending on the mushroom species. Different substrate compositions can directly affect the quality and quantity of mushroom production yields. Consequently, the microbial dynamics and communities of the composting substrates can significantly affect mushroom production. Therefore, changes in both substrate composition and microbial diversity during the cultivation process can impact the production of high-quality substrates and result in a high degree of biological efficiency. A brief review of the current findings on substrate composition and microbial diversity for mushroom cultivation is provided in this paper. We also summarize the advantages and disadvantages of various methods of mushroom cultivation by analyzing the microbial diversity of the composting substrates during mushroom cultivation. The resulting information will serve as a useful guide for future researchers in their attempts to increase mushroom productivity through the selection of suitable substrate compositions and their relation to the microbial community.

Sexual Crossing, Chromosome-Level Genome Sequences, and Comparative Genomic Analyses for the Medicinal Mushroom Taiwanofungus Camphoratus (Syn. Antrodia Cinnamomea, Antrodia Camphorata)

Taiwanofungus camphoratus mushrooms are a complementary and alternative medicine for hangovers, cancer, hypertension, obesity, diabetes, and inflammation. Though Taiwanofungus camphoratus has attracted considerable biotechnological and pharmacological attention, neither classical genetic nor genomic approaches have been properly established for it. We isolated four sexually competent monokaryons from two T. camphoratus dikaryons used for the commercial cultivation of orange-red (HC1) and milky-white (SN1) mushrooms, respectively. We also sequenced, annotated, and comparatively analyzed high-quality and chromosome-level genome sequences of these four monokaryons. These genomic resources represent a valuable basis for understanding the biology, evolution, and secondary metabolite biosynthesis of this economically important mushrooms. We demonstrate that T. camphoratus has a tetrapolar mating system and that HC1 and SN1 represent two intraspecies isolates displaying karyotypic variation. Compared with several edible mushroom model organisms, T. camphoratus underwent a significant contraction in the gene family and individual gene numbers, most notably for plant, fungal, and bacterial cell-wall-degrading enzymes, explaining why T. camphoratus mushrooms are rare in natural environments, are difficult and time-consuming to artificially cultivate, and are susceptible to fungal and bacterial infections. Our results lay the foundation for an in-depth T. camphoratus study, including precise genetic manipulation, improvements to mushroom fruiting, and synthetic biology applications for producing natural medicinal products. IMPORTANCETaiwanofungus camphoratus (Tc) is a basidiomycete fungus that causes brown heart rot of the aromatic tree Cinnamomum kanehirae. The Tc fruiting bodies have been used to treat hangovers, abdominal pain, diarrhea, hypertension, and other diseases first by aboriginal Taiwanese and later by people in many countries. To establish classical genetic and genomic approaches for this economically important medicinal mushroom, we first isolated and characterized four sexually competent monokaryons from two dikaryons wildly used for commercial production of Tc mushrooms. We applied PacBio single molecule, real-time sequencing technology to determine the near-completed genome sequences of four monokaryons. These telomere-to-telomere and gapless haploid genome sequences reveal all genomic variants needed to be studied and discovered, including centromeres, telomeres, retrotransposons, mating type loci, biosynthetic, and metabolic gene clusters. Substantial interspecies diversities are also discovered between Tc and several other mushroom model organisms, including Agrocybe aegerita, Coprinopsis cinerea, and Schizophyllum commune, and Ganoderma lucidum.