Holistic assessment of the microbiome dynamics in the substrates used for commercial champignon (Agaricus bisporus) cultivation

Abstract

Microorganisms strongly influence and are required to generate the selective substrate that provides nutrients and support for fungal growth, and ultimately to induce mushroom fructification under controlled environmental conditions. In this work, the fungal and bacterial microbiota living in the different substrates employed in a commercial crop (compost phase I, II and III, flush 1 and 2, and casing material on day 1, 6 and 8 after compost casing and during flush 1 and 2) have been characterized along the different stages of cultivation by metataxonomic analysis (16S rRNA and ITS2), analysis of phospholipid fatty acid content (PLFAs) and RT-qPCR. Additionally, laccase activity and the content of lignin and complex carbohydrates in compost and casing have been quantified. The bacterial diversity in compost and casing increased throughout the crop cycle boosted by the connection of both substrates. As reflected by the PLFAs, the total living bacterial biomass appears to be negatively correlated with the mycelium of the crop. Agaricus bisporus was the dominant fungal species in colonized substrates, displacing the pre-eminent Ascomycota, accompanied by a sustained increase in laccase activity, which is considered to be a major product of protein synthesis during the mycelial growth of champignon. From phase II onwards, the metabolic machinery of the fungal crop degrades lignin and carbohydrates in compost, while these components are hardly degraded in casing, which reflects the minor role of the casing for nourishing the crop. The techniques employed in this study provide a holistic and detailed characterization of the changing microbial composition in commercial champignon substrates. The knowledge generated will contribute to improve compost formulations (selection of base materials) and accelerate compost production, for instance, through biotechnological interventions in the form of tailored biostimulants and to design environmentally sustainable bio-based casing materials.

Influence of Agaricus Bisporus Establishment and Fungicidal Treatments on Casing Soil Metataxonomy During Mushroom Cultivation

“…At day D00 the most abundant fungal phylum was Ascomycota, but throughout the cultivation cycle, the phylum Basidiomycota became dominant as described in other studies [16,17]. As indicated in these works, A. bisporus replace the other species and colonized the casing soil material.…”

Control of Fungal Diseases in Mushroom Crops while Dealing with Fungicide Resistance: A Review

“…Although mechanisms involving biocontrol of green mold from biofungicides have been barely described, according to Pandin et al [ 121 , 122 ], the mechanisms acting in the antagonism of T. aggressivum by B. velezensis QST713 may be a combination of (i) competence in the environmental niche through the formation of competitive biofilm to exclude T. aggressivum , (ii) production and secretion of compounds with antifungal activity against the parasite, and (iii) release of signaling molecules, such as volatile organic compounds (VOCs) or the quorum-sensing-controlled processes, which can lead to defense response in A. bisporus or reduce parasite activity. The environmental niche where mushrooms develop and fructify is a highly dynamic and rich microbiome where multiple agents act and its configuration may have a direct impact on yield performance and disease occurrence [ 32 , 123 , 124 ]. Bacteria genera inhabiting casing material, including Bacillus and Pseudomonas , can be responsible for the casing fungistasis of mycoparasites observed in the absence of the host mycelium [ 125 ], however, the host mycelium modifies the microbiome structure breaking the fungistatic equilibrium and the native microbiota results inefficient to suppress mycoparasites under conditions of high disease pressure [ 32 , 48 ].…”

Mycoremediation of Soils Polluted with Trichloroethylene: First Evidence of Pleurotus Genus Effectiveness

“…The secretion of the extracellular enzymes laccase and MnP are another indication of fungal functioning [40]. Although P. ostreatus did not express laccase in the absence of TCE in liquid broth, low levels were detected in the presence of the contaminant (Figure 3A), despite the structural alteration of its hyphae.…”