Casing microbiome dynamics during button mushroom cultivation: implications for dry and wet bubble diseases

Abstract

The casing material required in mushroom cultivation presents a very rich ecological niche, which is inhabited by a diverse population of bacteria and fungi. In this work three different casing materials, blonde peat, black peat and a 50 : 50 mixture of both, were compared for their capacity to show a natural suppressive response against dry bubble, Lecanicillium fungicola (Preuss) Zare and Gams, and wet bubble, Mycogone perniciosa (Magnus) Delacroix. The highest mushroom production was collected from crops cultivated using the mixed casing and black peat, which were not significantly different in yield. However, artificial infection with mycoparasites resulted in similar yield losses irrespective of the material used, indicating that the casing materials do not confer advantages in disease suppression. The composition of the microbiome of the 50 : 50 casing mixture along the crop cycle and the compost and basidiomes was evaluated through next-generation sequencing (NGS) of the V3-V4 region of the bacterial 16S rRNA gene and the fungal ITS2 region. Once colonized by Agaricus bisporus, the bacterial diversity of the casing microbiome increased and the fungal diversity drastically decreased. From then on, the composition of the casing microbiome remained relatively stable. Analysis of the composition of the bacterial microbiome in basidiomes indicated that it is highly influenced by the casing microbiota. Notably, L. fungicola was consistently detected in uninoculated control samples of compost and casing using NGS, even in asymptomatic crops. This suggests that the naturally established casing microbiota was able to help to suppress disease development when inoculum levels were low, but was not effective in suppressing high pressure from artificially introduced fungal inoculum. Determination of the composition of the casing microbiome paves the way for the development of synthetic casing communities that can be used to investigate the role of specific components of the casing microbiota in mushroom production and disease control.

Growing edible mushrooms: a conversation between bacteria and fungi

“…For instance, it leads to enhanced growth of Proteobacteria, particularly pseudomonads, with a corresponding decrease in Firmicutes and Actinobacteria (Fig. 2; Carrasco et al, 2019), which indicates a synergistic interaction between members of the phylum Proteobacteria and A. bisporus.…”

“…Both bacteria and yeast were shown to increase significantly in basidiomes after harvest and during cold storage (Siyoum et al ., 2016). According to our results, Proteobacteria , Bacterioidetes , Actinobacteria and Firmicutes are the most abundant phyla in button mushroom basidiomes (Carrasco et al ., ). In addition, bacterial and fungal diversity in basidiomes appears to be more broadly configured by the microbial community present in the casing than by the compost microbiome (Carrasco et al ., ).…”

“…Thermotolerant, sulfur-reducing bacteria of the phyla Deinococcus-Thermus and Thermodesulfobacteria have been reported to be highly active up to the first flush, even though the temperature during phase III is typically reduced to 15-25 C (McGee et al, 2017b). Notably, the activity and relative abundance of the phyla Actinobacteria and Firmicutes was observed to increase as mushroom production progressed, indicating a potential role of members from these phyla in the conversion of complex carbohydrates to simple sugars suitable for the A. bisporus mycelium (McGee et al, 2017b;Carrasco et al, 2019). Unsurprisingly, A. bisporus occupies a dominant position in the fungal community from the beginning to the end of the crop cycle, which supports the hypothesis that the native microbiome facilitates colonization of the substrate by A. bisporus and helps to restrict the growth of competitors and parasites of the crop (McGee et al, 2017a;Carrasco et al, 2019).…”

“…Sequencing has revealed a more diverse bacterial population in casing than in the compost (Siyoum et al, 2016;Carrasco et al, 2019). Along the mushroom cropping cycle, the presence of the A. bisporus mycelium modifies the initial composition of the casing microbiome (Pecchia et al, 2014;Carrasco et al, 2019).…”

“…Sequencing has revealed a more diverse bacterial population in casing than in the compost (Siyoum et al, 2016;Carrasco et al, 2019). Along the mushroom cropping cycle, the presence of the A. bisporus mycelium modifies the initial composition of the casing microbiome (Pecchia et al, 2014;Carrasco et al, 2019). Casing at the beginning of the crop cycle (prior to A. bisporus colonization) shows statistically significant differences in microbiome composition from colonized casing (Carrasco et al, 2019).…”