Fungal and bacterial community dynamics in substrates during the cultivation of morels (Morchella rufobrunnea) indoors

Abstract

Morel mushrooms (Morchella, Pezizales) are highly prized edible fungi. Approaches to cultivate morels indoors in pasteurized composted substrates have been successful for Morchella rufobrunnea. We used DNA amplicon sequencing of the Internal Transcribed Spacer (ITS) ribosomal DNA and 16S rRNA gene to follow bacterial and fungal communities in substrates during indoor morel cultivation. Our goal was to determine changes in microbial communities at key stages of morel cultivation, which included primordia development, fundament initiation, differentiation and maturation. Additionally, we compared microbial communities between trays that successfully fruited to those that produced conidia and primordia but aborted before ascocarp formation (non-fruiting). The prokaryotic community was dominated by Firmicutes belonging to Bacillus and Paenibacillus with a lower abundance of Flavobacteria. At earlier stages, the fungal community was dominated by Pezizomycetes including Morchella and other species, whereas, later in the cropping cycle Sordariomycetes dominated. Additionally, differences were observed between trays with successful fruiting, which were dominated by Gilmaniella; compared to trays that did not fruit, which were dominated by Cephalotrichum. Our findings inform understanding of microbial community dynamics during morel cultivation, and show that fungal genera, such as Gilmaniella, and prokaryotic genera, such as Bacillus, are abundant in substrates that support M. rufobrunnea fruiting.

Build Your Own Mushroom Soil: Microbiota Succession and Nutritional Accumulation in Semi-Synthetic Substratum Drive the Fructification of a Soil-Saprotrophic Morel

“…The dung saprotrophic Basidiomycete mushroom A. bisporus grows on a substratum of compost covered with a thin layer of casing soil (Pardo-Giménez et al, 2017). A facultatively saprotrophic morel species, the M. rufobrunnea, requests a substratum with a relatively higher proportion of compost (soil to compost at 50%:50% (v/v)) (Longley et al, 2019), while the semi-synthetic substratum for M. importuna in this study is mostly composed of quartz particles with no more than 2% (w/w) of organicmatter supplementation. Compared with the substrata used for A. bisporus and M. rufobrunnea dominated by organicmatters, the semi-synthetic substratum for M. importuna is more analogous to sandy soils.…”

“…The major bacterial phyla Actinobacteria , Chloroflexi , and Proteobacteria in the semi-synthetic substratum in this study ( Figure 3A ) were also dominant in the soil beneath the fruiting bodies of Morchella sextelata , another black morel species ( Benucci et al, 2019 ). During the fructification period of Morchella rufobrunnea cultivated indoors, different profiles of bacterial communities were observed ( Longley et al, 2019 ). Among the fungal communities, a high abundance of Gilmaniella seemed associated with a successful fructification of M. rufobrunnea cultivated indoors, while the dominance of Cephalotrichum seemed responsible for a failure of the fructification ( Longley et al, 2019 ).…”

“…Bacterial OTUs were clustered against the SILVA reference database (Release 132), while fungal OTUs were clustered against the UNITE v7.2 (Full UNITE + INSD datasets) as described previously ( Tan et al, 2019 ). The 16S OTUs were assigned to bacterial taxa using the RDP classifier of the QIIME pipeline, while the ITS OTUs were assigned to fungal taxa using the CONSTAX classifier ( Gdanetz et al, 2017 ), as described by Longley et al (2019) . The sequencing depth was normalized among different samples.…”

“…β-diversity of the communities in different samples was estimated by Non-metric Multi-Dimensional Scaling (NMDS) analysis using Bray-Curtis distance. The OTU table was normalized using cumulative sum scaling prior to calculation of the Bray-Curtis distance matrix, as described by Longley et al (2019) . Dispersion of community groups was estimated by permutational multivariate analysis of variance (PERMANOVA), using the “adonis” command in the R package vegan ( Oksanen et al, 2016 ).…”

“…Species in the ascomycete genus Morchella are culinary delicacies widely prized in the world, commonly known as morels ( Pilz et al, 2007 ). With great ecological and economic importance, the nutritional strategies of morels vary from soil-saprotrophic to biotrophic ( Larson et al, 2016 ; Loizides, 2017 ; Longley et al, 2019 ). Their production was once quite dependent on collection from wild forests ( Pilz et al, 2004 , 2007 ).…”