Microbial communities associated with the black morel Morchella sextelata cultivated in greenhouses

Abstract

Morels (Morchella spp.) are iconic edible mushrooms with a long history of human consumption. Some microbial taxa are hypothesized to be important in triggering the formation of morel primordia and development of fruiting bodies, thus, there is interest in the microbial ecology of these fungi. To identify and compare fungal and prokaryotic communities in soils where Morchella sextelata is cultivated in outdoor greenhouses, ITS and 16S rDNA high throughput amplicon sequencing and microbiome analyses were performed. Pedobacter, Pseudomonas, Stenotrophomonas, and Flavobacterium were found to comprise the core microbiome of M. sextelata ascocarps. These bacterial taxa were also abundant in the soil beneath growing fruiting bodies. A total of 29 bacterial taxa were found to be statistically associated to Morchella fruiting bodies. Bacterial community network analysis revealed high modularity with some 16S rDNA operational taxonomic unit clusters living in specialized fungal niches (e.g., pileus, stipe). Other fungi dominating the soil mycobiome beneath morels included Morchella, Phialophora, and Mortierella. This research informs understanding of microbial indicators and potential facilitators of Morchella ecology and fruiting body production.

Keywords: Amplicon sequencing; CONSTAX; Microbial ecology; Microbiome; Morchella; Mushroom cultivation; Pedobacter; USEARCH.

Figure 1. Stacked bar plots.

Stacked bar plots showing fungal families (A) with relative abundance ≥1% detected in soil beneath ascocarps of mature and young Morchella sextelata fruiting bodies, and prokaryotic phyla (B) with relative abundance ≥1% detected in pileus, stipe, and soils beneath ascocarps of mature and young M. sextelata.

Figure 2. Principal coordinates analysis plots, using Bray–Curtis dissimilarity matrices, of prokaryotic (A) and fungal (B) communities associated with Morchella sextelata.

Figure 3. Heatmap of the relative abundances of the 29 indicator taxa significantly associated with Morchella sextelata pileus, stipe, pileus and stipe, pileus and soil, stipe and soil.

Samples are ranked according the clustering dendrogram. Blue and white blocks of the top annotation represent samples from young and mature morels, respectively. The side annotation barplot reports the square root of the cumulative relative abundance for each OTU across all the samples.

Figure 4. Venn diagrams showing core and unique OTUs among different sample groups.

(A) Prokaryotic communities in pileus, stipe, and soils beneath Morchella sextelata; (B) Prokaryotic communities in mature and young ascocarps of M. sextelata; (C) Fungal communities in mature and young M. sextelata ascocarps.

Figure 5. Microbial co-occurrence network showing the prokaryotic community structure of Morchella sextelata.

Each node (vertex) indicates a single OTU at 97% sequence similarity. Blue edges indicates positive co-occurrence, red edges indicated negative co-occurrences; (A) Network showing indicator species (see in Fig. 3), keystone OTU, and the first top five modules. (B) Network showing the taxonomic composition of each node and articulation points. Nodes size is the square root of the relative OTU abundance; (C) Barplot showing OTU frequency (OTU richness) and taxonomic composition for the first five modules.