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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.

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