Evaluating the Microbiome of Hemp

Cornell University

For each DESeq2 analysis, we used unrarefied OTU tables filtered to include only OTUs represented by at least five reads in at least one sample of the plant compartment-bulk soil set. We defined the core microbiome as bacterial and fungal OTUs that were ubiquitous in hemp plants and enriched significantly in a plant compartment relative to bulk soil. We defined a member of the core microbiome for a given plant compartment as an OTU that was ubiquitous across all plants in all sampling locations and enriched significantly in their plant compartment relative to the bulk soil. A number of the microbes that were highly abundant in the rhizosphere belong to taxa commonly found in plants; however, we only included in the core hemp microbiome those OTUs that were enriched significantly in the hemp rhizosphere relative to bulk soil. A leaf core fungal member, OTU_174, classified to the genus Epicoccum, was also highly abundant and ubiquitous in the flower community, though not significantly enriched in that compartment.

https://doi.org/10.1094/pbiomes-06-20-0046-r

Tags:

Rhizosphere

Microbiome

Phyllosphere

Polymerase chain reaction

Biology