Variations in Cannabis Microbiome: Time, Space, and Cultivar

Written by Lydia Kariuki

The legalization of cannabis in Canada in 2018 set the stage for widescale commercialization of the plant. This also paved the way for diverse research into the properties of cannabis. The cannabis microbiome has since become a subject of particular interest to researchers because it facilitates nutrient uptake, induces resistance to pathogens, modulates the production of secondary metabolites, and contributes to plant growth. [1]

A group of researchers from the University of Moncton, Ca. recently investigated the different factors responsible for the variations in the cannabis microbiome. [2] Cannabis cultivars are classified into chemotypes based on their concentration of the primary cannabinoids: delta-9-tetrahydrocannabinol (THC) and cannabidiol (CBD). The researchers looked at chemotypes and spatial and temporal changes that occur during the lifecycle of the plant.

Chemotype Considerations
Three cannabis chemotypes cultivated using standard commercial production conditions from the company Organigram’s facility (Moncton, NB, Canada) were used in this study:

  • CBD Yummy (<1% THC/13% CBD)
  • CBD shark (6% THC/10% CBD)
  • Hash (14% THC/ < 1% CBD)

Clones instead of seeds were used to circumvent genetic variations which may occur because cannabis is inherently “promiscuous.” This property can incidentally affect the microbiome.

Spatio-temporal Considerations
DNA from the rhizosphere (narrow region of soil influenced by root secretions and root microbiome), endosphere (inside plant tissues), and phyllosphere (total above ground surface of a plant) were included in the sampling to evaluate the spatio-temporal variations in the microbiome. The microbial DNA was extracted from the chemotypes at different lifecycle stages (four harvesting periods). The researchers could amplify fungal DNA but not bacterial DNA from the phyllosphere.

After analyzing 130 samples from each of the 3 cultivars, the researchers successfully identified spatio-temporal and cultivar dependent variations in the fungal and bacterial microbiomes of cannabis. The researchers found that the greatest diversity in the microbiome occurred belowground. This is during the vegetative stage, a period where the plant has no appreciable cannabinoid levels. While there was a concomitant appreciation in microbiome richness as the plant ages, a drop in those attributes was observed between the rhizosphere, endosphere, and phyllosphere.

CBD Shark appeared to be an outlier as far as the variation in its microbiome is concerned. The researchers thought this warranted further investigation.

All three chemotypes showed variation in their terpene production:

The researchers found that spatio-temporal variations affect the cannabis microbiome. They acknowledged that the plants were not exposed to biotic and abiotic stressors, having been grown in an indoor setup, which could potentially impact the cannabis microbiome. These findings can help to engineer plant growth in economically important crops. [2]


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1- Taghinasab M, Jabaji S. Cannabis microbiome and the role of endophytes in modulating the production of secondary metabolites: An overview. Microorganisms. 2020;8(3):355. [journal impact factor = 4.128; times cited = 21]

2- Comeau D, Novinscak A, Joly DL, Filion M. Spatio-temporal and cultivar-dependent variations in the Cannabis microbiome. Front Microbiol. 2020;11:491. [journal impact factor = 5.64; times cited = 11]

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Lydia Kariuki

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