The plant microbiome is defined as the key microbial organisms that are associated with the plant and important for its fitness. They are established through evolutionary mechanisms of selection and enrichment of microbial populations containing essential functions and genes contributing to the fitness of the plant in nature or improved performance in human cultivation. The   microbial partnerships with the medicinally and economically important crop Cannabis, has the potential to affect agricultural practice by improving plant fitness and production yield. Along with steadily growing research in cannabis healthcare science, there is an increasing interest in the plant microbiology and research connecting the plant microbiome and plant health to product yield, quality, and product safety.

When addressing the microbiome of cannabis, the immediate attention is directed towards the major fungal plant pathogens. From an economic standpoint, Botrytis cinerea (Gray rot), Erysiphe species complex (‘Powdery Mildew’- (PM)) and Fusarium spp. are the prominent three pathogens affecting yield, quality, safety, and the derived financial consequences.

Golovinomyces (Erysiphe Spp.) cichoracearum, the causal agent(s) of powdery mildew is the predominant pathogen affecting indoor production. Two pathways currently exist for limiting the extent of fungal invasion:

1. Various yet uncharacterized plant immune pathways originating from ‘hemp-type’ cannabis

2. Recessively inherited loss-of-function alleles of Mildew Locus O (Mlo) genes confer a prominent type of effective powdery mildew resistance. Application of both requires extensive breeding for trait introgression.

Botrytis is currently the most widespread pathogen of Cannabis worldwide, damaging flowering buds and stalks, causing gray mold and capable of producing two major phytotoxins: the sesquiterpene botrydial and the polyketide botcinic acid that pose a risk for human consumption.
Despite growing research in recent years, still, no effective management measure exists against B. cinerea or other cannabis-associated molds due to their genomic plasticity and development of drug resistance.
Fusarium sp. (mainly F. oxysporum and F. solani ) are soil fungal pathogens with devastating effects on contaminated production facilities and no clear genetic sources of resistance. One of the suggested methods for maintaining healthy plants is to enrich the plant microbiome for beneficial microorganisms.

Soil microbes play a major role in plant ecology by providing a variety of benefits such as nitrogen fixation, production of growth stimulants, improved water retention, and suppression of root diseases. Microbial composition in soil depends on complex interactions between the soil type, root zone location, and plant species. Rhizosphere microbiota are highly dynamic, and the composition of bacterial communities can fluctuate in response to seasonal and diel temperature changes, water content, pH, CO2 concentration, and O2 levels.

Publications (e.g., see here and here) in recent years have demonstrated that bacterial communities that colonize the root system (endorhiza) show significant cultivar-specificity and support plant growth and suppress plant diseases by providing phytohormones, small molecules or enzymes involved in regulating growth and metabolism.

Figure 1. Diversity of fungal and bacterial tax in the cannabis microbiome,
(A) left panel: Diversity of Cannabis fungal taxa, based on NCBI database, ≥2 ITS (internal transcribed spacer) rRNA sequences in NCBI
(B) right panel: Diversity of Cannabis bacterial taxa based on NCBI: ≥2 16S rRNA sequences

[From Vujanovic, Vladimir, et al. “Scientific Prospects for Cannabis-Microbiome Research to Ensure Quality and Safety of Products.” Microorganisms 8.2 (2020): 290]

Cannabis cultivar types have important structuring effects on both rhizosphere and endorhiza communities. Characterization and manipulation of the plant microbiome may help increase plant fitness, suppress disease, or augment desired metabolite production. For example, certain cannabis varieties support colonization by specific bacterial species that secrete Spinosyn D-like compounds, a natural toxin that deters insect pests.

Though the study of the cannabis microbiome involves complex population dynamics of multiple organisms (fig. 1), the plant’s ability to enrich for certain microbiome species has been demonstrated (reviewed here). While some of the factors affecting microbiome are controlled by the environment, there is also genetic component that allows to enrich beneficial organisms. In such cases, once an adequate phenotyping system is set-up, it is possible to analyze a segregating population, as done in ‘regular’ trait-mapping, and to identify genetic components controlling the plant -microbial interaction. This approach will generate a new strategy of resistance to plant pathogens and is currently being tested in several genetic backgrounds.

Oori Weisshaus, Ph.D.

Director of Genomic Solutions at NRGene Ltd. Oori has a rich background in genetics of plant secondary metabolism pathways and has been with NRGene since 2011, developing and applying genomic tools in marker development for breeding projects in various crops. In recent years Oori has specialized in development of genomic tools applicable to the dynamic needs of the emerging cannabis and hemp industries and collaborations with academic research of this unique plant.

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