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Cannabis Microcosm – The Microbiome of Cannabis

Cannabis Microcosm – The Microbiome of Cannabis

In the last decade, two facets of scientific understanding regarding the interconnected nature of life on Earth have been honed, catching my attention in their early hypothetical stages: the Hologenome Theory of Evolution and the concept of Phylosymbiosis. Hologenome Theory asserts that multicellular life—an individual human, insect, plant, fungus, et cetera—is better conceptualized as an entire ecosystem, a “holobiont” made up of the collective genomes encompassed within and with which it interacts. Most people have heard of the microbiome, and this term similarly encompasses smaller divisions: the mycome for fungi, bacteriome for bacteria, virome for viruses, as well as other “-omics” related to genomic expression just as the hologenome does. Essentially, the hologenome is all the genomes of all the organisms in a collective holobiont or ecological unit. The scale of the holobiont can vary, from the entirety of Earth’s collective hologenome to a single individual or population. It is not just the genome of a plant, for example, but all the microbes that exist inside like endophytes, or outside like epiphytes, and runs the gamut of symbioses from mutualistic to parasitic. Some of these microbes are obligate or facultative in their relationships with plants, meaning either they require the plant as a necessary part of their life like the parasitic powdery mildews, or they can switch between lifestyles, like the insect-infecting Beauveria bassiana which comes from a lineage that evolved to infect insects first, and colonize plants secondarily, and can now do both as a plant mutualist. Importantly, it is possible for some species of both mutualistic “good” microbes and parasitic “bad” microbes to have multiple lifestyles, and even switch between being mutualistic in one cultivation context and parasitic in another due to environmental or genetic changes.

In the same way that it is the interaction of multiple genes that impacts the expression of their traits in an organism, so too is it the case at higher levels of complexity, like those between different tissues of a plant and microbes that exist on, in, or around it. Phylosymbiosis is an non-universal approach to symbiotic relationships characterizing microbes that closely associate with an organism to reflect its developmental evolution and relationship with other organisms. For a simple example, two plant species in the same genus that only diverged from a common ancestor 1 million years ago would be more likely to have a similar microbiome due to their relatedness than two plant species in two different orders that diverged 100 million years ago. Space and time play a crucial role in symbiotic interactions, and changes can occur in a relatively short or long period of time, affecting the short-term and long-term development of plants. Cannabis is not unique in this regard, though research about microbiome relationships is currently growing. The family Cannabaceae in general has some unique plant-microbe relationships: Parasponia andersonii is the only non-legume plant species that has established a rhizobial mutualism wherein nitrogen-fixing bacteria colonize the roots. When compared with the distantly-related legume Alfalfa, Medicago truncatula, over 290 orthologous genes were found to be conserved related to this symbiosis. The implication is that for unknown reasons, this relationship is not new, but the same old symbiosis legumes retained into the present, somehow being simultaneously lost in all other plants, as well as other Cannabaceae which would be a bizarre turn of events and may be better understood with more research into the Cannabis and related microbiomes.

Several culturable microbial populations have been found in empirical research to associate with Cannabis already. In one study regarding industrial hemp endophytes in CRS-1, Anka, and Yvonne, the most common bacteria encountered were Bacillus and Pseudomonas in leaves, Pantoea and Pseudomonas in the petioles connecting leaves to stems, with seeds encountering Pantoea and Staphylococcus primarily. Endophytic fungi most prominently found in Cannabis leaves were Cochliobolus and Aureobasidium, Alternaria and Cryptococcus in the petioles, and only were Cladosporium and Aureobasidium found in the seeds at equal levels. Several of these groups contain both mutualistic and parasitic species and strains, and bacterial populations evaluated tended to come from the alpha-proteobacteria and gamma-proteobacteria, though 18 different bacterial genera and 14 different fungal genera were found in Cannabis tissues. Bacillus, Enterobacter, Enterococcus, and Pseudomonas were found that could make enzymes that break down cellulose and inorganic phosphate more soluble in water, as well as those that could chelate iron and produce the plant hormone indole acetic acid. Clearly, these traits can have physiological effects on the development of their host.

Not only beneficial, but detrimental microbes are affected by the genetic makeup of Cannabis. A group of genes associated with the name Mildew Locus O are referred to as susceptibility genes, as opposed to resistance genes, because they facilitate the colonization of powdery mildews and other fungal pathogens in plants. For a long time, their presence in the genomes of many diverse plants puzzled researchers because such detrimental genes would have strong selection pressure working against them. In recent research, one contributing factor for their presence was confirmed: MLO facilitates mycorrhizal fungal colonization as well as parasitic fungal colonization, and the absence of several of these genes severely impairs the colonization of both. Interestingly, powdery mildews encompass the fungal order Erysiphales, which have been shown to be most closely related to a detrivorous soil fungus order, Onigenales, implying that powdery mildews may have developed from fungi that processed decaying plant matter and that the basal ancestor became able to infect living plant matter. If true, it would be another example of a nominally neutral or even beneficial soil microbe evolving parasitic traits, changing its symbiotic lifestyle relationships, as mutualistic and parasitic microbes often use the same host genes to interact.

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