Pathogen Sampling: Turning Over a New Leaf on the Root of Your Problems

As the legal cannabis industry matures, we find ourselves encountering many of the same problems other agricultural industries run into. While producers of bananas fear the ever dreaded Panama Disease and orange growers contend with Citrus Greening Disease, cannabis has its own set of plant infections that keep cultivators up at night. Common pathogens like fusarium fungi leading to root and stem blights, and various waterborne bacterial pathogens that can fully block vascular tissues are eternally feared, but no pathogen is as discussed and maligned as much as the small ring of RNA responsible for “dudding,” known as Hop Latent Viroid. 

Hop Latent Viroid (HLVd) is a pathogen first encountered in the hops industry, where it was largely overlooked due to its “latent” nature within the plant host. While HLVd has spread to virtually every area in which hops are grown, the jump from its original host to cannabis has been particularly problematic. Certain cannabis plants seem resistant or even asymptomatic to HLVd, while others may express symptoms ranging from a reduction in THCA and terpenes to complete structural failure including the shedding of branches and total loss of the plant’s original growth habit. 

Although the threat of HLVd invading the grow is frightening to most cultivators, fortunately there are tools we can use to both avoid introducing this pathogen to the grow and remove it from production if it is discovered. Technologies like enzyme-linked immunosorbent assays (ELISA) and quantitative polymerase chain reaction (qPCR) make it possible for individuals to detect pathogens like viroids in extremely small amounts of plant tissues. With these technologies in mind, we are brought to the question – what plant tissue is the best to test? Root or shoot? 

Root vs. Leaf Sampling

Sampling from roots may yield the earliest and most consistent detection, but comes with its own set of risks. Due to the source/sink nature of plant tissues, all “below-ground” structures are considered “sinks” which require a “source” of carbohydrates to function and grow. Because mature fan-leaves are the most photosynthetically active structure on the plant, they are considered the “source” for the root tissue “sink.” This relationship is why pathogens can be so reliably detected in root tissues. Any infection that occurs in a leaf has a direct path through the plant’s phloem (the vascular tissue carrying carbohydrates from the leaf to the root). This leads to the root tissue directly around the crown of the plant typically carrying the same pathogens found in the shoots earlier than they can be detected in the remainder of the non-infected shoot tissues. 

While detection may be earlier and more consistent from these tissues, there is a significant risk to the plant any time root tissues are excised from a living crop. Open wounds near the crown are welcoming to any other pathogenic microbes, viruses, or viroids that may be present in the root zone. 

Sampling from leaves on the other hand, is typically much less destructive to the plant. De-fanning of cannabis is a common practice at most cultivation sites, and the small wound where a petiole is removed from the stem heals quickly and typically isn’t exposed to soil or irrigation water that may carry other pathogens. Leaf tissue also carries significantly less inhibitory compounds than root tissues, which are generally coated in various humic acids and other compounds found in soil that make processes like ELISA and qPCR challenging. 

While sampling and testing this tissue is much easier and less harmful to the plant than sampling from roots, there are downsides to this approach as well. Depending on the time between infection and sampling, there is a chance that a leaf selected for screening doesn’t yet carry the pathogen which has already made its way into the root tissues. Once viruses and viroids colonize the roots they make their way back up to any new growing tissues as a result of the source/sink dynamic between root starch (source) and new growing leaves and stems (sink), and over time will become detectable in virtually all above ground tissues. If you sample between the time of initial infection and full colonization of the pathogen however, you run the risk of missing a pathogen in a leaf sample that may have been detectable in root tissues. 

So, which of these approaches is better for the cultivator? That is an answer that depends on what the cultivator is hoping to achieve. If the survival of the plant is no matter, be it a post-harvest plant or a plant that was going to be culled anyway, a root tissue sample may provide the most robust test results. If you are trying to carry out basic surveillance or test new clones that have not yet established robust root systems, a leaf sample may be the better bet, and can be collected easily during standard de-fanning operations.