What We Find and Where: Molecular Tools for Fungal Identification in Cannabis

Michael Esposito – MCR Labs

Background:

Everyone who has grown cannabis has likely encountered at least a few fungal and bacterial plant pathogens. While some may be fairly easy to identify with the naked eye such as the pervasive “powdery mildews” or the common Botrytis “gray bud rot”, many more are organisms that appear virtually identical to each other. Molecular identification is a useful solution in the growers’ tool belt to help distinguish between a common Penicillium mold and a pathogenic Aspergillus that may appear identical but potentially lead to much worse outcomes both surrounding consumer health, and compliance at the state level. Even two powdery mildews that appear identical to the naked eye may be from two completely separate fungal genera, with one a common local fungus native to the ecosystem, and another an invader from a different region that our local plants have no natural resistance against.

Methods:

Through the use of common “molecular barcoding” approaches, we are able to identify individual fungi and bacteria at the species level in an affordable and rapid way. Well known microbial genes have been sequenced and uploaded by scientists worldwide for decades, providing us with a massive library of gene sequences to compare with sequences we obtain from sampled microbes. Reference of sampled DNA against the existing libraries allows us to determine if the bacteria sampled from an irrigation line is a harmless microbe or a plant pathogen that could cause every seedling germinated to dampen off or the stems of half of a grower’s crop to turn to wilted mush.

Discussion:

While simple molecular barcoding for species identification may not be as advanced as costlier approaches like metagenomics and shotgun sequencing, it is an extremely valuable asset to the industry while those more advanced technologies gradually become more affordable and accessible to the average consumer. Each species identified in a cannabis cultivation context is a piece of the puzzle we are all putting together to optimize cultivation in our region and maximize the quality and yield of each grower tending their crop in our state and the surrounding area.

Conclusion:

By obtaining species level identification of microbes collected from a wide variety of cannabis and environmental samples, we are able to notice certain trends which may help guide the future of cannabis cultivation in the region. A high abundance of anaerobic bacterial species, for example, may help a grower determine if their drainage and root-oxygen content is inadequate. A repeated detection of certain Penicillium species on samples matched to detection of those same species on unopened coco coir may help a grower realize they need to switch up their grow media supplier. Lastly, determining that outdoor growers and indoor growers may have very different species of microbes in their crops may also indicate that these different branches of the industry need to explore different approaches to things like cultivar selection or remediation solutions.