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Speciation for Cultivators

By Michael Esposito, Lead Microbiologist at MCR Labs


Cannabis cultivators struggle against a wide range of microbiological pathogens. Some organisms can cause cannabis to fail compliance testing, while other organisms can wipe out an entire crop. Unfortunately for growers, many of these organisms are either invisible to the naked eye, or indistinguishable from each other. The use of speciation via molecular barcoding allows us to identify exactly which organism or organisms are impacting a grow, saving time and effort by allowing a cultivator to direct their remediation or integrated pest management approach at exactly the species causing problems.


Speciation of microbes was carried out using common published primer sets utilized by a wide range of microbiological laboratories both within industry and academics. Primers designed to target conserved regions of microbial DNA coding for the 16s ribosomal subunit in bacteria and internally transcribed spacer (ITS) regions in fungi were utilized on DNA purified with qiagen spin kits to produce DNA amplicons. Amplicons were then sent to a contracted sanger sequencing lab to obtain the genetic sequence of the fungal or bacterial amplicons. Once the genetic sequence was obtained, the sequences were submitted to the Basic Local Alignment Search Tool (BLAST) database to identify the closest match. These matches represent the most likely species identification for a given produced amplicon, allowing us to positively identify exactly which microbes are present on any given cannabis sample.

Diagram example of a DNA barcoding workflow for speciation


Different microbes have different reactions to certain integrated pest management (IPM) approaches, and in certain cases an approach that works well on one pest may actually exacerbate problems when applied to a different pest. Additionally, speciation allows us to help pinpoint the vector by which a microbe made its way into the grow. Two prime examples of the benefit of speciation for cultivators presented themselves through our speciation analysis.

In the first circumstance, a cultivator was utilizing a common and effective radiation approach to attempt to remediate the microbiological contamination issue impacting their crop. While the remediation approach was effective in combating their bacterial issues, they noticed their yeast and mold counts were getting worse with each attempt at radiation-based remediation. Through speciation we were able to identify the yeast and mold organism giving them issues as Cladosporium sphaerospermum, a radiotrophic organism capable of utilizing radiation as a source of fuel to increase its proliferation.

The second example of speciation as a boon to growers came when a client with otherwise uncontaminated material continued to fail for total yeast and mold despite following agricultural best practices. We identified a species of yeast on their samples commonly associated with predatory mites. While predatory mites are a valuable aspect of IPM, many cultivators don’t realize that the predatory mites they order are typically packaged with feeder mites, with those feeder mites surviving off a blend of oat bran and baker’s yeast. By identifying the organism present on the samples, we were able to help this client backtrack to the vector carrying yeast onto their crops and remove it from their system.

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