Tag Archives: cells

3 Essential Components of Microbial Safety Testing

By Heather Ebling
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Microbial contamination on cannabis products represents one of the most significant threats to cannabis consumers, particularly immunocompromised patients who are at risk of developing harmful and potentially fatal infections.

As a result, regulatory bodies in the United States and Canada mandate testing cannabis products for certain microbes. The two most popular methods for microbial safety testing in the cannabis industry are culture-based testing and quantitative polymerase chain reaction (qPCR).

When considering patient safety, labs should choose a method that provides an accurate account of what is living on the sample and can specifically target the most harmful microbes, regardless of the matrix.

1. The Method’s Results Must Accurately Reflect the Microbial Population on the Sample

The main objective of any microbial safety test is to give the operator an indication of the microbial population present on the sample.

Figure 1: MA data collected directly from plant material before and after culture on 3M petrifilm and culture-based platforms.

Culture-based methods measure contamination by observing how many organisms grow in a given medium. However, not all microbial organisms grow at the same rate. In some cases, certain organisms will out-compete others and as a result, the population in a post-culture environment is radically different than what was on the original sample.

One study analyzed fifteen medicinal cannabis samples using two commercially available culture-based methods. To enumerate and differentiate bacteria and fungi present before and after growth on culture-based media, all samples were further subjected to next-generation sequencing (NGS) and metagenomic analyses (MA). Figure 1 illustrates MA data collected directly from plant material before and after culture on 3M petrifilm and culture-based platforms.

The results demonstrate substantial shifts in bacterial and fungal growth after culturing on the 3M petrifilm and culture-based platforms. Thus, the final composition of microbes after culturing is markedly different from the starting sample. Most concerning is the frequent identification of bacterial species in systems designed for the exclusive quantification of yeast and mold, as quantified by elevated total aerobic count (TAC) Cq values after culture in the total yeast and mold (TYM) medium. The presence of bacterial colonies on TYM growth plates or cartridges may falsely increase the rejection rate of cannabis samples for fungal contamination. These observations call into question the specificity claims of these platforms.

The Live Dead Problem

Figure 2: The enzyme is instantaneously inactivated when lysis buffer is added

One of the common objections to using qPCR for microbial safety testing is the fact that the method does not distinguish between live and dead DNA. PCR primers and probes will amplify any DNA in the sample that matches the target sequence, regardless of viability. Critics claim that this can lead to false positives because DNA from non-viable organisms can inflate results. This is often called the Live-Dead problem. However, scientists have developed multiple solutions to this problem. Most recently, Medicinal Genomics developed the Grim Reefer Free DNA Removal Kit, which eliminates free DNA contained in a sample by simply adding an enzyme and buffer and incubating for 10 minutes. The enzyme is instantaneously inactivated when lysis buffer is added, which prevents the Grim Reefer Enzyme from eliminating DNA when the viable cells are lysed (see Figure 2).

2. Method Must Be Able to Detect Specific Harmful Species 

Toxic Aspergillus spp., which is responsible for at least one confirmed death of a cannabis patient, grows poorly in culture mediums and is severely underreported by current culture-based platforms. And even when Aspergillus does grow in culture, there is a certain non-pathogenic Aspergillus species that look remarkably similar to their pathogenic cousins, making it difficult to speciate using visual identification alone.

Figure 3: The team spiked a known amount of live E. coli into three different environments

Conversely, qPCR assays, such as the PathoSEEK, are designed to target DNA sequences that are unique to pathogenic Aspergillus species, and they can be run using standard qPCR instruments such as the Agilent AriaMx. The primers are so specific that a single DNA base difference in the sequence can determine whether binding occurs. This specificity reduces the frequency of false positives in pathogen detection, a frequent problem with culture-based cannabis testing methods.

Additionally, Medicinal Genomics has developed a multiplex assay that can detect the four pathogenic species of Aspergillus (A. flavus, A. fumigatus, A. niger, and A. terreus) in a single reaction.

3. The Method Must Work on Multiple Matrices 

Figure 4: The team also placed TSB without any E. coli onto a petrifilm to serve as a control.

Marijuana infused products (MIPs) are a very diverse class of matrices that behave very differently than cannabis flowers. Gummy bears, chocolates, oils and tinctures all present different challenges to culture-based techniques as the sugars and carbohydrates can radically alter the carbon sources available for growth. To assess the impact of MIPs on colony-forming units per gram of sample (CFU/g) enumeration, The Medicinal Genomics team spiked a known amount of live E. coli into three different environments: tryptic soy broth (TSB), hemp oil and hard candy. The team then homogenized the samples, pipetted amounts from each onto 3M™ Petrifilm E. coli / Coliform Count (EC) Plates, and incubated for 96 hours. The team also placed TSB without any E. coli onto a petrifilm to serve as a control. Figures 3 and 4 show the results in 24-hour intervals.

Table 1: DNA was spiked into various MIPs

This implies the MIPs are interfering with the reporter assay on the films or that the MIPs are antiseptic in nature.

Many MIPs use citric acid as a flavoring ingredient which may interfere with 3M reporter chemistry. In contrast, the qPCR signal from the Agilent AriaMx was constant, implying there is microbial contamination present on the films, but the colony formation or reporting is inhibited.

Table 3: SenSATIVAx DNA extraction can successfully lyse the cells of the microbes
Table 2: Different numbers of DNA copies spiked into chocolate

This is not an issue with DNA-based methods, so long as the DNA extraction method has been validated on these matrices. For example, the SenSATIVAx DNA extraction method is efficient in different matrices, DNA was spiked into various MIPs as shown in Table 1, and at different numbers of DNA copies into chocolate (Table 2). The SenSATIVAx DNA extraction kit successfully captures the varying levels of DNA, and the PathoSEEK detection assay can successfully detect that range of DNA. Table 3 demonstrates that SenSATIVAx DNA extraction can successfully lyse the cells of the microbes that may be present on cannabis for a variety of organisms spiked onto cannabis flower samples.

Understanding Dissolved Oxygen in Cannabis Cultivation

By Aaron G. Biros
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Oxygen plays an integral role in plant photosynthesis, respiration and transpiration. Photosynthesis requires water from the roots making its way up the plant via capillary action, which is where oxygen’s job comes in. For both water and nutrient uptake, oxygen levels at the root tips and hairs is a controlling input. A plant converts sugar from photosynthesis to ATP in the respiration process, where oxygen is delivered from the root system to the leaf and plays a direct role in the process.

Charlie Hayes has a degree in biochemistry and spent the past 17 years researching and designing water treatment processes to improve plant health. Hayes is a biochemist and owner of Advanced Treatment Technologies, a water treatment solutions provider. In a presentation at the CannaGrow conference, Hayes discussed the various benefits of dissolved oxygen throughout the cultivation process. We sat down with Hayes to learn about the science behind improving cannabis plant production via dissolved oxygen.

In transpiration, water evaporates from a plant’s leaves via the stomata and creates a ‘transpirational pull,’ drawing water, oxygen and nutrients from the soil or other growing medium. That process helps cool the plant down, changes osmotic pressure in cells and enables a flow of water and nutrients up from the root system, according to Hayes.

Charlie Hayes, biochemist and owner of Advanced Treatment Technologies

Roots in an oxygen-rich environment can absorb nutrients more effectively. “The metabolic energy required for nutrient uptake come from root respiration using oxygen,” says Hayes. “Using high levels of oxygen can ensure more root mass, more fine root hairs and healthy root tips.” A majority of water in the plant is taken up by the fine root hairs and requires a lot of energy, and thus oxygen, to produce new cells.

So what happens if you don’t have enough oxygen in your root system? Hayes says that can reduce water and nutrient uptake, reduce root and overall plant growth, induce wilting (even outside of heat stress) in heat stress and reduce the overall photosynthesis and glucose transfer capabilities of the plant. Lower levels of dissolved oxygen also significantly reduce transpiration in the plant. Another effect that oxygen-deprived root systems can have is the production of ethylene, which can cause cells to collapse and make them more susceptible to disease. He says if you are having issues with unhealthy root systems, increasing the oxygen levels around the root system can improve root health. “Oxygen starved root tips can lead to a calcium shortage in the shoot,” says Hayes. “That calcium shortage is a common issue with a lack of oxygen, but in an oxygen-deprived environment, anaerobic organisms can attack the root system, which could present bigger problems.”

So how much dissolved oxygen do you need in the root system and how do you achieve that desired level? Hayes says the first step is getting a dissolved oxygen meter and probe to measure your baseline. The typical dissolved oxygen probe can detect from 20 up to 50 ppm and up to 500% saturation. That is a critical first step and tool in understanding dissolved oxygen in the root system. Another important tool to have is an oxidation-reduction potential meter (ORP meter), which indicates the level of residual oxidizer left in the water.

Their treatment system includes check valves that are OSHA and fire code-compliant.

Citing research and experience from his previous work, he says that health and production improvements in cannabis plateau at the 40-45 parts-per-million (ppm) of dissolved oxygen in the root zone. But to achieve those levels, growers need to start with an even higher level of dissolved oxygen in a treatment system to deliver that 40-45 ppm to the roots. “Let’s say for example with 3 ppm of oxygen in the root tissue and 6ppm of oxygen in the surrounding soil or growing medium, higher concentrations outside of the tissue would help drive absorption for the root system membrane,” says Hayes.

Reaching that 40-45 ppm range can be difficult however and there are a couple methods of delivering dissolved oxygen. The most typical method is aeration of water using bubbling or injecting air into the water. This method has some unexpected ramifications though. Oxygen is only one of many gasses in air and those other gasses can be much more soluble in water. Paying attention to Henry’s Law is important here. Henry’s Law essentially means that the solubility of gasses is controlled by temperature, pressure and concentration. For example, Hayes says carbon dioxide is up to twenty times more soluble than oxygen. That means the longer you aerate water, the higher concentration of carbon dioxide and lower concentration of oxygen over time.

Another popular method of oxidizing water is chemically. Some growers might use hydrogen peroxide to add dissolved oxygen to a water-based solution, but that can create a certain level of phytotoxicity that could be bad for root health.

Using ozone, Hayes says, is by far the most effective method of getting dissolved oxygen in water, (because it is 12 ½ times more soluble than oxygen). But just using an ozone generator will not effectively deliver dissolved oxygen at the target levels to the root system. In order to use ozone properly, you need a treatment system that can handle a high enough concentration of ozone, mix it properly and hold it in the solution, says Hayes. “Ozone is an inherently unstable molecule, with a half-life of 15 minutes and even down to 3-5 minutes, which is when it converts to dissolved oxygen,” says Hayes. Using a patented control vessel, Hayes can use a counter-current, counter-rotational liquid vortex to mix the solution under pressure after leaving a vacuum. Their system can produce two necessary tools for growers: highly ozonized water, which can be sent through the irrigation system to effectively destroy microorganisms and resident biofilms, and water with high levels of dissolved oxygen for use in the root system.