Microbial Considerations for Cannabis Cultivation in Controlled Environments

Controlled environment agriculture offers a number of advantages over traditional outdoor agriculture. Temperature, humidity, light, and nutrition can be tightly controlled and optimized.  But an environment optimized for plant growth will also meet the needs of many other organisms. Microbial organisms are the most problematic and difficult to control.

Mold is the most difficult problem for most cannabis cultivators because it can live and grow on plant material and even inside the plant. It can spread quickly, and it may not become obvious until the problem is very bad. Also, the worst documented cannabis related health outcomes have been due to mold, specifically Aspergillus.

Mold infection may also be a problem during drying and curing, but the greater challenge is usually harvesting healthy flower to begin with. If flower is harvested free of mold and handled properly, there should be minimal risk of mold growth during the curing process.  

One reason mold spread so easily is that spores tend to be durable and stay viable for a long time. They can cling to surfaces or even float in air and dust, and then awaken under the right conditions. Many different mold species would be able to flourish in a humid cannabis grow room.

Limiting Exposure to Microbes

Steps can be taken to limit plant exposure to mold. HVAC systems should use frequently changed air filters and positive pressure. Nutrient delivery systems should be thoughtfully designed and maintained. Personnel access should be limited, and equipment and tools should not be transferred between rooms. Preventative measures like these will keep most mold out but are unlikely to be 100% effective. Therefore, additional steps should be taken to prevent any mold that does enter the environment from flourishing. 

Plant Growing Environment

Constant temperature and humidity monitoring systems can optimize the operation of an HVAC system by analyzing fluctuations in different areas as systems cycle on and off. Humidity and temperature monitors at multiple locations can assess environmental uniformity. Lack of uniformity or wide fluctuation ranges may mean that some areas of the room are not getting proper circulation. 

Another way to address mold that is often overlooked is through plant nutrition. Monitoring levels of N, P, and K is enough to keep plants alive; but there are many other mineral nutrients that plants need in small quantities. A lack of these micronutrients might not prevent a plant from growing, but could make it less able to fight off even a small mold infection on its own. 

Even if the environment and nutrition are well-managed, additional factors work against cannabis cultivators. These include the plant’s unique breeding history and the widespread use of clonal propagation techniques. 

Plant Sourcing and Lineage

Clandestine breeding has led to many wide crosses without systematic genetic stabilization of desirable cultivars. As a result, there is great variety of simple traits like terpene content. Complex traits like mold resistance, which depend on more complex genetic combinations,  have sometimes been lost. 

Passing a clone over many generations will also eventually weaken a plant and make it more susceptible to infection. Therefore, if a particular cultivar struggles with mold, or if successive generations of clones begin to show increasing signs of mold, it may be time to let those plants go. It is not worth the risk of keeping a problem cultivar, especially if others are growing mold-free in the same system.

Even if healthy and well nourished plants are living in a well controlled environment, there can still be problems. Surfaces and plants can be tested for the presence of mold throughout the growth cycle. Precautionary testing identifies problems early and enables a cultivator to address issues before they impact a harvest.

Bacterial Problems

After mold, the next most likely microbes to cause problems at commercial cultivations are Enterobacteriaceae and Coliform bacteria. While mold can grow on the plant and flower itself, these bacterial species are more likely to grow in nutrient-rich solutions. And, whatever the source of contamination, relatively low levels of these organisms can cause a lot to fail regulatory compliance tests.

Most Enterobacteriaceae and Coliform bacteria are not harmful to humans. They are written into regulations at a relatively low threshold as indicator organisms because they are present in the digestive systems of many animals. The presence of these organisms indicates there may have been exposure to unsanitary conditions.

Bacterial contamination could happen during the handling and processing of harvested materials, but this type of contamination is unlikely to be systemic. Unless a cultivation has failed to implement standard Good Agricultural Practices (GAP) and Good Handling Practices (GHP), it will be rare for multiple lots of material to be contaminated this way over an extended period.

Systemic problems are more likely to arise with Enterobacteriaceae and Coliform bacteria if water sources are contaminated. The source of contamination is likely as simple as insufficient handwashing, contamination from the floor, or contamination from insects or other animals; but in this case the contamination inoculates a nutrient-rich water system. 

Even with contaminated water systems, flower material could remain free of contamination since these organisms can’t infect and travel through the plant. However, small splashes, drooping branches, or other contact could contaminate many lots of flower material.

A Defensive Strategy is Best

Clearly, extreme caution should be taken to avoid contamination. But with well-designed nutrient delivery systems, occasional spot checks should be sufficient to avoid problems with Enterobacteriaceae and Coliform bacteria.

Enterobacteriaceae and Coliform bacteria should not be present, but a nutrient solution will also not be sterile. Nature abhors a vacuum, and sterile nutrient-rich water is a vacuum ripe for infection. A healthy and balanced microbial community is more likely to resist infection.  This is part of the reason many cultivators turn to plant growth promoting microbes (PGPM).

PGPM can prevent infections by more problematic organisms and can also promote nutrient uptake by the plant. Researchers are just beginning to understand these complex interactions. They present many promising opportunities for future development; however, they are currently difficult to predictably manipulate. 

E. coli and Salmonella are found in similar environments as Enterobacteriaceae and Coliform bacteria, but they are pathogenic and much rarer. Cannabis products should never contain any level of E. coli or Salmonella, and their presence in a controlled environment agricultural setting indicates a major problem. Any detection of these organisms should be immediately and thoroughly investigated. These organisms are unlikely to cause any kind of systemic or ongoing problem, but they threaten public health.

Microbial environments will always be more difficult to control than light, temperature, humidity, and nutrient levels. Major problems that can cause regulatory failures can be avoided by taking the precautionary steps noted here. These steps will also contribute to overall production efficiency and therefore profitability. 

Variability in Microbial Test Results

Analytical measurements always have some uncertainty. If the same test is run repeatedly on the same sample, the uncertainty of microbial quantification by culture plating is around 20%. This uncertainty is not drastically different from uncertainties in analytical chemistry, but there are some additional factors that affect microbial results. 

Results from different samples across a given lot of cannabis may vary more than the inherent measurement uncertainty (due to sampling variation), but they will likely be similar for many analytes. Even with trace adulterants such as pesticides, a signal that shows up in one sample will likely be detectable in other samples from the same lot (even if the quantification value varies a bit more than the inherent measurement uncertainty of the test).

Microbial testing, on the other hand, may give a negative result for one sample from a lot, while another sample from the same lot may show contamination above regulatory limits. Imagine you grow five lots of cannabis in the same room, submit five samples for testing, and one out of five fails microbial analysis. You consider them all the same group of product, how can only one lot be contaminated?

The reason is sampling variability. The truth is that failure of one gram of sample does not mean that a whole five-pound lot is contaminated. Likewise, one gram of a lot passing microbial testing does not mean that every gram in that 5lb lot is free of contamination. If 4 out of 5 lots pass, the most likely explanation is that there is some mold contamination across all of the lots. The actual proportion of those 5 lots that is contaminated is impossible to determine without a great deal of additional testing. 

To understand why sampling causes greater variability in microbial detection than pesticide detection (which also looks for low levels of adulterants not expected to be found in the sample) consider how microbes and pesticides are distributed.

Pesticides, whether applied through roots or leaves, are applied systemically by the cultivator. The level may be low, but the distribution is somewhat even. 

Microbes, by contrast, grow wherever they get a foothold, and they distribute themselves, usually unevenly, to the next foothold. Like patches of mold in the shower, or one moldy strawberry at the bottom of the box, growth is concentrated in pockets.

Statistics can be used to calculate confidence scores based on sampling procedure. But, a cultivator’s best option is to take any microbial detection seriously. If there is a small amount of microbial signal, there might be more. 

Effective microbial management programs will incorporate temperature, humidity, and nutrient monitoring programs. Ongoing microbial monitoring provides an opportunity for constant improvement, and processes or cultivars that are not working must be readily abandoned.

Successful microbial management results not only in regulatory compliance, but also increased efficiency. Cannabis cultivators will benefit from engagement with academic research and communication with experts from other agricultural industries where consistency and efficiency are essential for profitability.

Good Agricultural Practices/ Good Handling Practices Resources



Other References

Cannabis Safety Institute

Beneficial Bacteria Review https://www.researchgate.net/publication/283440637_Beneficial_bacteria_and_fungi_in_hydroponic_systems_Types_and_characteristics_of_hydroponic_food_production_methods

PGPM in Aquaponics

Environmental Control of Root Systems

Research priorities for harnessing plant microbiomes in sustainable agriculture

Software for Nutrient Monitoring https://www.researchgate.net/publication/325341121_Software_for_Calculation_of_Nutrient_Solution_for_Fruits_and_Leafy_Vegetables_in_NFT_Hydroponic_System

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