It’s Not Too Late: Post-Harvest Solutions to Microbial Contamination Issues

Published on: 
Cannabis Science and Technology, November/December 2019, Volume 2, Issue 6

Columns | <b>The Cultivation Classroom</b>

Use the techniques described here to pass the state tests and ensure safe cannabis for consumers.

Passing state regulations for microbial contamination can be challenging. Excessive levels of mold, yeast, and bacteria can cause health problems for consumers. What happens when your flower doesn’t measure up to your state’s standards? You do have post-harvest treatment options that can save your buds. Microbial contamination can be remediated without damaging your final product.

Now that cannabis cultivation has become accepted as a legal business across most of the United States, growers have come face-to-face with the consequences of failing state tests for microbial contamination. It is a huge disappointment and financial burden to lose your profits and reputation to an unseen enemy-the microscopic menace of the microbial world. During author Roger Kern’s 22 years with The National Aeronautics and Space Administration (NASA), he worked in the area called planetary protection. This lofty-sounding subject ensures that we do not contaminate our planetary neighbors with microbes from Earth when we send exploration spacecraft for science missions. It was his job to ensure that our spacecraft were clean of living and dead microbes. Figuring out how to clean and sterilize sensitive materials was a daily job. Now, it is gratifying to apply that knowledge to help ensure that the cannabis we supply to the consumer is clean and free from microbial contamination. What could be better than using the NASA-studied techniques to ensure the cleanliness of our cannabis?

In this “Cultivation Classroom,” we explore how you can reduce your post-harvest microbial contamination and identify techniques to enhance your chances of passing state-mandated tests all along the supply chain from your cultivation facility to the consumer. Using the techniques described in this column you will be able to pass the state tests and ensure safe cannabis for the consumers, thus protecting your profits and your reputation (1).

Microbial Contamination in Cannabis

There are two points in the cannabis product supply chain when failure of the microbial contamination test is most likely:

  • Testing that occurs post-harvest on cured products that have not yet been packaged

  • Testing that occurs on products after they have been packaged. They may have even passed the microbial contamination tests before packaging (1, above).

In general, about 10% of cannabis fails the microbial contamination test at the cultivation facility post-harvest. This 10% can be the difference between profits and business failure. The grower must decide how a failure because of microbial contamination will be addressed. This percentage may be acceptable to a grower who will use the failed plant materials for concentrates to make up some of the lost profits. However, when faced with post-harvest microbial contamination, you may want to implement remediation techniques to ensure that such an event does not occur in the first place and have confidence that your products will pass the state-mandated tests every time products leave the facility.

Let’s take a closer look at the two main threats causing microbial contamination in post-harvest cannabis. The threats are environmental conditions during the harvest, drying, curing, and prepackaging storage; and the microenvironmental conditions of the packaged product across the supply chain from cultivator to consumer.

Microbial growth is enhanced or reduced by environmental conditions. Favorable conditions of temperature and relative humidity can cause microbes to grow and thrive after the plants have been harvested. It is obvious that microbial growth can occur in the large-scale environment of the grow, drying, curing, storage, transport, and retail shelf conditions. However, we must also consider the microenvironment of the cannabis in its final packaging for sale. The cannabis may also experience environmental conditions inside its packaging that promote additional microbial growth. As unusual as it sounds, this microenvironment must also be controlled to ensure that clean and safe cannabis is delivered to the consumer.

Once the cannabis has been packaged in sealed containers and sent to the dispensaries, additional tests for microbial contamination may show an increase in yeast and mold, even to the extent of causing a failure of the state-mandated requirements for microbial contamination. This recently happened in Colorado when state regulators inspected products from 25 dispensaries in Denver (2). There were unanticipated microbiological contamination failures of packaged product taken right from the shelves of these dispensaries: 20 of the 25 dispensaries had failed products. These products were not contaminated at the time of delivery from the supplier, as evidenced by METRC documentation. The origin of this contamination is likely because of conditions within the sealed packages that were favorable to microbial growth. When you consider the large-scale environmental conditions in which the cannabis is grown, harvested, dried, cured, and stored and compare it to the internal microenvironment of the packaging, it makes sense that similar environmental conditions would affect the packaged products in the same way. Just as we have seen that controlled environment agriculture (CEA) is necessary for successful indoor cultivation, we find that a form of CEA is necessary for the microenvironment inside the packaging of the harvested cannabis. You must consider both the large-scale and the microenvironments of the products across the entire supply chain from grower to consumer. Along with your best practices in cultivation, you must work as a team across the supply chain to ensure your products reach the consumer in the pristine state in which they left your grow facility. Plan to work closely with the various people or businesses that handle your product to ensure optimal environmental conditions that support clean cannabis. Mistakes made along the supply chain, by other people, can negatively affect microbial contamination test results, leading to the product being returned to you for reprocessing or destruction, and potentially leading to increased costs and possible questions about the cleanliness practices in your cultivation facility. In the worst case, not considering this source of “down the supply chain” microbial contamination may cause harm to sensitive consumers. Secondary to this is the loss to your profits and reputation that accompany a failure of this type.

Methods to Reduce Microbial Contamination in Post-Harvest Cannabis

Cannabis cultivators are the beneficiaries of decades of technology developments for consumer safety, including those developed for food safety across its supply chain (3). With cannabis in the mainstream of the consumer products, it is time to take advantage of those developments and use them to create safe cannabis that will always pass the state-mandated tests for microbial contamination. These methods are used to eliminate or greatly reduce the microbial contamination on the post-harvest cannabis and help to create the controlled microenvironment inside the cannabis packaging, necessary for ensuring safe cannabis across the supply chain.

The first step in the process is to kill the microbes in the post-harvest cannabis before it is packaged. The second step is to create the right microenvironment for the packaged cannabis. In sections below, we discuss two microbe-killing methods that will maximize your readiness to pass the state-mandated tests for cannabis post-harvest, before packaging. This is followed by a discussion of a method to ensure that you maintain the right microenvironment in the packaging. By following this two-step process, you will maintain your microbial cleanliness across the supply chain.

Killing Microbes in Post-Harvest Cannabis

There are many methods to reduce total mold and yeast count (TMYC) in post-harvest cannabis, but the two written about below seem to have no impact on the quality of the flower (terpenes, cannabinoids, and appearance). They are effective treatments and are not cost-prohibitive. The decontamination machines may be leased or purchased.


X-Ray Chamber Decontamination
X-ray chamber decontamination is highly effective and has a history of use in medicine and even airport security. X-rays are a form of high-energy electromagnetic radiation, that is, short wavelength light. X-ray wavelengths are shorter than those of ultraviolet (UV) radiation. This means they pack more punch with an intrinsically higher level of energy and therefore are much more effective in killing microbes than UV. The instrumentation for X-ray decontamination is well-tested and uses technology that has been proven for decades. The cannabis is placed in a lead-lined chamber that ensures the safety of the operator during the decontamination process. X-rays are produced from an internal vacuum tube once the lead lined chamber is sealed. The X-rays penetrate the cannabis and kill the microbes. The system is foolproof and does not allow the operator to be exposed to X-rays. It is highly effective in the destruction of the full complement of microorganisms to be tested at the state level. After the processing by X-ray chamber decontamination, your cannabis will be ready to pass the state tests.

Ozone Chamber Decontamination
Ozone chamber decontamination has a history of use in agriculture to help keep the food supply safe. Ozone is highly effective in reducing the levels of TYMC to meet state standards. Ozone gas (O3) is a highly reactive oxidizing molecule, meaning it is harmful to cells. It destroys the microbes’ cell wall, which enables the ozone to destroy all of the cell’s components: enzymes, proteins, DNA, and RNA. An ozone chamber generates its ozone gas as needed in a foolproof sealed chamber that cannot be operated until the door is sealed. Once placed in the chamber and sealed in, the cannabis will be exposed to ozone, and the microbes on the surface will be killed. Any ozone not consumed by the disinfection process is deactivated by the system before the door can be opened. This method greatly reduces the number of microbes but does not reduce the number to zero. Ozone chamber decontamination has been demonstrated to be effective against the full range of microorganisms expected to be tested by the states (4).

Controlling Microbial Growth Inside Packaged Cannabis Products

In the rare instances when regulators find contaminated products, such as flower and pre-rolls, on the shelf from lots that have previously met state standards, it is likely because of post-harvest environmental control of the products. A measurable value, called water activity, must be considered in assessing the probability of on-going microbial growth even while packaged. With an out-of-spec water activity value, plant material that passed the 10,000-count-limit test with a count of 7000 need only double over a period of weeks to render the material noncompliant with a measure of 14,000. The microbial growth that can take place after packaging is the reason that 11 of 29 states now require the testing of water activity, a measure that indicates whether continued microbial growth of the packaged cannabis is likely. We anticipate that additional states will include water activity in their slate of mandated testing.

Our home state of California has established an upper limit for the water activity for flower of 0.65. If flower material is not cured to a water activity measure of at least 0.70, yeast and mold can grow on it. We expect that in the coming years all states will require the same water activity limits for packaged cannabis. If this level of water activity is maintained throughout the cultivation processes and into packaging it prevents incidents such as the recent Denver dispensary test failures (2). Similar to food products, a lower water activity measure should also extend the overall shelf life of the product. If you are interested in a more in-depth understanding of water activity in cannabis, we encourage you to read further about it in a recently published article (5).

How do you achieve the desired water activity of ≤0.65 post-harvest if, and when, your state mandates this test? This is not easy; it will require dedication and determination on your part and compliance from all of your team members. This will be a standard operating procedure (SOP) to ensure you are taking all necessary steps to achieve the desired water activity prior to packaging. Ideally, all of your post-harvest processes must be performed in a controlled environment where the relative humidity (RH) is maintained between 55–65%. To achieve the desired water activity in the cannabis of  0.65, you will need to have a stable humidity across your entire set of post-harvest processes in this range of 55–65% RH. This stable relative humidity is called equilibrium relative humidity (ERH). If the relative humidity is not stable and controlled, you will not be assured of the desired water activity when the cannabis is packaged. To accomplish the ERH, you will need to monitor and control the potential effects on relative humidity from the weather, temperature, and people entering and exiting your processing rooms-to name just a few factors. With excellent practices, codified in your SOP, you will be assured that you have done all that can be done to achieve the water activity necessary to pass the state-mandated tests and prevent microbial growth in the packaged products.

Once packaged, the microenvironment in the package can be controlled by including relative humidity control packets, such as Boveda and Integra brands. Both products are designed to maintain relative humidity inside the package at 62%. This will be the ERH in the packaging that translates into the desired water activity measure that will prevent further microbial growth. The packets contain proprietary materials that can both absorb and release water into the packaging based on the relative humidity. The relative humidity will be affected by the temperature, so these packets are protective against some of the negative impact of temperature fluctuations along the supply chain. The packets are encased in a breathable membrane that permits them to release and absorb pure water with no contaminants. The result is a microbiologically stable cannabis product with longer shelf life and a total yeast and mold count that will pass the state-mandated test.

Expert Point of View

We spoke with the Executive Vice-President and a scientist at Radsource Technologies, Inc., George Terry and Justin Czerniawski, PhD, as well as the Engineering Manager of Willow Industries, Adrian Alvarez, to learn about their microbial remediation technologies and gain their perspectives on post-harvest microbial decontamination. Their insights are invaluable as we work to solve this threat that can be costly and lower your profit margin.

How big is the need for post-harvest decontamination technology?

George Terry and Justin Czerniawski: Huge! Many cannabis regulators require cannabis samples pass total yeast and mold testing before they can be sold in dispensaries. The standards many states use to determine pass or fail criteria for microbial testing, is in the range of less than 10,000 CFU/g on cannabis plant material and 1000 CFU/g on extracts. Although there are many methods to try to reduce the amount of pathogens during the grow (such as approved bacteria sprays, UV light, ozone sprays), mold is a spore, and a living organism that thrives on the moisture in grow operations and proliferates. Post-harvest is the last chance to treat the product prior to it being packaged for consumption. If the packaging process is aseptic, then decontamination at that point is the best option to keep the material clean to the consumer. There are a few articles related to this (6–8).

Adrian Alvarez: There is an ever-growing need for post-harvest remediation and decontamination technology in the cannabis industry today. A few years ago, there were less stringent regulations surrounding cannabis contamination, so the market wasn’t really there. But as regulators learned more, new testing laws were created, and the $3B cannabis contamination problem was born. In terms of the numbers, industry estimates state that 10–20% of commercially grown cannabis fails microbial testing, which means there’s a significant need for a decontamination step in post-harvest production.

There are a lot of factors that influence a cultivator’s decision to implement decontamination technology, but in the commercial grows, where a test failure could mean 100+lbs of cannabis is pulled from the supply chain, the need is clear. The only reliable alternative to decontamination technology is turning contaminated flower into concentrates, but these products sell at a lower margin, so businesses usually prefer to have a nonextraction-based decontamination solution on hand.

How effective is your decontamination approach?

Terry and Czerniawski: While no system can make the legal claim that the product is sterile, we believe our method is the most effective means of reducing the microbial bioburden available. We have used X-rays to decontaminate medical devices and even blood supply for immune compromised patients. Using Aspergillus niger as a test strain, one of our clients has shown the eradication of spores from the material to zero.

Alvarez: Our technology reduces mold and pathogens on cannabis flower without altering potency, cannabinoids, or terpenes, making it an extremely effective decontamination solution for cultivators. When used for remediation, that is, cleaning flower that has already failed testing once, we have a roughly 89% pass rate, but when our technology is implemented as a kill-step, our pass rate is 94%. There are a lot of factors that explain this difference, but to put it simply, decontamination is most effective when implemented preventatively, as this stops mold from growing in the first place. In terms of the numbers, a 6-hour WillowPure treatment provides an average microbial count reduction of over 97% (P < 0.001), and that’s when used on heavily contaminated flower (TYMC greater than 75,000 CFU/g).

Are there any negative effects, for example, terpene degradation?

Terry and Czerniawski: We have a cold process that does not introduce heat so there is no premature conversion of THCA, no mycotoxin stimulation from pathogen stress, no oxidative aging of the flower, and no accelerated evaporation of volatile organics like terpenes.

Alvarez: WillowPure treatment has no negative effects on flower terpene profiles or cannabinoid concentrations, as the plant’s natural, organic resin protects it from the oxidizing effects of ozone and no residue is deposited on the flower during treatment as ozone decomposes into oxygen. Three years were spent optimizing ozone concentrations and run times, but with hundreds of positive customer experiences behind us, we’re confident in our system’s ability to eliminate mold and pathogens without negatively affecting the product.


Clean cannabis starts with clean cultivation practices (9). Clean practices, combined with the post-harvest decontamination methods described here, should enable every cultivator to pass state-mandated tests for microbial contamination 100% of the time. To maintain state compliant levels of microbial contamination, you should maintain a stable water activity measurement across the full supply chain from grower to consumer. However, with at least 10% of the flower material not passing state-mandated tests for total mold and yeast count, we need safe decontamination steps that do not compromise the quality of the final product. We have highlighted two examples here, X-ray chamber decontamination and ozone chamber decontamination methods. Whether you choose to remediate only the plant material that fails the state test and is returned to you for post-failure processing or introduce a microbial decontamination process for each lot before you send it out is up to you. A conservative approach would be to decontaminate every lot with one of the decontamination methods and use the relative humidity control packet in the packaging materials. This approach will give you confidence that your products will be state compliant and avoid expensive transport and return to your facility for reprocessing should they fail state testing further down the supply chain. Starting clean and staying clean will improve your profitability and maintain your excellent reputation along the supply chain all the way to the consumer.


  1. K. McKernan, Y. Helbert, H. Ebling, A. Cox, L.T. Kane, and L. Zhang, “Microbiological examination of nonsterile Cannabis products” (2018).
  2. T. Mitchell, Westworld, October 30, 2019
  3. G.D. Molim, M. de Souza Braga, et. al., Curr. Pharm. Des.22(27), 4264–4287(24) (2016).
  4. A.J. Brodowska and K. Smigielski, “Ozonation-an alternative decontamination method for raw plant materials” Food Sciences and Biotechnology (2013).
  5. B.P. Carter, Cannabis Science and Technology2(4), 30–35 (2019).
  6. C. Hellerman, PBS News Hour,
  8. Y. Gargani, P. Bishop, and D.W. Denning, Mediterr. J. Hematol. Infect. Dis. 3(1), e2011005, (2011).
  9. R. Kern, Cannabis Science and Technology2(4), 16–29 (2019).

About the Coauthor

Dr. Jacklyn R. Green is a project manager, systems engineer, and scientist focused on today’s commercial cannabis enterprise. She is the cofounder and Chief Executive Officer of Agate Biosciences LLC, an agricultural consultancy. She earned her PhD at The University of Texas in astronomy, and subsequently applied her big-picture view and systems approach to problem solving at NASA’s Jet Propulsion Laboratory for more than 25 years. In her tenure there, she conducted detailed scientific research, managed complex projects and programs, and led teams of engineers and scientists to solve near impossible problems in a collaborative team setting. Now, she brings the best practices of management and systems engineering to cannabis businesses enhancing their financial and technical success in today’s stringent government-regulated environment.

About the Columnist

Dr. Roger Kern is a scientist and technologist who cares deeply about the cultivation and health of plants in the cannabis industry. With his PhD in microbiology from the University of California, Davis, Plant Growth Laboratory, he solves the most challenging problems in hydroponics, from studying the root microbiome to developing nutrients and lighting systems to ensure plant health and a disease-free lifecycle. He spent 22 years at NASA’s Jet Propulsion Laboratory as a scientist, technologist, and research leader before becoming the President of Agate Biosciences, a consulting firm for project management, systems engineering, and science in CEA for the past eight years. He leads developments to optimize sustainability, consistency, quality, and yield without compromising plant health. Direct correspondence to:

How to Cite this Article

R. Kern and J.R. Green, Cannabis Science and Technology2(6), 15-19 (2019).