Uploaded August 2025 | Updated September 2026, 2 weeks ago
Tags: Cannabis Plant Pathogens, Trichomes, HLVd, HPLVd, Hop Latent Viroid, qPCR Testing, Root Infection, Cannabis Yield, Cannabis Disease
Zamir Punja, PhD, presents "Microbial Endophytes are Abundant in Cannabis Plants as Revealed by Microbiome Analysis and Scanning Microscopy Studies – Implications for Plant Health and Product Quality" at CannMed 2025.
Learn More about CannMed: cannmedevents.com
Microbes that reside within cannabis tissues (endophytes) are thought to provide benefits to the plant although their presence has also raised concerns about possible negative impacts on plant quality. To determine the nature of these endophytes and their potential impact on cannabis growth, tissues of high THC-containing plants were subjected to Next-Generation Sequencing (NGS). Reads were classified using a metagenomics classification algorithm that assigns a taxonomic identification to each sequencing read and estimates the abundance of each species in the sample. The tissues analyzed included 90 samples of roots, stems, leaves and flowers representing 12 genotypes. A few seed samples were also included. Scanning electron microscopic studies were performed on stem tissues to examine the xylem and pith tissues for presence of endophytes. Up to 20 genera of fungi, 9 yeasts and 18 bacterial genera were present at varying frequencies (percent of total reads of the taxon relative to total reads of that microbe group) in the tissues. The highest frequencies were generally found in the roots, followed by stems. Seeds and flowers contained an abundance of endophytic and epiphytic microbes. The most frequently detected fungal genera were Penicillium, Fusarium and Rhizophagus (Glomus) while the most abundant bacterial genera were Bacillus and Pseudomonas. Penicillium chrysogenum and Fusarium oxysporum were present in all tissue samples. The microbiome of cuttings and vegetative plants mirrored that of mother plants, suggesting that transmission of endophytes was occurring through vegetative propagation. Scanning electron microscopy of sectioned stems from mother plants revealed the presence of fungal spores of a range of species within the xylem vessel elements and pith parenchyma cells. The cocofibre substrate in which mother plants were grown greatly influenced the microbes present, particularly in roots but also in other tissues. Application of biocontrol fungi, such Trichoderma harzianum, was followed by detection in roots, stems, leaves and flowers of treated plants. Applications of this biocontrol fungus to 2 week-old rooted cuttings resulted in a partial displacement of the pre-existing microbes, thus enhancing the frequency of T. harzianum in the roots but not in stems within 4 weeks after treatment. Sterilizing the cocofibre growing medium did not influence the microbiome of cuttings grown in them. Meristem tip culture eliminated almost all fungal endophytes but bacteria were still present. However, rapid recolonization by Fusarium species during the rooting phase resulted in a predominance of this pathogen in the tissues. These findings suggest that endophytic microbes are abundant in cannabis tissues and their composition is influenced by the growing substrate, as well as by applications of biocontrol agents. Meristem-derived plants should be treated with protective microbial products to occupy the biological vacuum before being used.
0:20 - What Are Microbial Endophytes?
1:57 - The Cannabis Production Cycle and Sampling
3:18 - Where to Find Endophytes in Plants
4:25 - Research Objectives & Methodology
7:10 - Chronoplots: Visualizing Microbial Data
8:09 - Fungal & Yeast Differences by Genotype and Stage
9:21 - The Influence of Growing Medium on Microbes
10:28 - Effect of Drying on Microbial Populations
12:56 - Summary: Endophyte Presence Across Plant Tissues
15:52 - Beneficial vs. Harmful Endophyte Species
16:30 - Pinpointing Where Microbes Hide in Plant Tissues
18:55 - How Microbes Move Within the Plant
22:24 - Microscopic View: Spores in Flowers
24:35 - The Role of Tissue Culture in Endophyte Elimination
26:22 - The Takeaway: Understanding Endophyte Behavior
27:48 - Research Support Acknowledgements
28:09 - Q&A Session & Conclusion
Learn More about CannMed: cannmedevents.com
Sign Up for Our Newsletter: share.hsforms.com/1oi57oJDnRN-Uqqc9YPByRA20xr2
The CannMed 25 Innovation & Investment Summit showcased its first international venue, the Wyndham Grand Rio Mar Golf & Beach Resort in Puerto Rico from June 17 - 20, 2025. Since its inception at Harvard Medical School in 2016, CannMed has earned a reputation as the premier destination for cutting-edge research, emerging technologies, and investment opportunities. CannMed 25 continues this tradition with medicinal plant researchers, clinicians and venture capitalists who view this Summit as the industry’s number one showcase for the latest advances in plant-based science, medicine, cultivation, and safety.
Tags: Cannabis Plant Pathogens, Trichomes, HLVd, HPLVd, Hop Latent Viroid, qPCR Testing, Root Infection, Cannabis Yield, Cannabis Disease
Zamir Punja, PhD, presents "Microbial Endophytes are Abundant in Cannabis Plants as Revealed by Microbiome Analysis and Scanning Microscopy Studies – Implications for Plant Health and Product Quality" at CannMed 2025.
Learn More about CannMed: cannmedevents.com
Microbes that reside within cannabis tissues (endophytes) are thought to provide benefits to the plant although their presence has also raised concerns about possible negative impacts on plant quality. To determine the nature of these endophytes and their potential impact on cannabis growth, tissues of high THC-containing plants were subjected to Next-Generation Sequencing (NGS). Reads were classified using a metagenomics classification algorithm that assigns a taxonomic identification to each sequencing read and estimates the abundance of each species in the sample. The tissues analyzed included 90 samples of roots, stems, leaves and flowers representing 12 genotypes. A few seed samples were also included. Scanning electron microscopic studies were performed on stem tissues to examine the xylem and pith tissues for presence of endophytes. Up to 20 genera of fungi, 9 yeasts and 18 bacterial genera were present at varying frequencies (percent of total reads of the taxon relative to total reads of that microbe group) in the tissues. The highest frequencies were generally found in the roots, followed by stems. Seeds and flowers contained an abundance of endophytic and epiphytic microbes. The most frequently detected fungal genera were Penicillium, Fusarium and Rhizophagus (Glomus) while the most abundant bacterial genera were Bacillus and Pseudomonas. Penicillium chrysogenum and Fusarium oxysporum were present in all tissue samples. The microbiome of cuttings and vegetative plants mirrored that of mother plants, suggesting that transmission of endophytes was occurring through vegetative propagation. Scanning electron microscopy of sectioned stems from mother plants revealed the presence of fungal spores of a range of species within the xylem vessel elements and pith parenchyma cells. The cocofibre substrate in which mother plants were grown greatly influenced the microbes present, particularly in roots but also in other tissues. Application of biocontrol fungi, such Trichoderma harzianum, was followed by detection in roots, stems, leaves and flowers of treated plants. Applications of this biocontrol fungus to 2 week-old rooted cuttings resulted in a partial displacement of the pre-existing microbes, thus enhancing the frequency of T. harzianum in the roots but not in stems within 4 weeks after treatment. Sterilizing the cocofibre growing medium did not influence the microbiome of cuttings grown in them. Meristem tip culture eliminated almost all fungal endophytes but bacteria were still present. However, rapid recolonization by Fusarium species during the rooting phase resulted in a predominance of this pathogen in the tissues. These findings suggest that endophytic microbes are abundant in cannabis tissues and their composition is influenced by the growing substrate, as well as by applications of biocontrol agents. Meristem-derived plants should be treated with protective microbial products to occupy the biological vacuum before being used.
0:20 - What Are Microbial Endophytes?
1:57 - The Cannabis Production Cycle and Sampling
3:18 - Where to Find Endophytes in Plants
4:25 - Research Objectives & Methodology
7:10 - Chronoplots: Visualizing Microbial Data
8:09 - Fungal & Yeast Differences by Genotype and Stage
9:21 - The Influence of Growing Medium on Microbes
10:28 - Effect of Drying on Microbial Populations
12:56 - Summary: Endophyte Presence Across Plant Tissues
15:52 - Beneficial vs. Harmful Endophyte Species
16:30 - Pinpointing Where Microbes Hide in Plant Tissues
18:55 - How Microbes Move Within the Plant
22:24 - Microscopic View: Spores in Flowers
24:35 - The Role of Tissue Culture in Endophyte Elimination
26:22 - The Takeaway: Understanding Endophyte Behavior
27:48 - Research Support Acknowledgements
28:09 - Q&A Session & Conclusion
Learn More about CannMed: cannmedevents.com
Sign Up for Our Newsletter: share.hsforms.com/1oi57oJDnRN-Uqqc9YPByRA20xr2
The CannMed 25 Innovation & Investment Summit showcased its first international venue, the Wyndham Grand Rio Mar Golf & Beach Resort in Puerto Rico from June 17 - 20, 2025. Since its inception at Harvard Medical School in 2016, CannMed has earned a reputation as the premier destination for cutting-edge research, emerging technologies, and investment opportunities. CannMed 25 continues this tradition with medicinal plant researchers, clinicians and venture capitalists who view this Summit as the industry’s number one showcase for the latest advances in plant-based science, medicine, cultivation, and safety.
