Restoring Lost Microbial Diversity in Cannabis
By Carolina Lobato, 18.02.2025
Domestication and intensive breeding have shaped modern crops, enhancing yield and specific traits like disease resistance and chemical composition. However, this process has also consequences for plant-microbe interactions. In our recent study, conducted at Graz University of Technology. We investigated how domestication has shaped the seed microbiome of Cannabis. We found that intensive breeding has led to a loss of seed microbial diversity and, with it, potentially valuable bacterial species. Notably, we were able to recover a beneficial bacterium from low-domesticated Cannabis varieties and demonstrate its potential to enhance plant growth — highlighting the importance of microbiome-based strategies for sustainable agriculture.
The Seed Microbiome: An Overlooked Factor in Plant Health
While the importance of root and soil microbiomes is well established, far less attention has been given to how plant breeding has influenced the microbial composition of seeds. Seeds are not just genetic repositories; they also harbor complex microbial communities that influence plant development by enhancing nutrient uptake, stimulating plant growth, and protecting against pathogens. Among these, seed endophytes — microorganisms that reside within seeds — can be passed down across plant generations, shaping the initial microbial landscape of emerging plants. By carrying both genetic and microbial legacies, seeds provide a crucial foundation for plant establishment and microbial colonization.
In our research, we analyzed the bacterial communities of 46 Cannabis varieties, from traditional landraces to modern cultivated varieties. The results revealed a clear pattern: as breeding intensity increased, microbial diversity declined. Landrace varieties harbored a more diverse microbiome, while inbred lines exhibited a homogenized composition dominated by fewer bacterial taxa. These findings suggest that breeding may have inadvertently led to the loss of microbes that once played a crucial role in plant health and stress resilience.
Reintroducing a Lost Beneficial Bacterium
One of the most striking discoveries in our study was the identification of Bacillus frigoritolerans C1141, a bacterial species strongly associated with low-domesticated Cannabis varieties, and largely absent from modern cultivated varieties. Whole-genome sequencing revealed that this bacterium possesses genes linked to plant growth promotion, including phytohormone production, nutrient solubilization, and stress resistance.
To test its potential, we reintroduced B. frigoritolerans C1141 to Cannabis plants in both controlled and field experiments. The results were remarkable: treated plants grew 43% taller, nearly doubled their stalk diameter, and produced three times the biomass compared to untreated plants. These effects surpassed those of Serratia plymuthica, a well-established plant-beneficial bacterium, demonstrating the power of rediscovering and harnessing lost microbial diversity.
Implications for Sustainable Agriculture
Our findings underscore the critical role of seed microbiomes in plant fitness and highlight the need for breeding programs to consider microbial conservation. Instead of relying solely on synthetic fertilizers and pesticides, integrating beneficial microbes into agricultural systems could enhance plant resilience while reducing chemical inputs.
Although this study focused on Cannabis, similar microbial shifts have been observed in other domesticated crops, suggesting broader implications for global agriculture. Future research should explore how microbiome restoration strategies can be applied across different plant species to promote sustainable and resilient farming.
By recognizing seeds as both genetic and microbial reservoirs, we can rethink breeding strategies and harness the full potential of plant-microbe interactions. This approach offers a promising path toward ecologically sound and productive agricultural systems — one where beneficial microbes play as important a role as the plants themselves.