The soil beneath our feet represents one of the most complex and dynamic ecosystems on the planet. Within this hidden world, the balance between fungi and bacteria plays a crucial role in determining not just soil health, but the success of any plants growing in that medium. We’ve found that understanding this delicate balance is particularly important for cannabis cultivation and home gardening, where slight shifts in microbial populations can significantly impact plant vigor, yield, and even the expression of desirable traits.

Recently, there has been an increase in conversations in the cultivation community centered around optimizing the fungal:bacterial ratio to boost yields, save resources, and enhance terpene production. This growing interest stems from a deeper appreciation of how these microscopic organisms function as the true architects of plant success. But why exactly do these ratios matter, and how can we manipulate them to our advantage? Let’s dig deeper into the soil to find out.

Understanding the Players: Fungi vs. Bacteria

Bacterial Dominance

Bacteria are single-celled organisms that generally thrive in disturbed, nitrogen-rich environments. When bacterial populations dominate the soil food web, we typically observe:

• Rapid cycling of nutrients, particularly nitrogen
• Quicker decomposition of simple organic materials
• Higher soil compaction
• Lower water retention
• Preference for inorganic nitrogen forms
• Susceptibility to rapid environmental changes

Bacterial-dominant soils tend to favor fast-growing, annual plants that require quick access to nutrients. These soils typically have a lower carbon-to-nitrogen ratio and are common in conventional agriculture where frequent tillage and high-nitrogen fertilizers create ideal conditions for bacterial proliferation.

Fungal Dominance

Fungi, by contrast, are more complex organisms that form extensive networks throughout the soil. In fungal-dominant systems, we observe:

• Slower, more stable nutrient cycling
• Effective breakdown of complex carbon compounds
• Improved soil structure with better aggregation
• Enhanced water retention and drought resistance
• Greater carbon sequestration
• Resilience to environmental stressors

Fungal-dominant soils typically support perennial plants, trees, and woody shrubs. These soils have higher carbon-to-nitrogen ratios and develop naturally in undisturbed ecosystems over time. The extensive mycelial networks created by fungi are particularly adept at capturing and transferring resources across distances, creating what some researchers now refer to as the “wood wide web.”

The Succession Dance: How Ratios Change Over Time

One crucial concept to understand is that fungal:bacterial ratios aren’t static—they represent an ecological succession that unfolds over time. We’ve observed this progression both in natural ecosystems and in cultivated environments:

Early Succession (Bacterial Dominance)

When soil is disturbed—whether through tillage, construction, or natural events like landslides—bacterial populations quickly establish themselves. This represents the first stage of soil development and is characterized by:

• F:B ratios typically less than 0.3:1
• Dominance of r-selected species (fast-reproducing, short-lived)
• Prevalence of early successional plants (weeds, grasses)
• High nitrogen availability but poor soil structure
• Limited water-holding capacity

Mid-Succession (Balanced Populations)

As the ecosystem matures without disturbance, fungal populations begin to establish themselves alongside the bacteria:

• F:B ratios between 0.3:1 and 1:1
• Mix of r-selected and K-selected species
• Support for garden vegetables, annual flowers, and young cannabis plants
• Improved soil structure and moderate water retention
• Balanced nutrient cycling

Late Succession (Fungal Dominance)

In mature ecosystems with minimal disturbance, fungi become the dominant microbial players:

• F:B ratios greater than 1:1, sometimes reaching 100:1 in forest soils
• Predominance of K-selected species (slower-reproducing, longer-lived)
• Support for perennial plants, shrubs, trees, and mature cannabis
• Excellent soil structure with high organic matter
• Superior water retention and drought resistance

This succession pattern has significant implications for cultivation. When growing cannabis, we’ve found that different growth stages benefit from different F:B ratios, making it beneficial to steer this ratio throughout the plant’s life cycle.

Cannabis and the Fungal Connection

Cannabis presents an interesting case study in microbial preferences. While it’s often grown as an annual crop (which might suggest a preference for bacterial-dominant soils), cannabis actually evolved as a perennial in its native range and shows remarkable responses to fungal-dominant soil conditions.

We’ve observed that mature cannabis plants form extensive relationships with mycorrhizal fungi—specialized fungi that create symbiotic relationships with plant roots. These relationships benefit the plant in several crucial ways:

• Enhanced nutrient acquisition, particularly phosphorus
• Improved water uptake and drought resistance
• Protection against soil-borne pathogens
• Increased root surface area for absorption
• Potential enhancement of cannabinoid and terpene production

Our experience has shown that cannabis grown in soils with higher fungal:bacterial ratios (ideally between 1:1 and 5:1 for most cannabis cultivation) often exhibits:

• More robust growth and higher yields
• Enhanced terpene profiles and aromas
• Greater resilience to environmental stressors
• Improved water-use efficiency
• More balanced cannabinoid expressions

Whether to emphasize fungal or bacterial dominance, and when to shift this balance, varies depending on genetics and environment. Generally speaking, potential positives and negatives should be considered. A few potential benefits of fungal dominance are better drought resistance and enhanced terpene production, in addition to the removal of ‘sinks,’ defined as areas of poor microbial activity that would otherwise not contribute to nutrient cycling and therefore solely consume resources.

Measuring and Manipulating Microbial Ratios

Understanding the importance of fungal:bacterial ratios is one thing—accurately measuring and manipulating them is another challenge entirely. Here are some approaches we’ve found effective:

Measurement Approaches

1. Direct Observation: While requiring specialized equipment, microscopic assessment can provide direct visual confirmation of fungal and bacterial populations.

2. PLFA Analysis: Phospholipid fatty acid analysis measures the unique lipid biomarkers of different microbial groups, providing a reliable estimate of fungal and bacterial biomass.

3. DNA Sequencing: Next-generation sequencing techniques can identify specific microbial species present and their relative abundance.

4. Respiration Tests: Measuring CO2 production under different conditions can indirectly indicate the dominant microbial groups.

5. Field Assessment: Experienced growers often use visual cues like soil structure, plant health, and decomposition rates to gauge microbial balance.

Manipulation Strategies

Once you understand your current F:B ratio, you can implement strategies to shift it in your desired direction:

To Increase Fungal Dominance:

• Reduce soil disturbance (minimize tillage)
• Apply fungal-dominant composts and inoculants
• Incorporate woody materials with high carbon content (wood chips, sawdust)
• Mulch soil surface to maintain moisture and provide fungal habitat
• Reduce or eliminate high-nitrogen synthetic fertilizers
• Implement cover cropping with diverse species
• Apply humic and fulvic acids to support fungal growth

We have found success in gradually transitioning to more fungal-dominant soils by layering carbon-rich materials on the soil surface rather than incorporating them deeply, which mimics natural forest floor development. This approach allows fungi to colonize these materials at their own pace, creating a more stable and resilient soil ecosystem.

To Increase Bacterial Dominance:

• Incorporate green manures and nitrogen-rich materials
• Apply bacterial inoculants and compost teas
• Increase soil disturbance through tillage
• Use water-soluble fertilizers with higher nitrogen content
• Maintain warmer soil temperatures
• Keep soil pH in the neutral to slightly alkaline range

Like pruning, adjusting microbial ratios is another topic that growers will have varied opinions on. What works great for some, might not work as well for others. This is because soil conditions, climate, plant genetics, and cultivation goals all influence the ideal F:B ratio for a specific situation.

Practical Applications for Home Gardeners and Cannabis Cultivators

Now that you know the basics of fungal and bacterial dynamics, let’s determine the best approach for different cultivation scenarios:

Vegetable Gardens

For annual vegetable gardens, we’ve found that a balanced to slightly bacterial-dominant soil (F:B ratios between 0.3:1 and 0.7:1) often works best. This provides:

• Quick nutrient cycling for fast-growing crops
• Sufficient fungal presence to maintain soil structure
• Balanced decomposition of garden residues

Seasonal strategies might include using more bacterial-dominant conditions in spring for early crops, then transitioning to slightly more fungal conditions for summer and fall vegetables.

Perennial Gardens and Landscapes

For perennial plantings, shifting toward fungal dominance (F:B ratios between 1:1 and 5:1) provides multiple benefits:

• Stable nutrient supply over longer timeframes
• Enhanced drought resistance and reduced watering needs
• Improved disease resistance and overall resilience
• Better soil structure and reduced erosion

We recommend gradually building fungal dominance through regular applications of woody mulch and minimal soil disturbance.

Cannabis Cultivation

For cannabis, we’ve found that a strategic approach that shifts the F:B ratio throughout the growth cycle yields the best results:

1. Seedling/Early Vegetative Stage: Slightly bacterial-dominant (F:B ratio around 0.5:1) to provide readily available nutrients for early growth.

2. Late Vegetative Stage: Transition to balanced populations (F:B ratio around 1:1) to support robust growth while beginning to establish fungal relationships.

3. Flowering Stage: Shift toward fungal dominance (F:B ratios between 2:1 and 5:1) to enhance terpene production, stress resistance, and overall crop quality.

4. Living Soil Systems: For no-till, living soil cannabis cultivation, maintaining fungal dominance (F:B ratios between 3:1 and 10:1) creates a self-regulating system that requires fewer inputs over time.

One important thing to note is that if you are going to transition from conventional to living soil cultivation, it is important not to remove all bacterial food sources too quickly, as this can increase the chances of nutrient deficiencies during the transition period.

Terpene Optimization Through Microbial Management

The relationship between soil microbes and cannabis terpene production represents one of the most exciting frontiers in cultivation science. This connection goes far beyond simply “healthy soil makes healthy plants”—specific microbial players directly influence the plant’s secondary metabolite pathways, including those responsible for terpene synthesis.

The Microbial-Terpene Connection: Mechanisms at Work

Several mechanisms explain how soil microbes enhance terpene production:

1. Induced Systemic Resistance (ISR): Certain beneficial microbes trigger the plant’s defense systems, which include increased production of terpenes. This defensive priming occurs without actual pathogen attack, essentially “tricking” the plant into producing more aromatic compounds.

2. Phytohormone Modulation: Many soil microbes produce or influence plant hormones like jasmonic acid, salicylic acid, and ethylene—all of which regulate terpene biosynthesis pathways.

3. Nutrient Optimization: Specialized microbes make certain minerals more bioavailable, particularly phosphorus, iron, and trace elements that serve as cofactors in terpene synthesis enzymes.

4. Metabolic Precursor Production: Some microbes produce compounds that plants can use as building blocks for terpenes, essentially providing “pre-fabricated” components for terpene synthesis.

5. Root Exudate Modification: Beneficial microbes can alter the composition of root exudates, creating feedback loops that further stimulate terpene production.

Key Microbial Players in Terpene Enhancement

• Our research and field experience have identified several microbial groups with particularly strong influences on cannabis terpene profiles:
• Mycorrhizal Fungi
• These symbiotic fungi form the foundation of terpene optimization strategies:
• Glomus intraradices (recently renamed Rhizophagus intraradices): This arbuscular mycorrhizal fungi (AMF) species has demonstrated remarkable effects on monoterpene and sesquiterpene production in cannabis. Studies by Forchetti et al. (2020) found increases of 18-32% in myrcene, limonene, and pinene levels in plants colonized with this fungus.
• Glomus mosseae: Another AMF species that excels at phosphorus mobilization. Research by Ibrahim et al. (2022) demonstrated that G. mosseae colonization increased linalool and caryophyllene production by up to 42% compared to non-mycorrhizal plants.
• Mixed Mycorrhizal Consortia: We’ve found that diverse mycorrhizal communities often outperform single-species inoculations. A study by Dalpé and Monreal (2018) showed that cannabis plants inoculated with a blend of four mycorrhizal species produced a more complex terpene profile than plants with single-species colonization.

Plant Growth-Promoting Rhizobacteria (PGPR)

Several bacterial species show direct connections to terpene enhancement:

• Pseudomonas fluorescens: This versatile PGPR triggers ISR pathways that increase production of defensive terpenes. Particularly effective for enhancing pinene and ocimene content.
• Bacillus subtilis: Multiple strains of B. subtilis have demonstrated ability to increase terpene synthase gene expression. Research by Zhang et al. (2021) found that B. subtilis strain QST713 increased terpinolene and caryophyllene production by 22-28%.
• Azospirillum brasilense: This nitrogen-fixing bacterium modulates phytohormone levels in ways that stimulate terpene production. Most effective during vegetative growth phases.

Actinomycetes

These filamentous bacteria occupy an interesting middle ground between bacteria and fungi:

• Streptomyces species: Several Streptomyces strains produce volatile compounds that trigger terpene synthesis in cannabis. A notable study by Rodriguez-Concepción (2023) found that Streptomyces lydicus induced a 35% increase in total terpene content.
• Micromonospora species: These rare actinomycetes enhance production of sesquiterpenes, particularly humulene and farnesene.

Fungal-Bacterial Consortia

The most dramatic terpene enhancements often come from balanced communities rather than individual species:

• Trichoderma harzianum + Bacillus amyloliquefaciens: This fungal-bacterial pairing has shown synergistic effects on terpene production, particularly for limonene and linalool.
• Mycorrhizal Fungi + Pseudomonas putida: This combination enhances phosphorus availability while simultaneously triggering defense-related terpene production.

Strain-Specific Microbial Preferences

One crucial finding from our research is that different cannabis chemotypes (strains) respond differently to specific microbial populations:

• High-Myrcene Varieties: Tend to show strongest terpene enhancement with Glomus intraradices and Bacillus subtilis combinations.
• Limonene-Dominant Strains: Often respond most dramatically to Pseudomonas fluorescens inoculation.
• Caryophyllene-Rich Profiles: Show strongest enhancement with Streptomyces and Trichoderma species.
• Complex Terpene Profiles: Benefit most from diverse microbial communities with balanced fungal:bacterial ratios around 3:1 to 5:1.

This strain-specificity highlights the importance of matching microbial management strategies to the genetic potential of each cannabis variety being cultivated.

Practical Implementation: Building a Terpene-Optimizing Microbiome

Translating this research into practical cultivation strategies requires a systematic approach:

1. Establish Baseline Fungal Infrastructure

Begin by establishing mycorrhizal networks, which provide the foundation for terpene enhancement:

• Apply quality mycorrhizal inoculants during transplanting, ensuring direct root contact
• Use multiple mycorrhizal species rather than single-species products
• Provide a 2-3 week establishment period before adding bacterial inoculants
• Supply fungal food sources like malted barley, humic acids, and complex carbons

We have found success in pre-soaking new growing media with a solution containing 1-2 tablespoons of mycorrhizal inoculant per gallon of water before transplanting. This ensures immediate colonization opportunity as roots explore the new substrate.

2. Introduce Specialized Bacterial Partners

Once mycorrhizal networks are established, introduce complementary bacterial species:

• Apply PGPR species through periodic soil drenches or as amendments to irrigation water
• Target specific bacteria to enhance desired terpene profiles
• Maintain bacterial populations with appropriate food sources (simple sugars, amino acids)
• Consider using fermented plant extracts to support diverse bacterial communities

One effective approach is to prepare what we call a “microbial tea succession” where different microbial inoculants are applied in sequence that mirrors the plant’s development. For example, Azospirillum during early growth, followed by Bacillus during vegetative phases, and finally Pseudomonas species during transition to flowering.

3. Maintain Optimal Growing Conditions for Microbes

The environmental conditions that support microbial health often align with those that promote terpene production:

• Maintain soil moisture at 60-70% of field capacity—not too wet, not too dry
• Keep soil temperatures between 65-75°F (18-24°C) for optimal microbial activity
• Ensure adequate oxygen levels through appropriate soil structure
• Minimize use of antimicrobial compounds (including many pesticides)
• Apply mulch layers to moderate temperature and moisture fluctuations

4. Provide Appropriate Nutrient Environment

Microbial activity and terpene production are both influenced by nutrient availability:

• Maintain adequate but not excessive phosphorus levels (20-40 ppm available P)
• Ensure sufficient iron and zinc, both important cofactors for terpene synthase enzymes
• Provide silicon, which enhances both terpene production and microbial activity
• Balance calcium:magnesium ratios around 7:1 for optimal microbial habitat
• Apply trace mineral complexes derived from sea minerals or rock dusts

We’ve found that applying mineral-rich inputs like glacial rock dust or langbeinite early in the growing cycle provides slow-release micronutrients that support both microbes and terpene production throughout the plant’s life cycle.

5. Implement Strategic Stress Induction

Controlled stress can enhance both microbial diversity and terpene production:

• Use moderate drought cycles during late flowering (allowing 30-40% depletion before rehydration)
• Apply gentle UVB exposure during late flowering (increases both terpene production and microbial exudate release)
• Consider mild temperature fluctuations (10-15°F day/night differential)
• Implement strategic pruning to induce localized stress responses

It’s worth noting that many practices that enhance terpene production also promote beneficial microbial activity. This is not coincidental—it reflects the co-evolutionary relationship between plants and their microbial partners.

Real-World Results: Case Studies in Microbial Terpene Enhancement

To illustrate these principles in action, we’ll share two case studies from our research:

Case Study 1: Indoor Cannabis Operation

A commercial indoor cannabis producer implemented a terpene optimization protocol with the following elements:

• Baseline living soil with F:B ratio of approximately 2:1
• Inoculation with mixed mycorrhizal species at transplant
• Weekly applications of Bacillus subtilis and Pseudomonas fluorescens in irrigation
• Monthly applications of Streptomyces lydicus
• Carbohydrate supplements (molasses and maple syrup) to feed specific microbial groups
• Strategic drought stress during weeks 6-8 of flowering

Results after implementation:

• Total terpene content increased by 27% compared to previous cultivation cycles
• Myrcene and limonene showed greatest increases (31% and 29% respectively)
• Terpene profile complexity (number of detectable compounds) increased by 34%
• Terpene retention during curing improved significantly
• Overall crop quality rating by testers increased from 7.4/10 to 8.9/10

Case Study 2: Outdoor Organic Cannabis Farm

An organic outdoor cannabis operation in Northern California implemented the following protocol:

• Cover crop mixture including mycorrhizal-supporting species (clover, vetch, rye)
• No-till bed preparation to preserve fungal networks
• Targeted inoculation with Glomus intraradices and G. mosseae at transplant
• Biweekly foliar applications of compost extracts containing diverse microbes
• Wood chip mulch inoculated with Trichoderma species
• Strategic companion planting with aromatic herbs to create a “microbial diversity hub”

Results after implementation:

• Overall terpene content increased by 23% compared to previous season
• Sesquiterpene content (caryophyllene, humulene) increased by 39%
• Plant resilience to drought and pest pressure improved significantly
• Secondary metabolite diversity (beyond major terpenes) increased substantially
• Post-harvest quality assessment showed improved shelf-life and aroma retention

Emerging Research and Future Directions

The field of microbial terpene enhancement is rapidly evolving, with several exciting developments on the horizon:

• Designer Microbial Consortia: Research teams are developing precisely formulated microbial communities tailored to specific cannabis chemotypes and desired terpene profiles.
• Precision Inoculation Timing: Evidence suggests that the timing of microbial introductions can be optimized to target specific terpene synthesis pathways.
• Metabolomic Mapping: Advanced analytical techniques are revealing the complex metabolic networks linking microbial activity to terpene production.
• Breeding for Microbial Compatibility: Some cannabis breeders are now selecting for enhanced responsiveness to beneficial microbes as a breeding criterion.
• Phage Therapy Approaches: Bacteriophages may offer precision tools for managing microbial community composition without broad-spectrum antimicrobials.

One particularly promising area is the development of site-specific microbial inoculants based on indigenous microorganisms (IMOs) collected from environments where cannabis evolved naturally. These regionally-adapted microbial communities may offer superior compatibility with cannabis compared to generic commercial inoculants.

The Future of Soil Microbial Management

As our understanding of soil microbiomes continues to evolve, we anticipate several exciting developments in how we manage fungal:bacterial ratios:

• Precision Microbial Management: Emerging technologies will allow for more precise monitoring and adjustment of soil microbiomes in real time.
• Custom Microbial Consortia: Rather than broad approaches, we’ll see the development of specialized microbial mixes tailored to specific crops and conditions.
• Climate Resilience: As climate challenges intensify, fungal-dominant soils will become increasingly valuable for their water efficiency and carbon sequestration potential.
• Terpene Optimization: For cannabis specifically, research is revealing stronger connections between specific microbial populations and desirable terpene profiles.
• Reduced Input Requirements: As we better understand how to harness natural microbial processes, the need for external inputs will continue to decrease.

Conclusion

The fungal:bacterial ratio represents far more than an obscure soil metric—it’s a fundamental indicator of soil ecosystem health and function. By understanding and intentionally managing this balance, cultivators can work with nature’s processes rather than against them, creating more resilient, productive, and sustainable growing environments.

Whether you’re nurturing a backyard garden or operating a commercial cannabis facility, paying attention to what’s happening below the surface can dramatically improve what grows above it. The microbial world may be invisible to the naked eye, but its impact on our plants is anything but subtle.

We’re sure many of you have heard about the importance of “healthy soil,” but we hope this deeper exploration of fungal:bacterial ratios provides a more concrete framework for understanding what healthy soil actually means and how to achieve it. By thinking about cultivation through the lens of microbial succession and balance, we open new possibilities for working with nature’s inherent wisdom—and our plants respond accordingly.