Mycelium Propagation as Ecological Negotiation
Why does the same spawn, on the same substrate, at the same rate, sometimes produce uniform colonization and sometimes patchy failure? Why do contamination issues that were resolved at the bench scale reappear at pilot scale, even when aseptic protocols are identical? The answer lies in recognizing that propagation is not a technical handoff but an ecological negotiation.
The Ecology Beneath Propagation Pipelines
Propagation (‘myceliation’, or the ‘mycelium run’) sits at the foundation of every mycelium process, and is often treated as a technical linear formality; prepare a substrate, add a spawn, control the environment, thus myceliation. Anyone who has worked with whole-thallus mycelium production (in solid-state fermentation in particular) long enough knows this framing is incomplete. Propagation is not a neutral handoff between steps in a pipeline, it is an ecological negotiation. Mycelium does not simply expand (or ‘run’) through a substrate; it competes, occupies, modifies, and defends. It is a sequence of ecological decisions that determine whether the organism will take hold, stabilize, and ultimately produce the product we are designing to.
Two organizing principles govern this negotiation. Inoculum potential shapes the ability of a fungus to establish itself early and with enough presence to matter. Resource-capture priority effects determine what happens next, when the first wave of growth begins to set conditions that either allow or prevent anything else from entering the system (and the practical impacts of that entry, if it occurs). Together, these principles define the logic of mycelium propagation just as specific growth rate and growth velocity define the logic of fungal physicality. They are the principles that decide whether a propagation pipeline will be stable, scalable, and capable of producing consistent material outcomes.
These principles are straightforward to describe, and profoundly difficult to fully reduce to controllable and quantifiable parameters. Real substrates, real environments, and real economic constraints introduce variation that no model can completely resolve. But learning to design with these principles, acknowledging what can be quantified, what cannot, and what must be understood intuitively, is a necessary and enabling effort.
Defining Inoculum Potential
In a previous essay I framed inoculum potential as more than a dosage term; it is not simply “how much inoculum” enters the system, but the capacity to establish, expand, and dominate a substrate under the specific ecological and operational conditions. From this perspective, inoculum potential integrates at least six dimensions: (1) the quantity and viability of propagules, (2) their geometric and spatial distribution, (3) their compatibility with the substrate, (4) the timing of their introduction relative to substrate history, (5) the resource landscape they encounter, and (6) the competitive community already present or emerging.
This framing is a rational extension of how inoculum potential has been treated in classical plant pathology and mycorrhizal ecology. In soilborne pathogen work, Baker describes inoculum potential as a composite property capturing the “energy of growth” available for infection at the host surface, distinguishing it from simple inoculum density [Baker, 1981]. In this scope it often expresses the relationship as
Inoculum Potential = Inoculum Density × Aggressiveness
where density is the number or length of propagules per unit substrate, and aggressiveness is their ability to initiate infection [van Bruggen, 2015]. Conceptually, this recognizes inoculum potential as a compound ecological quantity, not a single countable thing.
In arbuscular mycorrhizal research, the same concept appears under the banner of “mycorrhizal inoculum potential.” Liu and Luo’s New Phytologist paper reviews prior concepts of inoculum potential and proposes a quantitative method in which colonization structures (vesicles, hyphae) in bioassay roots are used to estimate the effective potential of a given inoculum source [Liu, 1994]. Andrango and co-authors compare multiple operational methods (infection units, mean infection percentage, most probable number, mycorrhizal soil infectivity) to estimate inoculum potential in field soils, emphasizing that different methods capture different facets of the same underlying property [Andrango et al., 2016]. Wiseman and Wells use soil inoculum potential as a way to explain differences in mycorrhizal colonization, showing how land-use history and soil disturbance manifest as changes in effective inoculum potential rather than simply in propagule presence [Wiseman, 2005].
Importantly, several consistent themes emerge:
Inoculum potential is context-dependent. The same propagule density can yield very different outcomes depending on substrate, environment, and host; i.e. propagule density and inoculum potential are independent.
It is inherently multidimensional. Any operational measure (spore count, root colonization percentage, most probable number) is at best a partial view.
It is ultimately about realized colonization capacity, not nominal inoculum. What matters is what the inoculum can do in situ, not what it is in isolation.
Translating this into whole-thallus mycelium propagation, inoculum potential becomes the situated probability of early ecological success. A kilogram of spawn does not carry a fixed inoculum potential across substrates and processes. Its effective potential is shaped by:
Physiological state and history of the mycelium at the moment of transfer.
Geometry and distribution of inoculation within the substrate.
Temporal alignment between substrate preparation, conditioning, external controls, and inoculation, which defines the context, access, and timing of competing organisms.
Substrate ecology, including nutrient profile, moisture, pH, and pre-existing microbial communities.
In practice, we can only ever measure slices of this; spawn rate per dry weight, viability tests, colonization assays, microbial community sampling. None of these alone are inoculum potential. Instead, they are proxies that help the mycelium engineer reason about a fundamentally ecological quantity.
For propagation design, the value of inoculum potential as a concept is not that it can be perfectly parameterized, but that it forces us to ask the right questions: What is the real colonization capacity of this inoculum in this substrate, under these conditions, against this competitive background, at this point in time?
Defining Resource-Capture Priority Effects
If inoculum potential describes the probability of early establishment, resource-capture priority effects describe what happens once that establishment begins. In fungal ecology, particularly in wood decay, priority effects refer to the advantage gained by the organism that colonizes a resource first. Early colonists preempt space, consume accessible resources, and exert pressure on how later arrivals establish. In the context of mycelium propagation, these dynamics determine whether early establishment becomes stable, exclusive, and resistant to invasion, ultimately impacting the practical performance of the resultant mycelial body.
Ectomycorrhizal systems provide a clear demonstration. Kennedy and Bruns showed that when two Rhizopogon species compete to colonize Pinus muricata roots, the species that arrives first typically dominates root tips, even if the other is a strong competitor under simultaneous inoculation [Kennedy, 2005]. Kennedy and co-authors later extended this work, confirming that priority effects play a major role in early ectomycorrhizal root tip colonization more generally [Kennedy et al., 2009]. In wood-decay systems, Hiscox and colleagues explicitly tested whether the identity of the first colonist in beech wood shapes subsequent community development. Pre-colonizing beech disks with different fungi and then exposing them to the same forest floor environment produced distinct and persistent fungal communities, confirming strong priority effects in wood decomposition [Hiscox et al., 2015].
Boddy and Hiscox synthesize these threads in the broader context of saprotrophic fungi: colonization success can be divided into (i) the ability to arrive at, enter, and establish within a resource and (ii) the ability to persist there against competitors over time. Priority effects emerge when early success in (i) is amplified through processes that secure (ii) [Boddy, 2017].
Across these systems, priority effects express through four interacting components:
Physical preemption
Early mycelium occupies physical space within the resource (wood lumens, pits, fibers, pores, root tips). Once these structures are filled, later arrivals have fewer accessible entry points and pathways. In wood, early colonists effectively “claim” internal territory that newcomers must either displace or work around, often at a competitive disadvantage.Resource depletion and monopolization
Primary colonists rapidly consume readily available carbon and nitrogen resources, and begin restructuring more recalcitrant substrates (cellulose, hemicellulose, lignin) in ways tied to their own enzymatic competencies. This creates an asymmetric landscape: the founder retains internalized reserves and a customized residual substrate, while invaders encounter a depleted or chemically altered resource base.Habitat modification
Fungi modify their environment through pH shifts, redox changes, water redistribution, extracellular enzymes, organic acids, and secondary metabolites. In wood-decay communities, such modifications can persist and condition which species are able to establish later. These changes constitute niche construction: the founder not only occupies the resource but rewrites its local rules.Stochastic arrival amplified by deterministic feedbacks
Once an early colonist begins to grow, deterministic feedbacks (physical preemption, resource capture, habitat modification) amplify that initial head start into long-term dominance. This is historical contingency: small differences in arrival time lead to large differences in community outcome, not because the founder is inherently “better,” but because early growth gives it leverage over the resource and the rules of subsequent engagement. Through this lens, a well designed inoculation strategy directed to maximizing inoculum potential is realized.
In this sense, resource-capture priority effects can be understood as the ecological mechanics by which early colonization is translated into durable control of a substrate. For mycelium propagation, they describe how the fungus that wins the first wave of growth sets the conditions under which all later biological events occur.
The Logic of Propagation and the Practical Reality of Design
The combination of these core principles, inoculum potential and priority effects, defines the ecological logic of mycelium propagation. These forces are linked through a sequence: inoculum potential, expressed within a total ecological and kinetic context, produces a realized early establishment. Priority effects then act on that early establishment to determine the stability, exclusivity, and trajectory of colonization. This chain captures the true structure of propagation dynamics.
Inoculum Potential → Total Context → Realized Early Establishment → Priority Effects → Propagation Outcomes
Inoculum potential provides the probabilistic capacity for early establishment. It represents what the inoculum could do: the ability, in principle, for the fungus to initiate growth and assert a meaningful early presence. It is not self-realizing, being shaped and constrained by the conditions in which it is introduced; the substrate’s physical and chemical composition, its preparation and history, moisture and gas conditions, microbial background, the strain’s physiological responsiveness, and the geometry and timing encoded in the inoculation strategy.
Total context determines how inoculum potential becomes actualized. The same inoculum can behave differently under different substrate histories, conditioning regimes, or environmental gradients. The effective magnitude of inoculum potential (its real expression in the system) depends on how well the early context aligns with the strain’s kinetic and ecological requirements. In this step of the chain, inoculum potential and context combine to produce a realized early establishment; the actual biological foothold.
Priority effects act on the realized early establishment, not on inoculum potential itself. Once colonization begins, the mechanisms of priority effects - physical preemption, resource restructuring, habitat modification, and deterministic feedback - operate on whatever early establishment exists. If early establishment is strong and well distributed, priority effects tend to consolidate it into durable resource control. If early establishment is weak or uneven, priority effects may struggle to stabilize it, allowing competing organisms to gain influence or disrupt the developmental trajectory. In this sense, priority effects amplify or diminish what early establishment provides, but cannot create establishment where it does not exist.
Propagation outcomes emerge from the behavior of this entire chain. Two systems can differ dramatically in performance even if their inoculum potential appears similar, because their context differs, altering the realized early establishment. Conversely, two systems with identical context can diverge because their inoculum potential differs in viability, distribution, or timing. And systems with similar early establishment can diverge further based on how strongly or weakly priority effects manifest. Propagation is not strictly a linear sequence but a phase of ecological sensitivity during which small differences in any part of the chain can lead to large differences in eventual system behavior.
This causal structure also clarifies why full quantification is difficult. Each term in the chain (potential, context, establishment, priority dynamics) is inherently multidimensional. They span physical, chemical, biological, temporal, and spatial factors, many of which are nonlinear or strain-specific. Real-world substrate heterogeneity, environmental drift, microbial communities, and economic conditions introduce complexities that no single model can resolve. The chain is mechanistic, but not fully parametric.
Yet fully resolving the dimensionality of this sequence in quantitative terms is practically inaccessible. The interactions among potential, context, establishment, and consolidation span too many physical, chemical, biological, and temporal dimensions for complete parameterization. But this does not diminish the value of the framework. Instead, it clarifies where attention should be placed. Designing effective propagation pipelines means strengthening inoculum potential where feasible, shaping or stabilizing the context to allow that potential to be expressed, and ensuring that early establishment can transition into the stabilizing mechanics of priority effects. Even if the system cannot be exhaustively modeled, organizing what can be measured around an intuitive understanding of these principles improves experimental design, reinforces ecological literacy, and increases the probability of developing propagation systems that perform reliably.
Through this lens, mycelium propagation becomes a process defined by the alignment of potential, context, and consolidation. The aim is not to eliminate ecological complexity, but to engage with it: to recognize what is knowable, what is estimable, and what must ultimately be understood through intuition. Successful pipelines emerge from respecting this causal chain and designing with it in mind, rather than attempting to override or ignore the ecological reality embedded within it.
References
Baker, R. (1981). Inoculum Potential and Soilborne Pathogens: The Essence of Every Model Is Within the Frame. Phytopathology, 71(4), 363–372. American Phytopathological Society.
van Bruggen, A., with contributions from Stevenson, K. (2015). Lecture 6: Influence of pathogen on disease development: soil-borne pathogens. PLP 6404 – Epidemiology of Plant Diseases, University of Florida, IFAS. Retrieved from https://plantpath.ifas.ufl.edu/classes/plp6404/lectures/handouts/Jan26_LEC06_Influence%20of%20pathogen-%20soil-borne%20pathogens.pdf plantpath.ifas.ufl.edu
Liu, R.-J., & Luo, X.-S. (1994). A new method to quantify the inoculum potential of arbuscular mycorrhizal fungi. New Phytologist, 128(1), 89–92. https://doi.org/10.1111/j.1469-8137.1994.tb03990.x
Andrango, C., Cueva, M., Viera, W., & Duchicela, J. (2016). Evaluación de métodos para estimar el potencial de inóculo micorrízico en suelos agrícolas. INIAP – Instituto Nacional de Investigaciones Agropecuarias, Departamento de Suelos y Aguas.
Wiseman, P. E., & Wells, C. (2005). Soil inoculum potential and arbuscular mycorrhizal colonization of Acer rubrum in forested and developed landscapes. Journal of Arboriculture, 31(2), 67–72.
Kennedy, P. G., & Bruns, T. D. (2005). Priority effects determine the outcome of ectomycorrhizal competition between two Rhizopogon species colonizing Pinus muricata seedlings. New Phytologist, 166(2), 631–638. https://doi.org/10.1111/j.1469-8137.2005.01355.x
Kennedy, P. G., Peay, K. G., & Bruns, T. D. (2009). Root tip competition among ectomycorrhizal fungi: Are priority effects a rule or an exception? Ecology, 90(8), 2098–2107. https://doi.org/10.1890/08-1291.1
Hiscox, J., Savoury, M., Müller, C. et al. Priority effects during fungal community establishment in beech wood. ISME J 9, 2246–2260 (2015). https://doi.org/10.1038/ismej.2015.38
Werner, G. D. A., & Kiers, E. T. (2015). Order of arrival structures arbuscular mycorrhizal colonization of plants. New Phytologist, 205(4), 1515–1524. https://doi.org/10.1111/nph.13092
Hiscox, J., & Boddy, L. (2017). Fungal ecology: principles and mechanisms of colonization and competition by saprotrophic fungi. In C. K. Watkinson, L. Boddy, & N. P. Money (Eds.), The Fungi (3rd ed., pp. 23–51). Academic Press / Elsevier.