This is the last post of the series.:
Phytochemical Ratios Emerge as Terroir
Ratio Control as Emergent
Plant genes encode enzymes, regulatory elements, and signaling capacity. They do not encode the final distribution of products across competing pathways under variable environmental conditions. The observed ratios among secondary metabolites arise from competing pathway flows across pathways that are themselves responsive to environmental, microbial, and physiological inputs (Fernie & Tohge, 2017; Nikoloski et al., 2015; Tohge et al., 2013). This strongly suggests ratio control is emergent.
Integrative transcriptomic–metabolomic analyses of ginsenosides (triterpene saponins) indicate that these ratio changes arise from differential regulation of shared biosynthetic pathways, where environmental inputs modulate expression of key enzymes and redirect flux between competing branches (Di et al., 2023). This leads to synchronized increases in some ginsenosides alongside decreases or redistribution in others, reflecting pathway partitioning rather than independent compound regulation. Similar patterns of coordinated accumulation and transfer of individual saponins across tissues and growth stages further support the view that ratios emerge from dynamic flux redistribution within a shared precursor pool (Li et al., 2023).
This interpretation extends to alkaloid biosynthesis, where many medicinal compounds arise from shared amino acid–derived precursors and diverge through branch-point enzymatic steps. In benzylisoquinoline alkaloid pathways, central intermediates such as (S)-reticuline are directed toward multiple end products, including berberine, morphinan alkaloids, and related structures, (Hagel & Facchini, 2013). Changes in enzyme expression or substrate availability shift flux across competing branches, resulting in altered ratios among structurally related alkaloids.
A similar pattern is observed in phenylpropanoid and flavonoid pathways, which produce a wide range of medicinal compounds including flavonols, anthocyanins, and lignans from common phenylalanine-derived intermediates. Flux partitioning at key enzymatic steps, such as chalcone synthase and downstream branch enzymes, determines the relative abundance of these compound classes, with environmental and regulatory inputs modulating pathway balance and resulting metabolite ratios (Tohge et al., 2013).
In terpenoid indole alkaloid pathways, such as those in Catharanthus roseus, monoterpenoid and indole precursors converge to form strictosidine, which then branches into multiple alkaloid classes including vinblastine and ajmalicine. The relative distribution of these metabolites depends on coordinated regulation of pathway enzymes and transport processes, demonstrating that final metabolite ratios emerge from dynamic control of shared biosynthetic networks rather than discrete genetic specification (De Luca et al., 2012).
Evidence in medicinal species under strict genetic control is limited, but model systems isolate these effects. In Arabidopsis thaliana, where genotype is held constant, variation in soil conditions and microbial community composition alters biosynthetic gene expression and shifts metabolite profiles, demonstrating that pathway output and metabolite ratios can change independently of genetic variation through microbiome-mediated regulation (Kliebenstein et al., 2001; Lebeis et al., 2015; Zhalnina et al., 2018).
The consistent observation that wild plants exhibit different metabolite ratios compared to cultivated plants can be interpreted as ratios may be appear stable within a given context but remain condition-dependent but vary across contexts. This framework clarifies why attempts to standardize medicinal plant products based on single marker compounds often fail to capture functional equivalence. If biological activity depends on interactions among multiple compounds arising from a coupled network, then controlling one metabolite does not ensure control of the system. Variation in metabolite ratios across environmental and developmental contexts is consistent with models of flux partitioning across shared biosynthetic pathways (Weng et al., 2012; Fernie & Tohge, 2017). The variability exists across multiple plant genus and phytochemical classes including Arabidopsis, Medicago, Solanum, Catharanthus, and Papaver, spanning phenylpropanoids, flavonoids, alkaloids, and terpenoids, and is consistently explained by flux partitioning across shared biosynthetic pathways under changing environmental and developmental constraints. Ratios provide more information because they show how activity is distributed across connected pathways, but they depend on the conditions shaping the system rather than being fixed outputs.
From a mechanistic perspective, emergent ratio control is supported across multiple plant systems in which measured phytochemicals derive from shared precursor pools. In Arabidopsis thaliana, flux through the phenylpropanoid pathway partitions among flavonoids, lignin precursors, and related phenolics, demonstrating competition among branches for common intermediates (Weng et al., 2012; Nikoloski et al., 2015). In Medicago truncatula, isoflavonoid profiles shift in response to symbiotic and defense signaling, reflecting coordinated regulation of pathway enzymes through hormone-mediated transcriptional control (Pieterse et al., 2012). In Solanum lycopersicum and Petunia hybrida, flavonoid and anthocyanin ratios vary with developmental and environmental cues, illustrating regulatory nodes that integrate signaling across biosynthetic branches (Chezem & Clay, 2016). In specialized metabolism, Catharanthus roseus (terpenoid indole alkaloids) and Papaver somniferum (benzylisoquinoline alkaloids) provide canonical examples where environmental and biotic inputs shift flux among structurally related compounds derived from shared precursors (Weng et al., 2012). Across these systems, nutrient status and rhizosphere-mediated interactions further modify resource availability and signaling states, altering the constraints under which these pathways operate (Badri & Vivanco, 2009; Zhalnina et al., 2018). The combined effect is the production of metabolite distributions, whether flavonoids, alkaloids, or terpenoids, that represent transient equilibria defined by interacting regulatory, environmental, and metabolic constraints rather than fixed biochemical outputs (Weng et al., 2012; Milo & Phillips, 2015).
Finding Terroir
Terroir is most usefully defined not as a descriptive attribute of place, but as a set of interacting, measurable constraints that govern plant metabolic state. Across the systems reviewed, plant chemistry does not arise from isolated variables. Root exudate’s structure microbial assembly, microbial communities feedback on host gene expression, and environmental and nutritional conditions shape carbon allocation and signaling. Together, these factors define the range of possible metabolic outcomes rather than determining any single fixed profile.
In grapevine systems, variations in soil microbiota have been associated with differences in berry composition, including phenolic compounds that contribute to flavor and quality (Zarraonaindia et al., 2015). These associations persist even when other variables are controlled, indicating that microbial community structure is a significant component of terroir. While such studies are often interpreted in terms of correlation, they are consistent with a model in which microbial communities act as part of the constraints shaping plant metabolism. Soil properties, microbial communities, and environmental conditions jointly influence plant metabolic profiles and can be treated as interacting determinants of plant chemistry (Zarraonaindia et al., 2015; Bokulich et al., 2016)..
Within this framework, microbial communities are a functional component of terroir. Controlled systems demonstrate that defined microbial assemblages can alter transcriptional programs and metabolite profiles, providing evidence consistent with causal relationships at the component level. In contrast, field observations—such as variation in grape or medicinal plant chemistry across soils—remain largely associative, even when patterns are consistent. The evidence therefore supports component-level causality embedded within system-level correlation.
Secondary metabolite profiles, and especially their internal ratios, are best interpreted as outputs of a constrained system. Across pathways drawing from shared precursors, environmental inputs, microbial signaling, and regulatory networks redistribute flux, producing coordinated shifts in related compounds. Apparent stability of ratios reflects stable conditions, not fixed biochemical programming. When constraints change, ratios shift accordingly, consistent with a model of dynamic, flux-dependent equilibrium.
Treating terroir as a set of measurable conditions has practical implications. Reproducibility in medicinal plant products requires defining and managing the key variables that shape metabolism, including soil chemistry, climate, and microbial community structure. A
The central limitation is not lack of evidence for individual mechanisms, but lack of integration. Carbon allocation, microbial composition, transcriptional regulation, and metabolite output are typically measured in isolation. As a result, the proposed distributed regulatory network remains only partially resolved, and predictive capacity is limited.
Advancing terroir from description to prediction requires integrated, flux-aware, and experimentally controlled validation. This includes simultaneous measurement of microbial communities, host gene expression, carbon allocation, and metabolite profiles; causal manipulation of microbial assemblages; and direct assessment of pathway flux and ratio shifts. Only through such approaches can the constraint system be defined quantitatively and tested for reproducibility across environments and species.
Under this interpretation, terroir becomes a governable system of constraints that defines metabolic possibility. The remaining question is whether those constraints can be sufficiently resolved and controlled to produce predictable chemical outcomes.
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