The farm as a holobiont

The farm as a holobiont: activating/stimulating biochemical pathways for agroecological regeneration

What if the farm were not a simple sum of fields, crops, inputs, and machines, but a unique living organism, endowed with its own physiology, ecological memory, and intrinsic capacity for adaptation?
This question no longer belongs solely to agricultural philosophy.
In recent years, systems biology, microbial ecology, and agroecology are converging toward a vision in which agricultural life is interpreted as an integrated system of relationships, rather than a sequence of independent technical interventions (Gilbert et al., 2012; Vandenkoornhuyse et al., 2015).

From the concept of holobiont to the eco-holobiont
The concept of holobiont describes a biological entity consisting of a host organism and the set of stably associated microbial communities, considered as a single functional unit (Bordenstein & Theis, 2015; Rosenberg & Zilber-Rosenberg, 2016).
In the agriecology field, this vision has profoundly changed the understanding of nutrition, defense, and stress adaptation, highlighting the central role of rhizosphere, endosphere, and phyllosphere microbiomes (Vandenkoornhuyse et al., 2015).
With their paper “Eco-holobiont: A new concept to identify drivers of host-associated microorganisms,” Singh, Liu, and Trivedi (2020) introduce a crucial conceptual extension: the microbiome is not merely a property of the host, but the dynamic result of ecological and management drivers such as soil, climate, biodiversity, disturbances, and agricultural practices.
The eco-holobiont thus becomes an open, flexible system, continuously reorganized by environmental conditions and decisions made by the farmer (Singh et al., 2020).

The Farm as a Holobiont
Translating this paradigm to agroecology means shifting our perspective:
the farm can itself be considered a holobiont.
A system in which:
• crops,
• soil and microbiomes,
• beneficial insects, soil fauna, and wild plants,
• water, air, and agronomic practices
do not act separately, but as a living network of biochemical and informational interactions.
From this perspective, fertility, resilience, and agroecological productivity emerge from the functional coherence of the system, not from the simple addition of external inputs (Altieri et al., 2015; Wezel et al., 2020).
Every intervention is a signal, not just an input.
If the farm is a holobiont, then every agronomic intervention becomes a biological signal.
Organic fertilizers, biostimulants, plant extracts, microorganisms, soil cultivation: everything is perceived, interpreted, and integrated by the system as a whole.
Here, however, a key distinction emerges: quantity of matter versus quality of biological information.

Dilutions: From Matter to Information
The use of biotic components of the holobiont, such as microbes and their consortia, secondary metabolites individually or as a phytocomplex, and plant extracts in highly diluted form, should not be interpreted as a reduction in effectiveness, but rather as a change in language.
Dilution:
• reduces the direct chemical impact and therefore inputs,
• limits ecological and agroecological disturbances,
• amplifies the signaling function of the biochemical stimulus.
It is not a matter of “feeding” the system, but of activating endogenous responses already present in the physiological repertoire of the holobiont (Compant et al., 2019).

Hormesis: Small Stimuli, Big Responses
This logic finds a solid foundation in the biological principle of hormesis, which describes nonlinear dose-dependent responses in which weak, nontoxic stimuli induce positive adaptations, while high doses are inhibitory or detrimental (Calabrese & Baldwin, 2003; Calabrese, 2014).
In agriculture, hormesis has been documented for:
• biotic elicitors,
• secondary metabolites,
• microbial signals,
• moderate abiotic stresses,
with effects on metabolic efficiency, defense, and resilience (Vargas-Hernández et al., 2017).

Metabolic Signaling: The Real Target
The real target of dilutions is not the direct growth of the plant, but the biochemical pathways, the metabolic pathways.
Phenols, terpenes, alkaloids, transient ROS, redox signals, and phytohormones constitute the biochemical language through which plants, microbes, and fauna communicate, recognize each other, and mutually modulate their functions (Pieterse et al., 2014; Erb & Reymond, 2019).
Dilutions:
• reactivate existing signaling pathways,
• reestablish plant-microbe-soil dialogues,
• strengthen positive feedback loops,
• reorganize the system’s metabolic priorities.

Operational Conceptual Framework
Corporate Holobiont
→ Highly Diluted Biotic Stimulus
→ Nonlinear Hormetic Response
→ Activation of the Metabolic Pathway
→ Metabolic and Microbial Cascades
→ Functional Reorganization of the Holobiont
→ Greater Stability, Resilience, and Agroecological Coherence
The above framework directly integrates the holobiont, dilutions, hormesis, and signaling into a single systemic logic, consistent with the eco-holobiont theory (Singh et al., 2020).

Why This Vision Is Crucial for Agroecology
Adopting a holobiont/agroecological vision of the farm means:
• reducing dependence on external inputs,
• enhancing internal biological resources,
• working with complex natural processes,
• building long-term resilient agricultural systems.
This is not a technical shortcut, but a shift in perspective, requiring observation, listening to the system, and the ability to interpret weak signals.

Francesco Di Lorenzo
Agronomist

Key References
Altieri, M. A., Nicholls, C. I., Henao, A., & Lana, M. A. (2015). Agroecology and the design of climate change-resilient farming systems. Agronomy for Sustainable Development, 35, 869–890. https://doi.org/10.1007/s13593-015-0285-x

Bordenstein, S. R., & Theis, K. R. (2015). Host biology in light of the microbiome: Ten principles of holobionts and hologenomes. PLoS Biology, 13(8), e1002226. https://doi.org/10.1371/journal.pbio.1002226

Calabrese, E. J., & Baldwin, L. A. (2003). Hormesis: The dose–response revolution. Annual Review of Pharmacology and Toxicology, 43, 175–197. https://doi.org/10.1146/annurev.pharmtox.43.100901.140223

Compant, S., Samad, A., Faist, H., & Sessitsch, A. (2019). A review on the plant microbiome. Journal of Advanced Research, 19, 29–37. https://doi.org/10.1016/j.jare.2019.03.004

Gilbert, S. F., Sapp, J., & Tauber, A. I. (2012). A symbiotic view of life. Quarterly Review of Biology, 87(4), 325–341. https://doi.org/10.1086/668166

Pieterse, C. M. J., et al. (2014). Induced systemic resistance by beneficial microbes. Annual Review of Phytopathology, 52, 347–375. https://doi.org/10.1146/annurev-phyto-082712-102340

Singh, B. K., Liu, H., & Trivedi, P. (2020). Eco-holobiont: A new concept to identify drivers of host-associated microorganisms. Environmental Microbiology, 22(2), 564–567. https://doi.org/10.1111/1462-2920.14900

Vandenkoornhuyse, P., et al. (2015). The importance of the microbiome of the plant holobiont. New Phytologist, 206(4), 1196–1206. https://doi.org/10.1111/nph.13312

Vargas-Hernández, M., et al. (2017). Plant hormesis management with biostimulants. Frontiers in Plant Science, 8, 1762. https://doi.org/10.3389/fpls.2017.01762