The action of bacteria in the soil
The action of bacteria in the soil is a function of the microbiological ecosystem present therein
For many years, agriculture has regarded bacteria as “specific tools.”
A strain, a function, an expected effect.
Specific bacteria are usually used to achieve:
• nitrogen fixation;
• phosphorus solubilization;
• phytohormone production;
• antagonism towards specific pathogens.
This list, however, has significant qualitative limitations.
In particular, it proposes a linear vision.
I have written several times that in agroecosystems, the responses to our actions as farmers or technicians are never linear.
They are systemic, networked, or, if you will, circular, because they are context-dependent.
Today, specifically, we know that the behavior of a bacterium in the soil depends not only on its genetic makeup, but above all on the biological context into which it is introduced (Fierer, 2017; Hartmann & Six, 2022).
Soil, therefore, is not simply a living container; it is an ecosystem –
An extremely complex, dynamic, and adaptive ecological system (Clagnan et al., 2024).
And this is precisely where one of the great misunderstandings of modern agriculture arises: thinking that a microbial inoculum consisting of a single bacterial strain can function the same way in all soils and in all contexts.
This is not the case.
The same bacterium, the same strain, can produce different effects depending on the microbiological biodiversity already present, soil structure, organic matter, pH, moisture, existing crops, the quality of root exudates, and the agronomic history of the field (Hartmann & Six, 2022; Francioli et al., 2025).
In other words, the resident microbiota profoundly influences the ability of an introduced bacterium to actually colonize the system.
And here a fundamental concept must be recalled: quorum sensing and, more generally, biochemical communication in the rhizosphere.
Microorganisms do not live in isolation. They communicate, perceive signals, and respond to signals.
They modify their behavior in relation to microbial density, the presence of the plant, and other organisms in the rhizosphere (Venturi & Keel, 2016).
Soil is not a sterile laboratory –
This is probably the most important point to understand and to make others understand.
Many microorganisms show extraordinary performance in vitro.
But when transferred to the open field, the results often become inconsistent.
Why?
Because in the soil, the introduced bacteria must compete, cooperate, adapt, communicate biochemically, and find available ecological niches in which to establish themselves.
That is, they must interact with thousands of other microbial species already present (Francioli et al., 2025).
And here a profoundly agroecological concept comes into play: the microbiological function emerges from the ecological network, not from the action of the single inoculated organism.
The plant itself can no longer be interpreted as an isolated organism.
It should be interpreted as a holobiont.
A functional unit composed of the plant and its associated microbiome (Vandenkoornhuyse et al., 2015).
A Bacillus can act as a growth promoter in biologically mature soil but be much less effective, or not at all, in degraded soil.
A Pseudomonas can support plant resilience in an agroecosystem rich in organic matter but become less effective in compacted, oxidized, and biologically poor soil.
This does not mean that the microorganism “doesn’t work.”
It means that the ecosystem capable of supporting its function is missing.
The soil microbiome is a communication system –
The most recent research shows that the microbiome is not a simple sum of microorganisms.
It is a metabolic network.
Bacteria continuously communicate through secondary metabolites, volatile organic compounds, siderophores, extracellular polysaccharides, quorum-sensing signals, and nutritional and redox exchanges (Fierer, 2017; Venturi & Keel, 2016; Clagnan et al., 2024).
In this scenario, introducing a microbial inoculum means altering a pre-existing ecological balance.
This is why modern agroecology should not limit itself to “administering individual bacteria.”
It should rather create the conditions for those bacteria to express their functions.
The real question, therefore, is not simply:
“Which bacteria should I use?”
But:
“What microbiological ecosystem should I build?”
Or, even better:
“What microbiological ecosystem is present on the farm where I need to intervene?”
Microbiological Biodiversity and Resilience –
Biologically complex soils tend to be more resilient.
More resilient to drought, oxidative stress, climate change, and plant diseases.
This happens because microbiological biodiversity increases functional redundancy, metabolic stability, ecological complementarity, and the system’s ability to adapt to perturbations (Fierer, 2017; Hartmann & Six, 2022; Clagnan et al., 2024).
A rich microbiota is not just “bigger.”
It is ecologically smarter.
And this is where Nature-Based Solutions take on a central role.
NBS must nourish not only the plant, but the entire system –
In an advanced agroecological approach, NBS cannot be considered simple technical inputs.
They must become tools for biological regeneration.
For example,
• Mature compost.
• Fermented extracts.
• Multispecies cover crops.
• Biochar.
• Mycorrhizae.
• Microbial consortia.
• Organic amendments.
• Plant extracts rich in secondary metabolites;
can profoundly alter the structure and function of the soil microbiome (Hartmann & Six, 2022; Clagnan et al., 2024).
And often the most important result is not the direct effect on the crop.
It is the reconstruction of biological complexity.
Because a biologically impoverished agroecosystem becomes fragile.
Dependent on inputs.
Metabolically unstable.
While a microbiologically active soil tends to progressively acquire self-regulation.
From microbiology to a systems vision –
The biggest mistake would be to reduce everything to simple microbial inoculation.
The real challenge is much broader.
We must move from microbiology to microbial ecology.
From a single strain to a functional consortium.
From the logic of input to the logic of relationship.
From fertilization to the biological regeneration of the system.
Therefore, the actual effectiveness of bacteria in agriculture may not depend on the microorganism we introduce, but on the agroecosystem’s ability to accommodate, integrate, and make it functional (Francioli et al., 2025).
Ultimately, biological fertility does not arise from the presence of a single organism.
It arises from the quality of the connections between all the organisms that inhabit the soil.
And this is precisely where the agronomy of the future should start.
Not from the bacterium as a product, but from the soil as an ecosystem.
Not from inoculation as an isolated solution.
But from the microbial community as a living infrastructure of fertility.
Francesco Di Lorenzo
Agronomist
Essential Bibliography
Clagnan, E., Costanzo, M., Visca, A., Di Gregorio, L., Tabacchioni, S., Colantoni, E., Sevi, F., Sbarra, F., Bindo, A., Nolfi, L., Magarelli, R. A., Trupo, M., Ambrico, A., & Bevivino, A. (2024).
Culturomics- and metagenomics-based insights into the soil microbiome preservation and application for sustainable agriculture.
Frontiers in Microbiology, 15, 1473666. DOI: 10.3389/fmicb.2024.1473666
Fierer, N. (2017).
Embracing the unknown: disentangling the complexities of the soil microbiome.
Nature Reviews Microbiology, 15(10), 579–590. DOI: 10.1038/nrmicro.2017.87
Francioli, D., Kampouris, I. D., Kuhl-Nagel, T., et al. (2025).
Microbial inoculants modulate the rhizosphere microbiome, alleviate plant stress responses, and enhance maize growth at field scale.
Genome Biology, 26, 148. DOI: 10.1186/s13059-025-03621-7
Hartmann, M., & Six, J. (2022).
Soil structure and microbiome functions in agroecosystems.
Nature Reviews Earth & Environment. DOI: 10.1038/s43017-022-00366-w
Vandenkoornhuyse, P., Quaiser, A., Duhamel, M., Le Van, A., & Dufresne, A. (2015).
The importance of the microbiome of the plant holobiont.
New Phytologist, 206(4), 1196–1206. DOI: 10.1111/nph.13312
Venturi, V., & Keel, C. (2016).
Signaling in the rhizosphere.
Trends in Plant Science, 21(3), 187–198. DOI: 10.1016/j.tplants.2016.01.005