Far below what we see on the surface, the ground harbors a a vast network of microorganisms that acts as a true natural immune systemThis underground biodiversity not only sustains the fertility of the fields, but also helps to protect both crops and human health from dangerous bacteria.
Two major international studies, co-led by the Institute of Natural Resources and Agrobiology of Seville (IRNAS-CSIC)They have quantified and mapped this protective role. After analyzing more than 1.600 soil samples from 59 countries, scientific teams have demonstrated that soils with a diverse microbiota contain fewer pathogens capable of harming plants and people, and have produced the first global atlas of soil pathogenic bacteria.
A “natural shield” that starts in the ground
The research, published in Nature Communications and Cell Host & MicrobeThey agree on a key idea: when the soil harbors a rich and balanced microbial community, it acts as a shield that prevents the establishment and spread of harmful bacteria. This is very similar to what happens with the microbiota of the skin or digestive system in animals and humans.
According to the IRNAS-CSIC researcher Miriam Muñoz RojasIn the so-called "microbiome era," it has been proven that the biological defense we see in our own bodies has its equivalent under our feet. A diverse soil microbiota makes it difficult for pathogens to find a place to colonize and limits their ability to multiply to dangerous levels.
During field and laboratory work, the scientific teams analyzed 1.600 soil samples from 59 countries from all continents. From this data they generated 1.602 metagenomes, that is, massive sets of microbial genetic information extracted directly from the soil, which have made it possible to identify both beneficial bacteria and potentially pathogenic species.
The result is a global atlas of bacterial soil pathogens This map shows where they are concentrated, how they relate to the climate, and how microbial biodiversity responds. This global map, in which Spanish researchers played a prominent role, opens the door to new monitoring and prevention systems in both agriculture and public health.
Microscopic guardians: Actinobacteria and Bacillota
One of the most striking findings is the central role of two major bacterial groups that act as true “natural guardians” of the soil: Actinobacteria and Bacillota (a broad group that includes numerous species of the genus Bacillus, among others).
Actinobacteria They are notable for their ability to naturally produce a wide variety of chemical compounds—some similar to antibiotics—capable of inhibiting or eliminating pathogenic bacteria. Many of the molecules used in human and veterinary medicine to combat infections were originally discovered in these types of microorganisms found in the soil.
BacillotaThese beneficial bacteria, for their part, outcompete pathogens: they vie for physical space, consume available nutrients, and prevent harmful bacteria from establishing themselves comfortably. In soils where these "allies" are abundant, the likelihood of pathogenic bacteria proliferating decreases significantly.
The abundance of these microscopic guardians can increase for various reasons, such as contribution of organic matter of animal or human originCertain agricultural practices that favor microbial life or the arrival of wind-borne spores can contribute to this. When the system is functioning well, the community of beneficial microorganisms keeps problematic species in check.
However, in degraded soils or with low microbial diversityThe balance is disrupted. The lack of natural competitors and regulators allows pathogens to easily establish themselves, integrate into the soil microbiome, and increase their presence to levels capable of threatening agricultural production and, in certain contexts, human health.
Direct protection of key crops such as tomatoes, potatoes, and rice
The results of the study published in Nature Communications show that the Soils with greater bacterial biodiversity are more resistant to pests and plant infectionsIn particular, this protective effect has been observed in crops that are strategic for global food security, such as tomatoes, potatoes, and rice, and in systems of ecological production.
In plots with rich microbiota, the pathogens that affect these plants are clearly limited. The presence of Actinobacteria and Bacillota, along with other beneficial microorganisms, prevents invasive bacteria from reaching sufficient densities to trigger epidemics in the fields.
When the soil is impoverished by the intensive use of agrochemicalsWith aggressive tillage or loss of organic matter, the scenario changes. Pathogens encounter less competition and find it easier to establish themselves.This increases the risk of disease outbreaks that can ruin entire harvests and reduce food availability.
According to the leader of the Biodiversity and Ecosystem Functioning Laboratory (BioFunLab) at IRNAS-CSIC, Manuel Delgado BaquerizoPromoting native soil biodiversity is a promising way to reduce dependence on chemicals and foster more resilient crops. The idea is to harness the soil's own ecological processes to control infections, rather than systematically using pesticides and antibiotics.
From a European perspective, this approach fits with the EU strategies aimed at more sustainable agriculturewhich reduces the use of pesticides and promotes nature-based solutions. Protecting and restoring soil life is emerging as an essential element for sustaining production in key agricultural regions, such as Spain, which are highly exposed to water stress and the effects of climate change.
When the soil also takes care of human health
The work published in Cell Host & Microbe expands the approach and demonstrates that the Soil biodiversity also protects peopleThe researchers identified 80 potentially pathogenic bacterial species for humans present in soils around the world, of which 25 were considered dominant for appearing in 80% of the samples analyzed.
These bacteria include well-known names such as Mycobacterium tuberculosis (causing tuberculosis), different types of Salmonella o Bacillus anthracis, responsible for anthrax. Although many of these species behave as opportunistic pathogens —that is, they only cause serious problems when conditions favor them or when they find weakened organisms—, their control is a priority from the point of view of public health.
According to Delgado Baquerizo, Many pathogenic bacteria live naturally in the soil without necessarily causing disease. The determining factor is the context: if the soil is diverse and healthy, the microbial community as a whole limits their proliferation. If the ecosystem degrades, the balance tips in favor of these at-risk species.
This behavior has direct implications for rural and agricultural areas, where there is closer contact between soils, food, and population. Fresh produce from contaminated soils or poorly managed, they can act as an entry point for pathogens into the food chain, particularly where hygiene practices and post-harvest treatment are insufficient.
The authors emphasize that human health and environmental health are closely linked. Caring for the soil's microbial biodiversity translates not only into more stable harvests, but also into a first line of health defense at an ecosystem scale, especially relevant in a context of increasing antibiotic resistance and the emergence of new diseases.
Rain, heat and climate change: factors that tip the scales
The global atlas compiled by the researchers also allows us to understand how climatic conditions influence the presence of dangerous bacteria. The data points to the rain as the most determining factor: 82% of the dominant pathogens show a clear correlation with rainfall.
Increased soil moisture facilitates both the movement and survival of these microorganisms. In moist soils, pathogens can move more easily through the pores, reach new roots, or emerge at the surface. Hence, Humid and tropical ecosystems concentrate higher levels of risky bacteria, as reflected in the atlas.
Temperature is the other major factor. As the thermometer rises, Many pathogenic bacteria increase their growth rateThis translates into larger populations and a greater likelihood of infection. This pattern is concerning in the current context, given that climate change is raising average temperatures and altering rainfall patterns across much of the planet.
The predictive models developed from the atlas suggest that, in future climate scenariosThe proportion of dominant pathogenic bacteria will increase in many regions, especially in tropical and subtropical areas. Although Europe and Spain are not located in these climatic zones, the progressive increase in heat waves and extreme weather events makes it necessary to be attentive to possible changes in the soil microbiota.
Given this scenario, the authors believe that the results provide a solid scientific basis to strengthen preventive surveillance systemsIntegrating information on soil microbiota, climate, and the presence of pathogens can help anticipate disease outbreaks, adjust agronomic practices, and guide public health and environmental policies.
Nature-based agriculture: strengthening the soil's "immune system"
Beyond the diagnosis, the work co-led by IRNAS-CSIC points to a change in approach to agricultural management. The key lies in apply nature-based agricultural strategiesthat strengthen soil biodiversity instead of damaging it.
Among the practices that favor this recovery are the regular contribution of organic matter (compost, well-managed manure, crop residues), the maintenance of plant cover, and the reduction of intensive tillage. All of these help create a more stable and rich environment for microbial life, which is essential for Actinobacteria, Bacillota, and other beneficial microorganisms to perform their protective role.
Also key are crop rotations and plant associationswhich prevent nutrient depletion and break the cycles of specific pests. The integration of trees and hedgerows into agricultural systems, through agroforestry, improves soil structure, provides shade, and promotes deep roots that mobilize nutrients from lower layers. Furthermore, the presence of auxiliary fauna It helps with the biological control of pests and promotes ecosystem stability.
Conversely, the intensive use of synthetic fertilizers and broad-spectrum pesticides It damages the soil's "natural guardians". and can create an ecological vacuum that pathogens exploit. The gradual reduction of these inputs, in line with European sustainability strategies, is emerging as a necessary step to restore the biological functionality of agricultural soils.
For Mediterranean regions like Spain, where the Recurrent drought and erosion These are chronic problems; investing in regenerative agriculture focused on soil life can make the difference between vulnerable systems and systems capable of adapting to new climatic conditions without losing productivity or compromising public health. The dissemination of practices from agroecology is key in this process.
A strategic resource in the face of the climate and health crisis
Soils harbor more than 25% of the planet's biodiversity and concentrate a substantial part of its biomass. Despite this, it is estimated that We only know a tiny fraction of the microbial species that live undergroundWhat recent studies do show is that this invisible life is crucial for tangible issues such as the food that reaches our table or the appearance of certain diseases.
By protecting the soil's microbial biodiversity, several ecosystem services are strengthened simultaneously: food production, water regulation, carbon sequestration, and natural pathogen controlIn a climate change scenario, this multifunctionality makes soil a strategic resource that should be cared for with special attention.
The authors of the studies insist that the work has only been possible thanks to a broad international collaboration networkThis has allowed for the integration of data and methodologies from multiple regions of the world. This scientific cooperation is fundamental not only for identifying global patterns but also for designing solutions tailored to each territory.
Looking ahead to the coming decades, the available evidence points in a clear direction: maintain and restore soil biodiversity It will be essential for maintaining food security, reducing the risks associated with pathogenic bacteria, and increasing resilience to global warming. Caring for subterranean life means, in practice, reinforcing a silent but crucial layer of protection upon which much of our well-being depends.
