If we were to take a spoonful of soil, it would contain more organisms than there are people on the planet—a hidden universe of which we know only a fraction, and upon which our food and climate depend. In that tiny handful coexist bacteria, fungi, protists, nematodes, earthworms, and countless other organisms whose This activity keeps ecosystems alive and it sustains agriculture. Soil biodiversity is not a scientific curiosity: it is the silent engine of fertility, of water infiltration into the soil, and of plant health.
However, this treasure is under pressure. Climate change and certain human practices—intensive tillage, monocultures, excessive fertilizer and pesticide use, soil compaction by machinery, and urban sealing—are diminishing soil biodiversity at an alarming rate. Sources such as FAO and IPBES warn of a extinction rate between 100 and 1.000 times higher to the natural state and that soil is lost between 13 and 18 times faster than it is formed. In parallel, Europe is promoting strategies to curb this degradation, reduce inputs, and recognize the value of soil for what it is: a complex and living systemand not merely a substrate where roots can anchor.
What do we mean by soil biodiversity?
Soil biodiversity is the variety of organisms that live beneath our feet and their interactions, including species, genetic, and functional diversity, as well as the ecological niches they occupy. It encompasses everything from microbes and microfauna (less than 100 microns) to mesofauna (100 microns to 2 mm) and macrofauna (greater than 2 mm), with groups as diverse as bacteria, fungi, protozoa, mites, springtails, rotifers, tardigrades, nematodes, insect larvae, and earthworms; even plant roots are considered part of the system due to their symbiotic relationships. It is estimated that the soil harbors around a quarter of Earth's biodiversityand in general terms between a quarter and a third of all living organisms on the planet.
The reality is that we have identified only a tiny fraction of that subterranean life: approximately 80% of plants are known, but barely around 10% of the species. 1% of microorganisms of the soil. This gap in knowledge makes it difficult to assess its value and, above all, to understand how the networks that connect these beings are organized—networks that are essential for the proper functioning of the ecosystem. This intricate biological web is not static, but highly dynamic and multifunctional.
Ecosystem functions and services: why we care
The soil community carries out essential processes: it decomposes organic matter, recycles nutrients (nitrogen, phosphorus, potassium, sulfur, calcium, magnesium, and micronutrients), regulates soil structure, improves porosity and water retention, and reduces erosion. Through symbiotic and asymbiotic relationships with roots, it helps the plant to feed and defend itself, acting collectively as a natural barrier against pests and pathogensFurthermore, soil is a significant carbon reservoir, capable of sequestering it and, therefore, modulating greenhouse gas emissions.
The data provided by FAO is conclusive: soil contributes directly or indirectly to 95% of food that we consume and processes around 90% of the organic matter. In other words, without soil biota, the foundation of our food security and agricultural productivity would be severely compromised. It is no coincidence that when the soil is healthy, so are the plants and the value chain that surrounds them, from stable yields and quality even less need for supplies.
There are powerful images that help solidify this idea: in every handful of soil there can be more living organisms than stars in our galaxy. Some are ecosystem engineers, like earthworms, which They excavate galleries that facilitate infiltration and aeration, or mycorrhizal fungi, which extend the reach of the roots and improve the absorption of nutrients and water.
Warning signs: loss and threats
In the last century, significant increases in productivity have been achieved, especially since the 50s, but often without considering the ecological cost. Intensification based on deep tillage, monoculture, and synthetic chemicals acts like a boomerang: it may increase yields for a time, but it degrades the soil, reduces its biodiversity, and ultimately affects profitability. In intensively managed lands, the following have been recorded: declines of 50% to 60% in soil biodiversity, with more fragile and less resilient soils.
Erosion, salinization, compaction by machinery, loss of organic matter from crop residue removal, chemical imbalance from over-fertilization, burning of residues, inadequate irrigation—including salinization in saline soils and the use of wastewater—and biological invasions These are factors that erode soil health. Added to this is the sealing of the land (roads, buildings, parking lots), which prevents the entry of water and air and kills off the subterranean biota.
The problem is not limited to agriculture: certain livestock management practices can compact soil or trigger erosion. The FAO estimates that 33% of the world's soils are degradedA 2022 European report documents soil biodiversity losses of up to 70% in areas with intensive pesticide use and monocultures. In Europe, soil compaction has halved some earthworm populations, with all the implications this has for soil structure and fertility.
The global situation is pressing: we have already surpassed 8.000 billion inhabitants, and the response cannot be more of the same. Increasing inputs without considering the biological basis of the soil leads, in the long run, to less productive and lower-quality soils. In fact, there is evidence that soil is being lost. 13 to 18 times faster of what nature regenerates, and along with that loss, millions of key organisms disappear.
Policies and approaches that set the course
The paradigm shift is already emerging in Europe. Strategies such as Biodiversity, Farm to Fork, Circular Economy, and Soil Management are pushing towards a model that Reduces fertilizers and pesticidesIt diversifies and cares for the biological base. Behind the scenes, there is a cultural shift: the soil is no longer seen as mere inert support but is understood as a living system that demands delicate and contextualized management.
There are also symbolic milestones that help to highlight its importance. Every December 5th, World Soil Day is celebrated; the last edition fell on a Monday and served as a reminder that soil is essential for the balance of terrestrial ecosystems. On the international agenda, the COP15 on Biological Diversity—held in Montreal from December 7th to 19th—addressed overexploitation, invasive species, and the need for reduce the use of pesticides, a clear statement of intent towards a model that is more respectful of underground life.
Top-level scientific evidence
Science strongly supports the role of soil biodiversity. A study coordinated by the Pablo de Olavide University, published in Nature Ecology and Evolution, combined sampling in nearly one hundred ecosystems worldwide—from deserts to tropical forests and polar regions—with laboratory experiments to demonstrate that multiple components of soil biodiversity (from bacteria to earthworms) support key ecosystem functions.
These functions include climate regulation, soil fertility, food production, waste decomposition, and maintaining soils with lower pathogen loads and fewer antibiotic resistance genes. The study also underscores the need to identify and protect species with particular functional importance and strong connections within the food web, because their disappearance could have serious consequences. cascading effectsAnd it provides a valuable conclusion: the impact of plant biodiversity on ecosystem functioning is largely catalyzed through the biodiversity that resides in the soil.
Innovation in progress: the European project SoildiverAgro
Funded by the European Union, SoildiverAgro evaluated farming practices and systems in six soil and climate zones across Europe, with fifteen case studies focusing on potatoes and wheat, both in monoculture and diversified systems. One of the findings was the use of biostimulants based on plant growth-promoting rhizobacteria and non-mycorrhizal soil fungi: chemical inputs were reduced and soil biodiversity, fertility and potato quality were simultaneously improved, with a lower incidence of pests and diseases.
The project also reported a 40% reduction in CO2 emissions while maintaining yields and economic viability, a particularly relevant fact for the climate transition. In another case, the introduction of mycorrhizal fungi into potatoes increased soil biodiversity and improved its structure, boosting productivity and farmers' profits, while pollution decreased of water and soil thanks to less external fertilization.
To support decision-making, the consortium developed a low-cost predictive tool that estimates soil biodiversity parameters using infrared spectroscopy and climatic (rainfall and temperature) and soil (pH, organic matter, and texture) variables. This solution helps to understand the relationship between soil organisms and the provision of ecosystem services at a European scale and can contribute to the proposed EU Soil Monitoring Act, which aims to have all healthy soils by 2050.
In addition, a decision-support tool was created that integrates wheat management practices with machine learning models to estimate yield and indices of bacterial, fungal, and nematode biodiversity. The project published guidelines with best practices and a white paper with policy recommendations, facilitating the adoption of management practices that simultaneously reduce external inputs, improve biodiversity, and are cost-effective.
Conventional agriculture versus organic and regenerative agriculture
Costs of conventional intensification
Deep plowing breaks up aggregates and destroys pores, making the soil more vulnerable to erosion and reducing its capacity to store water and nutrients; compacting machinery and synthetic chemistry alter biogeochemical cycles and eliminate beneficial microorganismsMonocultures reduce the plant diversity that feeds multiple soil organisms. The result: soils that are more dependent on inputs, less resilient, and have a poorer structure.
- In intensively cultivated soils, a loss of 50%-60% of soil biodiversity.
- 33% of the planet's soils are degraded, and in Europe, the following have been reported: drops of up to 70% in soil biodiversity in regions with high pesticide use and monocultures.
- Soil compaction has reduced some earthworm populations by 50%, worsening aeration and infiltration, with increasing recovery costs.
Advantages of ecological and regenerative approaches
Organic and regenerative agriculture prioritize soil health: less tillage, cover crops, extended crop rotations, agroforestry, organic fertilizers, pasture management, and biological control. These practices promote microbial and macrofauna diversity, increase organic matter, and improve soil structure, making the system more fertile. productive and resilient.
There are figures to support this: increasing organic matter by 1% can increase water retention by about 19.000 liters per hectare, crucial in water-stressed areas. Organic farming systems have shown up to 40% more organic matter than conventional ones. In pest control, crop rotation can reduce infestations by 30-50% and increase the functional biodiversity 40%, while diversified landscapes favor pollinators, with increases of around 25%.
In the climate dimension, sustainably managed soil can sequester between 0,3 and 0,6 tons of carbon per hectare per year, and there are estimates that link a 1% increase in soil carbon with significant reductions in atmospheric CO2. Eliminating synthetic fertilizers and composting reduce N2O and CO2 emissions; these have been observed 50% decreases in N2O and 20-30% in total GHG emissions on organic farms, also improving competitiveness in markets that value sustainability.
Habitat conservation within the farm—hedges, flower strips, ecological corridors—creates shelter and food for beneficial insects and pollinators. Agroforestry, integrating trees and crops, provides shade, a microclimate, and soil improvementThese systems increase biodiversity by around 30% compared to conventional systems, and corridors can increase beneficial fauna by 60%.
Food quality and human health
The connection between healthy soil and quality food is becoming increasingly clear. Large-scale sensory analyses comparing vegetables from conventional, organic, and no-till systems have found better flavor, aroma, and texture profiles in the management practices that They protect soil biodiversityA rich soil microbiota facilitates plant nutrition and increases its content of beneficial compounds.
Higher concentrations of antioxidants such as polyphenols and vitamins (for example, increases of up to 20% in vitamin C) have been detected in organic vegetables. This translates into more nutritious foods, with the capacity to support the immune system and modulate inflammation. Scientific literature also explores how soil and human microbiota are related. diets from living soils They appear to promote a more diverse and stable gut microbiota.
Among practical tools, worm castings stand out for their ability to regenerate depleted soils, boost microbial activity, and improve soil structure. This type of input, along with biostimulants, probiotics, and agricultural prebiotics, are useful components in a strategy that aims to fertile soils and quality food.
Tools and management recommendations
The transition from discourse to action requires a menu of proven practices. Crop rotation “breaks” pest and disease cycles and distributes nutrient demands: alternating cereals with legumes, for example, improves nitrogen fixation and can increase yields by up to 20% compared to monocultures, in addition to promoting a more stable soil structure.
No-till farming or minimum tillage preserves soil architecture and its biota. In contexts with a high risk of erosion, it has reduced soil loss by up to 60% compared to intensive tillage. Combined with permanent plant cover, it helps to retain moisture already mitigating extreme weather.
Cover crops—clovers, oats, and others—protect the soil between seasons, provide roots and biomass, improve structure, and feed microorganisms. There is evidence of reductions of nearly 30% in nitrate leaching and a reduction of compaction on farms that use them systematically, reinforcing water quality and soil health.
Organic fertilizers (compost, well-rotted manure) provide slow-release nutrients, increase organic matter, and stimulate a diverse microbial community. In organic gardens, productivity increases of around 25% have been observed in the medium term, along with a improved structure and porosity of the soil versus exclusively mineral fertilization.
Agroforestry integrates trees and crops—or livestock—to generate synergies: windbreaks, shade, leaf litter, and deep roots that mobilize nutrients. In coffee and cacao, for example, a 30% increase in biodiversity and yield improvements associated with more favorable microclimates have been observed. improved soil health.
Integrated Pest Management combines biological control, cultural practices, and mass trapping (pheromones, traps) to reduce reliance on insecticides. [The following appears to be unrelated and possibly a separate document:] 40% reductions in pesticide use with IPM, keeping pests below economic thresholds and favoring natural enemies.
Promoting beneficial insects with hedges, flower strips, and insect hotels increases pollination and natural pest control; in vegetables, pollination increases of nearly 20% have been observed when suitable habitats are created. Regarding biological inputs, the following become increasingly important: biostimulants, probiotics and prebiotics that take care of the soil microbiota.
To certify sustainable agroecosystems in a context of ecological transition, robust and operational soil biodiversity indicators are needed. Initiatives like SOILBIO work to measure the effect of management practices in extensive rainfed agriculture, building metrics for biodiversity, soil function, and health—essential information for scale up regenerative practices with guarantees.
Inspiring cases and lessons learned
In the Ribera del Duero region, the inoculation of mycorrhizal fungi in vineyards has increased the absorption of water and nutrients, improved drought resistance, and allowed reduce fertilizers by 30%Microbial biodiversity and soil structure have improved, with measurable impacts on quality and productive stability.
In Galicia, farms that adopted regenerative agriculture—planned grazing, minimum tillage, crop rotation, and cover crops—have recovered degraded soils and achieved 40% increases in organic matter over five years. The presence of earthworms and microorganisms has multiplied, water retention has improved, and overall, the system resilience.
Agroforestry systems in various regions of Latin America and Europe have demonstrated average increases of 30% in biodiversity compared to conventional systems, with reductions in erosion and runoff. By creating mosaics of habitats, they provide resources for pollinators and natural predators and confer climate robustness to the farms.
Where agroecological practices have been implemented holistically—green manures, cover crops, crop rotations, and IPM—microbial activity has increased by up to 50%, and soils are better able to withstand extreme weather events. All of this confirms that agroecology not only restores soil biodiversity and reduces dependence on inputs, but also improves... productive stability.
Soil biota can withstand impacts and recover, but it has its limits. If balance is not restored after severe disturbances, we are talking about lost soils. Therefore, combining ambitious public policies, digital diagnostic tools, cutting-edge research, and field management adapted to each territory is the sensible path to guaranteeing fertile soils, stable food systems, and a more habitable climate. Caring for soil biodiversity means ensuring food, nature and climate future in a single move.