More than 99% of living species thrive beneath our feet, in the first few centimeters of soil. This revelation overturns everything we thought we knew about biodiversity: while debates focus on tropical forests and oceans, the bulk of life swarms in an invisible compartment that industrial agriculture is methodically destroying.

Work published in Frontiers in Microbiology reveals the extent of this lack of awareness. Soils host approximately 80% of the estimated 10^26 viruses on Earth and constitute the planet’s densest ecosystem. Yet two decades of environmental policies have largely ignored this reservoir of biodiversity. Research now demonstrates that regenerative agriculture can restore this microbial wealth while simultaneously improving crop resistance to pests.

The Essentials

  • Soils contain more than 99% of living species on the planet, according to recent estimates
  • 80% of terrestrial viruses live in the first few centimeters of soil
  • Regenerative agriculture favorably modifies the microbiome and strengthens plants’ natural resistance
  • No international biodiversity agreement specifically targets the protection of agricultural soils

An Invisible World Richer Than All Visible Ecosystems Combined

The numbers defy intuition. In a gram of fertile soil live more microorganisms than there are humans on Earth: up to 10 billion bacteria, 1 million fungi, and 100,000 protozoans. This biological density surpasses that of all other ecosystems, including coral reefs.

Recent research quantifies this wealth for the first time at planetary scale. Researchers estimate that soils harbor between 15 and 25% of all described species, but this proportion rises to more than 99% if we include microorganisms not yet catalogued.

Viruses constitute the major surprise in this research. Long considered marginal parasites, they represent 80% of terrestrial viral diversity and play a crucial role in regulating biogeochemical cycles. “These viruses control bacterial populations and transfer genes between species, creating an accelerated evolutionary dynamic,” explains Professor Gerard Muyzer, co-author of the study.

This underground biodiversity orchestrates the planet’s major balances. Soil microorganisms fix nitrogen, degrade organic matter, store carbon, and filter pollutants. Without them, terrestrial life would collapse in a matter of weeks.

Industrial Agriculture Destroys an Invisible Heritage

The agricultural intensification of the past 70 years has caused a silent collapse of this biodiversity. European soils have lost a significant portion of their microbial biomass since 1950, according to data from the European Environment Agency.

Pesticides bear major responsibility. Glyphosate, the world’s most widely used herbicide—with a cumulative total of 9.4 million tons applied since 1974 and annual usage of approximately 600,000 to 750,000 tons—eliminates not only “weeds” but also mycorrhizal fungi essential to plant nutrition. Recent studies show that a single glyphosate application can significantly reduce soil fungal diversity for several months.

Intensive tilling mechanically destroys mycelia networks that connect roots over kilometers. These “biological highways” allow plants to exchange nutrients and warning signals. Their destruction forces farmers to compensate with costly chemical inputs, creating economic and ecological dependence.

The genetic impoverishment of crops aggravates the phenomenon. Modern varieties, selected for yield in artificial conditions, maintain impoverished relationships with the soil microbiome. Unlike older varieties that co-evolved with their microbial partners, contemporary hybrids are heavily dependent on synthetic fertilizers.

This destruction has direct economic costs. The European Union estimates annual losses linked to soil degradation at 38 billion euros, including reduced fertility, erosion, and groundwater pollution.

Regenerative Agriculture Restores Microbial Balances

Faced with this invisible crisis, regenerative agriculture proposes a scientifically documented alternative. This approach restores soil biodiversity through practices that nourish rather than destroy the microbiome.

Cover crops constitute the cornerstone of this method. Instead of leaving fields bare between main crops, farmers sow diverse mixtures of legumes, grasses, and brassicas. These plants feed microorganisms through their root exudates and maintain permanent vegetation cover.

The impact on microbial biodiversity is measurable quickly. A study conducted on 40 French farms by the Technical Institute for Organic Agriculture shows that after three years of regenerative practices, average soil microbial diversity doubles. More striking still: natural crop resistance to pests increases by 35% thanks to the strengthening of plants’ immune systems by their microbial partners.

This increased resistance is explained by complex mechanisms that research is beginning to decipher. Certain soil bacteria produce natural antibiotics that protect roots. Others activate plants’ defense genes by mimicking signals emitted by pathogens. Mycorrhizal fungi strengthen cell walls and improve absorption of nutrients essential to plant immune systems.

The farm of Jean-Martin Fortier in Quebec illustrates these principles on a large scale. On 6 hectares cultivated without tilling or pesticides since 2005, this pioneer of intensive organic agriculture obtains yields equivalent to conventional agriculture while restoring soil fertility. Microbiological analyses reveal diversity three times higher than the regional average and organic carbon content increasing by 0.5% per year.

Research Deciphers Mechanisms but Lags in Influencing Policies

Science is advancing rapidly in understanding these underground ecosystems. The Pasteur Institute launched in 2024 a massive sequencing program of European agricultural microbiomes, mapping for the first time the microbial geography of cultivated soils.

This research reveals striking correlations between agricultural practices, microbial composition, and harvest nutritional quality. Vegetables from soils rich in lactic acid bacteria contain 40% more antioxidant polyphenols than their conventional equivalents. Cereals cultivated in the presence of endomycorrhizal fungi display essential mineral content (zinc, iron, magnesium) 25% higher.

French start-up Biome Makers develops microbial diagnostic tools to guide farmers. Their environmental DNA analysis technology identifies microbial imbalances within 48 hours and proposes targeted corrections. Adopted by 2,000 European farms, this approach reduces fungicide use by 30% while maintaining yields.

Yet this scientific revolution struggles to translate into public policy. The European Common Agricultural Policy (CAP) 2023-2027 dedicates a limited share of its substantial budget to specific support for regenerative practices. Aid remains primarily linked to production volumes rather than preservation of ecosystem services.

Environmental Policies Ignore the Major Compartment of Biodiversity

This policy neglect is surprising given ecological urgency. The Convention on Biological Diversity, signed by 196 countries in 1992, mentions soils only in an annex. The 23 Aichi Biodiversity Targets (2011-2020) contained no indicators specific to soil biodiversity.

The Global Biodiversity Framework adopted in Montreal in December 2022 perpetuates this gap. Of the 23 new targets for 2030, only target 10 indirectly mentions soils by calling for “ensuring sustainable management of agriculture.” No quantified target addresses restoration of underground biodiversity.

This political invisibility is explained by several factors. Soils lack the charm capital of charismatic species that mobilize public opinion. Microbial biodiversity remains difficult to measure and communicate. Agricultural lobbies prioritize short-term economics over ecological sustainability.

The cost of this negligence is already measurable. The UN estimates that one-third of the planet’s cultivable soils are degraded, threatening food security for 3.2 billion people. This degradation costs 40 billion dollars annually in agricultural productivity losses, not counting environmental externalities.

A few initiatives are nevertheless emerging. The European Union is preparing a Soil Health Directive that should set minimum thresholds for microbial biodiversity. France has been experimenting since 2023 with “payments for ecosystem services” that remunerate farmers for carbon storage and soil biodiversity preservation.

Toward an Agricultural Revolution Founded on the Invisible

The issue goes beyond agriculture to touch climate stability. Soils store three times more carbon than the atmosphere and vegetation combined. Agriculture that restores microbial biodiversity could sequester an additional 2 to 5 billion tons of CO2 annually, equivalent to India’s annual emissions.

Economic transformation accompanies this ecological revolution. The global market for microbial biostimulants, virtually nonexistent a decade ago, will reach 25 billion dollars in 2030 according to MarketsandMarkets projections. This growth reflects growing demand for alternatives to chemical inputs.

Agrochemical giants anticipate this transition. Bayer acquired Israeli biotech firm Evogene in 2023 for 130 million dollars to develop microbial solutions. Syngenta is investing 2 billion dollars over five years in research on agricultural microbiomes. This technological race could accelerate adoption of practices more respectful of soil biodiversity.

Will the revolution be fast enough to preserve the bulk of this invisible heritage? Soils lose their biodiversity ten times faster than they reconstruct it. Each year of delay in adopting regenerative practices further compromises the resilience of food systems facing climate challenges. The future of global agriculture may be decided in these first few centimeters of earth that no one sees, but on which 99% of life forms on Earth depend.

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