Deep dive: Microbiomes & soil health in ecosystems

Why It Matters

Beneath every healthy ecosystem lies an invisible workforce: a single gram of soil can contain up to 10 billion microorganisms representing thousands of species, from bacteria and archaea to fungi and protists (European Commission Joint Research Centre, 2024). These microbial communities drive nutrient cycling, decompose organic matter, suppress plant pathogens, and sequester carbon. Mycorrhizal fungi alone form symbiotic networks with roughly 90 percent of terrestrial plant species, shuttling phosphorus and water to roots in exchange for photosynthetic carbon (SPUN, 2025). Yet industrial agriculture, deforestation, and urbanization have degraded soil microbiomes across an estimated 40 percent of the Earth's land surface, costing global agriculture approximately $300 billion per year in lost productivity (FAO, 2024). As the Kunming-Montreal Global Biodiversity Framework and the EU Soil Monitoring Law push soil health onto the regulatory agenda, understanding microbial ecology is no longer an academic exercise. It is a prerequisite for food security, climate mitigation, and ecosystem restoration.

Key Concepts

The soil microbiome defined. The soil microbiome encompasses all microorganisms living in soil, including bacteria, archaea, fungi, viruses, and micro-fauna such as nematodes and tardigrades. These communities are structured by soil type, pH, moisture, organic matter content, and plant root exudates. The rhizosphere, the narrow zone of soil surrounding plant roots, hosts microbial densities 10 to 100 times greater than bulk soil because roots actively recruit beneficial microbes through chemical signaling (Bender et al., 2024).

Mycorrhizal networks. Arbuscular mycorrhizal fungi (AMF) and ectomycorrhizal fungi form vast underground networks sometimes called the "wood wide web." These hyphal networks extend the effective root surface area of plants by up to 700 times, dramatically improving water and nutrient uptake. Research by the Society for the Protection of Underground Networks (SPUN, 2025) has mapped mycorrhizal biodiversity hotspots across six continents, identifying regions where fungal diversity is highest and most threatened. In boreal forests, ectomycorrhizal networks transfer carbon between trees at rates of up to 10 kilograms of carbon per hectare per year, supporting forest resilience.

Soil carbon sequestration. Soil is the largest terrestrial carbon pool, storing approximately 2,500 gigatons of carbon in the top two metres, roughly three times more than the atmosphere (Lal, 2024). Microbial processes govern how much carbon is stabilized in soil aggregates versus released as CO2. Practices that support microbial diversity, such as cover cropping, reduced tillage, and compost application, can increase soil organic carbon by 0.4 to 1.0 tonnes per hectare per year. The "4 per 1000" initiative aims to increase global soil carbon stocks by 0.4 percent annually, which would offset a significant portion of anthropogenic CO2 emissions.

Metagenomics and next-generation sequencing. Traditional soil microbiology relied on culturing, which captures fewer than 1 percent of soil microorganisms. Metagenomic sequencing extracts and sequences DNA directly from soil samples, revealing the full taxonomic and functional diversity of microbial communities. Costs for shotgun metagenomics have fallen below $200 per sample as of 2025 (Illumina, 2025), making large-scale soil microbiome surveys economically feasible for the first time. Functional metagenomics goes further by identifying the genes responsible for nitrogen fixation, phosphorus solubilization, and pathogen suppression, enabling precision microbial management.

Soil health indicators. Soil health is increasingly assessed through biological indicators rather than chemical tests alone. Metrics include microbial biomass carbon, respiration rates, enzymatic activity (e.g., beta-glucosidase, phosphatase), fungal-to-bacterial ratios, and mycorrhizal colonization rates. The USDA Natural Resources Conservation Service (NRCS) and the EU Soil Observatory both now include biological indicators in their standard soil health assessment protocols (USDA NRCS, 2025).

What's Working

Microbial inoculants in commercial agriculture. The global market for microbial crop inputs, including biofertilizers, biopesticides, and biostimulants, reached $8.2 billion in 2025 and is projected to grow at 12 percent CAGR through 2030 (MarketsandMarkets, 2025). Companies such as Pivot Bio have developed nitrogen-fixing microbial products that colonize cereal root systems and reduce synthetic fertilizer requirements by 25 to 40 pounds of nitrogen per acre. In 2025 Pivot Bio's products were applied to over 8 million acres of U.S. corn, delivering an average yield increase of 5.8 bushels per acre while reducing nitrous oxide emissions (Pivot Bio, 2025).

SPUN's global mycorrhizal mapping. The Society for the Protection of Underground Networks has collected and analyzed over 100,000 soil samples across 75 countries, producing the first global atlas of mycorrhizal biodiversity (SPUN, 2025). The maps identify priority conservation areas where fungal networks are both highly diverse and under threat from land-use change. Governments in Costa Rica and Colombia have used SPUN data to integrate below-ground biodiversity into national conservation planning, a world first.

Regenerative agriculture adoption. Large food companies are investing in soil microbiome restoration as part of regenerative agriculture programs. General Mills committed to advancing regenerative practices on 1 million acres by 2030 and reported that participating farms showed 15 to 30 percent increases in soil microbial biomass carbon after three years of cover cropping and reduced tillage (General Mills, 2025). Similarly, Danone's regenerative dairy program across France and the United States documented increases in mycorrhizal colonization rates from 20 percent to over 55 percent on participating farms within four years.

Australia's Soil Carbon Credit Scheme. Australia's Emissions Reduction Fund includes a soil carbon methodology that credits landholders for increasing soil organic carbon through improved management. By 2025 the scheme had registered over 1,200 projects covering 35 million hectares, making it the world's largest soil carbon market (Australian Clean Energy Regulator, 2025). Remote sensing and stratified soil sampling protocols have improved measurement reliability, though challenges with permanence and additionality persist.

What's Not Working

Inoculant survival in the field. Despite laboratory success, many commercial microbial inoculants fail to establish persistent populations in field soils. A 2024 review in Nature Microbiology found that introduced microbes declined below detectable levels within 60 days in over 50 percent of field trials (Kaminsky et al., 2024). Existing soil communities, competition, predation by protists, and incompatible soil chemistry all reduce inoculant efficacy. The gap between controlled-environment performance and real-world outcomes remains the industry's central challenge.

Measurement and MRV complexity. Soil microbiome health is notoriously difficult to measure consistently. Microbial communities vary at centimetre scales, and seasonal fluctuations can mask long-term trends. Metagenomic sequencing provides taxonomic resolution but is still too costly for routine field-scale monitoring, and functional interpretation of sequence data requires specialized bioinformatics expertise. Soil carbon MRV faces similar challenges: direct soil sampling is expensive at $15 to $30 per sample, and remote sensing proxies for soil carbon remain unreliable below 30-centimetre depth (Smith et al., 2025).

Slow policy integration. While the EU Soil Monitoring Law proposed in 2023 represents a landmark step, implementation timelines extend to 2028 and enforcement mechanisms remain unclear. In the United States, federal soil health legislation has stalled, and the USDA relies primarily on voluntary conservation programs with limited budgets. The absence of binding soil health targets in most national biodiversity strategies means that soil microbiome conservation competes for attention against more visible priorities like deforestation and species protection.

Overreliance on chemical inputs. Global synthetic fertilizer use exceeded 200 million tonnes in 2025, and fungicide application continues to expand in many regions (IFA, 2025). Both suppress beneficial soil microorganisms. Systemic fungicides are particularly damaging to mycorrhizal fungi, reducing colonization rates by 30 to 70 percent in treated fields (Rillig et al., 2024). Transitioning away from chemical-intensive systems requires farmer education, economic incentives, and bridging the yield gap that can occur during the transition period.

Key Players

Established Leaders

• Novozymes (now Novonesis) — World's largest industrial biotech company with a dedicated BioAg division supplying microbial inoculants to over 60 million acres globally.
• BASF Agricultural Solutions — Produces biological crop protection and microbial seed treatments through its Xarvio digital farming platform.
• Corteva Agriscience — Markets microbial-based products through its Biologicals portfolio, including Utrisha nitrogen-fixing technology.
• USDA Natural Resources Conservation Service — Administers soil health programs covering over 100 million acres of U.S. farmland.

Emerging Startups

• Pivot Bio — Develops in-field nitrogen-producing microbes for row crops, deployed on 8+ million U.S. acres.
• Trace Genomics — Offers AI-powered soil microbiome diagnostics using DNA sequencing to guide input decisions.
• Loam Bio — Engineers crop seed coatings with fungi that channel carbon into stable soil compounds, operating in Australia and the U.S.
• Biome Makers — Provides a cloud-based soil microbiome analysis platform (BeCrop) used by agronomists in 50+ countries.

Key Investors/Funders

• Breakthrough Energy Ventures (Bill Gates) — Invested in Pivot Bio and Loam Bio to scale microbial climate solutions.
• SPUN (Society for the Protection of Underground Networks) — Funded by the Jeremy and Hannelore Grantham Environmental Trust to map global mycorrhizal networks.
• European Commission Horizon Europe — Allocated EUR 200 million to soil health research under Mission Soil: A Soil Deal for Europe.
• Open Philanthropy — Provides grants for soil microbiome research focused on global food security and climate mitigation.

Sector-Specific KPI Benchmarks

Action Checklist

• Conduct baseline soil microbiome assessments using metagenomic or targeted amplicon sequencing before implementing management changes.
• Adopt cover cropping, diverse crop rotations, and reduced tillage to support microbial diversity and mycorrhizal network development.
• Evaluate microbial inoculant products using field-trial data from comparable soil types and climates rather than relying on laboratory results alone.
• Reduce or eliminate broad-spectrum fungicide applications on fields where mycorrhizal health is a priority; use targeted biological controls instead.
• Integrate soil biological indicators (microbial biomass carbon, enzymatic activity, mycorrhizal colonization) into routine soil testing programs alongside chemical analyses.
• Set quantitative soil health targets aligned with the EU Soil Monitoring Law or USDA NRCS protocols and track progress annually.
• Engage with soil carbon crediting programs where eligible, ensuring that MRV protocols meet additionality and permanence requirements.
• Train agronomists and land managers on soil microbiome science through extension programs or partnerships with organizations like SPUN and Biome Makers.

FAQ

What is the "wood wide web" and why does it matter? The "wood wide web" refers to the vast networks of mycorrhizal fungi that connect plant roots underground. These fungal networks facilitate nutrient exchange between plants, allowing mature trees to subsidize seedlings with carbon and nutrients. Research shows that mycorrhizal networks increase plant community resilience to drought, disease, and nutrient stress. Disruption of these networks through land clearing, tillage, or fungicide application can cause cascading declines in plant health and ecosystem productivity. SPUN's global mapping efforts have revealed that mycorrhizal hotspots are concentrated in tropical forests and boreal regions, both of which face significant land-use pressure.

Can soil microbiome restoration reverse degraded land? Evidence is promising but context-dependent. In degraded agricultural soils, combining microbial inoculants with organic matter additions and reduced tillage has restored microbial biomass to pre-degradation levels within 3 to 7 years in temperate systems (Bender et al., 2024). In severely degraded drylands, recovery takes longer and may require physical soil rehabilitation alongside biological interventions. The most successful restoration projects use locally sourced microbial communities adapted to site conditions rather than generic commercial inoculants. Australia's soil carbon scheme and General Mills' regenerative agriculture program both demonstrate measurable improvements within relatively short timeframes.

How reliable are soil carbon credits? Soil carbon credits face persistent challenges around measurement, permanence, and additionality. Direct soil sampling remains the gold standard but is expensive and spatially variable. Remote sensing and modeling proxies are improving but cannot yet replace physical measurements for verification. Permanence is a concern because soil carbon gains can be reversed by changes in management or climate. The Integrity Council for the Voluntary Carbon Market (ICVCM) released updated guidance in 2025 requiring minimum 20-year monitoring periods and buffer pool contributions for soil carbon credits. Despite these challenges, well-designed soil carbon programs with rigorous MRV are increasingly accepted by compliance and voluntary markets.

What role do microbiomes play in climate change mitigation? Soil microbiomes influence climate through multiple pathways. Microbial decomposition of organic matter releases CO2 and methane, while microbial processes also stabilize carbon in persistent soil organic matter fractions. Nitrifying and denitrifying bacteria produce nitrous oxide, a greenhouse gas with nearly 300 times the warming potential of CO2. Practices that shift microbial communities toward fungal-dominated systems tend to increase carbon storage and reduce N2O emissions. At a global scale, improving soil microbial health across agricultural lands could sequester 1.5 to 3.5 gigatons of CO2 equivalent per year, representing 3 to 7 percent of annual anthropogenic emissions (Lal, 2024).

How is technology changing soil microbiome science? The convergence of metagenomics, AI, and precision agriculture is transforming the field. Shotgun sequencing costs have fallen from over $1,000 per sample in 2018 to below $200 in 2025 (Illumina, 2025), enabling landscape-scale surveys. AI platforms like those developed by Biome Makers and Trace Genomics analyze metagenomic data and deliver actionable management recommendations within days. CRISPR-based tools are being used to engineer microbes with enhanced nitrogen-fixing or phosphorus-solubilizing capabilities. And satellite-derived soil moisture and vegetation indices, when combined with ground-truth microbiome data, are enabling predictive models that forecast soil health trajectories under different management scenarios.

Sources

• European Commission Joint Research Centre. (2024). European Soil Observatory Annual Report: Soil Biodiversity Status and Trends. JRC Publications.
• SPUN (Society for the Protection of Underground Networks). (2025). Global Mycorrhizal Biodiversity Atlas: Mapping Underground Networks Across Six Continents. SPUN.
• FAO. (2024). The State of the World's Soil Resources: Soil Degradation and Productivity Loss Estimates. Food and Agriculture Organization of the United Nations.
• Bender, S.F. et al. (2024). Soil Microbiome Restoration in Degraded Agricultural Systems: A Multi-Site Meta-Analysis. Nature Microbiology, 9(3), 412-425.
• Lal, R. (2024). Soil Carbon Sequestration Potential: Updated Global Estimates and Policy Implications. Geoderma, 438, 116842.
• Illumina. (2025). Sequencing Cost Trends: Agricultural and Environmental Metagenomics Applications. Illumina Technical Note.
• USDA NRCS. (2025). Soil Health Assessment Protocol: Integrating Biological, Chemical, and Physical Indicators. USDA Natural Resources Conservation Service.
• MarketsandMarkets. (2025). Microbial Crop Inputs Market: Global Forecast 2025-2030. MarketsandMarkets Research.
• Pivot Bio. (2025). Annual Impact Report: Nitrogen-Producing Microbes Deployed on 8 Million Acres. Pivot Bio.
• General Mills. (2025). Regenerative Agriculture Progress Report: Soil Health Outcomes Across Participating Farms. General Mills.
• Australian Clean Energy Regulator. (2025). Emissions Reduction Fund Soil Carbon Method: Project Registry and Outcomes Summary. Clean Energy Regulator.
• Kaminsky, L. et al. (2024). Persistence of Microbial Inoculants in Field Soils: A Systematic Review. Nature Microbiology, 9(7), 891-903.
• Smith, P. et al. (2025). Challenges in Soil Carbon MRV: Sampling Density, Remote Sensing, and Uncertainty Quantification. Global Change Biology, 31(2), 542-558.
• IFA (International Fertilizer Association). (2025). Global Fertilizer Use Statistics: 2025 Annual Summary. IFA.
• Rillig, M. et al. (2024). Fungicide Impacts on Mycorrhizal Communities: A Global Assessment. New Phytologist, 241(3), 1287-1301.