Soil health certification & assessment

01Overview and value chain

Markers: [EC: Soil Deal for Europe & Horizon Europe | OECD: Soil health & biological inputs | Regulator: USDA (US), EFSA (EU), MARA (China)]

Soil health certification and assessment uses high-throughput metagenomic DNA sequencing of soil samples to generate a standardized, verifiable “passport” of microbiome composition and function — replacing subjective visual soil assessment with data that can support carbon-credit verification, biological-input recommendations and government soil-health compliance programs. Biome Makers, dual-headquartered in the US and Spain, launched BeCrop 4.0 in March 2026, a major upgrade to its AI-powered soil-intelligence platform improving DNA taxonomic assignment precision by over 30% and identifying more than 44,550 fungal species; the company’s underlying BeCrop platform was originally developed with EU Horizon 2020 funding for early biological-threat detection in agriculture. Trace Genomics, a Bay Area soil-metagenomics pioneer, was acquired by Canadian company Miraterra in July 2025 to combine molecular soil biology with Raman spectroscopy into an integrated “soil-to-table intelligence” platform. Pattern Ag continues expanding its predictive soil-pathogen and nematode testing service, having grown into cotton-specific predictive analytics for the US Delta region. Loam Bio, an Australian agricultural microbial company, markets CarbonBuilder, a fungal furrow treatment applied to wheat, barley and canola that uses root-associated fungi to sequester CO2 into stable soil carbon, with university trials demonstrating soil carbon gains as high as 9.4%. In China, the Institute of Soil Science, Chinese Academy of Sciences (based in Nanjing, tracing its origins to a 1930 soil research office), hosts the National Key Laboratory of Soil and Sustainable Agriculture and continues to publish foundational soil-health research, including 2025-2026 work on soil microbiome-function relationships for sustainable agriculture and ecosystem resilience.

The key directions of soil health certification and assessment are:

1. Metagenomic soil health passporting: next-generation sequencing (16S/ITS marker genes) of soil DNA to generate a standardized, comparable digital record of microbial community composition.
2. Predictive pathogen and pest risk scoring: using sequencing data to forecast disease and pest pressure several months ahead of visible symptoms, informing preventive input decisions.
3. Soil carbon sequestration verification: analyzing fungal-to-bacterial biomass ratios and melanized endophytic fungi content to verify that carbon has been stably fixed in soil, supporting carbon-credit issuance.
4. Government soil-health standardization: national programs (such as USDA soil-health initiatives) that fund and standardize biological soil-activity assessment methods across farms.

Sectoral value chain

[GPS-gridded soil sampling] ──> [DNA extraction] ──> [16S/ITS library prep & NGS sequencing]
                                                                        │
                                                           (Bioinformatic taxonomic & functional analysis)
                                                                        │
     [Soil regeneration & carbon credit issuance] <──── [Agronomic consulting & prescription] <───┘

Value chain levels

Cross-cutting technologies of the sector:

• Soil metagenomic sequencing: high-throughput NGS of soil DNA using 16S (bacterial) and ITS (fungal) marker genes to census the soil microbial community and decode its functional gene networks.
• Fungal-to-bacterial biomass ratio analysis: measuring the relative abundance of fungal versus bacterial biomass as a proxy indicator of soil structural stability, organic-matter turnover and carbon-sequestration capacity.
• Endophyte carbon verification: confirming the presence and activity of melanized endophytic fungi that convert plant-derived carbon into stable soil aggregates, a key evidence requirement for soil-carbon-credit certification.

02US

The United States hosts the world’s leading soil-metagenomics platforms, increasingly consolidating through acquisition and expanding into crop-specific predictive analytics.

Biome Makers’ BeCrop 4.0 upgrade, Trace Genomics’ acquisition by Miraterra, Pattern Ag’s cotton-specific expansion

• Biome Makers: launched BeCrop 4.0 in March 2026, improving DNA taxonomic assignment precision by over 30% and identifying more than 44,550 fungal species for better detection of beneficial and pathogenic organisms.
• Trace Genomics: acquired by Canadian company Miraterra in July 2025, combining Trace’s molecular soil biology with Miraterra’s Raman spectroscopy into an integrated “soil-to-table intelligence” platform.
• Pattern Ag: continues expanding its predictive soil-pathogen and nematode testing service, having grown from row-crop pathogen detection into cotton-specific predictive analytics for the US Delta region.

03CN

China channels soil health research through its national academic soil-science infrastructure, anchored by one of the world’s oldest dedicated soil research institutions.

ISSCAS’s century-old soil science mandate, national soil-health laboratory infrastructure, sustainable agriculture research focus

• Institute of Soil Science, Chinese Academy of Sciences (ISSCAS): based in Nanjing and tracing its origins to a 1930 soil research office, hosts the National Key Laboratory of Soil and Sustainable Agriculture and the National Engineering Research Center for Soil Nutrient Management and Pollution Remediation.
• Research output: continues to publish foundational soil-health research, including 2025-2026 work on the relationship between soil microbiome function and ecosystem resilience for sustainable agriculture.
• National infrastructure: operates multiple national field observation and research stations across China (including sites in Henan, Jiangxi and Jiangsu provinces), forming the backbone of China’s long-term soil-monitoring network.

04EU

The European Union funds soil-microbiome assessment technology directly through Horizon research programs and increasingly ties soil health verification to carbon-farming payment schemes.

Horizon Europe-funded BeCrop origins, EU carbon-farming certification demand, Loam Bio’s endophyte carbon verification

• Horizon Europe BeCrop origins: Biome Makers’ underlying soil-microbiome platform was originally developed with EU Horizon 2020 funding for early biological-threat detection in agriculture, illustrating direct European public investment in soil-metagenomics infrastructure.
• Carbon-farming certification demand: EU carbon-removal certification schemes increasingly require metagenomic verification that sequestered carbon is stably fixed by beneficial fungal communities rather than simply added as organic matter subject to rapid mineralization.
• Loam Bio (Australia, EU-relevant model): markets CarbonBuilder, a fungal furrow treatment for wheat, barley and canola using root-associated fungi to sequester CO2 into stable soil carbon, with university trials demonstrating soil carbon gains as high as 9.4% — a verification and product model increasingly referenced by European carbon-farming certification schemes.

05Leading companies and research institutes

06Tech stack and innovations

The soil health certification and assessment stack combines DNA sequencing with bioinformatic and carbon-verification analytics:

1. Soil metagenomic sequencing:
   • High-throughput next-generation sequencing of soil DNA using 16S bacterial and ITS fungal marker genes generates a comprehensive census of the soil microbial community, decoding functional gene networks that predict nutrient cycling and disease-suppression capacity.
2. Fungal-to-bacterial biomass ratio analysis:
   • Measuring the relative abundance of fungal versus bacterial biomass serves as a proxy indicator for soil structural stability and long-term carbon-sequestration capacity, since fungal-dominated soils typically retain organic carbon in more stable forms.
3. Endophyte carbon verification:
   • Confirming the presence and activity of melanized endophytic fungi that convert plant-derived carbon into stable soil aggregates provides the evidentiary basis required for soil-carbon-credit certification and payment.

07Value chains and production pipelines

Industrial pipeline for generating a metagenomic soil-health passport and carbon-credit verification report

┌───────────────────────────┐      ┌───────────────────────────┐
│ 1. GPS-gridded soil        │ ───> │ 2. DNA extraction &        │
│    core sampling                │      │    purification                 │
└───────────────────────────┘      └───────────────────────────┘
                                                 │
                                                 ▼
┌───────────────────────────┐      ┌───────────────────────────┐
│ 4. Bioinformatic taxonomic │ <─── │ 3. Library prep & NGS      │
│    & functional analysis        │      │    sequencing                    │
└───────────────────────────┘      └───────────────────────────┘
              │
              ▼
┌───────────────────────────┐      ┌───────────────────────────┐
│ 5. Agronomic prescription  │ ───> │ 6. Regeneration &          │
│    & carbon scoring             │      │    carbon-credit verification   │
└───────────────────────────┘      └───────────────────────────┘

Stage 1: GPS-gridded soil core sampling

Field technicians collect standardized 0-20 cm soil cores across a precision GPS grid, using automated samplers and sterile collection bags to prevent cross-contamination between sampling points.

Stage 2: DNA extraction and purification

Soil microaggregates are mechanically disrupted, bacterial and fungal cell walls are lysed with specialized extraction kits, and total genomic DNA is purified to a concentration and quality suitable for downstream sequencing.

Stage 3: Library preparation and NGS sequencing

Purified DNA undergoes 16S (bacterial) and ITS (fungal) marker-gene amplification to build sequencing libraries, which are run on Illumina or Oxford Nanopore platforms to generate raw genetic read data.

Stage 4: Bioinformatic taxonomic and functional analysis

Raw sequencing reads are filtered for noise, assembled and classified against reference databases (SILVA for bacteria, UNITE for fungi), with AI-driven analysis mapping functional gene networks into an interactive digital soil-health passport.

Stage 5: Agronomic prescription and carbon scoring

The soil-health passport data is translated into practical recommendations for biological-input dosing, cover-crop selection and tillage practice, alongside a carbon-sequestration score based on fungal-to-bacterial ratios and endophyte content.

Stage 6: Regeneration and carbon-credit verification

Farmers apply the recommended microbial consortia and regenerative practices, with follow-up sampling confirming microbiome recovery and providing the metagenomic evidence required to verify and issue soil-carbon credits.