Soil health certification & assessment

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.

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.