Decoding the Soil "Black Box": Introducing VITA SoilMicrobiome

Singapore, December 2025 – Soil is the most complex and biodiverse ecosystem on Earth. Every year on December 5, the World Soil Day, we are reminded of the enormous ecological engine beneath our feet — driving global food security, carbon cycling and climate resilience. ¹²³

Yet for decades, the microbial machinery powering these processes has remained a black box.

A single gram of soil contains tens of thousands of microbial taxa, many with distinct ecological roles. However, more than 99% of these microbes cannot be cultured², and traditional bulk metagenomics averages away crucial cell-to-cell heterogeneity. Gradients in oxygen, pH, and nutrients create micro-niches where even genetically similar microbes behave very differently.

Figure 1. Key ecological roles of soil microorganisms. This diagram illustrates the major microbial groups found in soil and their central functions in nutrient cycling, plant interactions, and environmental processes.⁴

To truly understand soil, we need to move beyond averages, into the functional reality of individual cells.

Why Soil is the "Final Frontier" for Single-Cell Biology

As highlighted by Pountain & Yanai (Science, 2025), single-cell transcriptomics is redefining how we study microbial communities today.⁵

However, soil remains the most technically challenging sample type of all: dense, heterogenous, and filled with diverse cell wall architectures and enzymatic inhibitors.⁶ Isolating intact microbial cells while preserving their native transcriptional states has been a long-standing unmet need.

Introducing VITA SoilMicrobiome

Today, M20 Genomics is proud to introduce VITA SoilMicrobiome — the world’s first high-throughput single-cell transcriptomics solution designed specifically for soil ecosystems.

VITA SoilMicrobiome Solution

Built on M20 Genomics’ proven VITA platform and powered by smRandom-seq, VITA SoilMicrobiome delivers whole-transcriptome profiling across bacteria, fungi and non-coding RNA far beyond the limits of poly(A)-based methods.

This technology unlocks a new era for soil microbiome research: multi-kingdom, unbiased, high-resolution single-cell analysis.

Case Study: Profiling the Soybean Rhizosphere

Using the full VITA SoilMicrobiome workflow, from VITApilote sample and library prep to the VITAseer analysis suite, we have generated one of the most detailed soil single-cell datasets to date:

• 5,931 microbial cells captured from a single rhizosphere sample.
• 299,033 unique genes detected in total
• Median of 124 genes per cell, enabling high-confidence subpopulation resolution (Table 1).

Table 1. Summary metrics for the soybean rhizosphere single-cell dataset

This granular resolution reveals the true diversity and functional states of microbial communities that bulk sequencing is unable to achieve.

What We Found: Hidden Microbial Structure & Function

1. Real Taxonomic Diversity: We detected both dominant species and rare functional groups as shown in Figure 2, including critical players like Nitrosospira, Pseudomonas, Mesorhizobium, and Azospirillum, all key players in nitrogen cycling and plant interaction.

2. Distinct Single-Cell Populations: UMAP embeddings cleanly separated microbial groups based solely on transcriptomic signatures, with no reference genome needed, confirming preserved transcriptional identity even in complex soil matrices.

Figure 2. Overview of captured cells and microbial composition. Left: Relative abundance of microbial taxa with >1% representation. Right: UMAP embedding of single-cell transcriptomes. Each dot corresponds to an individual microbial cell, grouped into distinct clusters based on gene expression similarity, demonstrating clear resolution of taxonomic and functional populations in the rhizosphere soil sample.

3. Functional Division of Labor

Single-cell KEGG pathway analysis revealed clear ecological specialization: (Figure 3)

• • Nitrogen Turnover: Ammonia-oxidizing bacteria enriched for amino acid catabolism.
  • Root Colonization: Specific groups (e.g., Nitrosomonas eutropha) exhibited molecular signatures for chemotaxis and membrane remodeling, which are critical for early-stage plant interaction.
  • Carbon & Energy Pathways: Specialized roles in organic matter breakdown and carbon fixation.

Figure 3. KEGG functional enrichment of microbial taxa in the rhizosphere sample. Bubble plot showing enriched KEGG pathways across major microbial clusters. Bubble size reflects the number of associated genes; color indicates adjusted p-value.

These insights highlight a multi-layered division of labor in nutrient cycling impossible to resolve with bulk methods.

A New Chapter for Soil Science

At M20 Genomics, we believe ecosystem understanding begins at the level of individual cells. With VITA SoilMicrobiome, researchers can finally observe the true functional dynamics of the soil: taxonomical, transcriptional and ecological, at single-cell resolution.

This World Soil Day, we look forward to partnering with researchers around the world to accelerate discoveries in agriculture, climate science, biogeochemistry, and environmental biotechnology.

The soil microbiome is no longer a black box.

Now, we can see its inner workings, one cell at a time.

Ready to explore the soil microbiome at single-cell resolution? Contact us at info@m20genomics.sg to learn more.

Reference:

1. Fierer, N. Embracing the unknown: disentangling the complexities of the soil microbiome. Nat. Publ. Gr. 15, 579–590 (2017).

2. Stewart, E. J. Growing Unculturable Bacteria. J. Bacteriol. 194, 4151–4160 (2012).

3. Banerjee, S. & van der Heijden, M. G. A. Soil microbiomes and one health. Nat. Rev. Microbiol. 21, 6–20 (2023).

4. Jansson, J. K., McClure, R. & Egbert, R. G. Soil microbiome engineering for sustainability in a changing environment. Nat. Biotechnol. 41, 1716–1728 (2023).

5. Pountain, A. W. & Yanai, I. Dissecting microbial communities with single-cell transcriptome analysis. Science. 389, (2025).

6. Blainey, P. C. The future is now: Single-cell genomics of bacteria and archaea. FEMS Microbiol. Rev. 37, 407–427 (2013).