The Life Beneath Our Feet: Organic Matter and Soil Biodiversity

The ground beneath your feet is far from lifeless. It is one of the most biologically active ecosystems on the planet. According to the FAO, soils are home to more than 25 percent of our planet’s biodiversity, and a single tablespoon of soil contains more living organisms than there are people on Earth. At the heart of this underground ecosystem lies soil organic matter (SOM) – a dynamic mix of living and dead materials that fuels nutrient cycling, supports soil structure, and sustains a staggering diversity of organisms. Understanding SOM and the creatures that depend on it is fundamental to understanding how ecosystems function and how we grow our food.

What is soil organic matter? 🔗

Soil organic matter is the organic component of soil made up of plant and animal residues at various stages of decomposition, living organisms, and substances produced by those organisms. It typically makes up a small fraction of total soil volume – often between 1% and 6% in agricultural soils – but its influence on soil health is disproportionately large.

SOM can be broadly divided into three categories. Active organic matter consists of recently deposited materials like fresh plant roots, leaf litter, and animal residues that are still being broken down. This fraction is the primary food source for soil microorganisms. Slow organic matter includes partially decomposed materials that are somewhat resistant to further breakdown. And humus, the most stable fraction, is highly decomposed material that persists in soil for decades or even centuries. Research from the University of Minnesota Extension highlights that most of the active organic matter cycling through soil originates from plant roots rather than aboveground residues.

Why does SOM matter so much? 🔗

SOM affects the physical, chemical, and biological properties of soil simultaneously. Physically, it binds mineral particles into aggregates, improving soil structure, water infiltration, and aeration. Chemically, it serves as a reservoir for essential plant nutrients – particularly nitrogen, phosphorus, and sulfur – and enhances the soil’s ability to retain nutrients through cation exchange capacity (CEC). The University of Missouri Extension notes that soil organic carbon, the main component of SOM, acts as a unifying metric for evaluating changes in soil health over time, since it drives the biological, chemical, and physical processes that underpin soil productivity.

From an ecological perspective, SOM also plays a major role in the global carbon cycle. According to SARE (Sustainable Agriculture Research and Education), soil organic matter holds an estimated four times as much carbon as all living plants, and the total carbon stored in soils worldwide is two to three times the amount found in the atmosphere. When soils lose organic matter – through intensive tillage, deforestation, or erosion – that stored carbon is released as CO₂, contributing to climate change.

Mineralization vs. immobilization: the nutrient tug-of-war 🔗

One of the most important processes in soil is the conversion of nutrients locked in organic matter into forms that plants can actually absorb. This process – and its opposite – form a constant push-and-pull that determines how much nutrition is available to growing crops at any given time.

What is mineralization? 🔗

Mineralization is the process by which soil microorganisms decompose organic matter and release nutrients in simple, inorganic (mineral) forms that plants can take up. For example, organic nitrogen in dead plant tissue gets converted first to ammonium (NH₄⁺) and then, through nitrification, to nitrate (NO₃⁻). Similarly, organically bound phosphorus and sulfur are released into plant-available mineral forms during decomposition. Penn State Extension explains that weather plays a significant role in this process, as microbial activity accelerates in warmer, well-drained soils and slows considerably in cold or waterlogged conditions.

What is immobilization? 🔗

Immobilization is essentially the reverse. When soil microbes are breaking down organic material that is rich in carbon but low in nitrogen, they need more nitrogen than the material itself provides. So they absorb inorganic nitrogen (ammonium and nitrate) from the surrounding soil and lock it into their own biomass. This temporarily reduces the pool of plant-available nitrogen, which can lead to nutrient deficiency in crops.

The C:N ratio: the deciding factor 🔗

Whether mineralization or immobilization dominates depends largely on the carbon-to-nitrogen (C:N) ratio of the organic material being decomposed. The C:N ratio of soil microbes themselves is approximately 8:1 to 10:1, and they function best when their food source has a C:N ratio around 24:1.

Here is how it works in practice:

C:N ratio below ~25:1 → The organic material has enough nitrogen to satisfy microbial needs, and excess nitrogen is released into the soil as mineral nitrogen. This results in net mineralization. Young legume residues, with C:N ratios around 15:1 to 17:1, are a good example – they release available nitrogen almost immediately upon decomposition.

C:N ratio above ~30:1 → The organic material does not contain enough nitrogen for the microbes. They pull inorganic nitrogen from the surrounding soil to meet their needs, resulting in net immobilization. Materials like wheat straw (C:N around 80:1) or sawdust are classic examples. South Dakota State University Extension explains that when such high-carbon residues are incorporated into soil, they can temporarily make it harder for crops to access nitrogen.

C:N ratio between 25:1 and 30:1 → This is a transitional zone where mineralization and immobilization roughly balance each other out.

The good news is that immobilization is temporary. As microbes continue to decompose carbon and respire CO₂, the C:N ratio of the remaining material gradually drops. Eventually, microbial demand for nitrogen decreases, and mineralization takes over, releasing the previously locked-up nitrogen back into the soil.

The soil food web: organisms that make it all happen 🔗

SOM would just sit there doing nothing if it were not for the vast community of organisms that break it down, transform it, and redistribute it. SARE estimates that the living organisms in the top 6 inches of an acre of soil with 3% organic matter weigh about 1.5 tons – equivalent to two Holstein dairy cows. This underground community ranges from microscopic bacteria to visible earthworms and insects, and each group plays a distinct role.

Bacteria: the tiny powerhouses 🔗

Bacteria are the most numerous organisms in soil. A teaspoon of productive soil can contain anywhere from 100 million to 1 billion individual bacteria. Despite being microscopically small – comparable in size to clay particles – their combined biomass in a single acre of soil can equal the weight of two cows.

Ohio State University’s fact sheet on soil bacteria explains that these organisms are directly involved in recycling carbon, nitrogen, phosphorus, and sulfur. Specific groups of bacteria perform specialized functions: nitrogen-fixing bacteria convert atmospheric nitrogen into forms plants can use, while nitrifying bacteria convert ammonium to nitrate. Bacteria also produce polysaccharides that help cement soil particles into microaggregates, directly improving soil structure.

Because bacteria are small and reproduce quickly, they can adapt rapidly to changing environmental conditions. They tend to dominate in tilled or disturbed soils, where conditions favour fast-cycling organisms over slower-growing fungi.

Fungi: the network builders 🔗

Fungi are the second major group of soil microorganisms, and they are especially important for decomposing tough, carbon-rich materials like lignin and cellulose that bacteria struggle to break down. Fungi grow as long, thread-like structures called hyphae, which can extend far beyond the root zone and create vast underground networks.

Mycorrhizal fungi form symbiotic partnerships with plant roots. The fungus extends the plant’s effective root system, helping it access water and nutrients – especially phosphorus – from a much larger volume of soil. In return, the plant supplies the fungus with sugars produced through photosynthesis. Oregon State University Extension notes that fungi tend to dominate in undisturbed soils, such as those under no-till or reduced-tillage management, because their hyphal networks are easily destroyed by ploughing.

Protozoa and nematodes: the nutrient recyclers 🔗

Protozoa are single-celled organisms that primarily feed on bacteria. As they consume bacteria, they excrete excess nitrogen as ammonium – a plant-available form. This makes protozoa an important part of the nutrient mineralization pathway.

Nematodes are tiny, unsegmented worms found throughout the soil. While some species are plant parasites, the majority are beneficial. Bacterial-feeding and fungal-feeding nematodes contribute significantly to nutrient cycling. SARE reports that nematode feeding may account for 50% or more of the mineralized nitrogen in soil – a remarkable contribution from organisms invisible to the naked eye.

Earthworms: the ecosystem engineers 🔗

Earthworms are perhaps the most well-known soil organisms, and for good reason. Charles Darwin himself called them one of the most important animals in the history of the world. The Earthworm Society of Britain describes their primary function as breaking down dead organic matter and making its nutrients accessible to bacteria, fungi, and plants. They do this by ingesting organic material and soil, grinding it in their guts, and excreting nutrient-rich castings.

Beyond decomposition, earthworms profoundly influence soil structure. Their burrows create channels that improve water infiltration and aeration, and their castings help form stable soil aggregates. Science Learning Hub (New Zealand) reports that when earthworms are introduced to soils that previously lacked them, water infiltration rates can increase up to tenfold. Earthworms also enhance microbial activity – soils with earthworms generally contain more active bacteria and fungi than soils without them.

How soil organisms work together: the soil food web 🔗

No soil organism works in isolation. They are all connected through a complex network of feeding relationships known as the soil food web. Plants provide root exudates and residues that feed bacteria and fungi (primary consumers). Protozoa and nematodes feed on bacteria and fungi (secondary consumers), releasing nutrients in the process. Predatory nematodes, mites, and other small arthropods feed on the secondary consumers (tertiary consumers). At every level, nutrients are transformed and recycled.

This food web is not just about nutrient cycling. It also provides natural disease suppression. A diverse microbial community creates competition for resources and space, making it harder for any single pathogenic organism to dominate. Some fungi actively trap and kill nematodes, while others produce antibiotics that suppress harmful bacteria. The more diverse the soil food web, the more resilient the soil ecosystem becomes.

The German Federal Environment Agency emphasises that biological processes in soil ecosystems integrate plant residues, break them down, and release fixed nutrients as minerals available for plant uptake. At the same time, these organisms help create favourable physical conditions, tying together organic matter management and soil structure improvement into a single, interconnected system.

Threats to soil organic matter and soil biodiversity 🔗

Despite their importance, soil organic matter and soil organisms face serious threats from human activities. Intensive tillage physically disrupts fungal networks and earthworm burrows, accelerates organic matter decomposition, and exposes previously protected carbon to oxidation. Monoculture farming limits the diversity of organic inputs, reducing the range of food sources available to soil organisms and narrowing microbial diversity. Excessive use of synthetic pesticides and fertilisers can suppress beneficial organisms and reduce the soil’s natural capacity for nutrient cycling.

Practices that support SOM and biodiversity include reduced or no-till systems, diversified crop rotations, cover cropping, composting, and the application of organic amendments like manure and biochar. These approaches maintain a steady supply of organic inputs, protect soil structure, and encourage the development of a diverse, resilient soil food web.

Why this matters for sustainability 🔗

Soil organic matter and the organisms that process it are not just technical topics for soil scientists. They are central to global challenges including food security, climate change, and water quality. Healthy, biologically active soils grow more nutritious food, sequester more carbon, filter water more effectively, and resist erosion and drought better than degraded soils.

Investing in soil health – by protecting and building organic matter and supporting soil biodiversity – is one of the most effective strategies available for creating sustainable agricultural systems. It is a long-term investment, but one that pays dividends for generations.

What do you think? How much attention does your local farming or gardening community give to the life beneath the soil surface? And if soil organisms are responsible for so many critical ecosystem functions, should policies do more to protect soil biodiversity alongside aboveground wildlife?

References

1. https://www.fao.org/global-soil-partnership/resources/highlights/detail/en/c/1309274/
2. https://extension.umn.edu/soil-management-and-health/soil-organic-matter-cropping-systems
3. https://extension.missouri.edu/publications/g9071
4. https://www.sare.org/publications/building-soils-for-better-crops/what-is-organic-matter-and-why-is-it-so-important/
5. https://extension.psu.edu/immobilization-and-mineralization-of-nitrogen-in-agricultural-soils
6. https://extension.sdstate.edu/carbon-nitrogen-ratio-healthy-soils
7. https://www.sare.org/publications/building-soils-for-better-crops/the-living-soil/
8. https://ohioline.osu.edu/factsheet/anr-36
9. https://extension.oregonstate.edu/catalog/em-9409-understanding-soil-health-biota-farms-gardens
10. https://www.earthwormsoc.org.uk/earthworm-function
11. https://www.sciencelearn.org.nz/resources/9-earthworms-role-in-the-ecosystem
12. https://www.umweltbundesamt.de/en/topics/soil-land/land-a-precious-resource/soil-biodiversity-loss