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Soil Health: The Simple Guide to Understanding, Measuring, and Monitoring Using eDNA

The soil is the fertile layer surrounding our planet, it is the skin of our Earth –  a living, complex substance. And just like our skin protects us and breathes for us, we could not live without soil health either. Paul Valéry once said: Skin is the deepest in man. And the same applies to soil: Soil is the deepest on earth. There is a reason our planet is called Earth. Because the soil does not only host a large amount of life – it forms the basis for all terrestrial life.

Why Soil Health Matters

Our soils are a true biodiversity hotspot, with 25% of global diversity hosted by soils. In just one cup of this “dirt”, researchers have counted up to highlighting the vivid life below ground. But this life is not just worth protecting for its richness and beauty – our living soil provides vital ecosystem functions:

  • Nutrient mineralization: Microbes transform nutrients into bioavailable forms for plant uptake
  • Bioremediation: Microbial activity can detoxify from heavy metals, preventing contamination of water sources
  • Basis of the ground food chain: Small invertebrates feed on soil microbes and are, in turn, consumed by birds, etc.
  • Building up soil organic carbon: Carbon must be processed through the microbiome to build up soil organic carbon stocks

Healthy soils are characterized by their ability to provide these vital ecosystem functions – and were built up via a long biochemical process. Soils are the largest carbon storage on land, directly or indirectly providing 95% of our food.  To preserve life on Earth as we know it, including our own, soils must be protected.

Man crouched besides crops, holding soil in his hands

Measuring Soils From Below 

Since the Kunming-Montreal Global Biodiversity Framework was adopted in 2022, biodiversity and ecosystem health have finally been starting to receive the attention it deserves. However, when measuring progress in biodiversity, the methods used often mostly rely on remote sensing. This means we look at ecosystems from above and assess their health based on the parameters we can see from space. We look at canopy density, spatial parameters, land management changes – and when it comes to soil, maybe color or structure.

But this way, we overlook two points: First, our soils constitute the basis for all above-ground biodiversity, making them an integral pillar of every biodiversity analysis. Many biodiversity frameworks at the moment, however, do not include soil indicators for measuring biodiversity – or if they do, they make the analysis optional.

This is a huge problem since healthy soils, characterized by their ability to provide vital ecosystem functions such as nutrient and carbon cycling, are the base layer for healthy ecosystems. They must be understood to derive insights about the effect of land management changes and biodiversity progress.

Second, if soils are included as important pillars, they cannot be analyzed solely via remote sensing. The soil is a living, complex substance which we are only now beginning to understand – thanks to new analysis tools like environmental DNA (eDNA) and progress in science.

Valley Farm, West Wratting
Source: Valley Farm, West Wratting

Soil Data As An Early Indicator Of Carbon Trends & Biodiversity 

So soil health matters – but why should we start measuring it? It’s very simple: The soil is the basis for all above-ground biodiversity – and with that, an incredible data treasure chest. Changes in above-ground biodiversity (like an increase in a specific species, e.g., rabbits) can often be predicted far in advance by looking at changes in the Soil Food Web. While bioacoustics and camera traps can help us understand how many rabbits we can find in an ecosystem right now, they can only assist with quantifying the status quo.

But for an increase in rabbits to occur, there must be new food sources that rabbits can eat. And what birds and animals feed on, e.g., worms or plants, all have been provided for by the soil – and can be tracked by looking at the soil microbiome.

Everything starts in the soil, and everything leaves traces in the soil. Understanding changes in the soil food web allows us to predict changes early on and assess the success of, e.g., changed land management practices early in advance. What happens below ground will directly impact the above-ground ecosystem—it might just take some time for the changes to become visible in a the variety of plants, trees, animals, or birds.

But decoding soil life is not something easy, soil is the most complex substance on Earth. Changes in its functionality cannot be tracked by looking at it from above. This is why you need to zoom into the soil and look at its organic layer and at the part of the soil that lives, communicates, and constantly evolves.

This is done via analyzing eDNA from soil samples collected from the ground and comparing the organisms with a wide range of libraries. In this way, we can understand exactly what happens in the soil and how it functions and develops. This allows us to understand what is in the soil and what it does.

Understanding eDNA

But what exactly is eDNA, and how do we analyze it? Just like humans have their own genetic footprint and their unique DNA, so does our environment. Living things leave their traces wherever they are, through various secretions, skin, or hair, all containing DNA. Environmental DNA (eDNA) is nothing other than DNA released by organisms into the environment.

eDNA, which is deposited in soil, water, or even air, can be extracted and used as a barcode for the organism, enabling its identification using molecular biology tools. Companies specializing in soil MRV can extract and analyze eDNA from soil samples, providing the biological fingerprint of soils.

Using eDNA helps us to decode the soil microbiome. It enables us to understand its health and its ability to provide core ecosystem functions. A healthy soil is full of life – and an important carbon sink. With eDNA analysis, we can understand how the microbial processing unit in the soil functions and thereby derive important insights with regard to the future carbon storage potential.

We must not only understand how much carbon is stored in the soil right now (which is the standard way of looking at soil organic carbon at the moment) – but also analyze the ability of soil to continuously and effectively store carbon in the future. By assessing the soil’s carbon use efficiency (CUE), companies like Soilytix have developed a completely new early indicator allowing us to make future predictions – and change our land management practices early on according to the findings.

This video from Illumina AMEA can explain more.

To Protect Our Soil, We Must Evaluate It

Everything starts in the soil. Everything ends in the soil. But our soils are being depleted around the globe: More than 40% of global soils are degraded. The main reason for that is intensive agricultural activity.

Luckily, society is finally starting to recognize that we need to change our way of farming and that in the interest of food security and climate regulation. Regenerative agriculture must actively promote, restore, and enhance soil health. However, when it comes to promoting regenerative agriculture, often the soil is treated as a standard organism which can be treated via one-size-fits-all solutions.

However, these do not look at the soil as a living substance that always looks and functions differently, depending on your geography and geology. Even within one field, you can find many different types of soil and many different states of soil functional biodiversity.

Also, we live in a time where we only value what can be quantified. This means that in order to protect something, we need to be able to track changes and progress adequately.  Soil is usually only analyzed by its chemical parameters, while its biology is often overlooked.

But to truly assess its health, we must look at its ability to provide core ecosystem functions. We must also make better choices when it comes to land management practices. Quantifying the benefits of healthy soils and the effect of its degradation will also help us understand the tremendous costs we will face if we do not take action to protect our soils now.

Soil science

In Summary

We need to understand the soil like we now can understand human blood. Only in this way can we protect it and enhance its health, reduce pesticides, and sustainably increase yields. We can also predict future ecosystem-level developments and food chain effects.

We urgently need to act and safeguard our soils, but first, we must understand them. Our soils are not dirt; they are not just a layer one can assess from space. Our soils live – and we urgently need to get to know them.


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