Soil Biodiversity Now Tracked Globally

Soil biodiversity is a hot topic in science. Find out how a new global database is helping to track the role of soil in fighting climate change and mass extinctions.

Being born on a farm and having spent my life in a community where we use about half of our land area for agriculture, I have a deep grasp of the role of soil. One of the first things I learned as a boy was not to call soil dirt.

The reason is that dirt implies something both lifeless and worthless. Soil, on the other hand, is a priceless living thing.

Some people prefer to refer to soil as earth and I can understand that. Just as we can see our planet Earth as one connected organism, we can think of the earth under our feet in the same way.


Soil is complex and all the things that make up soil relate to one another. Scientists think of soil as its own ecosystem, in the same way that they think of the Earth’s biosphere.

More than a million creatures live in a spoonful of soil. You’ll find over a thousand different species of minute critters in one square metre of a farmer’s field.

Plant roots feed the rest of plants from the nutrient cycling these tiny beings do. Everything depends on everything else in nature and agriculture done properly is part of the web of life.


Soil biodiversity does four things in nature. It’s a home for all those little organisms, it helps plants grow, it stores water and it adjusts our atmosphere.

As the soil does all these things, it changes too as part of the circle of life. Soil biodiversity affects the earth’s crust, the atmosphere and the biosphere and they affect soil in return.

We can find all three of the traditional states of matter in soil. The minerals and tiny life forms are solid, the water is liquid and the nitrogen, oxygen and carbon dioxide in the soil are gases.


Scientists who study soil biodiversity look at it in two broad ways. One way to think about soil is how it supports living things. The other way is to consider how soil forms and to describe and group the different kinds of soils there are.

Soil biodiversity is a hot topic these days with ecologists and geneticists. They’re thinking about soil as a microbiological community made up of tiny roundworms , bacteria and other single-celled soil microorganisms.

The trouble is that nobody thought ahead to these days of big data. As a result, the records about soil biodiversity from different places don’t have the same quality.


They’re also hard to pull together. This stands in the way of scientists finding ways to improve land management practices to build up soil quality.

Now, researchers at the Helmholtz Centre for Environmental Research in Germany have set up a global soil biodiversity database to fix this. Their announcement in last week’s edition of Nucleic Acids Research explains that the system went live last November. It holds more than 15,000 soil biological datasets from around the world.

The two main older soil biodiversity databases held all of the genetic information from more than 202,000 soil biota samples. The soil structures they sampled could be from under the sea, forest floors, grassland topsoil or from rocks.


Researchers could quickly compare their own findings on soil organic matter with what was in those databases. They saved some time by not delving into questions about the diversity of soil that someone else had already answered.

Even with the older soil biodiversity databases, users looking at microbial diversity sometimes had trouble with inconsistency. It could be anything from recording temperatures in Fahrenheit versus Celsius to the short forms samplers used to record measurements.

Bigger issues came from things like different definitions of terms like biome or food web. Dr. Ulisses Nunes da Rocha, one of the soil biodiversity study‚Äôs lead authors explains, “This makes it more difficult for interested users to further process the data.”


To start with, the team separated out marine data. That gave them a more workable database focused on soil biodiversity on land like forests, grasslands and the subsoils in 84 countries.

Dr. de Rocha went on to say, “The metadata-database helps researchers whose work centres on the terrestrial environment and who want to incorporate data of this kind into their own work.” Now, researchers looking at threats to soil biodiversity can check the database for experiments others have done and what they found.

The team calls the new soil biodiversity database TerrestrialMetagenomeDB and it’s open to everyone. Users can narrow searches based on things like origin, sample type or data source. There are 33 more filters in the advanced search.


Users can also approach the soil biodiversity database as a geographical information system. There’s an interactive map that lets users search based on topographical features.

They plan to update the new soil biodiversity database in January and July every year. This will include land-based data added to the two older systems as long as the quality is up to snuff.

Our land and water use is the primary cause of species extinction worldwide. Things like soil erosion and soil compaction from human activity destroy existing habitats and agricultural yields.

database helps scientists preserve soil biodiversity

The function of soil also includes ecosystem services like carbon sequestration to fight climate change. Courtney White discusses this as part of a strategy she calls “carbon farming” in her book, Grass, Soil, Hope: A Journey Through Carbon Country.

This new database will help scientists get to the bottom of how to preserve soil biodiversity.

Even so, it’s only the beginning. There are another 100,000 soil biodiversity datasets on hold that don’t measure up to the quality standards. The team hopes to get these cleaned up and added to their public database as well.

Part of the new story we all need to tell each other about life is that soil is a living thing. Grasping soil biodiversity builds our awareness of the interconnectedness of all life.


This new database will give scientists the information to ground our understanding of the living soil in facts and evidence. It’s all part of our growth toward one story that we can all believe in and share.

We always have more to learn if we dare to know.

Learn more
Helmholtz Centre for Environmental Research
TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes 
Food Ethics: An Embarrassment of Choices
Agricultural Biodiversity Under Threat Worldwide
Finding New Ways to Share the Land
Biodiversity Always Wins
Predators Decline First From Land Use
Mass Extinction Happening Again


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