Uncovering the hidden life in soil

By looking at the eDNA present in the soil of each site, we’ve found thousands of fungi, bacteria and insects as well as a whole range of new species we know nothing about called dark taxa.

What is eDNA?

As organisms move around, they leave behind traces of their DNA known as environmental DNA or eDNA for short. This eDNA can then be sampled from the air, water or surfaces such as a building wall or flower petals.

‘We can identify organisms from the traces of DNA they leave in their environment using DNA barcoding,’ says Sam Thomas our UK Biodiversity Officer.

‘We can barcode an individual specimen, seek DNA from a single species in a sample or extract and sequence all of the DNA present in a sample using a process known as meta-barcoding,’ he adds.

Collecting urban soil samples 

We’ve taken soil from urban sites around the UK. These include grassy patches in Glasgow and Newcastle, urban nature reserves in west Kent and chalk grasslands in London. 

We’ve also sampled a wildlife meadow and a mowed lawn at the National Museum of Wales in Cardiff.

When Sam travels to these places, he meets up with local volunteers or researchers.  

‘We want to make sure that the methods we are developing in the Museum are practical and relevant all over the UK,’ says Sam. 

His work involves digging little holes in the soil as well as taking water samples from creeks. With our community partners, Sam also puts up a small insect traps.

Last year, transporting the samples back to the Museum proved the most challenging part of the experience. Making sure that that frozen samples stayed frozen on the road was difficult, as was organising a way of transporting the samples that were stored in ethanol, given the flammability of pure alcohol.

After the samples finally made it back to London, Sam and his team at the Museum have been analysing the tiny life living within them. 

What did we find living in the soil? 

We found a vast range of life living in our urban sites. Across the soil samples from six urban nature reserves we found eDNA from between 650 and 1,200 animals, plants, fungi and protists as well as 800–1,900 types of bacteria.

Put another way, the eDNA found in the soil spans 34 phyla of plants, animals, fungi and protists, including a bewildering range of microscopic life. 

Finding bacteria 

We found a great diversity of bacteria living in the soil, including:

• proteobacteria – a group of bacteria that ranges from pathogens to nitrogen-fixing bacteria in plants
• actinobacteria – a group of bacteria that is fundamental to soil fertility and helps with nutrient cycling and nitrogen fixation in plants
• firmicutes – a highly varied group of bacteria that helps to promote plant growth and with the biocontrol of plant pathogens
• planctomycetes – these bacteria are central to the nitrogen cycle and are involved in anaerobic oxidation of ammonium
• acidobacteria – we still don’t fully understand the ecological function of this common soil bacteria group.

Finding fungi

We’re often finding more than 50 different species of fungi in a single soil sample. This includes species such as the colourful waxcap fungi that are associated with ancient grasslands.

Finding dark taxa

As we expand the ways we study soil life, it’s easy to see how much we don’t know about what lives in one of the most biodiverse ecosystems on the planet.

Much of the life we’re finding in soil can’t be seen with our eyes or even under a microscope. But by looking at eDNA, we can uncover life that was previously unknowable. 

‘We’re finding whole groups of organisms that we know very little about as well as numerous species that haven’t been properly described and are only known from their DNA. We call these dark taxa,’ says Sam.

A taxon – plural taxa – is a taxonomic grouping at any rank. So, this could be a species, genus, family or any higher rank such as an order or class of organisms.

‘Now we can see a whole range of new groups in soil, we need to know the role these groups have in the ecosystem,’ he adds.

A new way of looking at biodiversity

eDNA is still a relatively new way of looking at biodiversity and we still don’t understand its full potential. 

Our researchers are looking at how eDNA can be used, including understanding what a typical eDNA signal for different habitats might look like and what indicates good biodiversity.

‘We’re also still learning about how long DNA can persist in different types of soil and how that affects the species we’re detecting,’ Sam explains.

Using this data to help urban biodiversity

Studying soil biodiversity allows us to see if our efforts to improve places for nature is working. By looking at the data we collect over time, we can see if creating and restoring habitats is changing what lives in the soil. 

The sheer number of organisms that live in soil means we need to collect a lot of data. To store this data, we’re currently building a biodiversity monitoring platform to enable researchers to store and access a range of biological surveys. Called the Data Ecosystem and sponsored by Amazon Web Services (AWS), it will allow us to gather biodiversity data from a range of sources and create new ways to study and understand urban nature. 

This work is part of a long-term monitoring project in our gardens here in South Kensington and in sites around the UK, where we hope to learn more about the biodiversity on our own doorstep.