Joe Llanos : worm DNA soil

Meet the earthworm CSI & discover how worm DNA can help soil health

In this interview with ‘earthworm CSI’ Joe Llanos we learn about a technique he is pioneering collects worm DNA to help soil health. 

Interview with Joe Llanos, the ‘earthworm CSI’

Joe in a field finding worm DNA in the soil
Joe in the field at Leeds University farm, collecting soil samples for eDNA analysis

When Joe was younger he didn’t expect to study for a PhD, let alone one focusing on earthworms, though he’s always loved nature.

Born in Derby, Joe is a first-generation university student who worked in various jobs before getting into research, including selling TVs in an electrical store and labouring on construction sites. And despite his PhD he still gets family and friends asking when he’s going to get a ‘proper job’!

We interviewed Joe remotely during lockdown as he completed a fellowship with POST (UK parliament’s in-house source of analysis of public-policy issues). While at POST Joe wrote a briefing paper on creating a resilient food system in the UK, which you can read here.

Read on to find out about Joe’s work with eDNA, the problem with soil health in the UK, and everything you ever wanted to know about worms.

1 eDNA, worms and farms

Joe explains the eDNA technique, and why it is that eDNA can play a vital role in measuring soil health on agricultural land. Plus he sets out why this measure could be important for policy in the UK.

Why are worms the focus of your research?

Joe: There is currently worldwide concern about the threat of soil degradation and about how we are going to feed the growing world population. But worms could offer natural solutions to both of these problems.

But despite their vital role in soil health, worms are understudied.

Joe: That’s right. There’s still a lot we do not know about worms, despite the fact that Charles Darwin spent 40 years studying them in his garden. Darwin even wrote a book about worms that was so popular it initially outsold The Origin of Species!

Darwin concluded his study saying this about worms: “It may be doubted whether there are many other animals which have played so important a part in the history of the world, as have these lowly, organised creatures.”

So your project aims to fill some of these gaps in our knowledge using DNA earthworms leave behind in soil?

Joe: Yes. The problem is that earthworms live in an opaque soil environment we can’t see into. As a result little sampling has been done worldwide. But we know earthworms are incredibly important in many places for soil health. So it’s really important to ‘burrow’ into these knowledge gaps – sorry! – to utilise the benefits worms can bring.

However, currently to find out about worm populations we have to dig a pit and count worms by hand. This is labour intensive and has other problems. For instance, in most cases to identify an earthworm to species level we have to take them to the lab and examine them under a dissecting microscope. This process is time consuming and requires taxonomic training – worms are quite hard to identify. Plus pit sampling can introduce bias and a lot of pits need to be dug to get a representative picture. Further, many worms can sense the vibrations from digging, and may flee the pit area before they are found.

So we are working on a new technique that can identify what species of worms have been in a sample of soil. This technique extracts a type of DNA – what we call environmental DNA (eDNA) – that worms leave behind.

So you can tell what worms have been in soil from traces of DNA? That sounds like something out of CSI!

Joe: Yes, it does, doesn’t it? Not many people know about eDNA, but it’s very useful. Already eDNA has been established in marine and aquatic environments but much less so in soils. So our work is new.

The best thing about this technique is that we can use eDNA to get a picture of the organisms that live in a particular environment but without having to find the organisms themselves. And worms are a good choice because they leave many traces behind, like skin cells and mucus. And also soil moves through their guts.

How does this eDNA technique work?

worm DNA in a tube
The tiny amount of liquid in this tube contains hundreds of thousands of DNA sequences from hundreds of soil samples. This is what Joe ended up with after all the field and lab work. The sample is then sent for next generation sequencing.

Joe: We get soil samples and analyse them in the lab, being careful about contamination. Then we isolate the eDNA, purify it and sequence the DNA using the latest next-generation sequencing techniques. We end up with hundreds of thousands of sequences (in some cases millions) which we can then ID to species level.

This list of species and sequence numbers can answer all sorts of questions about the worm populations and their environment.

Though we can’t currently tell exactly how many individuals of each species are present (the number of sequences does however give a rough proxy measure of numbers), it can accurately tell us the different species of worm that are present.

What are the practical outcomes of knowing how many types of worm are living in your soil samples?

Joe: Abundant and diverse earthworm populations are a great measure of biological soil health.

And worms can also play a huge role in boosting food production in agriculture. For instance there is a 25% boost in crop yields from having them present in soil.

Although further development of the technique is needed, the fact that we’ve been able to apply it to agricultural soils is exciting. Because farmers, land managers, scientists and policymakers could all use it to more accurately measure soil biodiversity and health.

Being able to measure soil health is important because both the Agriculture Bill and Environment Bill that are going through parliament talk about measuring soil health and biodiversity. But it is yet to be decided how this will be done. Measuring eDNA to detect soil earthworm populations is a good candidate to measure soil health as it can potentially be widely deployed in an efficient, standardised and scientific way. And it’s not too invasive or disrupting to organisms and habitats.

You have been doing fieldwork at the University of Leeds site Spen Farm, what have your tests there shown?

Joe: We have shown that the technique can be used successfully on farms. And importantly we have shown that different management practises can have big effects – even at a small scale (within the same field).

At Spen Farm there are crop fields with strips of grass and clover (leys) in them. We examined the impact of leys and how they help improve soil quality by giving the soil a break from nutrients being taken out through crop growth. We sampled both the crop fields and strips, and showed that the eDNA technique is sensitive enough to show a difference in worm populations between these two closely related areas.

Further, we found there were way more worms in the grass-clover strips, both in the number of species found and the rough abundances. These strips were around two years old. So we also know eDNA sampling is sensitive enough to detect differences in this relatively short amount of time.

But there are still lots of unanswered questions that need working on. For example, we don’t yet know how long eDNA can last in the soil. The danger is it can survive for quite some time, which means you could be sampling populations that are no longer there. We’d like to get an idea of this and hone the technique further.

2 Hermaphroditic, herding, hunters – it’s not all about worm DNA

We couldn’t talk to Joe without picking his brains about earthworms. These creatures are incredibly important to ecosystems and human health, but much about them remains a mystery. Here Joe opens up the secret life of earthworms. 

Earthworm anatomy is pretty complicated right?

Joe: People assume worms are simple because they look simple, like a long tube. And it’s true that earthworms have had the same physical anatomy for millions of years – some of the earliest fossils of multi-cellular animals show evidence of animals that look very similar to the earthworms we find today.

But earthworms are an example of honed evolutionary design. They have a closed circulatory system and haemoglobin, so their blood is red just like humans. Plus they have five ‘hearts’ that pump the blood around, can breathe through their skin and have a specialised digestive system that includes a crop and gizzard for grinding up tough food, similar to birds.

Although they might not be obvious to the naked eye, they are also covered in backwards facing hook-like hairs called setae. Satae can anchor the worms in their burrows, help them move and stop predators pulling them out. This makes worms rough to the touch if you stroke them a certain way!

And though they only have a primitive brain, as we’ve seen they show complex behaviour and intricate systems.

A photo of a live worm labelled with anatomical details
Anatomy of an earthworm: labelled are some of the distinctive features of worms. Note this worm is a juvenile as it lacks the distinctive ‘saddle’ feature on its upper body.

Is it true they have an interesting love life?

Joe: Their mating behaviours are pretty complex. Earthworms are hermaphrodite, meaning individuals have both male and female sex organs. And some species of earthworms are able to reproduce parthenogenetically without a partner and create clones of themselves.

But most go in search of a partner when they are ready to mate. And some species can be choosy. They visit the burrows of their prospective mates repeatedly before deciding who to choose. We think earthworms use these visits to judge the size of their mates, as they seem to prefer to mate with similar sized individuals. This may be because they don’t want to risk being pulled out of their own burrows by bigger, stronger mates.

All of this is likely going on in your back garden or the local park!

And what about other earthworm behaviours?

Joe: Earthworms show some sophisticated behaviours we do not fully understand yet. For example, some species exhibit a type of herding behaviour. They organise themselves into groups by touch and smell alone (as they have no ‘eyes’) and then move off as a herd to find food or new habitats. It turns out that earthworms may be surprisingly social!

And they can also act as predators, detecting certain microbes in the soil and hunting them down. They have interactions with larger species too, like dung beetles.

3 Worms, DNA and soil health

Here Joe explains why his eDNA technique should be used to help maintain worm populations and agricultural soil health.

Why are earthworms so good for soil?

Joe: Earthworms are keystone species and ecosystem engineers – they have a huge impact on the environment they inhabit. They are hugely important for soil health in most temperate soils, particularly in the UK and Europe.

One of the reasons they are good for soil is that burrows and worm casts contain concentrated nutrients. This is because organic matter has been pulled down into the earth by worms and then broken down. These nutrients would otherwise remain locked away and others wouldn’t be able to access them. Their role in breaking down organic matter helps to stimulate the soil microbial community and allows other plants and animals to access the nutrients released.

Worm casts (worm poo) also stick soil particles together to form aggregates which improves the soil structure. Plus worm’s deep vertical burrows help water get deep into the ground and allow gas exchange to occur. And we know burrows are used by other organisms to reach moisture and shelter.

Can we have soil health without worms?

Joe: Soil health is currently gaining a lot of attention, because soil degradation threatens our ability to grow food in many places. A lot of research on soil biodiversity (an essential part of soil health) focuses on soil microbes. But there is not much that focuses on soil meso and megafauna. However, both are hugely important to soil health and should be studied.

In UK agriculture worms are an integral part of healthy soils. Importantly worm research shows that we don’t always need sophisticated technological solutions to solve our problems. Natural solutions already exist  – like harnessing the power of our existing soil biodiversity. These natural solutions could be more effective than any sophisticated futuristic technology.

However, earthworms are not in every soil and are invasive species in some soils, causing trouble. For example, in parts of North America, invasive European earthworms are changing the productivity and dynamics of boreal forest soils. This is affecting the plant diversity above ground, meaning that animals and plants that have adapted to live there are being out-competed. The worms are putting those ecosystems at risk.

What should the UK do about soil health?

Joe at COP14
Joe at the UN COP14 Biodiversity summit with other Grantham Scholars. Global policy must reflect the importance of soil health and biodiversity if we are to feed the world population.

Joe: We need to emphasise soil health and soil biodiversity more than we have been doing. Not many people know that over a quarter of the world’s biodiversity is found in soil. And biodiversity loss is just as big a problem as climate change. Further, soil – this tiny layer on the surface of the earth – is vital to us. After all, most of our food (98.8%) is grown in soil.

The UK has committed to improving soil health in the latest Agriculture Bill. And the 25-year environment plan talks about leaving biodiversity in a better state than we found it.

So, increasing soil health measurements on farms, incentivising management practises that increase soil health, and promoting soil biodiversity in other ways (such as earthworm introductions) will be key to achieving these aims. They could also help to make our food system more sustainable.

Why focus on agricultural soil?

Joe: Intensive agriculture can damage soils and lead to soil degradation. Regular ploughing kills worms and destroys their burrows. If crop residues are not left in the field earthworms can struggle to find enough organic matter to eat. So there can be a positive feedback problem on farms. As earthworm populations are reduced, we lose the benefits they provide, which means the soil degrades further and so on.

If left unchecked this problem can spiral.

The result can be the that the soil loses all its nutrients and structure – and blows away. A classic example of this was the American dust bowl in the 1930’s.

Frighteningly, soil degradation causes the loss of millions of tonnes of once healthy soil every year. So it is important that we get on top of this problem. We need to find alternative ways to grow our food: without destroying the soil we need and the earthworms that look after it.

So measuring soil health on farms is important. But we currently don’t have many standardised ways to do this. Hopefully our work can help towards this.

Find out more about soil research at the Grantham Centre. And for more on worms, try the Earthworm Society of Britain where Joe received his taxonomic training.

Interview by Claire Moran. Images from Claire/Joe.