‘These lowly organised creatures’: Earthworm sample collecting at the Sanger Institute

For many people, these animals are seldom seen and probably underappreciated. Yet few organisms have, as Darwin himself wrote, played such an important role in the history of the world. On an earthworm sampling visit to the Wellcome Sanger Institute, I got to find out more about their vital role as ecosystem engineers, how we have (unwisely) used one species to test the safety of agricultural chemicals, and how the sequencing of their genomes will help to answer fundamental questions about their biology.

When talking about the Darwin Tree of Life Project to a new audience, Professor Mark Blaxter (who leads the Tree of Life Programme here at Sanger) often describes how Darwin spent a great part of his life honing his theory of evolution by observing what was going on in his back garden.

In fact, Darwin spent decades studying earthworms at Down House in Kent, culminating in his final published work in 1881, The Formation of Vegetable Mould through the Action of Worms, with Observations on their Habits. One of Darwin’s earthworm experiments, where he set out to discover the rate at which a stone was buried by the activity of ‘these lowly organised creatures’, lasted for 29 years.

The stone Darwin used in one of his earthworm experiments.
Credit: Wellcome Collection (CC BY 4.0)

Darwin was among the first scientists to fully appreciate the importance of earthworms, observing that they had been working the soil long before humans conceived of such a thing as the plough. Yet 139 years after Earthworms was published, we still don’t have a clear idea of the numbers and types of earthworms that inhabit our fields, parks and gardens.

Within the next few years, however, this is likely to change. Whole genome sequencing of earthworm species as part of the Darwin Tree of Life Project will allow scientists to begin to answer fundamental questions about earthworm biology.

A visit from the earthworm experts

Though the Sanger will be involved in much of the sequencing for the Darwin Tree of Life Project, sample collection is something that tends to happen elsewhere. So it was great to get our hands dirty for a change and tick some species off the list. Our aim was to collect as many species of native earthworm as we could find on campus.

Earthworm experts Professor Pete Kille (University of Cardiff) and Dr Dave Spurgeon (UK Centre for Ecology & Hydrology) came down to lead the sampling, ably assisted by two members of the British and Irish Earthworm Society on the Wellcome Genome Campus, Mark Blaxter and Head Gardener, Lee Outhwaite. Gardener Chris Evans and I completed the party.

We headed out on a fine spring day armed with pitchforks and sample trays. Lee suggested a few spots on campus to try – the needle-fall beneath a large cedar, some semi-wild fringe habitats, the shore of the lake and the campus compost heap (which Mark was particularly excited about).

Mark Blaxter and Pete Kille searching the needle-fall under the watchful eye of Head Gardener Lee Outhwaite

Part of the challenge of monitoring earthworm populations is their inaccessibility. They spend most of their time below ground or beneath leaf litter, so the only way to survey them is to turn over a clod of soil or mulch and get your hands dirty.

Fortunately, you don’t have to go far to find them. The soil beneath our feet is packed full of worms. A single badger can consume 200 in one night. Darwin estimated that in a single year, earthworms can bring up to 15 tons of soil to the surface per acre. This figure may seem unbelievable given their size, until you consider the fact that earthworms make up a larger proportion of UK terrestrial biomass than any other class of species. Dave Spurgeon told me he once calculated that there are approximately five billion kilograms of earthworm living in our soils – that’s equivalent to roughly 1.7 million Ford Transit vans. Or, at a guess, 66,666,666 David Attenboroughs.

A few minutes beneath the cedar turned up a couple of species, 20 minutes exploring the fringe habitats another five. Some are readily identifiable even to a novice such as me, particularly the giant Lumbricus terrestris. Others are a little more challenging – even to the experts.

L. Terrestris (left) is unmistakable due to its size. Other species are trickier to identify

There are thought to be 27 species of earthworm that are native to Britain and Ireland, though nobody knows for sure whether some rare finds that we think may be introduced could be native. As Dave told me, “Earthworms don’t have many distinguishing physical characteristics, so there may be more diversity to be discovered. This is one way that whole genome sequences for all the known species of British and Irish earthworm will help us to better understand their biology. It could be that what we currently categorise as a single species is actually made up of several.”

Ecosystem engineers

Though they can’t hope to match the Instagram-friendly, fuzzy cuteness of a bumble bee clambering over a flower, earthworms are as important to our soil as pollinators are to plants and trees. But whereas the sight of bees doing what they do best is as much a part of summer as short sleeves and ice-cream, the ecological services provided by worms are difficult to observe.

“Earthworms’ title of ecosystem engineers is well-earned. To put it simply, they create the soil,” Dave explained to me. Burrowing beneath the surface aerates the soil, allowing air and moisture in and letting carbon dioxide out. Earthworm casts (faeces) help to create fine-textured soil that is an important part of soil structure. They break down dead organic matter into smaller pieces through bioturbation, allowing fungi and bacteria to finish the job and in the process returning nutrients to the soil required for plant growth. Not to mention feeding many a hungry mustelid, hedgehog and owl.

This robin spied an opportunity for an easy meal in the patches we’d uncovered

Unfortunately, it is quite possible that earthworms are declining alongside many other invertebrate families due to human impact on the environment. Pete was unequivocal about the impact losing our earthworms would have: “The loss of our earthworms would be every bit as catastrophic for our survival as losing our bees. Without the ecosystem services they provide, soil function and food production would plummet. One reason we’re so excited about the genomes is that we’ll be able to gauge how earthworms respond to their environment. With the right evidence we’ll be better able to influence policy to ensure ecosystems are protected.”

The worm turns: toxicity testing and neonicotinoids

Dave Spurgeon assesses his latest find among the daffodils near Hinxton Hall

Earthworms are also an important barometer for ecotoxicologists like Dave Spurgeon. Historically, a single species of earthworm, Eisenia fetida, has been used to test the toxicity of agricultural chemicals on soil. If the chemical in question did not adversely affect E. fetida within certain parameters, it would be deemed safe for use. One class of chemicals tested in this way was neonicotinoids. Now infamous as the chemicals linked to huge bee population declines, ‘neonics’ were banned in the European Union in 2013*.

In recent years the work of Dave Spurgeon has shown that what is ‘safe’ for one worm isn’t necessarily safe for all. “Because different earthworm species can have very different sensitivities to the same chemical, measuring soil toxicity using only Eisenia fetida can produce misleading results,” Dave told me. “While earthworms can adapt to toxic soils, we need to know exactly how sensitive individual species are to chemicals like neonicotinoids.”

The worst case scenario would be if the worm turns and earthworms can no longer provide the vital ecosystem services that we depend on. Reference genomes for earthworm species will help researchers like Dave Spurgeon assess the effect of chemicals on their DNA and help us to safeguard ecosystems from chemicals that are not safe for use.

Eight more species added to the Project

Mark Blaxter and Dave Spurgeon separate the earthworms by species ready for sampling

In total our morning produced eight species of earthworm, which is about what Pete and Dave were expecting: Aporrectodea caliginosa, Aporrectodea longa, Aporrectodea rosea, Eisenia fetida, Lumbricus castaneus, Lumbricus rubellus, Lumbricus terrestris and Octolaision cyaneum.

Of these, A. caliginosa, L. rubellus, L. terrestris and O. cyaneum will have their DNA sequenced to create Darwin Tree of Life genomes, with the other species coming from samples donated by the Centre for Ecology & Hydrology. The E. fetida sample we collected turned out not to be – apparently the absence of yellow-green coelomic fluid when the specimens were dissected was a key marker. Dave did say that some earthworms could be difficult to identify from similar types.

It's a nice idea that one day, decisions will be made about what is and isn't safe to put in our soil based on the DNA of the individual earthworms we collected that day. And that, perhaps, reference genomes created from these samples will help scientists discover new earthworm species.