Life Underground: How Earthworms and Springtails Build Soil Ecosystems

"Underground" Is Where Life Is Most Concentrated on Earth

Soil is not simply a collection of minerals. The FAO's report "The State of Knowledge of Soil Biodiversity" classifies the soil biome into microbiota — bacteria, fungi, protozoa, and nematodes — mesofauna such as mites and springtails, and macrofauna such as earthworms and termites. By one estimate, more than 99.9% of the world's terrestrial species interact with soil at some stage of their life, and over 40% of terrestrial organisms depend directly on soil during their life cycle. Just as marine biodiversity is nurtured by ocean currents such as the Kuroshio and Oyashio, the foundation of terrestrial biodiversity is supported by this invisible underground ecosystem.

The invisible majority: bacteria, fungi, and protozoa

A single gram of healthy soil is said to contain billions of bacteria and several kilometers' worth of fungal hyphae. These organisms break down organic matter and mineralize nutrients into forms plant roots can absorb, functioning like an underground digestive system. Some, such as mycorrhizal fungi, form symbiotic relationships with plant roots, helping them absorb water and nutrients like phosphorus and nitrogen. Mycorrhizal networks can even connect the roots of multiple plants, and some research suggests they serve as channels for exchanging nutrients and information.

Protozoa and nematodes are often overlooked but play important roles. Protozoa prey on bacteria, regulating bacterial populations and creating what's known as the "microbial loop," in which nitrogen released through predation is recycled as a nutrient for plants. Nematodes include species that feed on plant roots as well as species that feed on bacteria, fungi, or other nematodes, forming short food chains within the soil.

Soil microbes are even behind the smell of earth after rain. Actinomycetes, a group of bacteria, produce a volatile compound called geosmin, which is released into the air by falling raindrops to create that distinctive earthy scent. The human nose is remarkably sensitive to geosmin even at extremely low concentrations, meaning we unconsciously perceive the presence of invisible microbes through smell.

The mid-sized workers: springtails and mites

Springtails — insect relatives just a few millimeters long — and oribatid mites feed on leaf litter and fungi, shredding them into pieces that microbes can more easily decompose. Research from the Research Institute for Humanity and Nature has found that many springtails feed mainly not on dead leaf litter itself, but on fungi and root exudates containing "new carbon" recently produced through photosynthesis. This finding shows that springtails are not simply "decomposers of leaf litter," but play a role in linking living plants to soil microbes.

The large-scale engineers: earthworms, termites, and millipedes

Earthworms and termites are large enough to dig tunnels through the soil, changing its aeration and drainage, which is why they are called "ecosystem engineers." The tunnels they leave behind become channels for water and air, and shelters for other organisms. Millipedes and beetle larvae physically break down leaf litter and fallen wood, making it easier for microbes and fungi to colonize. How stag beetle larvae decompose rotting wood is one example of this kind of macrofauna activity.

A special world around the roots: the rhizosphere

The few millimeters surrounding a plant root are known as the "rhizosphere," a special zone where bacteria and fungi congregate in numbers far exceeding those in the surrounding soil, drawn by sugars and amino acids secreted by the root. Plants form symbiotic relationships with some of the microbes gathered in the rhizosphere, exchanging photosynthesized sugars for help absorbing nutrients. In discussions of soil biodiversity, it's important to consider not just the average across the whole soil, but also this "micro hotspot" that is the rhizosphere.

Earthworms Are "Ecosystem Engineers" — Tilling Soil and Boosting Microbes

Earthworms ingest leaf litter and soil, break down organic matter together with microbes in their gut, and excrete it as castings. In this process, soil particles bind into ball-like "aggregates," producing soil that balances drainage with water retention. Charles Darwin, of evolutionary theory fame, spent his later years observing how much earthworms moved the topsoil, and compiled his findings into a dedicated book. Earthworms have long been recognized as "the first creatures to till the soil."

Three lifestyles, three types

Earthworms are broadly divided into three types based on where they live: "epigeic" species, which live in leaf litter near the surface and tend to be darkly colored; "endogeic" species, which move horizontally through shallow soil layers; and "anecic" species, which dig deep vertical burrows connecting the surface to deeper soil. The vertical burrows dug by anecic earthworms help rainwater infiltrate the ground quickly during heavy rain, improving surface drainage.

How the gut transforms the microbial community

Studies using an index (BIOTREX) that measures the diversity and level of decomposition activity in soil microbial communities have found that soil which has passed through an earthworm's gut shows a more than sixfold increase in microbial diversity and activity compared with soil that hasn't. Earthworms don't just move soil around — they act as a catalyst that boosts the very functioning of microbial life. This is thought to happen because earthworms selectively enrich certain microbes as they ingest soil and organic matter, and the special conditions inside the gut — oxygen levels, pH, and mucus — activate microbial activity.

How many earthworms live in a square meter?

Earthworm population density varies greatly depending on soil conditions and farming practices. Well-managed farmland is reported to have around 100 to 300 earthworms per square meter, while under favorable conditions, some surveys have recorded densities of several thousand per square meter within a 10cm-thick layer of soil. Conversely, fields subject to heavy pesticide use and frequent tillage can end up with almost no earthworms at all. Earthworm numbers are often used as a simple indicator that reflects the overall soil biodiversity of a field.

No-till farming and earthworms

Frequent tillage with machinery suppresses weeds, but it also physically destroys earthworm tunnels and soil aggregates. Under no-till, grass-covered farming — in which fields are not tilled and are managed with vegetation left in place — earthworm populations increase, soil aggregates increase, and this has been reported to result in greater soil carbon storage. Fields with more earthworms tend to allow crop roots to grow deeper, with reports of more stable growth during droughts, meaning earthworms matter for agricultural productivity as well.

Red wigglers: the stars of home composting

The earthworms typically used in home vermicomposting bins are not the Megascolecidae species commonly found in fields and gardens, but "red wigglers" (Eisenia fetida), which favor easily decomposed organic matter such as food scraps. Red wigglers are epigeic earthworms that live in leaf litter and compost near the surface, are highly prolific, and efficiently break down food scraps into high-quality "worm castings." Even in a limited space like a balcony, a dedicated bin and a population of red wigglers let you reduce food waste while experiencing the work of soil organisms firsthand.

Springtails and Soil Fauna Drive Decomposition and Carbon Cycling

Soil animals don't just act as "cleaners." Springtails and mites shred leaf litter, increasing its surface area and making it easier for microbes to decompose. This speeds up the rate of decomposition and accelerates the cycling of nutrients such as nitrogen that plants can use. A single fallen leaf goes through multiple stages before it fully returns to the soil — softening by fungi, shredding by soil animals, and final decomposition by microbes — and if any one stage is missing, the whole process slows dramatically.

What determines the speed of leaf-litter decomposition

Research from the Research Institute for Humanity and Nature shows that many soil animals don't simply function as "decomposers of leaf litter." Instead, by selectively feeding on fungi and fresh organic matter, they actively restructure the decomposition process itself. In experimental plots where soil animals were removed, the rate of organic matter decomposition dropped significantly — demonstrating how the presence or absence of these tiny, invisible creatures can determine the speed of an entire forest's or field's material cycle.

Speeding up the nitrogen cycle

FAO materials also position mesofauna such as springtails as organisms that accelerate leaf-litter decomposition and, in particular, promote nitrogen cycling and its availability — that is, converting it into a form plants can absorb. Nitrogen is an essential nutrient for plant growth, and activating this cycle without relying on chemical fertilizer can help maintain healthy growth while reducing the amount of fertilizer needed.

Mycorrhizal networks: the underground "wood wide web"

Research has increasingly shown that the roots of forest trees are loosely connected underground through the hyphae of mycorrhizal fungi. This network of fungal threads, sometimes called the "wood wide web," is being studied as a possible pathway through which plants exchange carbon and nutrients, and even transmit chemical signals about pest damage to neighboring trees. Just as coral reefs in the ocean provide shelter for fish and support complex ecosystems, mycorrhizal networks underground form a foundation that loosely connects an entire forest.

The soil food web of eating and being eaten

Just as terrestrial ecosystems above ground have food chains and food webs, so does the world beneath the soil. Springtails and mites that feed on fungi and organic matter are, in turn, preyed on by larger arachnids, centipedes, and moles, and some of these predators become food for birds and small mammals. If soil animal diversity is lost, the effects ripple outward from the bottom of this web, potentially affecting the food resources of organisms above ground as well.

Soil Is Earth's Largest Terrestrial Carbon Pool

Soil is both home to countless organisms and an enormous carbon reservoir. The organic carbon stored in the world's soils is estimated to be two to three times the amount of carbon in the atmosphere as carbon dioxide, making soil the largest terrestrial carbon pool. It far exceeds the amount of carbon stored in the plant biomass of forests and grasslands.

How carbon gets locked into soil

Some of the carbon dioxide plants absorb through photosynthesis enters the soil as roots, leaf litter, and organic compounds secreted by roots. As earthworms and microbes decompose this material, some of the carbon returns to the atmosphere as carbon dioxide, while the rest becomes locked away inside soil aggregates or bound to clay minerals for long periods. How much of this carbon can be kept "locked away" is key to using soil as a tool against climate change.

Peatlands: an extreme case of soil carbon

Peatlands, formed when dead wetland plants accumulate in thick layers without fully decomposing, are known for storing carbon far more densely than ordinary soils. The world's peatlands hold an estimated 550 gigatons of carbon — roughly twice the amount stored by the world's forests. When peatlands are drained or developed and dry out, the carbon locked within them rapidly oxidizes and decomposes, releasing large amounts of carbon dioxide, which is why simply keeping them wet is itself a form of climate action. In discussions of soil carbon, peatlands stand out as a prime example of a "carbon reservoir worth protecting."

What is the "4 per 1000" initiative?

Proposed at COP21 in 2015, the "4 per 1000" initiative is an international effort based on the idea that increasing the world's topsoil carbon by 0.4% (four parts per thousand) per year could offset the increase in atmospheric carbon dioxide caused by human activity. Adding compost and green manure, adopting no-till farming, and using cover crops are among the concrete measures identified for increasing soil carbon.

The connection to Japan's Green Food System Strategy

Japan's Ministry of Agriculture, Forestry and Fisheries also positions carbon storage in farmland and grassland — through the application of compost, green manure, and biochar — as one of the measures in its "Green Food System Strategy," established in 2021. Farming practices that activate soil organisms are one of the few approaches that can advance biodiversity conservation and climate action at the same time. Conversely, research has also reported that alternating cycles of drought and heavy rainfall increase carbon dioxide release from soil, underscoring the need for caution around the two-way relationship in which climate change itself affects the soil's carbon cycle.

What Lives in Japan's Soil? The Hidden Diversity of Megascolecidae Earthworms

The earthworms found in Japan are classified into families including Megascolecidae, Lumbricidae, and Moniligastridae, with Megascolecidae alone accounting for more than 95% of species. Megascolecidae is estimated to include more than 500 species, yet only about 10% have been formally given scientific names. It is highly likely that many "undescribed species" of earthworm — still without a scientific name — live in the soil of ordinary gardens, farmland, and coppice woodlands.

Why diversity is higher in the south

A research team at Kyoto University used genetic analysis to systematically organize Japan's Megascolecidae earthworms, revealing that they can be divided into more than 100 species based on morphological differences, and that their species diversity is strikingly high even compared with other regions such as Europe. Joint research by the University of Tokyo and Hirosaki University has also shown that earthworm species diversity in Japan is higher in the south, with many lineages concentrated in southern regions. The repeated glacial and interglacial periods in Japan's geological history, along with its long north-south geography, are thought to have generated this distinctive underground diversity as well.

Earthworms as a soil health checkup

Because earthworms have limited ranges of movement and respond sensitively to environmental change, they are also recognized as bioindicators of how healthy a given soil is. Tracking the species and numbers of earthworms in the same field over time can reveal how changes in farming practices or pesticide use are affecting the soil environment — information that chemical analysis alone cannot capture. Just as eelgrass beds serve as an indicator of marine water quality, earthworms can serve a similar role on land, as a readily accessible "health checkup" for the local environment.

The problems caused by earthworms that crossed the ocean

Some earthworms of the genus Amynthas, native to East Asia including Japan, have become established after being introduced to North America, where they are known as "jumping worms" for their vigorous, leaping movements. Northern North American forests were historically swept clean of earthworms during the ice age and evolved for a long time as ecosystems without them. When invasive earthworms move in, the thick layers of accumulated leaf litter are rapidly decomposed, and studies report declines in the plants, fungi, and ground-dwelling insects that depended on that layer. Earthworms, so familiar and unremarkable in Japan, illustrate how introducing a species to a land with a different ecological history can create a serious invasive species problem.

How Soil Animals Are Studied — From Homemade Devices to Genetic Analysis

The organisms living underground are hard to grasp in full simply by digging. Research and environmental education programs use a number of established methods to extract and observe soil animals.

The Tullgren funnel: observation with everyday tools

A "Tullgren funnel" is a device that uses the heat from an incandescent bulb to slowly dry out collected leaf litter or soil placed on top of a funnel. Soil animals, which avoid dryness, move downward to escape it and fall into a container below. This makes it an efficient way to collect mesofauna such as springtails and mites — around 0.2 to 2mm long and hard to see with the naked eye — and it's used in environmental education programs at the Forestry and Forest Products Research Institute as well as in school science lessons. Even without special equipment, a simple version can be made at home with a funnel, a light source, and a container.

Hand-sorting and the litter-bag method

Larger soil animals like earthworms are often studied by digging up soil of a set area and depth and sorting through it by hand — a method known as hand-sorting. Another widely used technique places leaf litter in a mesh bag (a litter bag) on the ground surface, then periodically retrieves it to measure weight loss over time, providing a quantitative way to evaluate the decomposition rate at that particular site.

The "hidden diversity" revealed by genetic analysis

In recent years, genetic analysis (DNA barcoding) has advanced research into distinguishing species that look similar and are hard to tell apart, and it has repeatedly revealed that what was once considered a single earthworm species is actually made up of multiple lineages. The research results from Kyoto University and the University of Tokyo mentioned earlier are examples of diversity that came to light only through this kind of genetic analysis. Underground biodiversity contains a great deal of "hidden diversity" that appearance alone cannot reveal.

Nature-observation events as an entry point

Even without advanced genetic analysis, observing soil animals with a Tullgren funnel or through hand-sorting is a familiar activity used by nature conservation groups and in school classes. Because the organisms that turn up can differ by season and management practices even at the same site, continued observation at a fixed location can help reveal changes in the local environment over time. Just as tidepooling and mudflat exploration are popular ways to observe marine life, observing soil animals offers an accessible "creature hunt underfoot" that's easy to build into children's nature experiences.

How Pesticides, Tillage, and Farmland Abandonment Affect Soil Organisms

Soil biodiversity is strongly affected by human land use. Heavy use of chemical pesticides, excessive tillage, monoculture cropping, and, conversely, the increase in abandoned farmland where management has stopped can all alter the composition and balance of soil organisms. The FAO estimates that about 33% of the world's soil resources are already moderately to severely degraded, due to factors including erosion, salinization, compaction, acidification, and pollution. Forming just one centimeter of soil naturally is thought to take hundreds to a thousand years, meaning regeneration is failing to keep pace with the speed of degradation.

Chemical pesticides and soil microbes

Japan's Ministry of Agriculture, Forestry and Fisheries has set a target, under its Green Food System Strategy, of reducing chemical pesticide use by 50% by 2050. Because pesticides can affect non-target organisms in the soil as well as the pests they are aimed at, reducing usage with biodiversity in mind has become a policy priority. The same strategy also sets a target of reducing chemical fertilizer use by 30% by 2050, pointing toward an overall reduction in the burden placed on soil.

How excessive tillage destroys soil aggregates

As noted earlier, frequent tillage destroys earthworm tunnels and soil aggregates, tending to release stored soil carbon. Striking a balance between appropriate tillage and no-till, grass-covered farming helps maintain soil biodiversity.

Climate change: a new pressure

Pressures on soil organisms don't come only from direct human land use. Recent research has reported that shifts in rainfall patterns — with repeated cycles of drought and heavy rainfall — increase the amount of carbon dioxide released from soil. Extreme dryness can temporarily halt the activity of soil animals and microbes, and the sudden onset of wet conditions afterward can trigger rapid decomposition of accumulated organic matter. Climate change is increasingly disrupting the rhythm of carbon cycling that soil organisms have stabilized over long periods of time.

Urbanization and farmland abandonment: risks at both extremes

When soil itself is lost to urbanization and paving, the habitat of soil organisms disappears physically. On the other hand, in abandoned farmland where management has stopped, vegetation grows in rapidly as ecological succession proceeds, and the composition of soil organisms once adapted to farmland can change substantially. Both over-management and a complete absence of management can affect soil biodiversity, each in different ways, and this warrants attention. Even in urban parks and street-tree planting strips, leaving some soil unpaved so it can "breathe," rather than covering it entirely in asphalt, matters for maintaining local soil biodiversity.

Restoring Soil Biodiversity — Organic Farming, Compost, and No-Till

As of FY2022, the area of farmland under organic cultivation in Japan stood at about 30,300 hectares, only around 0.7% of total farmland. Japan's Green Food System Strategy sets targets of expanding this to 63,000 hectares by 2030 and to 25% of farmland (one million hectares) by 2050.

Compost, green manure, and biochar as options

Using compost, green manure (incorporating cover crops as fertilizer), and biochar (a soil amendment made by charring organic matter) is expected to supply soil organisms with organic matter to feed on while keeping carbon locked in the soil for longer. Charring pruned branches for application to soil is a practice already adopted by local governments including Yamanashi Prefecture. Because biochar resists decomposition by microbes almost entirely, it can keep the carbon applied to soil locked away for something close to the very long term — a distinct feature compared with other organic materials. Compost and green manure, by contrast, decompose while directly feeding soil organisms, making them microbial food, whereas biochar focuses more on carbon fixation — each material plays a different role and is used accordingly.

Community composting of leaves and food scraps

At the municipal level too, efforts are spreading to collect fallen leaves from parks and street trees, along with household food scraps, and compost them for return to local farmland and flowerbeds. Returning organic matter that would otherwise be incinerated as waste both reduces waste and replenishes the organic matter that feeds soil organisms. Even on a small scale, building this kind of "circular loop" within a community helps strengthen soil biodiversity.

Rice paddies: an important stage for soil biodiversity too

The rice paddies that support the creatures that live in rice fields are also, from a soil biodiversity perspective, an important wetland ecosystem. Practices such as "winter flooding," in which fields are kept flooded through the winter, are being tried in various regions as a way to increase the diversity of soil animals and benthic organisms through careful water management.

What you can do at home

Even in a home garden or a planter, small steps such as composting food scraps and fallen leaves, or leaving some fallen leaves in the garden rather than removing them all, help support the habitat of soil organisms. Just as with the creatures that live under rotting wood and fallen leaves, paying attention to the work of these unseen decomposers is a first step toward protecting the nature close to home. Observing soil animals with a Tullgren funnel at school or a nature-observation event can also be a gateway that sparks children's interest in the ecosystem right beneath their feet.