Focus on Arts and Ecology

At the microscopic level, soil from Germany’s Black Forest is a fantastical realm—one that’s mirrored in wooded ecosystems worldwide. 

Scoop a handful of soil from the Black Forest in Germany, or the Tongass in Alaska, or the Waipoua in New Zealand. Lift it close to your eyes. What do you see? Dirt, of course—soft, rich, and dark as cocoa. Pine needles and decaying leaves. Flecks of moss or lichen. The pale concertina of an inverted mushroom cap. An earthworm wriggling away from the light, perhaps, or an ant perplexed by the sudden change in altitude. 

Sue Grayston knows there is so much more.

Grayston’s lifelong devotion to soil began in her backyard. As a young girl in Stockton-on-Tees, England, she helped her mother sow seeds and tend to the apple trees, roses, and rhubarbs in their garden. Grayston loved the author Beatrix Potter—not only for her children’s books about mischievous rabbits but also for her scientific illustrations of fungi and the many fabulous forms they thrust through the earth. 

In college, where Grayston had access to microscopes, she became fascinated by soil’s constellations of creatures too small to study with the naked eye. She knew she had found her calling. After earning a Ph.D. in microbial ecology from the University of Sheffield, in 1987, Grayston worked for an agricultural biotechnology company in Saskatoon, Saskatchewan, followed by a research position with the Macaulay Land Use Research Institute (now the James Hutton Institute) in Scotland. There she began collaborating with plant ecologists, sowing the seeds for an undertaking that would engross her for much of her career: the complex connections between soil’s smallest and largest inhabitants, microbes and trees. 

By combining innovative field studies with sophisticated techniques in genetic sequencing, Grayston and other ecologists have created a much richer portrait of a secret society hidden in the forest floor—a largely invisible community without which that ecosystem would collapse.

“A great deal of biodiversity is belowground, but historically, we have not known much about it,” Grayston says. “That’s really started to change in the past couple decades.” 

Far below the leafy canopies of many forests, webs of filamentous fungi link roots into mycorrhizal networks through which trees exchange water, food, and information. Single-celled amoebas fuse into shape-shifting blobs called slime molds, which ooze within or along the earth, hunting bacteria and fungi. Tiny arthropods known as springtails scurry around, occasionally catapulting themselves more than 20 times their own body length in a fraction of a second. Oribatid mites, each about one-tenth the size of a lentil, lumber along what to them are mountains and canyons, walking only half the length of a bowling lane in a typical lifetime of about one and a half years. 

Other creatures are so tiny that they can move only by squirming or paddling through the thin films of water that surround plants and particles of soil. Those bizarre beings include transparent, noodle-shaped roundworms; rotifers with whirling crowns of hairlike fibers that pull food into their vaselike bodies; and tardigrades, which resemble eight-legged gummy bears with claws and spiky suction tubes for mouths.

HOW WE MADE THESE IMAGES
The pictures in this article were taken with a scanning electron microscope, which uses electrons instead of light to capture fine details. SEMs produce grayscale images, so these have been colorized to showcase different life-forms.

Even tinier are the protozoans: a diverse group of single-celled organisms that sometimes move by fluttering their numerous appendages or by contorting their gelatinous interiors. The forest floor also teems with all manner of bacteria and archaea, which are superficially similar to bacteria but make up their own kingdom of life. A single gram of forest soil can contain as many as a billion bacteria, up to a million fungi, hundreds of thousands of protozoans, and nearly a thousand roundworms. 

Soil is not, as was once believed, an inert substance in which trees and other plants conveniently anchor themselves to extract whatever they need. It’s increasingly clear that soil is a dynamic network of habitats and organisms—an immense, ever changing tapestry woven with the threads of innumerable species. Soil is itself alive. 

Grayston and other ecologists now argue that this modern understanding requires substantial changes to forestry. The common practice of clear-cutting does far more widespread and long-lasting damage than ever imagined, they’ve discovered. It’s not enough to consider how felling trees alters the forest from the trunk up. To be truly sustainable, forestry also needs to reckon with the consequences for all that lies beneath.

Billions of years ago, Earth had no soil—only a rocky crust that rain, wind, and ice gradually wore down. As microbes, fungi, lichen, and plants populated the land, they greatly accelerated the erosion of rock by burrowing into it, dissolving it with secreted acids, and breaking it apart with roots.

At the same time, decomposing life enriched the mineral crust with organic matter. Recognizable forest soils first appear in the fossil record during the Devonian period, between 420 and 360 million years ago.

Today life continues to maintain Earth’s soils in all terrestrial ecosystems. The forest floor is full of essential nutrients, such as carbon, nitrogen, phosphorus, and potassium. Without the daily activities of tiny creatures, Grayston and her colleagues point out, many of these elements would remain locked in place or otherwise be inaccessible.

As plants photosynthesize, converting the sun’s energy into carbon-rich molecules, they exude a portion of these compounds through their roots into the dirt, where microbes and fungi consume them. In exchange, mycorrhizal fungi and certain rootbound microbes help them absorb water and nutrients and convert chemically recalcitrant forms of nitrogen into molecules the plants can use.

When plant parts wither and die, worms, arthropods, fungi, and microbes decompose their often resilient tissues into smaller components, returning their nutrients to the soil. In parallel, the continual movements of tiny animals—all their crawling, slithering, and tunneling— mix different layers of soil together, distribute nutrients throughout, and keep it aerated. By digesting huge quantities of dirt, secreting slimy substances, and depositing durable fecal pellets, worms, slugs, and arthropods imbue the earth with organic matter and help particles stick together, improving soil structure.

In 2000, while working for the Macaulay Institute, Grayston traveled to Tuttlingen, a German town that straddles the Danube River, so that she and her colleagues could investigate soils in the Black Forest. This roughly 2,300-square-mile region in the southwestern part of the country, known for its mountain woodlands, has long been prized by the mining and lumber industries. The researchers visited a few sites 
distinguished by 70-to-80-year-old beeches with supple, silver barks and gnarled trunks. Beech is one of the most common deciduous tree species in Europe, valued for firewood and timber. Some of the areas the team surveyed had been heavily logged; others were relatively untouched.

Grayston used metal augers to extract plugs of forest soil from the different sites, stored the samples in coolers, and whisked them back to Scotland for closer examination. Laboratory tests and cell cultures revealed that in one part of the woods, intensive harvesting had significantly diminished the abundance of microbes.

At the time, these connections were tantalizing but still rather mysterious in their details. In the past two decades, however, Grayston and other scientists have learned much more about the interdependence of plants and soil microbes and the importance of these relationships for forest ecosystems as a whole.

Grayston moved to Vancouver in 2003 to become a professor of microbial soil ecology at the University of British Columbia and has worked there ever since. She’s grown particularly fond of the region’s towering western red cedars and similar conifers, as well as the morels, chanterelles, and other delicious fungi that spring up between them like gifts from the forest. Here, Grayston and several collaborators have further investigated how different types of forestry change soil’s microbial communities. 

Many of their studies compare three types of logging: clear-cutting, which strips all trees from a given site; aggregated retention, which preserves clumps of trees; and dispersed retention, which selectively removes individual trees, retaining a uniform distribution.

To test soil health, Grayston and her colleagues buried nylon-mesh bags filled with fine roots in patches of forest that had been harvested in different ways. They left the roots to be decomposed by the tiny animals, fungi, and microbes and dug them up a few months to several years later. Back at the lab, the researchers performed various tests—such as sequencing DNA and measuring levels of essential nutrients—to identify the organisms associated with the roots and determine how active they had been. 

In many cases, clear-cutting reduced soil biodiversity and hindered nutrient cycles. Intensive logging also frequently shifted the demographics of soil communities, allowing a relatively small number of species to dominate.

But not all harvesting methods were equally detrimental. The abundance, diversity, and activity of microbes remained relatively high throughout stands that had been uniformly thinned. In sites reduced to clumps of trees, the researchers found similarly robust and lively communities of microbes only in the immediate vicinity of those clumps. The farther the researchers moved from the remaining patches of trees, the more lifeless the soil became.

Related research tracing the flow of carbon through tree roots revealed that the zone of influence of a tree or cluster of trees—the area across which they actively supply microbes and other tiny organisms with carbon-rich molecules—extends about 33 feet on average. Retaining patches of trees in otherwise naked soil—even large patches—can do only so much. Outside of a 33-foot zone surrounding those vegetal islands, microbial populations will suffer. Dispersed retention is better for soil health, Grayston says, because it typically preserves a tree every 46 to 52 feet, which allows their roots and respective zones of influence to overlap, providing carbon to microbes throughout the forest floor.  

Dispersed retention and other selective methods of harvesting are becoming more common in some regions of the world, but clear-cutting is still widely practiced in North America because it is more efficient, costs less, and requires less complicated machinery. Aggregated retention usually is favored over dispersed retention for similar reasons.

“We need to reconsider forestry practices,” says environmental microbiologist Petr Baldrian of the Czech Academy of Sciences’ Institute of Microbiology. “Clear-cutting is economical, but it comes at a huge cost to the state of the soil. We need to find a balance between the needs of industry and the needs of the forest.”

Reflecting on the future of Earth’s forests—in particular, their soils—Grayston is both excited and concerned. She’s thrilled by the grand mystery of all that remains to be discovered, which is essentially why she chose to study microscopic life in the first place. “We’ve made a lot of strides,” Grayston says, “but we still don’t know who is actually active at certain times and which specific organisms are really important for different processes in the soil.”

At the same time, she is alarmed by the continued decline of forests in many parts of the world because of overharvesting, poor land management, and the stresses of climate change. Given that Earth’s overlapping ecosystems are so highly interconnected and so integral to the survival of complex life, the damage we inflict on the planet’s trees and soils ultimately harms us too.

“We’d be buried knee-deep in litter if we didn’t have soil microorganisms,” Grayston says. “Without them, life on Earth would cease. They could do fine without us, but we couldn’t do much without them.” 

Ferris Jabr is a science writer based in Oregon. Photographer Oliver Meckes and biologist Nicole Ottawa document the microscopic world through their project Eye of Science.

This story appears in the September 2022 issue of National Geographic magazine.

(Sources: National Geographic)