(Jon Hughes for The Washington Post)
Gardening columnist

The gardener has a long, touchy-feely relationship with the soil. As every good cultivator knows, you assess the earth by holding it. Is it dark and crumbly, is there an earthworm or beetle in there, is it moist, and when you smell it, are you getting that pleasant earthy aroma?

All these signs are reassuring, and have been through the ages, but they are mere indicators of something much greater and infinitely mysterious: a hidden universe beneath our feet.

This cosmos is only now revealing itself as a result of scientific discoveries based on better microscopic imaging and DNA analysis. There is much still to learn, but it boils down to this: Plants nurture a whole world of creatures in the soil that in return feed and protect the plants, including and especially trees. It is a subterranean community that includes worms, insects, mites, other arthropods you’ve never heard of, amoebas, and fellow protozoa. The dominant organisms are bacteria and fungi. All these players work together, sometimes by eating one another.

The awareness of this biosphere should change the way gardeners think about cultivating plants and heighten everyone’s understanding of the natural world. In other words, don’t ever call it “dirt” again.

Nematodes convert nitrogen into a form that plants can use. (Jon Hughes for The Washington Post)

The sheer vitality of it is mind-bending: A teaspoon of good loam may contain a billion bacteria, yards of fungal strands, several thousand protozoas and a few dozen nematodes, according to Jeff Lowenfels, a garden writer based in Anchorage and co-author of “Teaming With Microbes.”

This is, basically, how it works: Plants manufacture carbohydrates through photosynthesis, but not just for themselves. They release some of their carbon sugars into the soil, which causes the bacteria and fungi to show up to feed. The bacteria crowd around the root zone, and the fungi form vast networks of interlocking strands that often link one plant to another. The bacteria convert nitrogen and other nutrients into forms the plants can use, often by getting devoured by other microbes.

The fungal strands, the mycelium, effectively increase the root mass of its host plant by as much as a thousand times and transport a bevy of goodies to the host plants, including phosphorus, copper, calcium and zinc. There is also evidence that trees use this network to send signals to one another if, say, leaf-eating pests have arrived.

In his Ted Talk, mycologist Paul Stamets referred to mycelium as “Earth’s natural Internet.”

Although some plant (and human) diseases are caused by soil-borne fungi and bacteria, most of these microbes are beneficial and keep the bad ones in check. The organisms assist in other ways, by increasing the size of soil particles, which improves the ability of the soil to hold water and air.

Even in the middle of a city, the subterranean world is thriving.

Scientists took almost 600 soil samples from across New York’s Central Park and discovered a surprising diversity and richness. They identified more than 120,000 types of bacteria and more than 40,000 species of fungi, protozoa and arthropods.

Fungi break down organic matter, which is why you will see mycelium strands in compost piles and under leaf litter. (Jon Hughes for The Washington Post)

Among the unexpected findings: The microbial species were the same, more or less, as those found in parts of the world with dramatically different flora and climates from New York’s, including Antarctic cold deserts, tropical forests and grasslands.

There was a strong association between the diverse organisms in each sample. “Unravelling these relationships will be critical to building a more integrated understanding of below-ground ecology,” the researchers wrote in a paper published by the journal for the British Royal Society. “Our work highlights that most of the diversity found in soil remains undescribed.”

Enough is known, however, to create a 21st-century subset of farming known as regenerative agriculture. The farmers have discovered that if you foster this biosphere, you don’t need expensive fertilizers because the microbes repay the plants with nutrients. They also, for obvious reasons, avoid pesticides that would kill this soil life.

The farmers do as little soil digging as possible because traditional tillage destroys the fungal networks and the desirable soil structure. Cover crops keep the soil life happy between growing seasons.

Advocates of this low-impact farming say it can restore soil carbon lost by the historic conversion of forest and prairie to farmland and help to mitigate greenhouse gases. In the 1990s, an Agricultural Research Service scientist in Beltsville, Sara F. Wright, discovered a sticky coating to fungal threads named glomalin that, it turns out, is a major reservoir for carbon.

Lowenfels says it’s also time for gardeners to adopt practices that nurture the soil biosphere. To say he thinks deeply about this subterranean world is an understatement. In addition to “Teaming With Microbes,” he has written “Teaming With Nutrients.” His latest title is “Teaming With Fungi,” which dwells on the type of fungi that directly associate with plant roots. They are known as mycorrhizal fungi, and he’s a big fan of adding them to his plants when they are installed, either as a spray or in powdered form available from the garden center. “It works. My tomato plants are bigger than the control, they’ve got more fruit on them, the plants are so healthy,” he told me. “My carrots are unbelievable this year.”

Some gardeners turn to compost tea to build soil microbes. This is made by aerating sugars, compost and humic acids in non-chlorinated water and then spraying the brew on plants and soil. Others are not convinced that this is needed, though everyone agrees that the way to foster the soil food web is to top-dress growing beds and lawns with organic matter such as shredded leaves or finished compost.

James Nardi, a biologist at the University of Illinois in Urbana, offers this advice: “Work with your fellow non-human gardeners. I never use synthetic fertilizers, and I never use pesticides.” Nardi’s 2007 book, “Life in the Soil,” remains an excellent introduction to the subject.

In the fall, he mixes horse manure with fallen leaves, shreds the mixture and applies it as a mulch to his growing beds. “In the spring, I have this lovely, spongy soil,” he said. Lowenfels shreds autumn leaves on his lawn and lets the biosphere use them over the winter.

The organic gardener’s mantra has never seemed more appropriate. Feed the soil, not the plant.

The players

Earthworms: Earthworms (and other worms) play an important role in the hidden biosphere. Most worm species in the garden were imported by Old World settlers, and some worms in certain regions have caused a problem by processing organic matter too efficiently. The latest culprit is a creature called the Japanese crazy worm (Amynthas agrestis), which multiplies like, er, crazy and damages the soil structure through mass feeding. It is long established in parts of the Southeast but has spread recently to Wisconsin and Illinois, where it is causing problems.

But the European earthworms familiar to most gardeners are helpful.

Worms provide critical assistance to smaller organisms by breaking down and incorporating leaves into the soil, so all may eat. Worm castings are rich in nutrients, including calcium, nitrogen, phosphorus and potassium.

The most famous observer of earthworms, Charles Darwin, estimated that they could add as much as 40 tons of casts per acre annually.

Insects: Thousands of insects (and spiders) live in a patch of soil. Some are considered pests by humans — Japanese beetle grubs, termites and weevils, for example — but others are beloved or at least beguiling and include the larvae of lightning bugs and cicadas. Dung beetles convert animal waste into humus, a service we take for granted. Ants are the most abundant soil insect. Although some species are pests or nurture pests such as aphids, ants with their highly organized colonies are essential members of the soil biosphere. They assist in the conversion of litter to humus, move and mix large quantities of soil, and spread the seed of bulbs and other desirable plants.

Other arthropods: The more conspicuous of these include millipedes and centipedes, as well as woodlice. Millipedes feed on plant debris and microbes; centipedes eat other arthropods. Woodlice, or sowbugs, are crustaceans that like soft plant debris and make quick work of green plant material and newly fallen leaves.

One of the most abundant, but barely visible, arthropods in the soil are springtails. They are named for a tail-like structure that allows them to jump when threatened. As many as a billion or more can live in an acre of soil. Depending on species, they cycle plant debris or feed on fungi, algae or other springtails.

Mites are generally regarded by gardeners as pests, and some are — sucking sap from plants and spreading disease. But the soil houses an immense community of non-pest species that are essential to the cycle of life. Half the known species of mites live in the soil, where they feed on decaying plant litter. Nardi writes that they “set the stage for smaller decomposers like bacteria and fungi to free most of the energy and nutrients stored in those leaves.”

Some mites are predatory and attack nematodes and other small creatures.

Nematodes: Nematodes are tiny wormlike creatures that have traditionally been viewed in agriculture as serious pests that harm plants by feeding on their roots. More recently, the view of nematodes has become more nuanced because some species are now commonly used (and purchased) as predators of garden pests such as slugs, vine weevils and white grubs, to name a few. In truth, the world of nematodes is much greater and can only be imagined. Experts believe there may be close to a million species, of which only a fraction have been described scientifically.

Some nematodes eat soil bacteria and fungi, while others prefer to consume other soil arthropods and protozoa. Their value to the garden is in converting nitrogen into a form that plants can use.

Protozoa: Protozoa are microscopic creatures that live in vast numbers in the film of water between soil particles. The most well known is the amoeba, but these microbes come in several forms, including species that move with a single flagellum or with hairlike cilia.

They are the major predator of bacteria, and in consuming them they release nitrogen and other nutrients to plants.

Protozoa, in turn, are eaten by nematodes and other small arthropods.

Bacteria: Historically, bacteria have been associated with germs. Some of the nastiest human diseases — anthrax, typhoid, tuberculosis and syphilis, for example — are the result of bacterial infections. But we have come to know too that our guts are full of beneficial bacteria and essential to our health.

The soil is the same way — the bad actors are outnumbered and usually outwitted by the good ones. Healthy soil is loaded with bacteria, and because they’re not very mobile, they tend to hang out in vast numbers on and around the roots of plants, a zone known as the rhizosphere. There can be as much as 100 times more bacteria around plant roots than elsewhere in the soil, and with good reason. The plants feed them carbon sugars. The microbes give back nitrogen.

Fungi: Fungi break down organic matter, which is why you will see mycelium strands in compost piles and under leaf litter. Two basic forms of fungi form a symbiotic relationship with plants. One exists in proximity to root tips and associates with hardwood trees and conifers. The other penetrates the cell wall of the roots and is found in plants of the domestic landscape — flowers, shrubs, grasses and vegetables.

The fungi grow tiny, fragile strands called hyphae. They are a tenth the thickness of human hair, but there are so many of them that they form a vast network, effectively extending the reach and efficiency of plant roots. In her book “The Soil Will Save Us,” science writer Kristin Ohlson says there can be as much as 320 miles of hyphae in a cubic foot of soil. At least 80 percent of the plants on Earth connect to these fungal partners.

“Gardeners need to know this stuff,” Lowenfels said. “A thinking gardener is a better gardener.”

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