The Underground Railroad - How Plants Work (2015)

How Plants Work (2015)

2 The Underground Railroad

TUCKED IN THE CORNER of my backyard is a small opening, covered with a thick layer of wood chips. It’s bounded by an arborvitae hedge on two sides, a redbud tree, a dogwood, and several smaller shrubs and groundcovers. Pulling back the moist, decomposing mulch, I can see a mass of fine white threads as well as fibrous roots. As I dig deeper, my trowel thuds against thicker, woodier roots. This complicated network of thick and thin roots, intersected by those fine white threads, runs in all directions like a city roadmap. Yet because it’s hidden underground, we often neglect this network—or worse, damage it—through our activities. And those white threads? They’re not roots but beneficial mycorrhizal fungi, which we’ll talk about later in this chapter.


Fungi and roots create an underground network.

Plant roots serve several functions: they anchor and stabilize the plant, store food, produce growth substances, and take up water and minerals. They represent the beginning of a plant’s internal transport system, somewhat similar to our own circulatory system. But rather than being driven by an active pumping heart, transportation in plants is passive and depends on a water gradient that begins in the soil and ends in the atmosphere.

Like the spokes on a wheel, roots radiate outward from the base of the stem, colonizing the soil and tapping pockets of water and nutrients. Some species have rhizomes (underground stems) that grow entwined with the roots. They serve as hidden growing points from which new roots and shoots arise. In fact, some of the clusters of goldenrod, poplar trees, and other common plants are nothing more than clones of a single individual whose roots and rhizomes have taken over a piece of land. We see this in our own gardens with spreading groundcovers and perennials.

How Far Roots Spread

One of the gardener’s standard reference points is the dripline, that invisible circle on the ground corresponding to the outermost leaves on a tree or shrub. We mulch, water, fertilize, and protect the soil between the trunk and the dripline, because the roots are there. But, in fact, roots grow beyond this circle. It’s estimated that woody plants may have root systems that are at least two to three times the diameter of the dripline. Most of this far-reaching system is made up of fine fibrous roots that are difficult to see when we’re digging in the landscape. It’s not surprising we don’t realize those tiny roots creeping into our annual border are from that maple tree 20 feet away.

Root growth is opportunistic. Fine roots that happen to hit pockets of water, nutrients, or oxygen in the soil will scavenge these resources and push onward. If roots hit a dead end, however, they die back to a larger root. If you were able to watch the root zone under time-lapse photography, you’d see a flurry of activity as tiny roots zoom in every direction, sometimes morphing into tiny starbursts of filaments when they hit the mother lode. Roots that survive the exploratory phase thicken and harden, eventually becoming permanent storage organs as well as parts of the transport system.


Roots were once thought to stop at the dripline of a tree, which is often where mulching ends.


We now know that roots extend far past the dripline, even to where the photographer was standing.

Unlike woody roots, fine roots can be transient. A good example of transient roots can be found in the mulch in my garden that we were exploring. In the wet months of the year, the mulch is always moist and roots find their ways upward to take advantage of the oxygen and nutrients in this upper layer. The aboveground parts of many plants undergo dormancy, but roots grow all year round. As the growing season approaches, temperatures get warmer, rains tend to decrease, and the top of the mulch layer will begin to dry out. The roots that are there will die back to deeper parts of the mulch and soil where it’s still moist enough to support growth.

This observation has led to well-intended but erroneous advice about using mulches. You may have been warned that you shouldn’t use deep organic mulches because the roots grow into them and eventually they’ll die. But the transient, opportunistic nature of the fine root system means this is okay—actually, it’s more than okay. The plant is able to absorb water, oxygen, and nutrients while conditions are favorable, if only for a short time. These resources are stored and contribute to increased growth and vigor of the entire plant. So mulch away!

Amending Soil before Planting


Adding organic matter, sand, gravel, or other materials to improve soil fertility, drainage, and/or reduce compaction.


Plants will establish better with richer, well-drained soil.


In limited spaces such as containers or raised beds where the entire soil volume can be amended, plants may establish better depending on the amendment chosen. In landscapes, however, only a fraction of the soil profile is changed by amendment. Where the amendment meets the native soil, you’ve created a discontinuity that slows down air and water movement. Imagine putting a handkerchief over your nose and mouth. You have to work harder to pull oxygen through it, and the inside of the cloth gets damp from the moisture in your exhalations. It’s the same phenomenon in the soil, and likewise plant roots will struggle to cross the barrier.

Although some plants don’t really care (heck, some plants grow through concrete), others are very picky about their root habitat and will grow only in the amended area. For smaller plants this might not be an issue, but it will be a problem for woody plants. Instead, use that great organic matter as part of your mulch layer, and leave the soil au naturel.

How Deeply Roots Grow

When I was growing up, I would often wander through the Douglas fir woods near my home. Once in a while, I’d find a tree that had blown down and I’d scramble onto the weblike mass of exposed roots. Even though I knew, subconsciously, that this was what tree root systems looked like, I still passively accepted the widely held notion that all plants except monocots (such as grasses and orchids), ferns, and mosses had a single taproot that descended far underground, with lateral roots branching off from the sides. Like a Rorschach blot, the symmetry of this appeals to us: a single trunk balanced by a single root.

Our misunderstanding of root systems arises from the fact that dicots have a taproot. But this taproot is transient. It’s dominant during the seedling growth phase, when a single root extends from the seed and grows downward. But over time, most taproots are absorbed into a maturing root system that extends laterally as well as downward. For trees and shrubs, the root system may not grow much deeper than a foot or two. As you now know, the lateral spread can extend far past the dripline of the crown.

Why are root systems so shallow relative to their spread? Unlike leaves, roots can’t make their own oxygen, so their growth is limited to areas of the soil that are well aerated. Gardeners who make the mistake of planting trees and shrubs too deeply will see these specimens become straggly and listless, until they eventually succumb to the pests and diseases that thrive on injured plants.

Obviously, soil structure and texture will determine how deeply oxygen, and thus roots, will permeate. Compacted soils, which are so common in our urban areas, hold little oxygen. Even seemingly harmless footpaths winding through parks compact soils to the point that they structurally resemble solid rock. The most tenacious weeds have a hard time getting established on these barren soils, much less any desirable species.


Mature trees and shrubs exploit water, nutrients, and oxygen with broad, shallow root systems.


A long taproot helps seedlings establish quickly.

In contrast, excessively drained, sandy, or rocky soils are highly aerated and the roots of naturally occurring trees might extend many feet into these unusual soils. The limiting factor for plants in highly aerated soils is water, rather than oxygen.

How Water Moves through Plants

To begin, we need to consider one of the amazing properties of water, specifically the asymmetry of the molecule, which contains two hydrogen atoms and one oxygen atom (H2O). Imagine your head is an oxygen atom and your hands are hydrogen atoms, joined by your arms in between (the bonds). Now make a Y with your arms (perhaps performing a molecular version of The Village People’s “YMCA”). There is a partial negative charge associated with the oxygen atom and a partial positive charge associated with each of the two hydrogen atoms, and this uneven electrical charge defines water as a polar substance.

Landscape Fabric (Geotextile, Weed Barrier)


Landscape fabric is laid on top of soil to keep weeds out while letting water and oxygen in.


Because the fabric is porous, water and oxygen will pass through to the roots of desirable plants but weeds can’t poke through.


Unlike the claims right on the packaging, these products do not let water and oxygen through for very long. Those little holes are quickly filled with soil particles, and water puddles on top of the fabric, only slowly dripping through to the parched roots below. Dust and soil blow in along with weed seeds, and within a few months—Voila! Weeds spring up like magic. Likewise, aggressive weeds like bindweed and horsetail slip underneath and pop right through the holes and seams. I guess they didn’t read where the package claimed “permanent weed control.”

Meanwhile, your tree and shrub roots are desperately seeking water, oxygen, and nutrients. They will creep up to the soil surface, sometimes growing through and on top of the fabric. This causes the fabric to break down even faster. If you try to remove it, you damage your trees and shrubs in the process. Do yourself a favor and don’t buy this stuff!


Weeds love landscape fabric.


Because of the slight positive and negative charges at the poles of water molecules, hydrogen bonds (dashed lines) form between them. Hydrogen bonds cause water molecules to cling to each other and to other polar molecules.

We know that opposites attract, and that’s exactly what happens with the charged areas of water molecules. Positive regions of polar molecules are attracted to negative regions of others, such that water molecules cling to one another (cohesion) as well as to other polar substances (adhesion). Cohesion allows water to form droplets. If a water droplet is placed on a material made of polar molecules, such as tissue paper, the droplet readily spreads out and adheres to the paper. But if that same water droplet lands on the waxy surface of a leaf, it remains in droplet form. That’s because waxes are made of nonpolar molecules, so there’s no electric charge to attract the water.

Tissue paper and plant cell walls are both made of cellulose, a polar material closely related to starch. The water uptake vessels in plants, collectively called xylem, are constructed of nonliving cells that essentially form hollow tubes of cellulose. Water adheres to the sides of the xylem tubes, creating an unbroken stream of water through the stem of the plant. You can think of them as giant straws, sucking the water from the roots to the leaves.

Finally, we need to understand how water can move from one place to another without the addition of energy. The basic rule is that water moves toward areas that contain less water. Many gardeners know what happens when they put salt on a slug. The slug shrivels up and dies as the water in its body moves outside toward the salt: the area of the body with salt on it has less water than the slug has on the inside. This passive diffusion works in plants, too. Moist soil contains lots of water, which diffuses into roots, where the presence of sugars, amino acids, and other dissolved substances means that water content is relatively lower compared to the soil. Leaves have even less water, because they have even more dissolved sugar. So water moves from the roots, through the stems, and into the leaves. The final pull comes from the atmosphere, where water concentrations can be quite low, especially when it’s sunny or windy. Water is pulled through the stomata, tiny pores in the leaf surface, into the atmosphere, dragging chains of water molecules behind in a process called transpiration. It’s estimated that 97 percent of the water taken up by the roots is lost to the atmosphere.

Why don’t plants conserve water more efficiently? Part of the answer is that transpiration is more than just a process for moving water through the plant. Minerals, nutrients, and other dissolved substances can all hitch a ride on the Transpiration Express. These tagalongs are especially noticeable in the spring, when the roots release materials they have stored all winter, as anyone who’s ever tapped a maple tree to make sugar or syrup will know. During the hot summer months, water loss from the leaves lowers the leaf temperature through evaporative cooling, keeping the photosynthetic machinery in a healthy state.


Water movement in plants is a one-way trip from the roots to the leaves.

Nevertheless, the apparent waste of water still puzzles both gardeners and scientists, who often wonder why plants haven’t developed a more efficient way to take up carbon dioxide for photosynthesis. For it is through the stomata that carbon dioxide enters the leaf, at the same time that water exits. Cacti and other succulent plants of arid climates have evolved water conservations strategies, such as closing the stomata during the day and only opening them at night. This adaptation affects the plants’ photosynthetic ability (as we’ll explore more in chapter 4).

Sheet Mulches


Placing newspaper or cardboard over weeds or bare soil. Sometimes compost or wood chips are put on top, often in many layers to create a sort of mulch lasagna.


Sheet mulches kill existing weeds and prevent weed seeds from germinating. They’re better than landscape fabrics because they break down and contribute to soil health.


It’s true that newspaper and cardboard sheet mulching is better than landscape fabric, but that’s not much of a compliment. Any sheet mulch creates a barrier to oxygen and water transfer between the soil and the environment. Roots in such a situation will grow closer to the surface of the soil to grab any oxygen that permeates through the sheets. Likewise, worms and other soil organisms move closer to the surface as the soil becomes more oxygen depleted, and gardeners mistakenly attribute their increased visibility to the attractiveness of the sheet much. When paper-based sheet mulches dry out, irrigation and rain water run off them, creating arid conditions underneath.

Paper-based sheet mulches do break down, but there is no scientific rationale behind their use. Chunky, coarse organic mulches are more effective in reducing weeds and create a more hospitable environment for roots and soil critters alike.


A virtual desert exists underneath dried-out cardboard mulch.


A visible root flare is crucial to tree longevity.

How to Tell When Roots Aren’t Happy

Plants can survive a long time with root problems. The key word here is survive, they certainly don’t thrive. Observant gardeners might notice that a recently planted Japanese maple just doesn’t seem to get much taller. Or maybe the new leaves on a favorite rhododendron seem to be getting smaller every year. These are signs that the root system isn’t supplying enough water and/or nutrients to support vigorous growth aboveground. Figuring out why is tricky, especially without exhuming the roots. There are some key symptoms, however, that gardeners should look for. Leaves may be smaller or sparser than normal, or they may have scorched tips and margins in the summer, all because they aren’t being supplied with enough water. Assuming there is enough water supplied to the soil, what else might be happening underground?


The burlap and twine on balled-and-burlapped trees protect them in the nursery, but they interfere with root establishment when the trees are planted.


The circling roots of container plants will continue their orbit unless straightened out upon planting. (New roots, however, will grow outward.)


Let’s start with the recently planted Japanese maple—or any other young tree—that stubbornly stays about the same size year after year. Can you see the root flare, the part of the tree where the trunk morphs into roots? This flare should be at the soil surface. If you can’t see it, the tree is planted too deeply. Although some tough tree and shrub species don’t mind this treatment, others have roots that will struggle for oxygen. Roots without enough oxygen aren’t very efficient at taking up either water or nutrients, effectively starving the trunk, branches, and leaves. You can commute the death sentence on these trees by digging them up and replanting them correctly. Do this within the first year after planting and you’ll probably be successful, but the longer you wait the more you reduce your chances of success.

Even properly planted trees and shrubs are in danger if their roots are suddenly buried due to changes in grade. Maybe you’ve put an addition on your house, widened a driveway, or done some other work where the soil level has been increased. Adding several inches of soil on top of existing fine root systems is literally burying them alive. Unlike leaves, roots don’t make their own oxygen and they depend on pockets of air trapped in the soil. When the soil suddenly becomes much deeper, it’s more difficult for oxygen to seep through from above and the roots suffocate. Mature, well-established trees might be able to survive this treatment, but younger plants will benefit from being exhumed and replanted at grade.


Now let’s consider that rhododendron whose new leaves are obviously smaller than those from the year before. You can see the flare of the roots, so you know it’s not buried too deeply. I call the next diagnostic tool the wiggle test. Gently grasp the plant near the base and wiggle it. Can you see soil movement around the root ball? Or can you feel movement through the trunk? Your fingers are exquisitely adapted to sense differences in resistance. With this rhododendron, you can see the root ball rock, so you know that the roots have not established in the soil. Now you have to figure out why.

Since the roots are obviously not exploring the surrounding soil, there’s no reason not to dig up the rhododendron. What you’re likely to find is a root ball surrounded in burlap or possibly shaped like the container it was originally planted in. Plants whose roots are isolated from the native soil have a difficult time establishing, and the best thing to do is release them from their solitary confinement. If it’s a balled-and-burlapped root ball, you’ll want to remove the twine, burlap, and as much of the clay as you can. Cylinder-shaped root balls from containers need to be cut and spread to correct the circling you’ll see. This might seem like plant abuse, but it’s the only way to deal with incorrigible root systems. The cool thing about roots is that pruning stimulates new root formation. So take the tough love approach with these anti-establishment trees and shrubs. They’ll thank you later!

Bare-Rooting Trees and Shrubs for Planting


Removing all foreign materials—containers, wire baskets, burlap, twine, and soil—from woody plant roots before planting.


By removing as much of the foreign material as possible, roots will be in direct contact with the native soil when planted.


This can be a stressful process for you as well as the tree or shrub. We’ve been taught for so long to leave the root ball intact that it’s very difficult to look at the issue objectively. But research has shown bare-rooting provides better long-term establishment and survival than leaving the root ball untouched.

Left intact, the clay or soilless media that is nothing like the site’s native soil will create barriers to water and air movement to the roots. By removing this material, plant roots are immediately able to establish in the native soil without passing through multiple barriers.

Poor root systems can be corrected before planting by removing circling, kinked, or otherwise deformed roots. The root system should look like spokes on a wheel. Also, pruning stimulates roots to grow once planted.

Removing all foreign materials will allow you to unearth the root flare. This structure needs to be planted at grade, not underground.

Finally, the transplanted tree will not need to be staked for more than a month or two, if at all, when planted in this manner.

This is a revolutionary approach and one that does not sit well with many home gardeners or nursery and landscape professionals. However, it is supported by research showing better long-term establishment and survival than conventional methods.


Washing the clay from roots of large and small trees will improve their establishment when planted.

Fungal Alliances

I’ve compared root systems to an underground railroad, but imagine upgrading that freight train to high speed rail. That’s what a certain group of fungi can do for your landscape and garden plants underground. We saw them in my backyard at the beginning of this chapter: those white threads too long and slender to be roots, yet cozily intertwined with the root system. These are the hyphae of fungi, and their associations with plants are collectively called mycorrhizae (meaning fungus roots). Before you grab the fungicide, let’s get to know these plant partners.

Mycorrhizae are ancient and beneficial associations that arose hundreds of millions of years ago, when plants first extended roots into soil. When first discovered in the late 1800s, mycorrhizal relationships were thought to be unusual oddities. We now know that they are the rule, rather than the exception, especially in woody plants. Mycorrhizal relationships are mutualistic in that both partners receive a significant benefit in exchange for sharing resources: you scratch my back, and I’ll scratch yours. Plants transfer carbohydrates and B vitamins through the hyphae to the fungi, which are not photosynthetic and can’t generate their own food. In return, the fungi extensively colonize the root surfaces and enhance the plant’s uptake of water and mineral nutrients.

Mycologists, scientists who study fungi, have divided mycorrhizal fungi into two categories depending on how cozy the relationship is. Those whose root-like hyphae surround and occasionally penetrate root tissues are ectomycorrhizae (ecto means outside), and those whose hyphae always enter the root cells are endomycorrhizae (endo means inside). Ectomycorrhizal fungi partner up with many woody plant species, forming an extensive hyphal network throughout mulch and topsoil layers; these are the networks we saw in my backyard soil. In contrast, endomycorrhizae are found in hundreds of plant families. You might see these delicate structures associated with the roots of your annual flowers or vegetables.


Healthy soils contain vast repositories of mycorrhizal spores in the coarse organic matter near the soil surface, where they germinate under moist, aerated conditions. As the hair-like hyphae emerge from the spores, rain and irrigation water create channels down through the soil toward growing plant root tips. Receptive roots release chemical cues that allow hyphae to penetrate the cell walls and create chemical passageways between the two partners. Multiple infection points and hyphal branching create a cottony sheath around the roots that extends far into the surrounding soil. Like microscopic miners, mycorrhizae discover and extract soil water and nutrients from otherwise inaccessible pockets.

The impact of mycorrhizal colonization goes far beyond an individual plant. Most plants are colonized by a variety of mycorrhizal fungi, and most of these fungi have multiple hosts. Mycorrhizae can link roots of different species, transferring nutrients to the plants with highest demand. At the same time, the dense network of fine hyphae increases soil aggregates and improves soil stability, while enhancing organic matter decomposition and acidifying the root zone. The resulting network is a virtual fungal freeway of nutrient and water acquisition and transfer.

As if extra water and nutrients weren’t enough of a benefit for plants, their fungal partners have some bonus gifts for joining the network. Mycorrhizal plants are more resistant to environmental stresses, such as drought and salinity, because their ability to find and extract soil water is improved. The dense fungal network created by mycorrhizal fungi limits the available space for colonization by pathogens or attack by nematodes, meaning that plants are less prone to disease and root pests.

But for this vital relationship to exist, plant roots need to be receptive to inoculation. The best way to ensure this is to avoid overwatering and excessive fertilization. Adding too much fertilizer, especially those containing phosphate, is by far the most damaging garden practice in terms of mycorrhizal health. Composted manure and many soilless potting mixes contain high levels of phosphate and other nutrients. With a plethora of nutrients, plants are less dependent on mycorrhizal connections. Mycorrhizal fungi retreat into the shadows, remaining inactive until more hospitable soil conditions return.

Not surprisingly, this mutually beneficial association between mycorrhizal fungi and plants has been marketed in the form of products that we’re told will improve soil health and plant establishment in gardens and landscapes. But scientific studies continue to show that these products have no value. We know that healthy soil will naturally contain a smorgasbord of beneficial microbes, including mycorrhizal fungi. And if a soil is in such bad shape that native mycorrhizal species don’t survive, adding packaged spores isn’t going to help.

Don’t Derail the Train

As you can probably tell by now, healthy vigorous root systems and their mycorrhizal partners will reward you with a garden full of lush, attractive plants that require few fertilizers or pesticides. Even though you can’t see this busy underground railroad, you need to constantly be aware of its presence and tread lightly. Activities associated with construction are extremely damaging to soil structure. Topsoil is removed, taking with it the beneficial microbes and all of the organic material. Adding insult to injury is the compaction caused by heavy equipment, which creates oxygen-depleted soils about as hospitable as cement. Of course, mycorrhizal colonization and plant communities will eventually recover, but unnecessary soil disruption should be avoided. This also means avoiding gardening activities that compact the soil, or worse, grind it into a lifeless powder.

Yes, I’m talking about rototilling. I know a lot of you enjoy your power tools and handling a rototiller is almost as fun as riding a bucking bronco. But as far as life in the soil is concerned, this is the equivalent of an underground tsunami. Rototilling destroys natural soil structure along with any plant roots and hapless animals in the path of destruction. Soils are more than just a medium for growing veggies: they are complex ecosystems containing beneficial bacteria, fungi, insects, nematodes, earthworms, and many other denizens. Well-structured soils, along with their natural living communities of organisms, benefit plant roots and enhance their establishment. Roots damaged by rototilling require energy and resources to repair, and when their protective outer tissues are torn they are exposed to diseases and pests.

In this case, less is more in terms of soil and plant health. Instead of revving up the rototiller, try using hand tools and digging only where you intend to place seeds or plants. When you’re getting rid of sod or other unwanted plants, cover them with a deep layer of arborist wood chips and let them die a sunless, hidden death. You’ll preserve soil integrity and reduce fossil fuel consumption as well. Add some mulch to protect any exposed soil, water well, and your impact on this complex ecosystem will be minimal.

Looking at the corner of my backyard again, it’s with new respect that we consider the landscape underground. Roots and their fungal helpers mine the soil for water and minerals, efficiently transporting this nutritious liquid to the tops of my redbud and the arborvitae hedge without a pump. Which gets us to wondering, what are all those nutrients used for?