Garden Allies: Soil Microbes

Mysterious soil organisms facilitate nutrient uptake by plants

In our last three forays into the under-world of the garden, our subject was decomposers: those organisms  that break down organic matter and build the gardener’s most precious resource, the soil that supports virtually all plant life. As we conclude our discussion of the soil foodweb, we explore rhizobia bacteria, actinomycetes, and mycorrhizae.

Endomycorrhiza. Illus: Craig Latker

Endomycorrhiza. Illus: Craig Latker

Certain bacteria and fungi form obligate mutualistic relationships with plants and are essential for optimal plant growth. Many plants can’t grow at all without their largely unseen partners, which facilitate nutrient uptake, while the mutualistic partner also derives essential sustenance. These partners provide nutrients such as nitrogen, phosphorus, and iron in an available form. Nitrogen gas (N2), for example, makes up 79 percent of our atmosphere, and nitrogen is an essential component  in DNA, proteins, and chlorophyll molecules. For nitrogen to be available to plants, however, it must first be converted, or “fixed” to a form that can be taken up by roots. In nature, this process is primarily accomplished by soil microbes and fungi converting N2 into ammonium (NH4+), nitrate (NO3-) and nitrite (NO2-). Lightning also fixes atmospheric nitrogen into a usable form for plants.

The nitrogen-fixing cyanobacteria (formerly known as blue-green algae) are among the first colonizers of bare land such as volcanic flows and glacial moraines, and are known as pioneer species. They create a hospitable environment for plants that succeed them; some are known to form mutualistic relationships with a few plant species. The Rhizobium bacteria associated with most leguminous plants are well-known to gardeners. Pull up peas and beans for instance, and the roots, if well inoculated with bacteria, will be covered with pale pinkish nodules. In order for the nitrogen contained in the nodules to become available in the soil, the roots must decompose.  For many years, I have increased the fertility and tilth of my vegetable garden with a fall crop of fava beans. When the fava beans begin to flower, I simply cut the plants down at ground level, bury the tops in the compost pile, and leave the fibrous root system to decompose in place (saving a few plants to harvest the delicious flowers and beans).  No tilling necessary! Other bacteria also fix nitrogen, but live free in the soil, not in plant roots.

Root nodules on legume. Illus: Craig Latker

Root nodules on legume. Illus: Craig Latker

Some  members of another group of microbes, the actinomycetes, are also capable of fixing nitrogen. One group of actinomycetes produces antibiotics such as streptomycin, while a different group is responsible for the earthy odor of forest humus and well-made  compost. The third group includes Frankia species that form large clusters of nitrogen-fixing nodules on the roots of some non-leguminous  plants, including some species of ceanothus, bayberry (Morella californica ), alder (Alnus spp.) and mountain mahogany (Cercocarpus spp.). Plants that fix nitrogen in partnership with actinomycetes are known as actinorhizal plants; there are over 200 plant species in eight families.

Twenty years ago, most gardeners had never heard the word “mycorrhizae,” although they were first documented in 1885 by a German scientist, Albert Bernhard Frank, in a simple experiment comparing pines grown in sterile soil to pines grown in forest humus. Mycorrhizae are fungi that have a mutualistic relationship with plants; the fungi use sugars produced by the plant, while they increase availability of water and of several nutrients, most notably phosphorus, to the plant. Ectomycorrhizae are associated with conifers and hardwoods, and grow in a web surrounding the roots of their host. The fruiting bodies are the familiar mushrooms of our woodland hikes—fungi such as Boletus, Cantharellus, and Morchella. Ectomycorrhizae are specialists on certain species of plants; any mushroom forager knows that their favorite mushrooms are only found in association with specific tree species.

Endomycorrhizae, on the other hand, are generalists, and the same species of fungus may be found on many species of plants. The fungal hyphae of endomycorrhizae penetrate into the cell walls of the hosts. The longer we study mycorrhizal relationships, the more we discover how ubiquitous mycorrhizae seem to be. Perennials, softwood trees, shrubs, and many vegetables have been discovered to be associated with endomycorrhizae, with the notable exception of all species of the large mustard family. Some plants may host dozens of species, and include both types of mycorrhizae

Mycorrhizae are reputed to add from 700 to 1,000 times the effective surface area to roots, greatly increasing the ability to take up water and nutrients. Unless the soil in your garden is highly impoverished, adding purchased mycorrhizae may be unnecessary as endomycorrhizae native to the soil should be present. In a new garden with poor soil, or added to a sterile potting mix, mycorrhizae can make a difference to success.

Armillaria ostoyae. Illus: Craig Latker

Armillaria ostoyae. Illus: Craig Latker

It has long been my practice, when planting native shrubs in my garden, to gather a handful or two of humus from the nearby woods and use it to inoculate the planting area. A walk in the woods is never in vain, and it is always rewarding to pull the aromatic bundle from my pocket and add it to my garden.