4.2: Soil Microorganisms

Microorganisms are very small forms of life that can sometimes live as single cells, although many also form colonies of cells. A microscope is usually needed to see individual cells of these organisms. Many more microorganisms exist in topsoil, where food sources are more plentiful, than in subsoil. They are especially abundant in the area immediately next to plant roots (called the rhizosphere), where sloughed-off cells and chemicals released by living roots provide ready food sources. Rhizosphere soil may have 1,000 times or greater the number of organisms than the soil just a fraction of an inch further away from the root. These organisms are primary decomposers of organic matter, but they do other things, such as provide nitrogen through fixation to help growing plants, detoxify harmful chemicals (toxins), suppress disease organisms and produce products that might stimulate plant growth. Soil microorganisms have had another direct importance for humans: they are the source of most of the antibiotic medicines we use to fight diseases.

Bacteria

Bacteria live in almost any habitat. They are found inside the digestive systems of animals, in the ocean and freshwater, in air, and certainly in compost piles (even at temperatures over 130 degrees Fahrenheit) and in soils. Bacteria are an extremely diverse group of organisms; a gram of soil (about 0.035 ounce) may contain many thousand different species. Although some kinds of bacteria live in flooded soils without oxygen, most require well-aerated soils. In general, bacteria tend to do better in neutral or alkaline pH soils than in acid soils. When colonies of bacteria develop they frequently produce a sticky material that, together with remnant cell walls of dead bacteria, help to form soil aggregates. In addition to being among the first organisms to begin decomposing residues in the soil, bacteria benefit plants by increasing nutrient availability. For example, many bacteria dissolve phosphorus, making it more available for plants to use.

Bacteria and nitrogen. Bacteria are very instrumental in providing nitrogen to plants, which they need in large amounts but is often deficient in agricultural soils. They do it in multiple ways. First, bacteria themselves tend to be rich in nitrogen (that is, they have a low carbon to nitrogen level) and when decomposed (or eaten) by other organisms, like protozoa, nitrogen is released to the soil in forms that plants can use.

You may also wonder how soils can be deficient in nitrogen when we are surrounded by it: 78% of the air we breathe is composed of nitrogen gas. And each percent soil organic matter in the topsoil contains about 1,000 pounds of nitrogen per acre. Yet plants as well as animals face a dilemma similar to that of the Ancient Mariner, who was adrift at sea without fresh water: “Water, water, everywhere nor any drop to drink.”

Unfortunately, neither animals nor plants can use nitrogen gas (N₂) for their nutrition. Nor can plants use the nitrogen tied up as part of an organic molecule. It needs to be converted to the inorganic forms of ammonium and nitrate to become available for plants to use. This process involves bacteria and is called nitrogen mineralization.

Another important conversion process is known as nitrogen fixation. Some types of free-living bacteria are able to take nitrogen gas from the atmosphere and convert it into a form that plants can use to make amino acids and proteins. Azospirillum and Azotobacter are two groups of free-living, nitrogen-fixing bacteria. Along with supplying N, Azospirillum attaches to the root surfaces and promotes plant growth by producing a number of substances that help plants better tolerate various kinds of stress. While these types of bacteria provide only a modest amount of nitrogen to the soil, this N addition is quite important to natural systems where nutrient cycling is efficient. Some innovative companies are now trying to enhance nitrogen fixation by free-living bacteria through soil additives and seed coatings.

Another type of nitrogen-fixing bacteria forms mutually beneficial associations with plants. One such symbiotic relationship that is very important to agriculture involves the nitrogen-fixing rhizobia group of bacteria that live inside nodules formed on the roots of legumes. People eat some legumes or their products, such as peas, dry beans, lentils and soybeans in the form of tofu or edamame. Soybeans, alfalfa and clover are used for animal feed. The symbiotic bacteria provide nitrogen in a form that leguminous plants can use, while the legume provides the bacteria with sugars for energy. It is common to apply rhizobia inoculant to seeds if the legume (or one with which it shares a strain of nitrogen-fixing bacteria) has not been grown in the field recently. Nodulation is enhanced in cool soils with lots of biological activity and plentiful growth-promoting bacteria. Clovers and hairy vetch are legumes grown as cover crops that enrich the soil with organic matter as well as nitrogen for the following crop. In an alfalfa field, the bacteria in the plant root nodules may fix hundreds of pounds of nitrogen per acre each year. With peas, the amount of nitrogen fixed is much lower, around 30 to 50 pounds per acre.

Relative Amounts of Bacteria and Fungi

All soils contain both bacteria and fungi, but they may have different amounts depending on soil conditions. Relative to their carbon contents, bacteria are higher in nitrogen than fungi. Bacteria also have short life cycles, and when they die or are consumed by another organism such as a nematode, plant-available nitrogen is released. But in the off season when no commercial crop is present in the field (fall through early spring) this nitrogen may be lost. Fungi live longer and less nitrogen is released when they are decomposed.

The ways in which you manage your soil—the amount of disturbance, the degree of acidity permitted and the types of residues added—will determine the relative abundance of these two major groups of soil organisms. Soils that are disturbed regularly by intensive tillage tend to have more bacteria than fungi. So do flooded rice soils, because fungi can’t live without oxygen, while many species of bacteria can. Tillage destroys the network of mycorrhizal hyphae, and in the absence of living plants (fall, winter, spring), viable spore numbers decrease, causing lower inoculation of spring-planted crops. Soils that are not tilled tend to have more of their fresh organic matter at the surface and to have higher levels of fungi than bacteria. Because fungi are less sensitive to acidity, higher levels of fungi than bacteria may occur in very acid soils.

Despite many claims, relatively little is known about the agricultural significance of bacteria versus fungal-dominated soil microbial communities. Therefore, it is difficult to state whether higher versus lower ratios are better or worse, just that soils that tend to have more bacteria relative to fungi are more characteristic of soils near or above neutral pH that are intensively tilled, enhancing rapid organic matter decomposition and temporary nutrient availability.

The actinomycetes, another group of bacteria, break large lignin molecules into smaller sizes. Lignin is a large and complex molecule found in plant tissue, especially stems, that is difficult for most organisms to break down. Lignin also frequently protects other molecules like cellulose from decomposition. Actinomycetes have some characteristics similar to those of fungi, but they are sometimes grouped by themselves and given equal billing with bacteria and fungi. That earthy scent you smell from healthy soils, especially after a rain, is produced by actinomycetes.Another important soil organism is cyanobacteria, frequently called “blue-green algae” although they are bacteria. They are found near the soil surface, in field puddles and in flooded soils. They can fix atmospheric nitrogen as well as photosynthesize. Oxygen is released as a byproduct of photosynthesis and cyanobacteria are believed to be the organisms living in ancient seas that oxygenated the Earth’s atmosphere, allowing plants and animals that need oxygen to evolve and survive. It was the oxygen pumped into the atmosphere by cyanobacteria that led to an incredibly wide proliferation of organisms, including all those you see around you on farms, in forests and prairies, in cities, and in lakes and oceans.

Note

Soils contain a group of organisms that look like bacteria under the microscope but have very different biochemistry and are now classified in their own group (called a “domain” by biologists), the Archaea (pronounced ar-key-uh). These organisms can live under all types of conditions, including extreme temperatures and in very salty environments. They are also commonly found in soil, some playing a major role in the nitrogen cycle by carrying out nitrogen fixation or by converting ammonium to nitrate, producing nitrite (NO₂^–).

The tree of life is made up of three domains (or “superkingdoms”):

• Archaea
• Bacteria
• All other organisms (this includes all the rest of life, such as fungi, algae, plants, single-cell organisms such as amoeba, and animals)

Fungi

Fungi are another group of soil organisms. Many are small, some even single celled. Yeast, an example of a single-celled fungus, is used in baking and in the production of alcohol. Other fungi produce a number of antibiotics. Some form colonies that we can see, such as when you let a loaf of bread sit around too long only to find mold growing on it. We have seen or eaten mushrooms, the very visible fruiting structures of some fungi. Farmers know that there are fungi that cause many plant diseases, such as downy mildew, damping-off, various types of root rot and apple scab. Fungi also initiate the decomposition of fresh organic residues. They help get things going by softening organic debris and making it easier for other organisms to join in the decomposition process. Fungi are also the main decomposers of lignin and are less sensitive to acid soil conditions than bacteria. None are able to function without oxygen. The low amount of soil disturbance resulting from reduced tillage systems tends to promote organic residue accumulation at and near the surface, which in turn encourages fungal growth, as happens in many natural, undisturbed ecosystems.

Once classified as fungi because they form filaments and live on decaying organic materials, oomycetes have cell walls that are chemically different from fungi. This group includes water molds, one of which, Phytophthora infestans (causing late blight in potatoes and tomatoes), is the organism that decimated the Irish potato crop in the 1840s, causing nearly 1 million deaths and massive emigration. Another oomycete group causes the downy mildew plant diseases in a number of vegetables and in grapes.

Mycorrhizal fungi are of special interest, and it is hard to overemphasize their importance in relation to plants. Roots of most crop plants occupy only 1 percent or less of the topsoil (grasses may occupy a few percent), but many plants develop a beneficial relationship with fungi that increases the contact of roots with the soil. Fungi infect the roots and send out root-like structures called hyphae (see figures 4.2 and 4.3). The hyphae of these mycorrhizal fungi take up water and nutrients that can then feed the plant. The hyphae are very thin, about 1/60 the diameter of a plant root, and are able to exploit the water and nutrients in small spaces in the soil that might be inaccessible to roots. This is especially important for the phosphorus nutrition of plants growing in low-phosphorus soils. While the hyphae help the plant absorb water and nutrients, in return the fungi receive energy in the form of sugars, which the plant produces in its leaves and sends down to the roots. This symbiotic interdependence between fungi and roots is called a mycorrhizal relationship. Mycorrhizal associations also stimulate the free-living, nitrogen-fixing bacteria such as azospirillum and azotobacter, which in turn produce both nitrogen that plants can use and chemicals that stimulate plant growth. They also stabilize soil aggregates by producing sticky proteins.

Crop rotations select for more types of, and better performing, fungi than does mono cropping. Some studies indicate that cover crops, especially legumes, between main crops help maintain high levels of spores and promote good mycorrhizal development in the next crop. And if flooding or very wet soils prevent planting a cash crop, it is important to plant a cover crop if conditions permit so that there will be high levels of mycorrhizal colonization of the roots of next year’s commercial crop. Roots that have lots of mycorrhizae are better able to resist fungal diseases, parasitic nematodes, drought, salinity and aluminum toxicity. All things considered it is a pretty good deal for both plant and fungus. But keep in mind that mycorrhizae do not associate with some crops, mainly those in the cabbage family, making it more important to follow these with cover crops that help build fungal spores for the next cash crop.

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  Figure 4.2. A soybean root heavily colonized with mycorrhizal fungi (Rhiziphagus irregularis). Photo by Yoshihiro Kobae.

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  Figure 4.3. A white fungal network called hyphae, not plant roots, is the principal structure for the uptake of many important nutrients by plants. Illustration by Michael Rothman, all rights reserved.

Algae

Algae, like crop plants, convert sunlight into complex molecules like sugars, which they can use for energy and to help build other molecules they need. Algae are found in abundance in the flooded soils of swamps and rice paddies, and they can be found on the surface of poorly drained soils and in wet depressions. Algae may also occur in relatively dry soils, and they form mutually beneficial relationships with other organisms. Lichens found on rocks are associations between fungi and algae.

Protozoa

Protozoa are single-celled animals that use a variety of means to move about in the soil. Like bacteria and many fungi, they can be seen only with the help of a microscope. They are mainly secondary consumers of organic materials, feeding on bacteria, fungi, other protozoa and organic molecules dissolved in the soil water. Protozoa—through their grazing on nitrogen-rich organisms (especially bacteria) and waste excretions—are believed to be responsible for mineralizing (releasing nutrients from organic molecules) much of the nitrogen in agricultural soils.

The Plant Microbiome

The human microbiome consists of the multitude of microorganisms living on our skin and inside us, especially in our gastrointestinal tract. It has become clear that these organisms that comprise roughly the same number of cells as the rest of our body play an important role in human health. Maintaining a diverse and healthy microbiome, especially among the bacteria in the gut, has multiple beneficial effects on our wellbeing.

Plants also have microbiomes, with organisms living on leaves and shoots, inside plant tissue, and on and immediately adjacent to root surfaces (the rhizosphere). As happened with animals, when plants evolved over the eons, they did so in tandem with microorganisms that depended on plants for their sustenance. In turn, many provide benefits to the plant: a truly symbiotic or mutualistic relationship. (The relationship of plants and mycorrhizae is thought to have begun hundreds of millions of years ago.) About half of the substances produced during photosynthesis are transported from the leaves to the roots, supporting root growth and maintenance. And about a third of what roots receive (approximately 15 percent of total production by the plant) is exuded (released) into the soil as a complex mixture of organic chemicals, which provides nutrition to the vast numbers of organisms in the rhizosphere. This large quantity of microbial food sources is the reason why there are such large quantities of organisms present in this zone immediately next to the root compared to the rest of the soil. As the numbers of bacteria and fungi increase, so do the populations of organisms that feed on microorganisms, such as springtails (collembola) and nematodes, thereby stimulating the reproduction of microbes. The type and amount of root exudates varies by plant species and variety, and shapes the composition of the microbiome. (By the way, mycorrhizae also have a microbiome living on their hyphae.) Clearly we want to grow plants in ways that favor a beneficial microbiome: more complex rotations, decreased compaction and soil disturbance, more use of cover crops, and so on.