THE LIVING SOIL: BACTERIA

Bacteria are tiny, one-celled organisms – generally 4/100,000 of an inch wide (1 µm) and somewhat longer in length. What bacteria lack in size, they make up in numbers. A teaspoon of productive soil generally contains between 100 million and 1 billion bacteria. That is as much mass as two cows per acre.

Bacteria fall into four functional groups. Most are decomposers that consume simple carbon compounds, such as root exudates and fresh plant litter. By this process, bacteria convert energy in soil organic matter into forms useful to the rest of the organisms in the soil food web. A number of decomposers can break down pesticides and pollutants in soil. Decomposers are especially important in immobilizing, or retaining, nutrients in their cells, thus preventing the loss of nutrients, such as nitrogen, from the rooting zone.

A second group of bacteria are the mutualists that form partnerships with plants. The most well-known of these are the nitrogen-fixing bacteria.

The third group of bacteria is the pathogens. Bacterial pathogens include Xymomonas and Erwinia species, and species of Agrobacterium that cause gall formation in plants.

A fourth group, called lithotrophs or chemoautotrophs, obtains its energy from compounds of nitrogen, sulfur, iron or hydrogen instead of from carbon compounds. Some of these species are important to nitrogen cycling and degradation of pollutants.

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WHAT DO BACTERIA DO?

Bacteria from all four groups perform important services related to water dynamics, nutrient cycling, and disease suppression. Some bacteria affect water movement by producing substances that help bind soil particles into small aggregates (those with diameters of 1/10,000-1/100 of an inch or 2-200µm). Stable aggregates improve water infiltration and the soil’s water-holding ability. In a diverse bacterial community, many organisms will compete with disease-causing organisms in roots and on aboveground surfaces of plants. 

A FEW IMPORTANT BACTERIA 

Nitrogen-fixing bacteria form symbiotic associations with the roots of legumes like clover and lupine, and trees such as alder and locust. Visible nodules are created where bacteria infect a growing root hair (see photo below). The plant supplies simple carbon compounds to the bacteria, and the bacteria convert nitrogen (N2) from air into a form the plant host can use. When leaves or roots from the host plant decompose, soil nitrogen increases in the surrounding area. 

Nitrifying bacteria change ammonium (NH4+) to nitrite (NO2-) then to nitrate (NO3-) – a preferred form of nitrogen for grasses and most row crops. Nitrate is leached more easily from the soil, so some farmers use nitrification inhibitors to reduce the activity of one type of nitrifying bacteria. Nitrifying bacteria are suppressed in forest soils, so that most of the nitrogen remains as ammonium. 

Denitrifying bacteria convert nitrate to nitrogen (N2) or nitrous oxide (N2O) gas. Denitrifiers are anaerobic, meaning they are active where oxygen is absent, such as in saturated soils or inside soil aggregates. 

Actinomycetes are a large group of bacteria that grow as hyphae like fungi (see photo below). They are responsible for the characteristically “earthy” smell of freshly turned, healthy soil. Actinomycetes decompose a wide array of substrates, but are especially important in degrading recalcitrant (hard-to-decompose) compounds, such as chitin and cellulose, and are active at high pH levels. Fungi are more important in degrading these compounds at low pH. A number of antibiotics are produced by actinomycetes such as Streptomyces. 

WHERE ARE BACTERIA? 

Various species of bacteria thrive on different food sources and in different microenvironments. In general, bacteria are more competitive when labile (easy-to-metabolize) substrates are present. This includes fresh, young plant residue and the compounds found near living roots. Bacteria are especially concentrated in the rhizosphere, the narrow region next to and in the root. There is evidence that plants produce certain types of root exudates to encourage the growth of protective bacteria. 

Bacteria alter the soil environment to the extent that the soil environment will favor certain plant communities over others. Before plants can become established on fresh sediments, the bacterial community must establish first, starting with photosynthetic bacteria. These fix atmospheric nitrogen and carbon, produce organic matter, and immobilize enough nitrogen and other nutrients to initiate nitrogen cycling processes in the young soil. Then, early successional plant species can grow. As the plant community is established, different types of organic matter enter the soil and change the type of food available to bacteria. In turn, the altered bacterial community changes soil structure and the environment for plants. Some researchers think it may be possible to control the plant species in a place by managing the soil bacteria community. 

BUG BIOGRAPHY: Bacteria That Promote Plant Growth

By Ann Kennedy, USDA Agricultural Research Service, Pullman, WA

Certain strains of the soil bacteria Pseudomonas fluorescens have anti-fungal activity that inhibits some plant pathogens. P. fluorescens and other Pseudomonas and Xanthomonas species can increase plant growth in several ways. They may produce a compound that inhibits the growth of pathogens or reduces invasion of the plant by a pathogen. They may also produce compounds (growth factors) that directly increase plant growth.

These plant growth-enhancing bacteria occur naturally in soils, but not always in high enough numbers to have a dramatic effect. In the future, farmers may be able to inoculate seeds with anti-fungal bacteria, such as P. fluorescens, to ensure that the bacteria reduce pathogens around the seed and root of the crop. 

THE LIVING SOIL: FUNGI 

Fungi are microscopic cells that usually grow as long threads or strands called hyphae, which push their way between soil particles, roots, and rocks. Hyphae are usually only several thousandths of an inch (a few micrometers) in diameter. A single hyphae can span in length from a few cells to many yards. A few fungi, such as yeast, are single cells. 

Hyphae sometimes group into masses called mycelium or thick, cord-like “rhizomorphs” that look like roots. Fungal fruiting structures (mushrooms) are made of hyphal strands, spores, and some special structures like gills on which spores form. A single individual fungus can include many fruiting bodies scattered across an area as large as a baseball diamond. 

Fungi perform important services related to water dynamics, nutrient cycling, and disease suppression. Along with bacteria, fungi are important as decomposers in the soil food web. They convert hard-to-digest organic material into forms that other organisms can use. Fungal hyphae physically bind soil particles together, creating stable aggregates that help increase water infiltration and soil water holding capacity. 

Soil fungi can be grouped into three general functional groups based on how they get their energy. 

  • Decomposers – saprophytic fungi – convert dead organic material into fungal biomass, carbon dioxide (CO2), and small molecules, such as organic acids. These fungi generally use complex substrates, such as the cellulose and lignin, in wood, and are essential in decomposing the carbon ring structures in some pollutants. A few fungi are called “sugar fungi” because they use the same simple substrates as do many bacteria. Like bacteria, fungi are important for immobilizing, or retaining, nutrients in the soil. In addition, many of the secondary metabolites of fungi are organic acids, so they help increase the accumulation of humic-acid rich organic matter that is resistant to degradation and may stay in the soil for hundreds of years.

  • Mutualists – the mycorrhizal fungi – colonize plant roots. In exchange for carbon from the plant, mycorrhizal fungi help solubolize phosphorus and bring soil nutrients (phosphorus, nitrogen, micronutrients, and perhaps water) to the plant. One major group of mycorrhizae, theectomycorrhizae (see third photo below), grow on the surface layers of the roots and are commonly associated with trees. The second major group of mycorrhizae are the endomycorrhizae that grow within the root cells and are commonly associated with grasses, row crops, vegetables, and shrubs. Arbuscular mycorrhizal (AM) fungi are a type of endomycorrhizal fungi (see fourth photo below). Ericoid mycorrhizal fungi can by either ecto- or endomycorrhizal.

  • The third group of fungi, pathogens or parasites, cause reduced production or death when they colonize roots and other organisms. Root-pathogenic fungi, such as Verticillium, Pythium, and Rhizoctonia, cause major economic losses in agriculture each year. Many fungi help control diseases. For example, nematode-trapping fungi that parasitize disease-causing nematodes, and fungi that feed on insects may be useful as biocontrol agents. 

WHERE ARE FUNGI?

Saprophytic fungi are commonly active around woody plant residue. Fungal hyphae have advantages over bacteria in some soil environments. Under dry conditions, fungi can bridge gaps between pockets of moisture and continue to survive and grow, even when soil moisture is too low for most bacteria to be active. Fungi are able to use nitrogen up from the soil, allowing them to decompose surface residue which is often low in nitrogen.

Fungi are aerobic organisms. Soil which becomes anaerobic for significant periods generally loses its fungal component. Anaerobic conditions often occur in waterlogged soil and in compacted soils.

Fungi are especially extensive in forested lands. Forests have been observed to increase in productivity as fungal biomass increases. 

MYCORRHIZAL FUNGI IN AGRICULTURE

Mycorrhiza is a symbiotic association between fungi and plant roots and is unlike either fungi or roots alone. Most trees and agricultural crops depend on or benefit substantially from mycorrhizae. The exceptions are many members of the Cruciferae family (e.g., broccoli, mustard), and the Chenopodiaceae family (e.g. lambsquarters, spinach, beets), which do not form mycorrhizal associations. The level of dependency on mycorrhizae varies greatly among varieties of some crops, including wheat and corn.

Land management practices affect the formation of mycorrhizae. The number of mycorrhizal fungi in soil will decline in fallowed fields or in those planted to crops that do not form mycorrhizae. Frequent tillage may reduce mycorrhizal associations, and broad spectrum fungicides are toxic to mycorrhizal fungi. Very high levels of nitrogen or phosphorus fertilizer may reduce inoculation of roots. Some inoculums of mycorrhizal fungi are commercially available and can be added to the soil at planting time.

THE LIVING SOIL: PROTOZOA 

Protozoa are single-celled animals that feed primarily on bacteria, but also eat other protozoa, soluble organic matter, and sometimes fungi. They are several times larger than bacteria – ranging from 1/5000 to 1/50 of an inch (5 to 500 µm) in diameter. As they eat bacteria, protozoa release excess nitrogen that can then be used by plants and other members of the food web. 

Protozoa are classified into three groups based on their shape: Ciliates are the largest and move by means of hair-like cilia. They eat the other two types of protozoa, as well as bacteria. Amoebae also can be quite large and move by means of a temporary foot or “pseudopod.” Amoebae are further divided into testate amoebae (which make a shell-like covering) and naked amoebae (without a covering). Flagellates are the smallest of the protozoa and use a few whip-like flagella to move. 

Protozoa play an important role in mineralizing nutrients, making them available for use by plants and other soil organisms. Protozoa (and nematodes) have a lower concentration of nitrogen in their cells than the bacteria they eat. (The ratio of carbon to nitrogen for protozoa is 10:1 or much more and 3:1 to 10:1 for bacteria.) Bacteria eaten by protozoa contain too much nitrogen for the amount of carbon protozoa need. They release the excess nitrogen in the form of ammonium (NH4+). This usually occurs near the root system of a plant. Bacteria and other organisms rapidly take up most of the ammonium, but some is used by the plant. (See figure below for explanation of mineralization and immobilzation.)

Another role that protozoa play is in regulating bacteria populations. When they graze on bacteria, protozoa stimulate growth of the bacterial population (and, in turn, decomposition rates and soil aggregation.) Exactly why this happens is under some debate, but grazing can be thought of like pruning a tree – a small amount enhances growth, too much reduces growth or will modify the mix of species in the bacterial community.

Protozoa are also an important food source for other soil organisms and help to suppress disease by competing with or feeding on pathogens. 

WHERE ARE PROTOZOA?

Protozoa need bacteria to eat and water in which to move, so moisture plays a big role in determining which types of protozoa will be present and active. Like bacteria, protozoa are particularly active in the rhizosphere next to roots.

Typical numbers of protozoa in soil vary widely – from a thousand per teaspoon in low fertility soils to a million per teaspoon in some highly fertile soils. Fungal-dominated soils (e.g. forests) tend to have more testate amoebae and ciliates than other types. In bacterial-dominated soils, flagellates and naked amoebae predominate. In general, high clay-content soils contain a higher number of smaller protozoa (flagellates and naked amoebae), while coarser textured soils contain more large flagellates, amoebae of both varieties, and ciliates.

NEMATODES AND PROTOZOA

Protozoa and bacterial-feeding nematodes compete for their common food resource: bacteria. Some soils have high numbers of either nematodes or protozoa, but not both. The significance of this difference to plants is not known. Both groups consume bacteria and release NH4+.

THE LIVING SOIL: NEMATODES 

Nematodes are non-segmented worms typically 1/500 of an inch (50 µm) in diameter and 1/20 of an inch (1 mm) in length. Those few species responsible for plant diseases have received a lot of attention, but far less is known about the majority of the nematode community that plays beneficial roles in soil. 

An incredible variety of nematodes function at several trophic levels of the soil food web. Some feed on the plants and algae (first trophic level); others are grazers that feed on bacteria and fungi (second trophic level); and some feed on other nematodes (higher trophic levels). 

Free-living nematodes can be divided into four broad groups based on their diet. 

  • Bacterial-feeders consume bacteria.

  • Fungal-feeders feed by puncturing the cell wall of fungi and sucking out the internal contents.

  • Predatory nematodes eat all types of nematodes and protozoa. They eat smaller organisms whole, or attach themselves to the cuticle of larger nematodes, scraping away until the prey’s internal body parts can be extracted.

  • Omnivores eat a variety of organisms or may have a different diet at each life stage. Root-feeders are plant parasites, and thus are not free-living in the soil. 

WHAT DO NEMATODES DO? 

Nutrient cycling. Like protozoa, nematodes are important in mineralizing, or releasing, nutrients in plant-available forms. When nematodes eat bacteria or fungi, ammonium (NH4+) is released because bacteria and fungi contain much more nitrogen than the nematodes require. 

Grazing. At low nematode densities, feeding by nematodes stimulates the growth rate of prey populations. That is, bacterial-feeders stimulate bacterial growth, plant-feeders stimulate plant growth, and so on. At higher densities, nematodes will reduce the population of their prey. This may decrease plant productivity, may negatively impact mycorrhizal fungi, and can reduce decomposition and immobilization rates by bacteria and fungi. Predatory nematodes may regulate populations of bacterial-and fungal-feeding nematodes, thus preventing over-grazing by those groups. Nematode grazing may control the balance between bacteria and fungi, and the species composition of the microbial community. 

Dispersal of microbes. Nematodes help distribute bacteria and fungi through the soil and along roots by carrying live and dormant microbes on their surfaces and in their digestive systems. 

Food source. Nematodes are food for higher level predators, including predatory nematodes, soil microarthropods, and soil insects. They are also parasitized by bacteria and fungi. 

Disease suppression and development. Some nematodes cause disease. Others consume disease-causing organisms, such as root-feeding nematodes, or prevent their access to roots. These may be potential biocontrol agents. 

WHERE ARE NEMATODES? 

Nematodes are concentrated near their prey groups. Bacterial-feeders abound near roots where bacteria congregate; fungal-feeders are near fungal biomass; root-feeders are concentrated around roots of stressed or susceptible plants. Predatory nematodes are more likely to be abundant in soils with high numbers of nematodes. 

Because of their size, nematodes tend to be more common in coarser-textured soils. Nematodes move in water films in large (>1/500 inch or 50 µm) pore spaces. 

Agricultural soils generally support less than 100 nematodes in each teaspoon (dry gram) of soil. Grasslands may contain 50 to 500 nematodes, and forest soils generally hold several hundred per teaspoon. The proportion of bacterial-feeding and fungal-feeding nematodes is related to the amount of bacteria and fungi in the soil. Commonly, less disturbed soils contain more predatory nematodes, suggesting that predatory nematodes are highly sensitive to a wide range of disturbances. 

NEMATODES AND SOIL QUALITY 

Nematodes may be useful indicators of soil quality because of their tremendous diversity and their participation in many functions at different levels of the soil food web. Several researchers have proposed approaches to assessing the status of soil quality by counting the number of nematodes in different families or trophic groups.* In addition to their diversity, nematodes may be useful indicators because their populations are relatively stable in response to changes in moisture and temperature (in contrast to bacteria), yet nematode populations respond to land management changes in predictable ways. Because they are quite small and live in water films, changes in nematode populations reflect changes in soil microenvironments. 

*Blair, J. M. et al. 1996. Soil invertebrates as indicators of soil quality. In Methods for Assessing Soil Quality, SSSA Special Publication 49, pp. 273-291. 

BUG BIOGRAPHY: Nematode Trappers

One group of fungi may be a useful biological control agent against parasitic nematodes. These predatory fungi grow through the soil, setting out traps when they detect signs of their prey. Some species use sticky traps, others make circular rings of hyphae to constrict their prey. When the trap is set, the fungi put out a lure, attracting nematodes that are looking for lunch. 

The nematode, however, becomes lunch for the fungus.