Soil is teeming with life, both macroscopic and microscopic. These life forms range in size from invisible microorganisms to easily visible insects, earthworms and plant roots (Figure 3.8). In a teaspoon of soil, there are millions of bacteria, hundreds of thousands of fungi, thousands of protozoa and many larger organisms. These soil organisms play essential roles in nutrient cycling and energy flow, both of which influence soil fertility and crop production.
Soil organic matter and soil organisms are inextricably connected. Microbial biomass is the living component of soil organic matter, and microorganisms are the catalysts for most nutrient-releasing processes. They make it possible for crops to grow and for soils to be productive. On the other hand, microbial growth and activities depend on available carbon and other mineral nutrients as well as a favorable physical and chemical environment. The way soil is managed through tillage and cropping systems has a profound impact on life below ground.
Soil Organic Matter as Food
Soil organisms form a complex food web, and soil organic matter is the base of the web. Most soil microorganisms use organic compounds in soil organic matter as carbon and energy sources. Some soil organisms feed directly on living roots, but most depend on dead plant matter [8]. Small insects such as the springtail, a micro-invertebrate, break up plant residue into small pieces, which accelerates further decomposition by microorganisms. Within the soil food web, there are also carnivores, parasites and predators. As in an aboveground ecosystem, these organisms are interdependent and help cycle nutrients from organic to inorganic forms that are available to crops.
Except for the area next to the root, called the rhizosphere, soil is a nutrient-poor environment for microbial growth. Nutrients and carbon, in the form of plant and animal residues, tend to enter the soil intermittently. Consequently, microorganisms are faced with a feast-or-famine existence. Soil microorganisms respond rapidly to the addition of plant and animal residues. They break down complex organic compounds, such as cellulose and lignin in plant residues, into simple organic compounds. Some of the carbon in these simple organic compounds becomes part of the microbial biomass and provides energy for microbial growth. Some becomes carbon dioxide.
The more stable fraction of soil organic matter, humus, is also a source of carbon for microorganisms. Organic compounds found in humus have complex chemical structures and are more resistant to decomposition than fresh plant or animal residues. Humus is also associated with mineral particles and forms materials called humate-clay complexes that protect the organic matter from decomposition by soil microorganisms. Therefore, humus serves as a slow-release source of carbon and energy.
In addition to carbon, soil organic matter contains substantial amounts of organic nitrogen, phosphorus, sulfur and many trace elements. Microorganisms perform an important function in cycling these nutrients. They convert organically bound elements to inorganic or mineral forms that are available for plant use. This process is called mineralization. Microorganisms, as well as plants, also immobilize nutrients in their biomass as they grow. These nutrients are unavailable to plants until the microorganisms and plants die and decompose. Mineralization and immobilization are key processes in nutrient cycling.
Nitrogen is the nutrient in highest demand by plants. Plants mainly use inorganic forms of nitrogen, such as ammonium and nitrate, which are products of microbial transformations. Plants and microbes use ammonium from nitrogen fixation and mineralization to form proteins, nucleic acids and cell walls. Nitrifying bacteria convert ammonium to nitrate in a process called nitrification. Microorganisms also convert nitrate to various gases, N2, NO, N2O, through a process called denitrification. This process occurs when soils are water saturated and oxygen is low. Denitrification causes nitrogen losses from the soil to the atmosphere.
Microorganisms compete with plants for nitrogen. During the decomposition of organic residues, microbial needs for nitrogen are met first. This is why with low-nitrogen residues, most nitrogen is immobilized and not available for plant use (Figure 3.7). Nitrogen not used by microbes is released to the soil and becomes available for plant use.
The increase in soil organic matter that occurs in conservation tillage systems results in greater soil biological activity and soil biodiversity. Generally speaking, microbial biomass increases along with soil organic matter and makes up 1–4 percent of the total organic matter. Reducing tillage increases the amount of microbial biomass in soil [45]. This improves soil quality and promotes a constant cycling of nutrients, some of which are available for crop growth.
Modification of Habitat
In addition to being a food source, soil organic matter modifies the habitat of soil organisms. Changes in water-holding capacity, porosity, infiltration, hydraulic conductivity and water-stable aggregation that occur with increased soil organic matter have a profound impact on microbial biomass development and its activity [21].
Changes related to soil water are particularly important. Soil organisms live in water films surrounding soil particles. Different types of organisms prefer different moisture conditions for growth. Consequently, changing moisture content alters the composition of soil microbial populations. For example, abundant soil moisture favors algae, protozoa and anaerobic bacteria, whereas low moisture favors fungi, actinobacteria and spore-forming bacteria [19]. The effects of soil-water content on microorganisms often result from changes in the amount of oxygen in the soil, because soil oxygen decreases as soil moisture increases. Generally speaking, total microbial activity is reduced when soil is either too dry or too wet.
Soil water also influences the movement of soil organisms. High water content makes movement easier for soil organisms. As water content increases, individual soil aggregates become connected by water and it is easier for bacteria to be eaten by predators such as protozoa [10]. In many cases, grazing by protozoa increases bacterial activity and increases the release of carbon and nitrogen bound in bacterial cells.
Soil aggregation increases with increasing organic matter and this modifies the microbial habitat. Large soil aggregates contain higher levels of nutrients than soil in general. Pores inside aggregates provide refuge for soil microorganisms, protecting them from predators and from drying. Soil aggregates vary in size as do the pores within them.
FIGURE 3.8. A soil habitat containing mineral particles, organic matter, water, plant roots with root hairs and soil organisms. The actual size of the soil in this drawing is slightly greater than 1 millimeter. Illustration courtesy of Wendy E. Giminski.
The size of pores determines the occupants, as illustrated by Figure 3.8. Bacteria usually live within micro-aggregates [20]. Fungi, nematodes and protozoa inhabit pores between micro-aggregates as well as pores within and between macro-aggregates. Most soil bacteria are physically separated from their predators, such as protozoa and nematodes. Soil mites are more abundant in macropores [9, 34]. Studies show that as protozoa, nematodes, fungi and mites feed on each other, nutrients are both released and incorporated into their bodies, affecting the fertility of soil.
Soil compaction crushes macropores and large micropores into smaller pores, reduces total pore space as well as air-pore space, and increases soil bulk density. Compaction limits the movement and abundance of larger soil organisms such as earthworms and soil insects. Microorganisms such as bacteria and fungi do not seem to be affected by soil compaction [49].
Disease Suppression
Most soils suppress soil-borne plant pathogens to some degree, including bacterial and fungal pathogens as well as parasitic nematodes. A soil’s ability to suppress pathogens is directly related to its microbial biomass and microbial activities since microbial populations compete with pathogens for nutrients and energy. Disease suppression is often enhanced by adding organic matter such as compost and fresh organic materials [51].