Soil Biota

1.1. Bacteria and Archaea: The Silent Majority

Let us begin with the most numerous component of soil biota. Imagine that a single gram of fertile soil can contain up to 10 billion bacteria and archaea (Eash et al., 2016; Weil & Brady, 2017). And these are not just cells—these are up to 100,000 different species! (Huang et al., 2012). This vast world is shared between two fundamentally different groups: Bacteria and Archaea.

What is important to understand about Archaea?

For a long time, it was believed that archaea only inhabited extreme environments—hot springs, salt lakes (Weil & Brady, 2017). However, with the development of molecular methods, we realized this is not the case. Archaea are common and active inhabitants of a wide variety of soils, often comprising about 10% of the entire microbial community (Huang et al., 2012).

The main difference between Archaea and Bacteria lies in the structure of their cell walls and membranes, as well as unique enzymes. But for us as soil scientists, their functional characteristics are more important.

• Role in the nitrogen cycle: Archaea are the primary nitrifiers in most soils (Huang et al., 2012). They oxidize ammonium (NH₄⁺) to nitrite (NO₂⁻), initiating the process that leads to the formation of nitrates (NO₃⁻)—the primary form of nitrogen available to plants. This is one of their key functions, and they are often more efficient than bacteria in this process.
• Adaptation to stress: Archaea often dominate under conditions of severe nutrient limitation (Huang et al., 2012), making them indispensable in poor soils.

Bacteria: Masters of All Trades

Bacteria are the most diverse group. They can be aerobes (living with oxygen) and anaerobes (living without oxygen) (Scheffer et al., 2018). They are divided into gram-positive and gram-negative, which affects their resistance and interaction with the environment. We will not delve into systematics but will focus on their functional groups:

1. Chemoorganotrophs—these constitute the majority of soil bacteria. They obtain energy by oxidizing organic compounds. These are the primary decomposers and reducers.

2. Chemoautotrophs—use inorganic compounds (iron, sulfur) to obtain energy and build their biomass from CO₂. They play an important role in the oxidation and reduction of mineral elements, affecting the availability of micronutrients (Foth, 1990).

3. Cyanobacteria (formerly blue-green algae)—photoautotrophs that, like plants, use solar energy. They are important for nitrogen fixation (N₂ fixation) in waterlogged and desert soils (Weil & Brady, 2017).

A small but important group—Actinobacteria. These are bacteria that form mycelium similar to fungi (Eash et al., 2016). Their role is the decomposition of the most complex organic molecules, such as lignin, cellulose, and chitin (Weil & Brady, 2017). It is actinobacteria that give soil its famous "earthy smell" due to the release of geosmin (Eash et al., 2016). But their main "asset" for humanity is the synthesis of antibiotics (Eash et al., 2016), which we will discuss later.

1.2. Fungi: Weavers of the Soil Network

If bacteria are the "chemists," then fungi are the "engineers" of soil. They belong to eukaryotes (their cells have a nucleus). The main difference between fungi and bacteria is their hyphal growth. Mycelium, or the mycelial network, is a network of thin tubes—hyphae. This network penetrates vast volumes of soil, connecting aggregates and plant roots into a single system.

Main functions of fungi:

1. Primary decomposers of lignocellulose. Fungi, especially basidiomycetes (Basidiomycota), are the only organisms capable of efficiently decomposing lignin (Eash et al., 2016; Weil & Brady, 2017). They secrete powerful enzymes that oxidize the complex aromatic rings of this polymer, making it available to other organisms. Without fungi, mountains of undecomposed wood would accumulate in forests.

2. Creators of soil structure. Fungal mycelium acts as a "superglue"—it mechanically binds soil particles into stable aggregates, which is the foundation for good structure, porosity, and water- and air-permeability (Eash et al., 2016). This role is especially important in natural ecosystems and under minimal tillage.

3. Symbiosis—Mycorrhizae. This is the most significant ecological achievement of fungi. About 80% of all terrestrial plants live in symbiosis with fungi, forming mycorrhizae (Weil & Brady, 2017). The fungus receives carbohydrates from the plant (up to 30% of photosynthetic products!), and in return, the plant receives from the fungus:

• Water and mineral nutrients, especially phosphorus, which the fungus extracts from soil pores inaccessible to roots (Weil & Brady, 2017; Huang et al., 2012).
• Protection from pathogens and drought.
• ere are two main types of mycorrhizae: ectomycorrhizae (characteristic of trees) and endomycorrhizae (arbuscular, characteristic of most agricultural crops) (Weil & Brady, 2017). We will return to this topic when we discuss symbionts.
• Biocontrol. Some fungi, e.g., Trichoderma, act as antagonists and hyperparasites, suppressing the growth of pathogenic fungi and bacteria, thereby protecting plants (Eash et al., 2016).

1.3. Functions of the Microbial Community: From Chemistry to Global Climate

Now let us summarize all the above and highlight the main functions that the microbial community performs in soil. These are processes without which soil would be merely geological parent material.

1. Decomposition and humus formation (C- and N-cycles). This is the foundation. Microorganisms decompose complex organic polymers (proteins, carbohydrates, lignin) into simple inorganic substances—this is mineralization (White, 2006; Foth, 1990).

• During the decomposition of carbohydrates, CO₂ is released (carbon returns to the atmosphere).
• During the decomposition of proteins, ammonium (NH₄⁺) is released—this is ammonification (Eash et al., 2016).
• Ammonium is oxidized by nitrifying bacteria and archaea to nitrates (NO₃⁻)—this is nitrification (Eash et al., 2016).

Concurrently, a process of immobilization occurs—when microorganisms capture available nitrogen to build their biomass, temporarily making it unavailable to plants (White, 2006). The balance between mineralization and immobilization determines the nitrogen supply to plants.

2. Atmospheric nitrogen fixation (nitrogen fixation). Some bacteria (e.g., symbiotic Rhizobium and free-living Azotobacter) and cyanobacteria can convert inert molecular nitrogen (N₂) into ammonium, available to plants. This process is of immense global significance (Eash et al., 2016; Weil & Brady, 2017).

3. Engineering and structure-forming role. We have already discussed fungal mycelium, but bacteria also contribute. Many bacteria secrete exopolysaccharides (EPS), which also bind soil particles, promoting aggregation (Scheffer et al., 2018).

4. Synthesis of biologically active substances. This includes antibiotics and various metabolites that stimulate plant growth (phytohormones), secreted by rhizobacteria (Weil & Brady, 2017). This is a direct contribution to fertility.

5. Detoxification and bioremediation. Soil bacteria and fungi can decompose many toxic substances: pesticides, petroleum products (Weil & Brady, 2017). This is one of the most important ecosystem services of soil.

6. Participation in global cycles. Bacteria, by oxidizing methane (methanotrophs) and releasing nitrous oxide (N₂O)—a powerful greenhouse gas—directly affect the planet's climate (Scheffer et al., 2018).

Summary of Chapter 1

We see that the microbial community is not just "dirt" of cells. It is a powerful metabolic system where:

• Bacteria and archaea are the primary agents of the nitrogen, carbon, and sulfur cycles, as well as "chemical factories" producing antibiotics and phytohormones.
• Fungi are the only decomposers of lignin, the foundation of soil structure, and the primary partners of plants in symbiosis (mycorrhizae).

Together, they initiate the main biochemical reactions, transforming dead organic matter into plant nutrition and creating conditions for the next level of life—microfauna, which will be discussed in the next lecture.

2.1. Protozoa: Shepherds of Bacteria

Protozoa are unicellular eukaryotes, free-living organisms, typically ranging from 4 to 250 μm in size (Weil & Brady, 2017). They move in the aqueous environment of soil pores using flagella (flagellates), cilia (ciliates), or pseudopodia (amoebae). They are divided into two main evolutionary lineages: Amoebozoa (Amoebozoa)—with broad pseudopodia, and Rhizaria (Rhizaria)—with thin filamentous pseudopodia (Huang et al., 2012). What matters to us is not their complex systematics but their colossal ecological role.

The primary role of protozoa is regulation of bacterial abundance.

• "Grazing" on bacteria. Most soil protozoa are bacteriophages. They actively consume bacteria, and this is not just consumption but a complex selection process: they prefer gram-negative bacteria and avoid gram-positive ones, as well as bacteria with pigments, toxins, or slime layers (Huang et al., 2012). Thus, they constantly shape the structure of the bacterial community.
• "Rejuvenation" of microbial populations. By removing old and slow-growing cells, protozoa stimulate the reproduction of young, actively growing bacteria that process organic matter faster. This leads to an increase in the overall metabolic activity of microorganisms (Weil & Brady, 2017).
• Acceleration of the nitrogen cycle. Bacteria typically have a narrow carbon-to-nitrogen ratio (C:N _{3–4), while protozoa have a wide ratio (C:N} 8–12) (Foth, 1990). By processing bacterial protein into their own biomass, protozoa excrete excess nitrogen in the form of ammonium (NH₄⁺). This ammonium becomes readily available to plants. This phenomenon is called the microbial loop and is a key mechanism of nitrogen mineralization in the rhizosphere (Eash et al., 2016; Huang et al., 2012).
• Reservoirs for pathogens. Some pathogenic bacteria (e.g., Legionella) can survive inside protozoan cysts, which protects them from unfavorable conditions and even promotes their multiplication. This is an important, though not always pleasant, aspect of their ecology (Huang et al., 2012).

2.2. Nematodes (Nematoda): The Most Diverse Group of Soil Animals

Nematodes, or roundworms, are the most abundant multicellular animals in soil. Up to 10 million individuals belonging to several dozen genera can inhabit a single square meter (Eash et al., 2016; Foth, 1990). Their size typically ranges from 0.5 to 2 mm, and they move in water films and along particle surfaces.

Their main feature is the enormous diversity of trophic (feeding) groups. Based on what they eat, nematodes can be divided into several categories (Eash et al., 2016; Weil & Brady, 2017):

1. Bacterivores. Feed on bacteria. Like protozoa, they are regulators of bacterial populations and a powerful factor in nitrogen mineralization. For example, analysis has shown they can provide up to 30–40% of mineralized nitrogen in some ecosystems (Weil & Brady, 2017).

2. Fungivores. Feed on mycelium and fungal spores. They regulate fungal abundance and are especially important in forest litter and during coarse organic matter decomposition (Foth, 1990).

3. Predators. Feed on other nematodes, protozoa, and small invertebrates. They play the role of "top regulators," controlling the abundance of herbivores and bacterivores (Weil & Brady, 2017).

4. Herbivores/Plant parasites. This is the most well-known and economically significant group. They feed on plant roots, piercing cells with a special stylet. Some are ectoparasites (living outside the root), others are endoparasites (penetrating inside) (Eash et al., 2016). This group includes notorious pests such as root-knot nematodes (Meloidogyne) and cyst nematodes (Heterodera), which cause enormous damage to agriculture (Foth, 1990). It is because of these species that agronomy often speaks of the "harmfulness" of nematodes, although in nature they are a vital component of the food web.

5. Omnivores. Feed on a mixed diet (bacteria, fungi, algae) and are often at higher trophic levels, serving as good indicators of soil health (Huang et al., 2012).

Ecological role of nematodes in general:

• Indicators of soil condition. Different nematode groups respond differently to stress (pollution, compaction, tillage). The ratios between groups (e.g., maturity index) are used to assess the biological health of soil. Abundance of bacterivores and fungivores indicates high carbon cycle activity, while abundance of predators and omnivores indicates ecosystem stability (Eash et al., 2016; Foth, 1990).
• Acceleration of cycling. Like protozoa, nematodes excrete mineral forms of nitrogen and phosphorus by consuming microbial biomass (Eash et al., 2016).
• Dispersal of microorganisms. Moving through soil, nematodes can carry fungal spores and bacteria on their surfaces or in their intestines, facilitating their dispersal (Foth, 1990).

Summary of Chapter 2

We see that microfauna, despite their microscopic size, are active regulators of microbiological processes:

• Protozoa are the primary "shepherds" of bacterial populations, stimulating their activity and accelerating nitrogen mineralization.
• Nematodes are a group with an extremely broad feeding spectrum. They are simultaneously regulators (bacterivores and fungivores), consumers (herbivores), predators, and valuable indicators of soil health.

Thanks to this group, the microbial biomass that accumulates nutrients is constantly "recycled," and these nutrients become available to plants. Without microfauna, mineralization processes would be significantly slower, and plants would suffer acute nitrogen deficiency.

We now move to the next, larger level—mesofauna—where new "engineers" of soil appear—mites and springtails.

3.1. Mites (Acari): The Most Diverse Group

Mites are a class of arachnids (Arachnida) and, after insects, are the most diverse group of animals on Earth. Most mite species inhabit soil (Weil & Brady, 2017).

Their main richness is the diversity of feeding strategies. Among soil mites, we find (Huang et al., 2012; Eash et al., 2016):

• Oribatida—or "beetle mites." This is the most abundant and diverse group of soil mites. They are the primary decomposers of plant litter in forest floors. Their powerful chelicerae allow them to gnaw even tough leaves and wood fibers. They play a key role in the primary decomposition of cellulose and lignin and, very importantly, in soil structure formation through the production of fecal pellets.
• Astigmata—often found in highly moist, organic-rich habitats. These are "scavengers" that feed on decaying organic residues and fungi. Many are "r-strategists" with rapid reproduction, capable of forming massive aggregations in composts and manure.
• Prostigmata and Mesostigmata—are primarily predators. They actively hunt springtails, nematodes, insect larvae, and other small invertebrates. They are an important link regulating the abundance of primary consumers. Many have piercing-sucking mouthparts.

Ecological role of mites:

1. Shredding and structuring. Like other mesofauna, mites chew plant residues, increasing their surface area for microbial attack. Their fecal pellets are microaggregates rich in organic matter and microorganisms, which become the foundation for forming larger soil aggregates (Foth, 1990; White, 2006).

2. Regulation of microbial populations. Some oribatid mites specialize in feeding on fungi, making them important regulators of fungal mycelium. Predatory groups control the abundance of nematodes and other arthropods.

3. Bioindicators. Oribatids are generally K-strategists—they reproduce slowly, have long life cycles, and are very sensitive to disturbances (tillage, pollution). Therefore, their diversity and abundance serve as excellent indicators of the degree of "wildness" and health of soil (Weil & Brady, 2017).

3.2. Springtails (Collembola): The "Feet" and "Tongue" of Soil

Springtails, or collembolans, are ancient wingless insect-like creatures that inhabit almost all terrestrial ecosystems. Their name comes from the characteristic "furca" (springing organ) on the abdomen, with which they make jumps.

Diversity of life forms. Springtails demonstrate remarkable adaptation to different soil horizons (Weil & Brady, 2017):

• Epiedaphic forms. Live on the surface. Large, brightly colored, with well-developed eyes and a jumping furca. They inhabit the litter layer and feed on fungi, bacteria, and decomposing plants.
• Hemiedaphic forms. Inhabit the upper soil layers and litter. They have less developed pigmentation and shorter antennae.
• Euedaphic forms. Permanent inhabitants of soil horizons. They are small (less than 1 mm), white, blind, without a jumping furca. They move exclusively in soil pores and feed primarily on bacteria and fungi.

Feeding preferences:

Most springtails are microphages (feed on microorganisms) or saprophages (feed on decomposing organic matter). They prefer fungi, especially molds, and bacteria that form colonies on the surface of plant residues. Thanks to their chewing mouthparts, they effectively "scrape" microbial biomass from the surface of leaves and roots.

Ecological role of springtails:

1. Primary decomposition. They do not digest tough cell walls, but by chewing plant tissues, they break them into small fragments and, more importantly, "consume" the soft internal tissues, leaving a "skeleton" of lignin and cellulose that becomes more accessible to fungi (White, 2006). This accelerates the decomposition process.

2. Regulation of fungal mycelium. By actively feeding on fungi, springtails stimulate the formation of new, more active mycelium, which, as with protozoa, increases the rate of organic matter mineralization.

3. Dispersal of microorganisms. Fungal spores and bacterial cells pass through the springtail gut and remain viable, facilitating the dispersal of microorganisms in soil (Foth, 1990).

Summary of Chapter 3

We see that mesofauna are not just "bugs" in the soil but active transformers of organic matter:

• Mites and springtails are the primary "shredders" of plant litter. They make coarse organic matter accessible to microbial attack.
• They regulate the abundance and activity of bacteria and fungi by feeding on them, thereby stimulating nutrient mineralization.
• Their fecal pellets and their very presence contribute to the formation of soil structure (aggregates).
• The composition of mesofauna is a sensitive indicator of soil condition, disturbance, or pollution.

It is the activity of mesofauna that creates the "fine earth"—the environment that will later be actively mixed and processed by earthworms and other representatives of macrofauna. We will turn to them in the next lecture.

4.1. Earthworms (Lumbricidae): Natural Plows

Earthworms are perhaps the most famous soil animals. Charles Darwin, in his last book "The Formation of Vegetable Mould through the Action of Worms," demonstrated their colossal role in soil formation. Their biomass in fertile soils can reach several hundred kilograms per hectare (White, 2006; Weil & Brady, 2017).

To understand their ecological role, it is important to distinguish three ecological groups of earthworms (Eash et al., 2016; Weil & Brady, 2017):

1. Epigeic. Live in litter and the upper soil layer. Do not dig deep burrows. Feed on plant residues on the surface. They are the primary "processors" of leaf litter. Example—compost worm Eisenia fetida.

2. Endogeic. Live in the upper mineral soil layer (10–30 cm). Construct horizontal, often temporary burrows. Feed on mineral soil rich in organic particles. They actively mix organic matter with the mineral fraction, creating "mull"—a homogeneous humus horizon. Example—Aporrectodea caliginosa.

3. Anecic. Build deep (up to several meters), permanent vertical burrows. At night, they emerge to the surface to collect fallen leaves and drag them into their burrows. They create "caches" of organic matter deep in the soil, and their burrows are large macropores. The most famous example—Lumbricus terrestris (the common earthworm).

Influence of earthworms on soil:

1. Creation of structure and pores (bioturbation). Worm burrows are large pores through which water and air penetrate deep into the soil. This improves drainage, aeration, and root growth (Weil & Brady, 2017). Their burrows are "highways" for root penetration into compacted horizons.

2. Aggregate formation (coprolites). By passing soil through their intestines, worms grind it, mix it with organic slimes and microorganisms, and then excrete it as coprolites—strong, structured granules. These coprolites are high-quality aggregates, resistant to disintegration and enriched with nutrients (Foth, 1990; Huang et al., 2012). In some ecosystems, worms bring up to 100 tons of soil per hectare to the surface annually (White, 2006; Weil & Brady, 2017).

3. Acceleration of nutrient cycling. By processing organic matter, worms sharply accelerate its mineralization. In their intestines, ideal conditions are created for bacterial multiplication. Coprolites are significantly richer in nitrogen, phosphorus, and calcium than the surrounding soil (Eash et al., 2016; White, 2006).

4.2. Termites (Isoptera): Tropical Engineers

In tropical and subtropical regions, the role of earthworms is largely performed by termites. These are social insects that live in huge colonies and, like worms, process gigantic volumes of soil.

Scale of activity:

Termites are the primary decomposers of wood and cellulose in the tropics. They can process up to 4000 kg of plant litter per hectare annually (Weil & Brady, 2017). Their earthen structures—termite mounds—can reach heights of 6 meters or more, and the building material is extracted from deep soil layers (Eash et al., 2016; Weil & Brady, 2017).

Influence on soil:

1. Bioturbation and profile alteration. Termites transport soil from deep horizons to the surface, completely mixing the profile. Over vast areas, their activity is comparable in scale to that of earthworms in temperate climates (Eash et al., 2016).

2. Creation of "fertility islands." Unlike uniformly working worms, termites create local zones of enrichment. Termite mounds are often richer in clay, calcium, phosphorus, and organic matter than the surrounding soil (Foth, 1990). Abandoned termite mounds often support lush vegetation.

3. Water permeability. Termite burrows, like worm burrows, serve as pathways for water infiltration into soil, especially in arid regions where the surface tends to form crusts (Weil & Brady, 2017).

4.3. Ants (Formicidae): Universal Bioturbators

Ants are found almost everywhere. Their role in soil formation is often underestimated, but it is enormous. They are active bioturbators in both temperate and tropical latitudes.

Their influence on soil:

1. Mixing and structuring. By building their nests, ants bring to the surface enormous quantities of soil from deep horizons, mixing the profile (Foth, 1990). Their activity is comparable to that of worms and can lead to the formation of characteristic microrelief.

2. Nutrient enrichment. Ant nests are local "fertility hotspots." They accumulate organic residues and excrement, making the soil in their nests richer in nitrogen and phosphorus (Weil & Brady, 2017; White, 2006).

3. Food web regulation. Ants are active predators, destroying huge numbers of small invertebrates, including pests. Some species (leafcutters) are powerful phytophages, directly affecting vegetation and the input of organic matter into soil (Eash et al., 2016).

Summary of Chapter 4

Macrofauna are the engineers of the soil landscape:

• Earthworms are the primary creators of structure and humus in temperate soils. They uniformly mix organic matter with the mineral fraction, creating macropores and stable aggregates.
• Termites perform the same role in the tropics, creating local "fertility islands" and altering the soil profile.
• Ants are universal mixers whose activity enriches soil and changes its physical properties.

Together with mesofauna, they are ecosystem engineers, creating the complex, porous, structured environment that allows water, air, and roots to penetrate deep into the soil. We will discuss the concept of "ecosystem engineers" in more detail in the next lecture.

5.1. Who Are the Ecosystem Engineers in Soil?

The main ecosystem engineers in soil are the already familiar representatives of macrofauna: earthworms, termites, and ants. Their activity creates the three-dimensional structure of soil that is the foundation for the life of all other organisms (Eash et al., 2016; Foth, 1990).

But not only them. In some ecosystems, smaller organisms also act as engineers:

• Plant roots. As they grow, they push apart and break up soil, create burrows and channels for water and air, and secrete organic compounds that alter the chemical environment (Weil & Brady, 2017).
• Vertebrates (rodents, moles). Their burrows and tunnels are also a powerful factor in soil formation and bioturbation (Foth, 1990).
• Bacteria and fungi. Although their influence is less obvious, the exopolysaccharides they secrete bind particles, creating microaggregates—the "bricks" of soil structure (Scheffer et al., 2018).

5.2. Mechanisms of Ecosystem Engineer Impact

The activity of engineers can be divided into several key processes:

1. Creation of biopores.

This is perhaps the most obvious function. Earthworms, termites, ants, and plant roots create a network of burrows and channels in the soil. These biopores have colossal significance:

• Water regime. Biopores are "highways" for rapid water infiltration into the soil. This is especially important during heavy rains when the surface tends to form crusts and runoff. Worm burrows can increase water infiltration by an order of magnitude (Weil & Brady, 2017).
• Gas exchange. Biopores are pathways for oxygen to enter deep soil and for carbon dioxide to exit. This is critically important for aerobic microorganisms and plant roots (Eash et al., 2016).
• Root growth. Roots use old worm and termite burrows as paths of least resistance, penetrating dense, compacted soil horizons (Weil & Brady, 2017).

2. Aggregate formation.

Engineers not only create macropores but also "build" the very structure of soil at the micro-level.

• Earthworm coprolites. By passing soil through their intestines, worms form strong, structured granules—coprolites—which are the foundation of water-stable aggregation (White, 2006; Eash et al., 2016).
• Fecal pellets of mesofauna. Mites and springtails, processing organic matter, leave behind small fecal pellets that also bind into aggregates (Foth, 1990).
• Binding by microorganisms. Bacterial exopolysaccharides and fungal mycelium act as biological "glue," connecting mineral particles into aggregates. This effect is greatly enhanced in the presence of engineers, who create favorable conditions for microbial life (Scheffer et al., 2018).

3. Mixing and transportation of material (Bioturbation).

Engineers actively move soil material through the profile.

• Earthworms bring soil from deep horizons to the surface while simultaneously dragging organic residues deep down. This leads to the formation of deep, dark, homogeneous humus horizons (mull) (White, 2006; Weil & Brady, 2017).
• Termites transport soil from deep layers to the surface for mound construction, completely altering the local soil profile. Abandoned termite mounds become "islands" with different texture and fertility (Eash et al., 2016; Foth, 1990).
• Ants also actively mix soil, bringing material from lower horizons to the surface and creating local enrichment hotspots (Foth, 1990).

4. Creation of microhabitats (Niche construction).

By changing the physical environment, engineers create new niches for other organisms.

• The walls of burrows and worm coprolites are colonized by specific communities of bacteria, fungi, and protozoa (the so-called "drilosphere"), which differ from microorganisms in the surrounding soil (Eash et al., 2016; Scheffer et al., 2018).
• Termite mounds and ant nests become shelters for many other arthropods, and their organic "gardens" serve as food for specialized fungi (Weil & Brady, 2017).

5.3. Scale of Impact

It is important to understand that ecosystem engineers do not work in a vacuum. Their activity has colossal scales:

• In one hectare, worms can process from 20 to 1000 tons of soil per year (Weil & Brady, 2017).
• Termites over vast savanna areas can process up to 4000 kg of plant biomass and move hundreds of tons of soil per hectare (Eash et al., 2016; Weil & Brady, 2017).
• Ant nests can occupy up to 1–2% of the surface area in some ecosystems and serve as local "hotspots" of biological activity (Foth, 1990).

Thus, ecosystem engineers create spatial and structural heterogeneity of soil, which is the foundation of its fertility and resilience.

Summary of Chapter 5

The concept of ecosystem engineers radically changes our perception of soil biota. We see that:

• Earthworms, termites, and ants are the primary architects of the soil profile.
• Their activity (creating pores, forming aggregates, mixing) creates the physical environment that determines the living conditions for all other organisms.
• They create niches for microorganisms, mesofauna, and plant roots, influencing the entire ecosystem.
• They are not just "neighbors" in the soil but active builders whose work is the foundation for mineralization, cycling, and fertility formation.

Now that we know all the "actors" and understand the principles of their interaction, we can move to the next, final stage of our course—classification of functional groups and a general overview of the soil food web.

6.1. Decomposers: Soil Chemists

Decomposers are organisms that carry out mineralization—the transformation of complex organic compounds into simple inorganic ones. This is the foundation of the entire soil cycle.

Who belongs to this group:

• Bacteria (especially heterotrophic ones, such as Pseudomonas, Bacillus).
• Actinobacteria (including Streptomyces).
• Fungi (especially saprotrophic ones—Penicillium, Aspergillus, as well as basidiomycetes that decompose lignin).

Their key function:

Decomposers secrete exoenzymes (extracellular enzymes) that break down high-molecular-weight polymers—cellulose, lignin, proteins, chitin—into low-molecular-weight compounds (monosaccharides, amino acids), which are then absorbed (Eash et al., 2016; White, 2006). They ensure the return of carbon to the atmosphere as CO₂ and mineral elements to the soil solution (nitrogen, phosphorus, sulfur).

An important nuance:

Decomposers do not just consume organic matter. In the course of their life activity, they themselves become part of the soil organic matter. Their biomass and metabolic products (exopolysaccharides, melanins) are the foundation for the formation of stable humus (Weil & Brady, 2017; Scheffer et al., 2018).

6.2. Consumers: Regulators and Shredders

Consumers are organisms that feed on other organisms or their metabolic products. They do not break down organic matter at the molecular level but redistribute and physically transform it, making it accessible to decomposers.

Who belongs to this group:

• Microfauna: Protozoa (eating bacteria), nematodes (bacterivores, fungivores, predators).
• Mesofauna: Mites (oribatids—feed on fungi and detritus; predatory mites—feed on nematodes and springtails), springtails (feed on fungi and bacteria).
• Macrofauna: Many insect larvae, centipedes, snails, as well as predatory beetles and spiders.

Their functions:

1. Regulation of microbial populations. By feeding on bacteria and fungi, consumers prevent them from growing uncontrollably and, more importantly, stimulate their activity. This is the so-called "grazing" effect: consumers remove old cells, freeing resources for young, actively growing microorganisms (Foth, 1990; Weil & Brady, 2017).

2. Shredding (comminution). Mesofauna and macrofauna physically chew plant residues, increasing the surface area for exoenzyme attack (White, 2006). This is a critically important step for accelerating decomposition.

3. Acceleration of nutrient cycling. As we already discussed in the microfauna lecture, consumers excrete mineral forms of nitrogen and phosphorus (ammonium, phosphates), which become available to plants (Eash et al., 2016).

4. Dispersal. By moving through soil, consumers carry spores and cells of microorganisms, facilitating their dispersal and colonization of new substrates (Foth, 1990).

6.3. Ecosystem Engineers: Architects of the Environment

We covered this group in detail in the previous lecture. These are organisms that create, change, or maintain the physical environment for other species. Their activity radically changes soil structure.

Who belongs to this group:

• Macrofauna: Earthworms, termites, ants.
• Plant roots.
• Vertebrates: Moles, rodents.

Their functions:

1. Creation of biopores (macropores).

2. Aggregate formation.

3. Mixing of the soil profile (bioturbation).

4. Creation of microhabitats (niches).

Engineers are "keystone species" in most soil ecosystems, as their presence or absence determines which other organisms can live there (Weil & Brady, 2017).

6.4. Symbionts: Partners

Symbionts are organisms that enter into close, mutually beneficial relationships with other organisms. This is not just "feeding" or "engineering" but a deep physiological and often structural integration.

Who belongs to this group:

• Mycorrhizal fungi. Symbiosis with the roots of higher plants. The fungus receives carbohydrates, and the plant receives water and mineral elements, especially phosphorus, as well as protection from pathogens (Eash et al., 2016; Weil & Brady, 2017).
• Nitrogen-fixing bacteria. Symbiosis with legumes (Rhizobium) and some other species (actinobacteria Frankia with alder). The bacteria receive carbohydrates, and the plant receives available nitrogen (Eash et al., 2016; Weil & Brady, 2017).
• Symbiosis with insects. Termites and leafcutter ants harbor symbiotic fungi and bacteria in their guts or in special chambers, helping digest cellulose (Eash et al., 2016).

Their function:

Symbionts expand the ecological capabilities of their partners. Thanks to mycorrhizae, plants can grow on poor soils; thanks to nitrogen fixation, legumes can do without nitrogen fertilizers; thanks to symbionts, termites can process wood.

Summary of Chapter 6

The functional approach allows us to see that there are no "unnecessary" organisms in soil. Each performs its own irreplaceable role:

• Decomposers initiate chemical reactions, transforming the dead into the living.
• Consumers regulate and accelerate this process, shredding organic matter and controlling microbial populations.
• Engineers create the physical structure—the "architecture" of soil space in which all other processes are possible.
• Symbionts establish "partnerships," expanding the capabilities of plants and animals.

Now that we have a complete picture of functional groups, we can move to the final lecture and examine how all these groups interact within the framework of the Soil Food Web.

7.1. What Is the Soil Food Web?

The food web is the totality of all feeding connections between organisms in an ecosystem. Unlike a simple food chain (e.g., "leaf → worm → mole"), the food web shows that most organisms have multiple food sources and multiple natural enemies. The soil food web is one of the most complex and diverse in nature (Foth, 1990; Weil & Brady, 2017).

Main trophic levels (according to White, 2006; Weil & Brady, 2017):

1. Producers (first trophic level). These are organisms that create organic matter from inorganic matter. In soil, these are:

• Plant roots. They are the main source of organic carbon in soil (up to 40–70% of all production in some ecosystems!) (Weil & Brady, 2017).
• Algae and cyanobacteria. Photosynthesize on the soil surface.
• Primary consumers (second trophic level). These are organisms that feed directly on producers or their dead remains. This includes:
• Saprophages and detritivores—feed on dead organic matter (leaf litter, root exudates). This includes most mesofauna (oribatid mites, springtails), as well as macrofauna (earthworms, termites) (Foth, 1990; Eash et al., 2016).
• Phytophages—feed on living plants. These are plant-parasitic nematodes, insect larvae, some rodents (Weil & Brady, 2017).
• Saprotrophic microorganisms—fungi and bacteria that decompose dead organic matter (White, 2006).
• Secondary consumers (third trophic level). These are predators and parasites that feed on primary consumers:
• Microphages—feed on microorganisms. These are protozoa (eating bacteria), bacterivorous and fungivorous nematodes, as well as some mites and springtails (Eash et al., 2016).
• Zoophages—predators that feed on other animals. These are predatory nematodes, predatory mites (Mesostigmata), spiders, ground beetles, centipedes (Foth, 1990; Weil & Brady, 2017).
• Tertiary consumers (fourth and higher trophic levels). These are large predators at the top of the food pyramid:
• Vertebrates—moles, shrews, birds that feed on earthworms, insects, and other invertebrates (Foth, 1990; White, 2006).

Important addition: The Microbial Loop.

In the soil food web, there is a special mechanism that sharply accelerates nutrient cycling. It is called the microbial loop (Eash et al., 2016; Weil & Brady, 2017). Its essence is that microorganisms (bacteria, fungi) "capture" nutrients from organic matter, and then they themselves become food for microfauna (protozoa, nematodes). When microfauna consume microbes, they excrete excess nitrogen and phosphorus in mineral form, which immediately becomes available to plants. Thus, nutrients do not stagnate in microbial biomass but rapidly "circulate" back to plants.

7.2. How Does the Soil Food Web Work in Practice?

Let us trace the path of one leaf that falls onto the forest floor to see the food web in action (model according to Weil & Brady, 2017; White, 2006; Eash et al., 2016):

1. Input of organic matter. The leaf falls onto the soil surface.

2. Primary decomposition (physical). Mesofauna (mites, springtails) gnaw the leaf, turning it into small fragments. Part of the leaf is dragged into burrows by earthworms (engineers). Plant tissues are shredded, and their protective waxy coatings are broken down. This is critically important for subsequent stages.

3. Secondary decomposition (chemical). Saprotrophic fungi and bacteria (decomposers) "attack" the shredded organic matter. They secrete exoenzymes and break down cellulose, hemicellulose, lignin, and proteins. In the course of their life activity, they consume part of the organic carbon and nitrogen, converting it into their biomass (immobilization).

4. Microbial loop. Rapidly multiplying bacteria and fungi attract protozoa and bacterivorous nematodes (primary and secondary consumers). These microfauna actively consume microbial biomass and, in processing it, excrete excess nitrogen (ammonium) and phosphorus into the soil solution. This mineral nitrogen becomes available to plant roots.

5. Engineering. Earthworms (engineers) pass the mixed organic matter and mineral soil through themselves, creating coprolites. These coprolites are highly structured aggregates in which organic substances are firmly bound to mineral particles. Part of the carbon in these aggregates becomes stable and protected from rapid decomposition (this is the basis of humus formation).

6. Regulation. Predatory nematodes and predatory mites (tertiary consumers) feed on bacterivores and fungivores, preventing them from multiplying uncontrollably and "eating up" all the microbial biomass. Thus, balance is maintained.

7. Higher consumers. Moles, shrews, and other vertebrates feed on earthworms and large insects, closing the cycle and returning nutrients to the ecosystem through their excrement.

As a result of this complex process, the leaf disappears; its carbon partially returns to the atmosphere as CO₂ (respiration of all participants), while most of the nitrogen and phosphorus are converted into forms available to plants, and part of the carbon is fixed as stable soil humus.

7.3. Key Principles of the Soil Food Web

The study of the soil food web allows us to formulate several important principles (Weil & Brady, 2017; Eash et al., 2016):

1. Functional redundancy. In healthy soil, the same function (e.g., cellulose decomposition) is performed by several species at once. If one species disappears, its function can be taken over by others, making the system resistant to stress.

2. Interdependence. No organism exists in isolation. The activity of engineers creates the environment for decomposers. The activity of decomposers creates food for consumers. The activity of consumers stimulates decomposers. Everything is connected to everything.

3. Energy flow. Energy moves through the food web from producers to consumers and is lost as heat at each trophic level. The longer the food chain, the less energy reaches its top. Therefore, the biomass of predators is always less than the biomass of their prey.

4. Nutrient cycling. The food web is not just an energy flow; it is a mechanism for nutrient cycling. Nitrogen, phosphorus, sulfur, and other elements circulate between organic and mineral forms, passing through the bodies of many organisms.

Summary of Chapter 7 and the Entire Module

We have completed our overview of the biological organization of soil. Let us summarize and answer our key question:

How do different groups of organisms collectively create functioning soil?

1. Decomposers (bacteria, archaea, fungi) initiate chemical reactions, transforming dead organic matter into mineral elements and humus. They are the "engine" of all soil processes.

2. Consumers (protozoa, nematodes, mites, springtails) regulate the abundance of decomposers, stimulate their activity, and shred organic matter, accelerating its decomposition. They are the "regulators" and "accelerators."

3. Engineers (earthworms, termites, ants, roots) create the physical structure of soil—pores, burrows, aggregates. They build the "house" in which all others live and work. Without them, soil would be an unstructured mass.

4. Symbionts (mycorrhizal fungi, nitrogen fixers) establish partnerships, expanding the capabilities of plants and other organisms. They make the soil ecosystem more efficient and resilient.

Together, through a complex network of interactions (the soil food web), these groups of organisms create what we call fertile, living soil. It is this collective, coordinated activity that ensures element cycling, structure, water regime, and the resilience of the entire terrestrial ecosystem.

Understanding the soil food web is the key to modern, ecologically conscious agriculture. Instead of viewing soil as a simple substrate for plants, we must see it as a complex, living system, and our task as agronomists is to maintain its health and diversity. This is the essence of sustainable soil resource management.