At the end of the last century, Russian biophysicist V. G. Gorshkov scientifically substantiated the real mechanisms of environmental regulation by biota and developed the concept of biotic regulation of the environment (without natural biota, there is no life itself). Within the framework of the concept of biotic regulation, the main property of life is the ability of species to perform work that maintains conditions suitable for life in the environment.
Russian scientist Vladimir Ivanovich Vernadsky, in his works, wrote: “Soil is saturated with life… On the surface of the Earth, there is no chemical force more consistently acting, and therefore more powerful in its ultimate consequences, than living organisms taken as a whole. Viable microorganisms can produce several generations of their kind per day.”
The soil microbiome refers to the community of microorganisms inhabiting the soil, including bacteria, fungi, protozoa, and nematodes. These microorganisms play a decisive role in the nutrient cycle, decomposition, and overall condition of the soil. They help break down organic matter, fix nitrogen, and suppress pathogenic microorganisms transmitted by the soil. A diverse and balanced soil microbiome is essential for healthy plant growth and the functioning of the ecosystem.
Simply put, the microbiome is the community of microbes—eukaryotes, archaea, fungi, viruses, and bacteria—that work together both with a given environment and within it. They are directly responsible for the health of that environment and how it functions, cooperating to provide benefits that can help the organism resist stressors and invaders, making it overall more resilient; conversely, when their composition changes, the environment changes as well, resulting in the suppression of the organisms living within it.
In the fertile soil horizon, a certain “layering” occurs: in the upper layer, aerobic microorganisms thrive, those that need oxygen. These are the active workers in the mineralization of organic remains. Deeper in the soil, other microorganisms inhabit the area—anaerobes, which can live without oxygen. They too process organic remains into mineral compounds, but they do so much more slowly than their aerobic counterparts. A prime example of the work of anaerobic microorganisms is peat at the bottom of a swamp, which takes a long time to form.
In the aerobic layer of the soil, the maximum multiplication of microorganisms occurs. In the aerobic humus layer, the formation of humus is 24 times greater than in the lower soil layers. When plowing or digging the soil, these layers are destroyed, and the soil microbiota is suppressed, which slows down the process of mineralizing organic matter. That’s why advocates of organic farming, rejecting the use of mineral fertilizers, resort to loosening the upper soil layer with a plow, hoe, or rake—this allows the aerobic microorganisms in the topsoil to quickly and effectively mineralize organic fertilizers, thus providing nutrients for the plants. Healthy soil can eliminate the need for fertilizers and protect plants from harmful diseases.
Bacteria and archaea, the smallest organisms in the soil (except for viruses), are prokaryotic. They are the most widespread microorganisms in the soil and serve many important purposes, including nitrogen fixation. Some bacteria can accumulate minerals in the soil and influence the weathering and breakdown of these minerals. The greater the number of minerals in an ecological niche, the higher the population of bacteria. These bacteria form aggregates, which improves the overall health of the soil.
In the process of photosynthesis, plants convert inorganic substances into complex organic compounds. Many soil bacteria, during their life activities, convert dead plant parts and dead organisms into humus. These are saprotrophic decay bacteria. By turning organic remains into humus, they perform a sanitary and soil-forming role in nature.
Another group of soil bacteria decomposes humus. These are saprotrophic fermentation bacteria. During their life activities, humus is converted into mineral salts, which are necessary for plant life.
All Bacteria Possess Biochemical Versatility. For example, the bacterial genus Pseudomonas can metabolize a wide range of chemicals and fertilizers. In contrast, another genus, known as Nitrobacter, can obtain energy only by converting nitrite to nitrate, a process also known as oxidation. The genus Clostridium is a model of bacterial versatility, as it can grow in the absence of oxygen, breathing anaerobically, unlike most species. Several Pseudomonas species, such as Pseudomonas aeruginosa, can breathe both aerobically and anaerobically, using nitrate as the terminal electron acceptor.
The permanent residents of the soil include various putrefactive, primarily spore-forming, aerobic (Bacillus subtilis, B. cereus var. mycoides, B. megaterium) and anaerobic (Clostridium sporogenes, C. putrificum) bacteria, as well as bacteria that break down cellulose, nitrifying, denitrifying, nitrogen-fixing, sulfur, and iron bacteria.
Soil microorganisms play a significant role in creating soil fertility. Microorganisms, in a sequence of changes, carry out the processes of the nutrient cycle in the soil. Organic materials entering the soil in the form of plant residues, animal carcasses, and other contaminants gradually mineralize. Carbon, nitrogen, phosphorus, and other elements from forms unavailable to plants are converted into substances they can absorb.
Soil is the natural habitat for microorganisms. They find all the conditions necessary for their development in the soil: food, moisture, protection from the harmful effects of direct sunlight and drying.
The soil microbiota varies significantly in terms of quantity and species composition, depending on the chemical composition of the soil, its physical properties, pH, moisture content, and degree of aeration. Climate conditions, the time of year, agricultural practices, the type of vegetation cover, and other factors also have a significant impact.
In ecosystems, as Barry Commoner stated, “everything is connected to everything.” The wise biota takes care of the plants. Soil microbes form symbiotic (mutually beneficial) relationships with plants, enhancing protection from pathogens and stimulating their growth in exchange for food sources. These microbes represent a special class of bacteria that occupy the rhizosphere (root zone) and have the ability to improve plant development and increase their defense mechanisms.
Plants Obtain Their Food from the Soil in Which They Grow. However, this food is only available to them thanks to the wide variety of microbes (especially bacteria and fungi) that can chemically and mechanically transform materials in the soil into nutrients. Thus, these bacteria directly influence plant growth by facilitating access to nutrients such as nitrogen, phosphorus, iron, and others.
Although nitrogen, phosphorus, and iron may be abundant in the soil, they are often in forms that plants cannot use. Plant-growth-promoting bacteria convert these nutrients into forms that plants can easily use for nourishment.
These bacteria can also produce plant hormones, such as auxins, gibberellins, and cytokinins. These hormones stimulate the growth of roots and shoots in exchange for nutrient sources obtained from the plant.
Furthermore, plant-growth-promoting bacteria have the ability to protect plants from pathogens. In their competition for nutrients, they outcompete pathogens and produce antibiotics and antifungal metabolites.
Such bacteria can help plants defend themselves from pathogens in a truly remarkable way. They trigger a signal within the plant that activates its defense system. This includes strengthening plant cell walls, producing antimicrobial substances, and synthesizing proteins related to pathogens.
Moreover, there is a direct and close connection between the soil microbiome and the human gut microbiome, both of which contain approximately the same amount of active microorganisms (there is also a connection between the human gut microbiome and the ocean microbiome, with about 73 percent of the same microbes). The soil microbiome is in harmony with the human microbiome and its estimated 39 trillion microbes that inhabit our bodies, mouths, noses, and especially our intestines — particularly our large intestines. Our health depends not only on the activity of microbes in our gut but also on the microbes we ingest both directly (through purposeful geophagy or accidental ingestion of dirt) and indirectly (via plant crops) from the soil.
Unfortunately, not all soils today have a healthy microbiome. This negatively impacts the human gut microbiome as well. This is especially true for products grown using hydroponics, where no soil microbiome is involved at all.
The soil microbiome is severely affected by the industrial, aggressive method of land treatment that is now widespread across the world. Soil is being destroyed and degrading at an unprecedented rate due to the use of plows (which turn the soil upside down, thus killing both aerobic and anaerobic bacteria), insecticides, herbicides, synthetic fertilizers, and a lack of organic matter. Without these vital microbial communities, ecosystems suffer on both small and large scales.
Human impact on the ecological situation is increasing. The situation is made worse by the regular synthesis of xenobiotics—substances that have no natural analogs. As a result, modern biota cannot process them, as they lack the natural mechanisms for doing so. The decay period of some waste products or polymers can span hundreds of years. Eventually, there may come a time when the volume of non-degradable waste reaches a critical mass, threatening the very existence of the biosphere over vast expanses of our planet. This is why it is important to understand the deep connection and interdependence of all the beings created by God for this planet.
All living organisms on Earth are divided into three major groups:
- producers of food (producers)
- consumers of food (consumers)
- and decomposers (detritivores).
From an abiotic perspective, any soil is a factory inhabited by decomposer organisms. Decomposers (also known as destructors, saprotrophs, or saprophytes) release primarily carbon dioxide (CO2) and nitrogen compounds from organic residues, returning mineral salts to the soil and water, making them available to producers (autotrophs). In this way, they close the biotic cycle. Therefore, ecosystems cannot function without decomposers. Decomposers differ from animals in that they do not leave behind solid undigested waste (excrements).
The fundamental condition for the existence of an ecosystem is the maintenance of the material cycle and energy transformation. The most complete material cycle occurs in terrestrial ecosystems, or biogeocenoses. This is ensured by trophic (feeding) relationships between organisms of different species belonging to different functional groups. It is based on these relationships that organic substances synthesized by producers from mineral substances, with the absorption of solar energy, are passed to consumers and undergo chemical transformations.
As a result of the activity of decomposers, organic substances from dead organisms are broken down into inorganic forms (CO2, NH3, H2S, H2O). These inorganic substances are then used by producers to create new organic compounds, which, with the help of consumers, are reintegrated into the cycle.
If these substances were not reused, life on Earth would be impossible. The stocks of substances absorbed by producers are not limitless. To maintain a full material cycle in an ecosystem, all three functional groups of organisms must be present. And there must be constant interaction between them in the form of trophic relationships, which form trophic (feeding) chains or food chains.
- The first trophic level of an ecosystem is formed by autotrophs, including green plants and photo- and chemosynthesizing bacteria.
- The second level of the chain consists of herbivorous animals, as well as parasitic higher and lower plants.
- The third trophic level includes carnivorous animals that feed on herbivores—these are first-order predators such as insectivorous birds, small mammals, reptiles, amphibians, and parasites of these animals.
- The fourth and subsequent trophic levels are represented by higher-order consumers—larger carnivorous animals, second-order predators, and their parasites, as well as humans.
- The last trophic level is occupied by decomposers (detritivores), which consume dead organic matter. These are invertebrate animals—saprophages, heterotrophic microorganisms, fungi, and protozoa.
It is the decomposers that complete the biosphere-forming function of biota and create the biogenic foundation for all the ecological pyramids used today to graphically represent ecosystems: 1) pyramids of numbers, based on counting organisms at each trophic level; 2) pyramids of biomass, which use the total mass (usually dry) of organisms at each trophic level; 3) pyramids of energy, which consider the energy content of organisms at each trophic level. However, when constructing these pyramids, decomposers are often forgotten or ignored for the sake of simplification.
Natural garbage collectors and cleaners, both in soil and water, suffer from human activities (harmful emissions from industrial enterprises into soil, water bodies, and the atmosphere, deforestation, plowing of meadows, etc.), which causes their total numbers and overall productivity to steadily decline. As a result, we are witnessing the so-called “decomposer crisis,” that is, the inability of natural destructors to fully process and return to the biosphere the growing mass of waste (primarily industrial, agro-industrial, and household waste), and ultimately—close the biotic cycles.
The balance of decomposers in the soil can be disrupted by various factors. Here are some of them:
- Improper soil treatment, which can disrupt the soil structure and destroy the natural communities of microorganisms.
- Failure to follow crop rotation: continuous cultivation of the same crops on the same plot of land leads to soil depletion and a reduction in microbial diversity.
- Competition for nutrients: pathogens often become stronger than beneficial microorganisms due to competition for nutrients. Therefore, it is important to systematically populate the soil with beneficial microorganisms.
- Use of chemical plant protection agents: chemical fertilizers and pesticides can disturb the balance of microorganisms, negatively impacting soil health.
Soil microbiomes also suffer from fires. Extreme temperatures, in addition to altering the physical properties and chemical structure of the soil, negatively affect the fungi and bacteria inhabiting its upper layer. Studies have shown that the composition of bacteria, fungi, and archaea in burned areas significantly differed from that of unburned soil. Research results have shown that the restoration of the physical and chemical properties and microbial communities in the soil after a fire can occur quite slowly. This means that fires have long-term consequences for the soil ecosystem.
Currently, the task of using the biological potential of plants and microbiomes to partially or fully replace agrochemicals is becoming more and more relevant. This would help successfully address the issue of providing nutrients and protecting plants from diseases and pests.
Ways to maintain soil microbiomes.
First and foremost, it’s the addition of organic matter. Modern soils are depleted of organic matter because livestock is now separated from crop production. Historically, plants and animals were always grown together, as they are in nature. Forests and meadows were filled with hooved animals and others, while traditional family farms worldwide have combined livestock with crops. Organic matter is any carbon-based material that comes from a once-living plant or animal. It is the most important source of “food” for microbes. Microbes feed on organic matter and then provide the extracted nutrients to plants.
Organic matter includes:
- Manure and bedding of any kind;
- Compost;
- Vegetable scraps;
- Crop residues (any part you don’t use);
- Mown grass;
- Tree leaves;
- Straw;
- Pine needles;
- Peat moss;
- Wood chips or bark;
- Stems and twigs;
- Plant roots and stubble;
- Animal by-products (remains of dead animals, etc.)
Any of these ingredients is well-suited to feed the soil food chain, but they differ in the speed at which they decompose. High-nitrogen materials, such as manure, vegetable waste, and mown grass, usually decompose the fastest because bacteria quickly consume them. However, these materials are typically not directly added to the soil because they may carry some pathogens or be too active for plants. Nitrogen-rich materials need to be balanced with carbon-rich materials to absorb excess moisture and nutrients, allowing them to decompose into a more stable compound like compost.
Composting is possibly the best way to improve the microbiome, as it creates a more closed cycle of localized microbes from vegetable waste. However, it may be necessary to bring manure or bedding from a local farm or neighbor to enhance the fertility of the compost.
Aeration is the most crucial part of the composting process because it continually introduces oxygen to nourish the “good” microbes. Most “bad” pathogenic microbes develop in anaerobic conditions, often creating that unpleasant rotten egg smell or stagnant, unturned compost pile.
Vermicomposting is the next best option. Worms have an incredible diversity of microorganisms in their intestines, and they can quickly contribute to improving the soil food chain. You can buy ready-made worm castings to enhance microbial activity or make your own worm compost.
The use of organic waste recycling products with the involvement of earthworms, in symbiosis with microorganisms, is a promising direction for restoring and maintaining soil fertility and biological intensification of agriculture. In natural soils, the decomposition of organic matter is carried out by earthworms, coprophages, and other organisms. But microorganisms are also involved in this process. The conditions in the worm’s intestines are more favorable for the performance of various functions than in the soil. Earthworms, in conjunction with microorganisms, convert various organic waste into highly effective biological fertilizers with good structure, enriched with macro- and micronutrients, enzymes, and active microflora, ensuring prolonged (long-lasting, gradual) effects on plants.
Secondly, minimizing soil disturbance. Soil disruption is the enemy of the microbiome. Every time the soil is heavily tilled with a shovel or heavy machinery, the fragile structure of the underground “factory” and all its microbial inhabitants are destroyed. Of course, soil preparation is necessary for agricultural activities, but it is possible to switch to primarily no-till or minimal tillage methods to minimize disruption to the soil food chain.
Destroying the soil layer to a depth greater than five centimeters, as happens with plowing or rototilling, significantly reduces biodiversity in the soil food chain and also leads to the loss of fertility and organic matter, soil erosion, and compaction.
Thirdly, abandoning synthetic fertilizers and chemicals. Synthetic fertilizers are the enemies of a healthy microbiome. While slow-release organic fertilizers can help feed microbes, synthetic chemical fertilizers are toxic to them. Synthetic fertilizers may appear to provide a great boost for plants, but they also pose a huge risk due to over-fertilization, nitrogen burn, and water pollution.
Furthermore, synthetic nutrients lead to salt accumulation in the soil. Since most chemical fertilizers are derived from petroleum products, they are overloaded with mineral salts that damage soil microbes, reducing overall biodiversity and depleting the soil’s natural fertility. Sometimes, you can even see a salt crust on the soil surface where a lot of fertilizers have been applied.
If natural soil fertility is to be created without relying on fertilizers, it is essential to first eliminate all synthetic chemicals, including synthetic fertilizers, pesticides, and herbicides. All these chemicals act in the soil like antibiotics, killing the microbes necessary for long-term plant nutrition. After removing these chemicals from agricultural practices, a recovery period may occur, where the ecosystem will struggle to return to balance. This will take time, but that’s okay.
Fourthly, aeration. Oxygen is critical for soil health. It’s quite difficult to ensure air flow in dense clay layers. Overly wet soils and plants struggling with root rot also suffer from a lack of oxygen in the root zone.
Pathogenic fungi thrive in soils with low oxygen content, which is why they tend to colonize roots in compacted soils. By adding more oxygen and loose organic material to the soil, root-borne diseases cannot survive. Instead, beneficial fungi and bacteria will flourish.
Wide fork loosening is a simple physical action in which long metal tines are pushed into the soil, without plowing or disturbing the soil structure. Each tine creates a channel for oxygen and water to reach deeper layers. Compost and microbes can follow these channels, working to break down compaction and creating positive feedback with increasing aeration.
Fifthly, planting cover crops. Cover crops are an excellent way to increase microbial activity in the soil, especially if nitrogen-fixing legumes are grown. Planting a cover crop between vegetable plantings can restore the soil and ensure that living roots are always in place to nourish the underground microscopic workers.
Cover crops should always be mowed or incorporated back into the soil to gain all their benefits. They can also be cut and added to compost. However, it’s important to ensure that invasive species are not used as cover crops, as this can also alter the soil structure.
Finally, sixthly, the use of soil microbiota-based products. The necessity of using the biological capabilities of plants and microorganisms to partially or completely replace agrochemicals makes it possible to effectively address the problem of providing nutrients and protecting plants from diseases and pests. When determining the productivity of the “plant-microorganism” interaction, it’s important to assess the compatibility of metabolic systems, such as nitrogen and carbon transport pathways, as well as the absence of active protective responses in plants to the presence or penetration of microorganisms. Bacteria located in the rhizosphere or “nodules” can synthesize both stimulating substances (phytohormones, vitamins) and inhibitory ones (rhizobiotoxins) that affect plant development.
Currently, products of the following classes are produced:
- Substances synthesized by specific soil microorganisms, such as phytohormones.
- Preparations made from artificially cultured soil microorganisms of certain strains, such as Bacillus subtilis or endophytic fungi.
- Preparations of artificially selected and reproduced communities of microorganisms, such as “effective microorganisms.”
- Preparations of natural communities of microorganisms from natural and artificial soils, such as concentrated soil solution.
In 1981, Vadim Ivanovich Nazarov’s book “Beyond the Threshold of Hostility” was published, discussing the friendship and cooperation of different, often very distant, beings that belong to different kingdoms of life. Not only do they not consume each other, but by living together, they make their existence easier. The book explores various forms of symbiosis and what studying them can teach us. Flowers and insects, algae and invertebrates, bacteria and multicellular organisms, ants and plants — these are just a few examples from the vast world of organism cooperation, which plays a crucial role in nature.
It is time for us, humans, to move from the discredited notion of “nature conservation” to a full-fledged interaction with the environmental regulation mechanisms through biota, in line with the concept of biotic environmental regulation by V. G. Gorshkov. This includes systematic interaction with decomposers. Specifically, this means a systematic approach, mediated by the natural levels and feedback networks of Earth’s biota. Because by destroying the Pyramid of Life and eliminating its stages, we inevitably descend directly to the decomposers and will meet them face to face. To avoid this, let’s take care of our Mother Earth and all the creatures living on it, because the health and well-being of humans depend on the well-being of all participants in these interdependent, complex, and balanced processes that sustain life on this planet.
Evgeny Lvovich Lebedev,
State Councilor of the Russian Federation, 2nd Class,
Former Head of the Department of the Federal Service for Supervision of Natural Resource Management in the Penza Region.
Literature:
- Biotic Regulation: Publications link
- Soil Pollution Poses a Greater Threat to Underground Biodiversity than Climate Change link
- N. Sukachev – Biogeocoenosis as an Expression of the Interaction of Living and Non-living Nature on the Earth’s Surface: The Relationship Between the Concepts of “Biogeocoenosis,” “Ecosystem,” “Geographic Landscape,” and “Facies” in Fundamentals of Forest Biogeocoenology, edited by V. N. Sukachev, N. V. Dylys. Moscow: Nauka, 1964. pp. 5–49.
- I. Vernadsky – Biosphere and Noosphere. Moscow: Nauka, 1989. 264 p.
- I. Nikitin – Soil Microbiology. Moscow: Kolos, 1979. 318 p.
- N. Winogradsky – Soil Microbiology. Moscow, 1952.
- Natural Resource Management: Dictionary-Reference Book by N. F. Reimers. Moscow: Mysl, 1990.
- F. Reimers – Hopes for the Survival of Humanity. Conceptual Ecology. Russia Young, Ecology, 1992.
- M. Gilyarov – Population Ecology: A Teaching Aid. Moscow: MGU Publishing House, 1990.
- Giller – Community Structure and Ecological Niche. Moscow: Mir, 1988. 184 p.
- Ecology by Yu. P. Odum. Moscow: Mir, 1986. Volumes 1–2.
- Barry Commoner – The Closing Circle. Moscow: Gidrometeoizdat, 1974. 280 p.
- Connection Between Soil Microbiomes and Gut Microbiomes link
- A. Tikhonovich, N. A. Provorov – Symbioses of Plants and Microorganisms: Molecular Genetics of Agroecosystems of the Future. St. Petersburg, 2009.
- Yu. Gelzer – Symbiosis with Microorganisms — The Basis of Plant Life. Moscow: MSHA, 1990.
- Beyond the Threshold of Hostility by Vadim Ivanovich Nazarov. Scientific Literature, Biology. Published: 1981. Moscow: Mysl.
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