Air and water pollution have long been in the crosshairs of news reports. Soil, however, has received less attention both in the media and in scientific research, despite being the third major habitat on our planet. On Google, the search term ‘soil pollution’ produces only a third as many results as the keywords ‘air pollution’ and ‘water pollution’. Although less conspicuously, this difference is also reflected on Google Scholar, one of the world’s largest search engines. The subterranean world is of less interest to people, even though it plays as important a role in maintaining ecosystems as wetlands and the atmosphere.

Soil biocoenoses are comprised of countless species of animals and plants, as well as a myriad of microbes and fungi. It is a hidden world that we pay little attention to, despite being at the heart of crucial issues such as climate change, biodiversity and food security. In the present analysis, we look at the impact of soil biocoenoses on these three processes.

Climate change

The complex ecosystem of soil binds carbon within itself and plant biomass through interdependent processes and prevents it from being released into the air as CO2, which contributes to global warming.

Plants and microorganisms capable of photosynthesis use carbon dioxide within the atmosphere to build their own organic matter, thus reducing the concentration of GHGs in the air during the building phase. In the decomposing phase, they would increase it by a similar amount; however, their organic matter is partly released into the soil.

Here it is used as a nutrient by soil-dwelling animals, bacteria and fungi. If the soil biocoenosis is complete, the carbon produced by decomposition is locked into a relatively closed cycle, remaining within the cycle of organisms consuming one another. Thus, it is released back into the atmosphere only after a very long period of time, if at all. Put simply, the richer the life is within the soil, the more carbon is stored underground at any given time, either as dead or as living organic matter.

One of the little-known consequences of this process is that, compared to tropical rainforests, the coniferous forests of the taiga contribute more to increasing oxygen concentration and reducing the concentration of carbon dioxide within the atmosphere. Biodiversity also reaches stunning levels along the equator.

Tropical rainforests boast an unparalleled richness of both species and numbers of individuals. These forms of life – mainly insects and microbes – consume most of the dead plants before they reach the soil. As a result, carbon dioxide sequestered during the life of the plant is released back into the atmosphere, where it can be used by new generations of growing plants during photosynthesis. The “carbon balance” of tropical rainforests is therefore close to zero. In contrast, the coniferous forests of the taiga have relatively low levels of soil diversity, with temperatures below freezing point for most of the year. A large proportion of dead branches and leaves are not immediately broken down by terrestrial animals and microbes, and consequently enter the soil and thus the carbon cycle. Although we tend to think of the Amazon basin as the lungs of the Earth, the reality is that there are more important biomes on the planet from a climate perspective. With that said, of course, there is a huge need for tropical rainforests, as we will later explain in more detail.

Paradoxically, the formation of fossil fuels is also a result of microbial activity within the soil, and soil microbes play a key role in carbon sequestration.

The long-term result of the processes outlined above – the sequestration of carbon by plants and the subsequent release of carbon into the soil – is the formation of abundant sources of carbon beneath the land and oceans over a period of hundreds of millions of years. This includes a broad variety of forms of carbon, including lignite, brown and black coal, oil and natural gas. The perspective of time is one of the problems implied by burning fossil fuels; oil, natural gas and coal are renewable energy sources over hundreds of millions of years. However, it takes only a few centuries, and usually no more than a few decades, to burn the carbon formed over a long period of time even from the perspective of geology.

The amount of carbon found in soil is around 2,500 gigatons, equaling about 80 percent of all carbon found in the Earth’s ecosystems. By comparison, human GHG emissions will amount to just over 40 billion tons of CO2 equivalent in 2021, containing roughly 11 billion tons of carbon.[2] This means that there is nearly 230 times more carbon in the planet’s soil than the amount emitted by mankind in a whole year, and the organic molecules in the soil contain over 140 times as much carbon. A significant amount of this may be released into the atmosphere of we continue destroying the biodiversity of our soils. This brings us to the role of biodiversity.


Increasing biodiversity brings about the enhancement of resilience to biotic and abiotic stresses.

The former includes various diseases; the latter mainly covers natural factors such as temperature, UV radiation and the abundance or scarcity of precipitation. The increase in resilience is due to the fact that diverse biocoenoses and natural ecosystems are able to withstand a wide range of environmental stresses or diseases; consequently, even if the individual count of a certain species decreases, others can increase their numbers. This is why tropical rainforests, with their unparalleled biodiversity, play an essential role in the global ecosystem. Rainforests provide the whole planet with adaptive capacity and are the centers of origin and dispersal of countless species (see, for example, Homo sapiens).

While resilience stemming from biodiversity appears evident in the case of animals and plants, the same is also true for microorganisms. If there are higher numbers of species and individuals of bacteria and fungi in the soil, a disease or environmental impact will not cause a drastic change in the structure of the soil microbiome.

Although soil biodiversity may also decline due to natural processes, we have a greater potential to influence human-induced soil pollution. One of the most significant forms of this is agriculture, including the use of pesticides and fertilizers.

Insecticides, fungicides and herbicides, collectively known as pesticides, are basic necessities of modern, industrialized agriculture. They are needed to ensure that crops are not damaged by pests, thus resulting in appropriate quality and quantity. However, these pesticides not only destroy forms of life that are harmful; they partly leach down into the soil, where they cause serious damage to beneficial microbial communities.

The soil microbiome is comprised of several groups of organisms, including prokaryotic and eukaryotic unicellular organisms, photosynthetic cyanobacteria, fungi and algae. These are far smaller and simpler organisms compared to multicellular forms of life; however, they share similar enzymatic reactions and other physiological processes at the cellular level, meaning that their metabolic activity and changes thereto can be assessed by studying the activity of enzymes selected by various microbes that are also active in soil. Several studies have been carried out to investigate the effects of various pesticides on the microbiome, based on enzyme activity and soil respiration (the latter measuring carbon dioxide produced by soil organisms during their respiratory processes).

One such study looked at the effects of an insecticide known as acetamiprid. This chemical is widely used in the cultivation of leafy vegetables, citrus fruits, apples, grapes, cotton, brassicas and decorative plants. Its use in both low and high concentrations has had negative effects on soil respiration and phosphatase enzyme activity. After two weeks of application, the chemical had a positive effect on dehydrogenase enzyme activity.[3] This is likely due to the fact that, with continued exposure, certain microbes are able to develop immunity to some chemicals; their life cycle is short and they multiply rapidly, meaning that beneficial (in this case, resistant) mutations are rapidly selected.

A further piece of research investigated the effects of a herbicide containing bromoxynil on soil life. The chemical caused a major and long-term reduction in soil biomass, reflected by a decrease in dehydrogenase enzyme activity.[4]

Yet another field study saw the investigation of an endosulfan-containing insecticide known as Thiodan. This chemical caused a severe reduction in the number of Actinobacteria, fungi and protozoa while increasing the number of bacteria.[5]

In conclusion, it is clear that various chemicals used in agriculture can even help a certain, highly reproductive and adaptive microorganisms to thrive. Overall, however, the scales tip heavily in the negative direction, as these chemicals are not selective enough for the target organisms and thus decimate many groups of organisms that are beneficial – sometimes even essential – for healthy soil life.

Food security

Soil fertility, as well as organic matter (and carbon) content, can also be determined by the number of microorganisms per 1 gram of soil. In the 1990s, the total mass of microorganisms was twenty times the total mass of humanity.[6] While we do not have precise data on how sharp the decline was, this ratio has definitely changed since in favor of humanity, due to both population growth and the continued destruction of the soil microbiome.

Soil biocoenoses are important for agriculture, and therefore food security, for the same reason that they carry significance for the entire terrestrial ecosystem. They bind and circulate organic and mineral matter in the upper layers of the soil, the root zones of plants. Consequently, it avoids being released into the atmosphere or washed down into deeper layers, and therefore remains available for use by natural vegetation and plantation crops.

Certain microorganisms, however, go beyond this preservatory process. One of the most important inorganic substances for plant growth is nitrogen, of which there is no shortage on Earth: it makes up 78 percent of the atmosphere. However, plants cannot use nitrogen in its N2 form, as it is present in the atmosphere; they require it in the form NH₄⁺, NO₃⁻ ions.[7] They are helped in this by nitrogen-fixing bacteria, which convert atmospheric nitrogen into ions that plants can use.[8] Of course, this symbiotic relationship is not detrimental to microorganisms either, as they have access to organic matter in plants’ root zone that they can use.

The destruction of microbial communities in the soil therefore also reduces the productive capacity of agricultural land, which we try to compensate through fertilization, using mainly artificial fertilizers. However, irresponsible use of such chemicals leads to further soil degradation and eutrophication (meaning excessive algal growth in wetlands). Preserving organic and inorganic matter within the soil is therefore a more sustainable way of working the land. Organic farming and soil regeneration farming, which we already discussed in a previous article, provide a method for this.


The soils of our planet are complex and fragile biocoenoses; their protection is in the vital interest of humanity in a variety of aspects.

Healthy soils boasting a high content of organic matter contribute to achieving our climate goals faster and more sustainably through microbial cycling and carbon storage. With its high diversity of species and large number of individuals, the soil microbiome has the potential of adapting to and withstanding biotic and abiotic stress effects, including those not caused by humanity.

Biocoenoses in natural and cultivated soils are essential for the growth of plants and thus for maintaining natural habitats and feeding humanity.

Industrialized agriculture and polluting industrial production make the protection of our soils difficult. However, our efforts at doing so will definitely yield results in the long term.