The microbial world and soil fertility

Microbial diversity in topsoil

The microbial community present in the soil is vast and includes protozoa, fungi, bacteria and archaea (a). Bacteria play a significant role in ecosystem processes such as atmospheric nitrogen fixation and the mineralisation of organic matter. Certain fungi and bacteria have a direct impact on plant health and growth through symbiotic processes.

Over the past decade, numerous scientific studies have shown that soil fertility is dependent on microbial diversity. And this diversity is also dependent on the physical characteristics of the soil and how it is maintained. A 30% loss of bacterial species leads to a 40% decrease in the mineralisation of organic matter and a 50% decrease in soil structural stability (1). A decline in microbial diversity also leads to a reduction in soil water reserves, making it more difficult for plants to take root. In addition, associations of microorganisms including bacteria are involved in the neutralisation of pollutants, particularly pesticides.

In well-maintained soil, pathogenic microbial populations represent a very small part of the vast microbial diversity. The presence of these pathogenic populations and other parasitic agents is natural and can affect all higher organisms. Pathogenic populations become invasive and pose serious health problems when they encounter certain environmental conditions. As for parasites, many of them live temporarily in the soil for a few weeks or even a few years, and they need a host to reproduce.

The environmental conditions that favour the development of a pathogenic microbial population are complex and often interdependent, such as farming methods (abundance of a single species grown on the same plot, lack of crop rotation, excessive nitrogen input), physical and biological soil conditions (such as soil texture, pH, humus depletion, soil that is too rich in limestone) and climate change. It is now generally accepted that high soil biodiversity results in a reduction in the activity of pathogenic organisms and an increase in beneficial interactions. (see the chapter on Rhizosphere, mycorrhizae and suppressive soils).

Soil biological activity and carbon sequestration

Soil biological activity plays a role in the carbon cycle and its concentration in the atmosphere. The carbon storage capacity of soil is determined by the input/output ratio. On the one hand, carbon is fixed in the soil through the decomposition of organic matter from plants or their root activities, and on the other hand, some of the carbon returns to the atmosphere during the mineralisation of organic matter by microorganisms

Natural and human factors influence carbon inputs and outputs, such as season, irrigation, ploughing and crop type. Some factors are uncontrollable, such as the weather. Others can be modified in a favourable way, such as simplified tillage, more frequent recycling of crop residues and the use of green manure between crops.

Deep aeration is certainly one of the factors that significantly alters the rate of carbon fixed in the soil and the evolution of microbial populations and other organisms present in the soil. Macrospores tend to accumulate a wide variety of organisms of varying sizes, while microspores select bacteria and viruses. In addition, within microspores, the scarcity of oxygen favours anaerobic bacteria such as clostridia, some species of which are involved in the putrefaction of organic waste, with the risk of producing toxic substances. In habitats where oxygen is frequently renewed, aerobic bacteria thrive. Oxygen is essential for certain important ecosystem services such as nitrogen fixation by bacteria.

Properties of organic matter and microbial population

It is well known that fungi present in the soil play a major role in the degradation of fresh organic matter, while bacteria play a more important role in the mineralisation of humus. The greater the microbial diversity in the soil, the greater the mineralisation of humus, and the more organic matter needs to be added each year to compensate for losses. This is a factor that must be taken into account in soil maintenance when seeking to increase soil biodiversity.

The vast majority of bacteria are heterotrophic, meaning they need organic matter to thrive, which is provided by plant roots, dead leaves, faecal matter from animals living in the forest, etc. Depending on the quantity and quality of organic matter added to the soil, some species will gain an advantage over others, altering the biochemical properties of the soil and its fertility. For example, easily decomposable organic matter favours copiotrophic bacteria, which have high nutritional needs over short periods of time.

Long-lasting humus-rich soil promotes oligotrophic bacteria with high biodiversity, characterised by specific strategies to meet their energy needs over longer periods. This entire microcosm is constantly evolving, subject to multiple local factors that are either random (such as rainfall) or stable (predominant minerals such as a high clay content) and the farmer’s actions on cultivated plots. Recent studies have shown that the great diversity of soils observed in France is home to a wide variety of habitats and therefore biodiversity, even in areas of intensive cultivation.

Microbial diversity is very abundant in regions such as Brittany, Normandy, the North, the Paris Basin, the Mediterranean coast, and parts of the South-East and South-West. Other regions, mainly mountainous and sandy areas, have lower diversity, such as the Landes, Gironde, Alsace and Lorraine, Sologne, Morvan and Cévennes. These significant differences in microbial diversity are positively influenced by pH and sand content and negatively influenced by a high carbon/nitrogen ratio and an unbalanced clay content. Studies have shown that soils with a neutral or alkaline pH, a texture rich in sand and easily degradable organic matter promote significant bacterial diversity. On the other hand, clay soils with an acidic pH and long-lasting humus have lower microbial diversity. In general, different organisms dominate in arable soils, forests and grasslands.