The microbial world and soil fertility

Microbial diversity in topsoil

The microbial community in soil is vast and includes protozoa, fungi, bacteria and archaea (a). Bacteria have a strong involvement in ecosystem processes such as atmospheric nitrogen fixation and mineralisation of organic matter. Some fungi and bacteria have a direct impact on plant health and growth through symbiotic processes. Over the last ten years, numerous scientific studies have shown that soil fertility is conditioned by microbial diversity. And this diversity is also dependent on the physical characteristics of the soil and the way 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 the structural stability of the soil (1). A decrease in microbial diversity also leads to a reduction in the soil's water reserve with greater difficulty in rooting. In addition, associations of micro-organisms including bacteria are involved in the process of neutralising pollutants, particularly pesticides.

In a well-maintained soil, pathogenic microbial populations represent a very small part of the immense 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 transiently in the soil for a few weeks or even years and need a host to reproduce.

The environmental conditions that favour the development of a pathogenic microbial population are complex and often interdependent, such as cropping patterns (abundance of a crop species on a plot, lack of rotation, excessive nitrogen supply), physical and biological soil conditions (such as soil texture, pH, depletion of humus, too much limestone) and climate change. In general, it is now accepted that high soil biodiversity results in a decrease in the action of pathogenic organisms and an increase in beneficial interactions (see the chapter on Rhizosphere, mycorrhizae and suppressive soil).

Soil biological activity and carbon fixation.

Soil biological activity is involved in the carbon cycle and its concentration in the atmosphere. The carbon storage capacity of the soil is determined by the input/output ratio. On the one hand, carbon is fixed in the soil by the degradation of organic matter from plants or their root activities, and on the other hand, part of the carbon is returned to the atmosphere through the mineralisation of organic matter by micro-organisms.

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

Deep aeration is certainly one of the factors that significantly modifies the rate of carbon fixed in the soil, the evolution of microbial populations and other organisms present in the soil. Deep aeration is certainly one of the factors that significantly modifies the rate of carbon fixed in the soil, the evolution of microbial populations and other organisms present in the soil. Les macrospores ont tendance à accumuler une grande variété d’organismes de dimensions variables alors les micropores sélectionnent les bactéries et les virus. In addition, within the microspores, the scarcity of oxygen favours anaerobic bacteria such as clostridium, 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.

Organic matter properties and microbial population.

It is known that fungi in the soil are strongly involved in the degradation of fresh organic matter, while bacteria play a more important role in humus mineralisation. The richer a soil is in microbial diversity, the greater the mineralisation of humus, and the more organic matter must 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, i.e. they need organic matter to thrive, such as plant roots, dead leaves, faeces from forest animals, etc. Depending on the quantity and quality of the organic matter brought to the soil, some species will take advantage over others modifying the biochemical properties of the soil and its fertility. For example, organic matter that is easily putrescible favours copiotrophic bacteria with high nutritional requirements over short periods of time.

A soil rich in humus of long duration favours oligotrophic bacteria with a high biodiversity characterised by specific strategies to cover their energy needs over longer periods. All this little world is constantly evolving, subject to multiple local factors, either random (such as rainfall) or stable (predominant minerals such as a high presence of clay) and the action of the farmer on the cultivated plots. Recent studies have shown that the great diversity of soils observed in France harbours a great diversity of habitats and therefore of biodiversity, including in areas of intensive cultivation.

Microbial diversity is very abundant in regions such as Brittany, Normandy, the North, the Paris basin, the Mediterranean region, and parts of the South-East and South-West. Other regions, mainly mountainous and sandy areas, have a lower diversity, such as the Landes, Gironde, Alsace and Lorraine, Sologne, Morvan and the Cévennes. These large differences in microbial diversity are positively influenced by pH and sand content and negatively by a high Carbon/Nitrogen ratio and an unbalanced clay content. Studies have shown that soils with a neutral or alkaline pH and a texture well supplied with sand and easily degradable organic matter favour high bacterial diversity. On the other hand, clay soils with an acid pH and a long-lasting humus content have a lower microbial diversity. In general, different organisms dominate in field crop, forest and grassland soils.