Until fairly recently, the living soil has been considered as a functional black box that is intrinsically too difficult to be unravelled into its core components. However, this concept has changed with the advent of the modern methodologies. The intricacies of microbial life in soil has been impacted by the advanced, mainly molecular-based, approaches that have been unleashed on the soil habitat in recent years. The application of molecular and other advanced methods (cultivation-independent analyses) has provided exciting new insights into microbial life in soil.

Soil is an extremely diverse and complex habitat containing many microsites and gradients that form a range of different biogeochemical interfaces. Depending on the proportion of sand, silt and clay, the surface area in soil can vary from 11 cm² up to 8 million cm² per gram of soil read more.... The aggregates formed by minerals, soil organic matter, fungal hyphae, roots and plant debris offer a range of potential niches for microorganisms with different lifestyles. The architecture of the soil pore network essentially defines the habitat colonized by the microorganisms and the pore space strongly influences the nature and extent of the interactions between the organisms inhabiting the soil. The heterogeneous physical structure of soil affects the spatial distribution of water, oxygen and nutrients, which in turn influences the composition and activity of the microbial communities themselves. As an example, the spatial distribution of bacteria in topsoil and subsoil was found to be different, but lateral variations in spatial distributions are also likely to occur.

In terms of their occurrence in microsites, bacteria can be found in soil as single cells but most often they occur as microcolonies, i.e. small agglomerates of cells that can be regarded as primative soil biofilms read more.... Microorganisms are the major drivers of geochemical and biotransformation processes in soil. In concert with the soil's inorganic and organic constituents, microbes are influential in actively shaping the architecture of the soil matrix by the formation and restructuring of soil aggregates. In addition, the diversity of microbial communities is extremely high in most soils. There are only a few quantitative estimates of the numbers of microbial taxa that can co-exist in just a single gram of soil, but an advanced analysis of nucleic acid-based analyses, based on re-association kinetics, has suggested that prokaryotic diversity can reach 1 million species genomes per g, which by far exceeds the common estimates of bacterial richness in soil obtained from cultivation-based studies read more....

A major driving force that spurs the microbial diversity of soil is the enormous heterogeneity of the soil habitat, allowing the formation of numerous niches. Different factors, such as the presence or absence of water, soil pH, temperature, redox potential and the soil organic matter content do not only influence the types of microbes colonizing the respective microniche but also their activity. All these factors can vary greatly between the different microhabitats and, thus, not only the composition but also the activity and interactions of the microbiota will largely vary due to the spatial and temporal heterogeneity between as well as within the microsites.

A key determinant of microbial fitness in soil is the ability of microbial cells to fine-tune their cellular metabolism to the abiotic and biotic conditions that prevail locally. In addition, the rate of adaptation of microorganisms to changing environmental conditions might be enhanced by horizontal gene transfer processes read more.... Undoubtedly, the most important prerequisite for microbial life in soil is the availability of water. Next to being indispensable for microbial life, the water in soil carries dissolved gases, ions and nutrients to microorganisms, and, in cases of saturation, may quickly establish anaerobic conditions. For instance, an increase of the moisture content of soil can greatly influence the microbial communities that are locally present, in particular by connecting pore spaces in and among aggregates that were unconnected without water, thus increasing the aggregate connectivity. Predation by protozoa or Bdellovibrio species will therefore be particularly enhanced in relatively wet soils.

from Kornelia Smalla and Jan Dirk van Elsas in Environmental Molecular Microbiology

Further reading:

• Environmental Molecular Microbiology
• Metagenomics: Theory, Methods and Applications
• Environmental Microbiology

Labels: Cultivation-independent analysis, microbial communities, microbial ecology, soil microbiology