Abstract
The living soil is instrumental to key life support functions (LSF) that safeguard life on Earth. The soil microbiome has a main role as a driver of these LSF. Current global developments, like anthropogenic threats to soil (e.g., via intensive agriculture) and climate change, pose a burden on soil functioning. Therefore, it is important to dispose of robust indicators that report on the nature of deleterious changes and thus soil quality. There has been a long debate on the best selection of biological indicators (bioindicators) that report on soil quality. Such indicators should ideally describe organisms with key functions in the system, or with key regulatory/connecting roles (so-called keystone species). However, in the light of the huge functional redundancy in most soil microbiomes, finding specific keystone markers is not a trivial task. The current rapid development of molecular (DNA-based) methods that facilitate deciphering microbiomes with respect to key functions will enable the development of improved criteria by which molecular information can be tuned to yield molecular markers of soil LSF. This review critically examines the current state-of-the-art in molecular marker development and recommends avenues to come to improved future marker systems.
Highlights
Given their often large and complex microbiomes, soils can be considered as hotspots for microbial biodiversity on Earth
Soils provide a large number of biological services that are essential for life on Earth, which are considered as life support functions (LSF)
These LSF include: (1) The provision of “fertile ground” as a basis for a sustainable bio-economy, including the growth of food, feed, fibers, and bioenergy crops; (2) The maintenance of a natural unthreatened plant biodiversity at sites which are not used for agricultural production; (3) The safeguarding of drinking water, by filtering and degrading pollutants in soil before they enter the groundwater body; (4) The protection from erosion; (5) The potential to act as a sink for atmospheric CO2
Summary
Given their often large and complex microbiomes, soils can be considered as hotspots for microbial biodiversity on Earth. If parts of the soil microbiome should serve as indicators for ecosystem services from soils, there is a need to address the issue “how to analyse microbial communities in soil” and “what is the required frequency of sampling” and “what is the optimal size of a sample.” Besides these technical issues, the lack of conceptual frameworks, like missing ecological concepts (e.g., with respect to the effect of diversity on the resilience of soil or on the stability of function), the absence of threshold values that define soil quality, and the lack of well-defined standard methods, have hampered developments in this area.
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