Dear Colleagues,

The soil is a very versatile habitat for microbes, plant roots and soil-dwelling animals. The soil contains numerous microhabitats with widely differing conditions in locations even very close to each other, allowing for example, strict anaerobes to cohabitate with strict aerobes in even very small soil particles. Soil conditions change rapidly with changes in soil moisture, temperature and other variables; thus, an important trait for soil organisms is to be able to adapt and, when necessary, enter dormancy until conditions suitable for growth return. The adaptation to a life shifting between active growth and dormancy presents challenges for soil molecular ecology research in that it is difficult to distinguish between actively metabolizing cells, dormant cells, or the mere presence of dead cells still retaining their DNA. Novel methods are now available to try to meet this challenge.

Soil organisms live in close proximity and interact actively with each other. This is particularly true in the plant rhizosphere, where the plant roots, in symbiosis with mycorrhizal fungi support a much higher microbial density and probably also diversity than the bulk soil. Soil was one of the first environments for which it was shown that the true diversity is very much higher than what could be demonstrated by cultivation methods. The diversity seen with nucleic acid based methods is at least one to two orders of magnitude higher than what could be demonstrated by plating. The new sequencing techniques now in use shift the bottle neck from the generation of sequencing data to the handling of the raw sequence data and, in particular, to make biological and ecological sense out of it. An additional challenge is to determine the phylogenetic position of the “unknown” microbes, that is, fungi, bacteria, and archaea that have no close relatives among the cultivated, well characterized organisms.

Finally, a group of biological entities whose ecological role is only beginning to emerge are the viruses. Their ecological and evolutionary roles are being explored in the oceans, but study of viruses in soil has been slow, possibly due to practical difficulties. Much waits to be explored regarding microbial dynamics in soil, particularly activities that may be significantly influenced by viruses.
This special issue “Soil Quality and Ecosystem” focuses on the microbial diversity in different soil types, and on the interaction of microorganisms with plants and soil animals that create the ecosystems and the organismal dynamics of studied soils.

Prof Dr. Martin Romantschuk
Dr. Janice E. Thies
Guest Editor