# Soil Is Still an Unknown Biological System
## 2 Properties of Soil as a Biological System
### Interactions between Microbes, between Microbes and Plants, and between Microbes and Fauna  
Interactions can be categorized not only by the interacting species (bacteria, fungi, plant, animal or virus) but also by how cells sense neighboring other cells of the same species. This can occur at (i) the physical level, because two cells occupy the same microenvironment; (ii) the biochemical level, because a cell responds to molecular signals released from the other one; and (iii) the nutritional level, due to metabolic interactions between the two cells [27]. Of course, these three types of interactions can occur simultaneously [27]. Interactions between microbes have been extensively studied in vitro but not in soil due to the complexity and heterogeneity of soil. However, it is plausible to hypothesize that these interactions are very important in soil habitable microsites, which are isolated each from the other in dry but not in wet periods, when water connections are established between two separate microenvironments [8]. Of course, mobile organisms (such as protozoans; nematodes and earthworms), fungi, with their hyphae, chain-forming organisms, (such as _Bacillus mycoide_, actinomycetes, and fungi), and plant roots, can visit different soil microenvironments [27]. Likely, in wet periods, there is the risk of increasing anaerobic microsites due to low oxygen diffusion in water [8]. One of the most studied molecular signals between bacterial cells is the quorum sensing (QS), discovered in 1980s; it involves the regulation of several bacterial processes, such as symbiosis, virulence, competence for transformation, conjugation, antibiotic production, motility, sporulation,and biofilm formation [25]. These signals are important in the assemblage of bacterial cells, because the cells of species with specific QS signals can exclude the cells of species with anti-QS signaling traits [25]. There are also interactions not mediated by QS, like the release of antibiotics, which can either kill or inhibit the growth of the microbial partner. Bacteria can interact with fungi both positively and negatively; fungi can promote the soil colonization of bacteria inhabiting the external surface of their hyphae and using fungal exudates. Other positive interactions involve the bacterial use of monomers or oligomers produced by the extracellular breakdown of polymers, such as the cellulose of plant residues, due to the activity of extracellular enzymes released from fungi [25]. Negative interactions can also involve several mechanisms, such as the predatory action of myxobacteria on fungi, the release of antifungal compounds by bacteria, and the use of bacterial cells as nutrient sources by some fungal species [25]. These are only few examples of the several interactions occurring among microbial species in soil. Of course, both fungi and bacteria can be used as nutrient sources by soil eukaryotic organisms, thus originating the soil food web. The microbial loop is an example of the complex interactions among bacteria, protists, and plants in nutrient dynamics [28]. Bacteria inhabiting the rhizosphere can grow due to the presence of the root exudates released from root tips; however, bacteria have to mine N from soil organic matter because root exudates are generally C-rich compounds [28]. Then, protozoa graze on bacteria, reducing their number and releasing ammonium-N because the C/N ratio of protozoa cells is higher than that of bacterial cells. The released ammonium is taken up by the plant, and thus the microbial loop shifts the competition for N between plants and bacteria in favor of plants [28]. This is just an example of the interactions between bacteria and protists, but other issues may be involved, such as selective grazing by predators [29]. The rhizosphere is the soil around the roots with a higher microbial activity than the bulk soil as the result of rhizodepostion, which includes root exudates, mucilage, root debris, and whole detached root cells [30].