# Soil Is Still an Unknown Biological System
## 2 Properties of Soil as a Biological System
### Microbial Diversity and Microbial Functions  
The microbial diversity is huge, as shown by the use of molecular techniques. According to [PERSON] and [PERSON] [9], \"A handful of soil contains, on average, more than a thousand million cells encompassing bacteria, archaea, fungi and protists--collectively called the soil microbiome\". However, molecular studies have revealed that a well-defined core set of taxa is present in soils sampled from different parts of the world [9]. Two percent of bacterial phylotypes were dominant and averaged 41% of the 16S rRNA gene sequences of surface soils from 237 locations across 18 countries of 6 continents [11]. Some of the ubiquitous and dominant phylotypes included Alphaproteobacteria (_Bradyrhizobium_ spp., _Sphingomonas_ sp., _Rhodoplanes_ sp., _Devosia_ sp., and _Kaistobacter_ sp. ), Betaproteobacteria (_Methylibium_ sp. and _Ramlibate_), Actinobacteria (_Streptomyces_ ssp., _Salinbacterium_ sp. and _Mycobacterium_ sp. ), Acidobacteria (_Candidatus_ sp., and _Salibacter_), and Plantctomyces. Less than 18% of the identified phylotypes matched an available genome at the 97% 16S rRNA sequence similarity level, and only 40% matched even at the 90% 16S rRNA sequence similarity level. However, the detection of a taxon does not mean it is active in soil [12]. Indeed, at least 95% of the total microbial biomass is inactive in soil, and microbial activity changes in time and space [13]. Additionally, the assumption that soil functions are those carried out by the dominant taxon under in vitro conditions may not be valid because rare taxa often play an important role in the measured microbial activity, as revealed for the alkaline phosphomonoesterase activity of soil [14] and the microbial activities of soil from a glacial retreat [15]. In addition to soil microorganisms, protozoa, nematodes, microarthropods, macroarthropods, Enchytraeidae, and Earthworms, collectively termed soil fauna, can inhabit soil [5; 7]. Among the soil fauna, earthworms are the most studied and act as ecosystem engineers, with significant effects on the structure and functions of soil [16]. Viruses are also present in soil, but they have been less studied than soil organisms; they are mainly bacteriophages and can infect pathogenic bacteria as well as beneficial bacteria for plants, such as rhizobia [17]. Both the abundance and diversity of viruses are markedly affected by agricultural practices [18], and the ratio between viral and bacterial abundances is higher in soil (330-470) than in water ecosystems (1-50), but the role of viruses in biological processes and the survival of organisms in soil is poorly known [17]. Among soil organisms, bacteria and fungi play the most important role in soil processes, such as the oxidation of organic matter, including xenobiotics, N, P, S, and micronutrient transformations, and have both beneficial and negative effects on plants. [8; 9]. Functional redundancy characterizes several soil metabolic processes being carried out by many different microbial species; for example, the loss of microbial diversity was thought not affect processes such as C and N mineralization [8], with a certain threshold value of microbial diversity being important [19]. However, a meta-analysis showed that the loss of diversity reduced soil C respiration by 25% [20]. It is important to underline that meta-analysis concerns different soils, plant covers, agricultural practices, and climatic conditions, whereas the comparison of the response of different microbial diversities obtained in the same soil studied under laboratory conditions avoids effects due to different parameters. However, [PERSON] et al. [21] found that the taxonomical variability was much higher than the functional variability in bacterial