## 2 Soil-Borne Plant Pathogens and Microbiota Determine Disease Suppression
### Omics Approach for Studying Soil Microbiome  
The issues related to the complexity and structure of microbial communities in the rhizosphere have been studied in the last 10 years [29]. From this perspective, the use and exploration of beneficial microorganisms in agricultural production systems provide new opportunities to increase crop productivity in a sustainable way by microbiome disturbance [82]. Although a lot of progress has been made in understanding interactions between plants and microorganisms, there is a need to increase the current knowledge of the microbiome ecology and functions. Thus, a detailed understanding of the soil microbiomes in order to limit inconsistencies, drawbacks and failures related to microbiota disturbance is needed. Two major approaches have been used to describe the soil microbiota diversity in combination with numerous identification strategies allowing to identify and quantify microorganisms at the various taxonomic levels, from the highest (kingdom and phylum) to the lowest (genus, species and strains) [41]. The first approach is \"culture-dependent.\" It involves isolation and purification of the microorganisms from soil or similar substrates as compost, biochar, digestate, etc. [49]. In this approach some basic morphological identifications using staining and microscopy techniques have been frequently employed to identify, for example, AM and other filamentous fungi. The morphological analyses have often been combined with the standard biochemical tests, such as those analyzing carbon source utilization and enzymatic assays in determining the microbial community-level physiological profiles of soil using Biolog EcoPlates(tm) (Biolog, Inc., Lyon, France) to identify bacteria, fungi and yeasts. Some more complex biochemical tests have sometimes been applied to confirm the microorganism's identity, such as the multi-locus enzyme electrophoresis for nitrogen-fixing bacteria, the fatty acid methyl esters gas chromatography for some bacterial isolates, and the matrix-assisted laser desorption ionization time-of-flight mass spectrometry for bacteria and yeasts. The second approach is \"culture-independent\". It regards the molecular-based methods, with DNA-DNA reassembling study as one of the first molecular methods employed by bacterial taxonomists since the 1960s to describe the relationships among bacterial species [166]. Up to now, it is still the \"gold standard method\" to identify new species as well as to discriminate bacterial isolates at the lowest taxonomic levels. These approaches were first studied generally in nosocomial microbiology for human illness in gut microbiota [167; 168; 169; 170]. With the development of the first-generation sequencing technologies (Roche 454-pyrosqueeing), DNA sequences comparison contributed to identify a number of microbial species in an unprecedented manner [171; 172]. Amplification and sequencing of simple genetic markers such as the rDNA gene repeats, the 16S rDNA of prokarya and bacteria, as well as the 18S or 26S/28S rDNA of eukarya and fungi and, more recently, the fungal nuclear ribosomal internal transcribed spacer (ITS) gene regions (ITS1, ITS2, ITS4, ITS5 and more) have been extensively used in soil metagenomics study [173]. Some housekeeping genes, like those coding the \(\beta\)-tubulin and TEF-1\(\alpha\) factors, were sequenced for specific fungal identifications as _Aspergillus_ spp. and _Penicillium_ spp. [174; 175]. More recently, the combination of several sequences in the multi-locus sequence typing was used to increase the reliability of the identification, as well as the NGS technology being employed to sequence the whole genome of soil microbiota [29]. This methodology does not require cultivation of the microorganisms. During its early development, it consisted in pooling DNA extraction, PCR-amplifying with DNA marker regions by universal/specific primer pairs, and then sequencing them after amplicon separation by the denaturing gradient gel electrophoresis or the cloning of single sequences.