## 2 Soil-Borne Plant Pathogens and Microbiota Determine Disease Suppression
### 3.1. Case Studies of Soil-Borne Pathogens and Diseases
#### 3.1.1. Contribution of Pathogenic Fungi and Oomycetes  
Nowadays, most of the soil-borne fungal diseases are well documented in both the intensive and CC systems as being generally caused by filamentous fungi and oomycetes. Ramie [100], soybean [101] and ginseng [102] monocultures showed a substantial reduction of the beneficial microbiota abundance under disease pressure against pathogenic fungi and oomycetes [103]. The beneficial microbiota diversity was also significantly reduced by ginseng monoculture during three years of cultivation. Evidences showed a negative correlation between the diseased plant rate and fungal diversity due to higher abundance, richness and biodiversity as key indicators of soil health, where the relative abundance of _F. oxysporum_ and _Phaeosphaeria rousseliana_ was positively correlated with the incidence and severity of ginseng monoculture [104]. Soybean monoculture was affected by root rot disease and associated with an increased level of _F. oxysporum_ load  
Figure 1: Flowchart of the main steps to study the disease-suppressive soil properties (modified by the author from [22]). in soil and reduction in fungal diversity where the CC may alter the fungal community composition [105]. This topic can be explained by some examples of the take-all decline of wheat by _G. graminis_ var. _tritici_[71], where long-term wheat monoculture increased fluorescent pseudomonad populations associated with biocontrol by production of toxic metabolites for the pathogen [106] and in reducing crop yield [107]. Other evidences confirmed an increased abundance of fungal pathogens that was positively correlated with the simplification of the biodiversity and a reduction of beneficial fungal microbiota, causing decreased growth and yield of continuous peanut crop [108]. Similarly, a large-scale study reported that soybean root rot disease increased dramatically after fewer than three years of CC in field condition in comparison to control soil under crop rotation condition [109]. Moreover, vanilla stem will disease outbreak was positively correlated to the increased and decreased abundance of pathogenic strains of _F. oxysporum_ and beneficial microbes in CC of vanilla, respectively [110]. Authors investigated the evolution of the bacterial and fungal communities in soils of banana crops where CC was significantly related to fusarium wilt outbreaks in China [111]. The same authors noticed that fungal microbiome abundance was more related to wilt suppression than the bacterial ones in banana monocultures. Unexpectedly, high fungal species richness was positively correlated with the highest incidence and severity of fusarium wilt on banana, _F. oxysporum_ f. sp. _cubense_ abundance and crop yield reduction, suggesting a weak antagonistic effect of the fungal community of the banana rhizosphere. In fact, the _Fusarium_ spp. and _Phylostica_ spp. abundances showed a significant correlation with the reduction of the banana yield [111]. Similarly, authors investigated the impacts of sweet potato monoculture on soil mycobiota, demonstrating that both fungal diversity and richness significantly increased in CC systems, while the ascomycota fungi and oomycetes abundance decreased over time [112]. These authors observed that abundance of the beneficial fungi belonging to the species of _Chaetomium_ decreased overall; but at the same time, more pathogenic fungi and oomycetes belonging to species of _Verticillium, Fusarium, Colletotrichum, Pythium_ and _Phylophthora_ increased in monocultured soil. The findings of [111] and [112] contrast partly with other studies that showed instead a positive trend of the relatively large richness and diversity of the microbiota in suppressing _F. oxysporum_ f. sp. _Iyocyersici_ in a mono-cultured Italian area with cherry tomato for at least five consecutive years showing severe fusarium wilt outbreaks [113].