Comparative Microbiome Analysis of a Fusarium Wilt Suppressive Soil and a Fusarium Wilt Conducive Soil From the Châteaurenard Region

Abstract

Disease-suppressive soils are soils in which specific soil-borne plant pathogens cause only limited disease although the pathogen and susceptible host plants are both present. Suppressiveness is in most cases of microbial origin. We conducted a comparative metabarcoding analysis of the taxonomic diversity of fungal and bacterial communities from suppressive and non-suppressive (conducive) soils as regards Fusarium wilts sampled from the Châteaurenard region (France). Bioassays based on Fusarium wilt of flax confirmed that disease incidence was significantly lower in the suppressive soil than in the conducive soil. Furthermore, we succeeded in partly transferring Fusarium wilt-suppressiveness to the conducive soil by mixing 10% (w/w) of the suppressive soil into the conducive soil. Fungal diversity differed significantly between the suppressive and conducive soils. Among dominant fungal operational taxonomic units (OTUs) affiliated to known genera, 17 OTUs were detected exclusively in the suppressive soil. These OTUs were assigned to the Acremonium, Chaetomium, Cladosporium, Clonostachys, Fusarium, Ceratobasidium, Mortierella, Penicillium, Scytalidium, and Verticillium genera. Additionally, the relative abundance of specific members of the bacterial community was significantly higher in the suppressive and mixed soils than in the conducive soil. OTUs found more abundant in Fusarium wilt-suppressive soils were affiliated to the bacterial genera Adhaeribacter, Massilia, Microvirga, Rhizobium, Rhizobacter, Arthrobacter, Amycolatopsis, Rubrobacter, Paenibacillus, Stenotrophomonas, and Geobacter. Several of the fungal and bacterial genera detected exclusively or more abundantly in the Fusarium wilt-suppressive soil included genera known for their activity against F. oxysporum. Overall, this study supports the potential role of known fungal and bacterial genera in Fusarium wilt suppressive soils from Châteaurenard and pinpoints new bacterial and fungal genera for their putative role in Fusarium wilt suppressiveness.

Network analysis infers the wilt pathogen invasion associated with non-detrimental bacteria

“…For example, Arthrobacter (49.7% and 19.1% reduction in infected bulk and rhizosphere soil, respectively) is known to have pathogen suppression potential for Fusarium wilt. 39 In the endophytic compartments, the relative abundances of Lactococcus, Pseudomonas, Bacillus, Falsibacillus, and Leuconostoc, often considered to be plant-beneficial microbes, [40][41][42][43][44][45][46] showed significant decrease compared to the healthy samples. These decreases suggest that the normal endophytic taxa were either actively excluded by the host immune system or outcompeted by moresuccessful colonizers.…”

Modulation of the Root Microbiome by Plant Molecules: The Basis for Targeted Disease Suppression and Plant Growth Promotion

“…Also, higher abundances of the Phyla Actinobacteria, Proteobacteria, Acidobacteria, Gemmatimonadetes, and Nitrospirae were found in soil with specific suppressiveness to Fusarium wilt of strawberry (Cha et al, 2016). More recently, it was shown that fungal and bacterial diversity differed significantly between a suppressive and a conducive soil of Fusarium wilt whereas several of the fungal and bacterial genera known for their activity against F. oxysporum were detected exclusively or more abundantly in the Fusarium wilt-suppressive soil (Siegel-Hertz et al, 2018). Interestingly, studies analyzing the rhizobacterial community composition in soils suppressive or conducive to R. solani revealed that relative abundance of specific bacterial taxa is a more important indicator of suppressiveness than the exclusive presence or absence of specific bacterial families (Mendes et al, 2011;Chapelle et al, 2016).…”

Phenolic Acid-Degrading Consortia Increase Fusarium Wilt Disease Resistance of Chrysanthemum

“…Soil disease suppressiveness primarily relies on the mechanisms of nutrient competition and specific antagonism caused by soil micro flora [8]. This disease-control capability can be abolished by soil sterilization, and is transferred into the disease-conducive soil by mixing the disease-suppressive soil, indicating that the microbial community confers the property of the soil to prevent the build-up of pathogens and its invasion [9,10].…”

“…In some cases, disease suppression is an inherent property of soils that exhibits the compatibility with crop rotation, while the extent of disease suppression is mediated by crop rotation, involving changes of soil microbial activity [14]. Natural suppression is well documented for some fungal diseases, such as Fusarium wilt disease and black root rot caused by T. basicola [8,12]. In other cases, crop monoculture induces soil disease suppressiveness, as evidenced by a decline of disease incidence, following earlier disease outbreak.…”

“…Some previous studies have attributed disease suppression to the Pseudomonas species that produce antifungal substances, such as 2,4-diacetylphloroglucinol and hydrogen cyanide [14,18]. More investigations have recently focused on the comparative analyses of the microbial community between the conducive and suppressive soils, and the identification of key indicators that participate in disease suppression [4,8]. In fact, unique soil situations lead to differential changes of microbial community, thereby contributing to variation in the ability of soils to suppress soil-borne pathogens [7,15,19,20].…”