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.
Highlights
Plant diseases caused by soil-borne microorganisms, including fungi, oomycetes, bacteria, nematodes as well as subterranean insects, regularly result in extensive losses in agricultural production every year
Fungal curves showed that: (i) the number of operational taxonomic units (OTUs) at 97% similarity increased with the number of sequences, and saturation was not reached for all soils; (ii) based on soil replicates, the number of sequences was sufficient to obtain a representative coverage of the major fungal groups; and (iii) differences among soils were recorded in the slope and level of the curves (Supplementary Figure 1A)
Rarefaction curves revealed that the number of OTUs increased with the number of reads, without reaching a plateau, and reads were in sufficient numbers to allow for an accurate description of the major bacterial genera in each of the soil samples (Supplementary Figure 1B)
Summary
Plant diseases caused by soil-borne microorganisms, including fungi, oomycetes, bacteria, nematodes as well as subterranean insects, regularly result in extensive losses in agricultural production every year. In addition to general suppressiveness, some soils exhibit an additional level of suppressiveness targeted to a specific soil-borne plant pathogen. Specific suppressiveness is attributed to the converging activities of specific members of the soil microbial community that interfere with the disease cycle of the pathogen. This is the case, for example, of bacteria in the Pseudomonas group that produce metabolites such as pyoverdins, iron-chelating siderophores, and make iron difficult to access for the pathogenic fungus F. oxysporum, this mechanism being added to the competition for carbon to which this same pathogen is confronted (Lemanceau et al, 1993; Alabouvette, 1999). The role of abiotic components cannot be ruled out (Amir and Alabouvette, 1993; Almario et al, 2013a), all of these demonstrations clearly indicate that a focus must be placed on the biotic component (Alabouvette, 1999)
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