Fusarium oxysporum f. sp. radicis‐vanillae is the causal agent of root and stem rot of vanilla

Root and stem rot (RSR) is a very detrimental disease of vanilla worldwide. Fusarium oxysporum is frequently associated with the disease but other Fusarium species are also reported. In this international study, 52 vanilla plots were surveyed in three of the most important vanilla producing countries (Madagascar, Reunion Island and French Polynesia) in order to determine the aetiology of RSR disease. Subsets from the 377 single‐spored Fusarium isolates recovered from rotten roots and stems in the surveys were characterized by molecular genotyping (EF1α and IGS gene sequences) and pathogenicity assays on Vanilla planifolia and V. ×tahitensis, the two commercially grown vanilla species. Fusarium oxysporum was shown to be the principal species responsible for the disease, representing 79% of the isolates recovered from the RSR tissues, 40% of which induced severe symptoms on inoculated plantlets. Fusarium oxysporum isolates were highly polyphyletic regardless of geographic origin or pathogenicity. Fusarium solani, found in 15% of the samples and inducing only mild symptoms on plantlets, was considered a secondary pathogen of vanilla. Three additional Fusarium species were occasionally isolated in the study (F. proliferatum, F. concentricum and F. mangiferae) but were nonpathogenic. Histopathological preparations observed in wide field and multiphoton microscopy showed that F. oxysporum penetrated the root hair region of roots, then invaded the cortical cells where it induced necrosis in both V. planifolia and V. ×tahitensis. The hyphae never invaded the root vascular system up to 9 days post‐inoculation. As a whole, the data demonstrated that RSR of vanilla is present worldwide and that its causal agent should be named F. oxysporum f. sp. radicis‐vanillae.     

Identification,pathogenicity and community dynamics of fungi and oomycetes associated with pea root rot in northern France

The pea root rot complex is a major concern for green pea production worldwide. This study aimed at characterizing its composition and dynamics throughout a cropping season in northern France. To this end, fungi and oomycetes were isolated from green pea plant roots with symptoms sampled at the flowering stage in 22 fields in 2017, and at the pea emergence, elongation and flowering stages in two fields in 2018. Out of 646 isolates collected, 317 were identified using molecular markers. Fusarium oxysporum, F. solani and F. redolens were highly predominant. Pathogenicity tests separated the isolates into four aggressiveness groups. F. solani isolates were the most aggressive. Phylogenetic analysis of their TEF1 sequences showed that they mainly belonged to the F. pisi lineage, and that F. oxysporum isolates were genetically close to isolates from the UK that did not belong to the forma specialis pisi. In addition, several Clonostachys rhizophaga isolates are reported for the first time to cause pea root rot. The oomycetes were rarely found and were represented by a few Pythium spp. isolates. Lastly, this study shows that the fungal and oomycete communities associated with pea root rot change during the cropping season. The level of dissimilarity of the root-rot-associated communities decreased throughout the cropping season towards a more similar composition at the flowering stage, dominated by F. solani, F. oxysporum and F. redolens. The proportion of nonpathogenic to weakly pathogenic isolates decreased progressively during the growing season in favour of moderately to highly pathogenic isolates.     

Risk assessment of Aphanomyces euteiches root rot disease: quantification of low inoculum densities in field soils using droplet digital PCR

European Journal of Plant Pathology - Fusarium verticillioides is a soil-borne plant pathogen of maize plants (Zea mays L.) responsible for major yield losses by causing root, stalk, and ear rot...     

Populations of Nonpathogenic Fusarium oxysporum Associated with Roots of Four Plant Species Compared to Soilborne Populations

ABSTRACT The effect of the plant on the diversity of soilborne populations of Fusarium oxysporum was assessed after successive cultures of flax, melon, tomato, and wheat in separate samples of the same soil. Forty soil-borne isolates of F. oxysporum and forty root-colonizing isolates of each plant species were sampled during the first (T0) and fourth (T1) cultures. The population structures were assessed by a genotypic method based on restriction fragment analysis of polymerase chain reaction-amplified ri-bosomal intergenic spacer (IGS) DNA. Sixteen IGS types were defined among the four hundred isolates analyzed. The distributions of soil isolates among IGS types were similar at both sampling times. The structure of F. oxysporum populations associated with the roots of flax or melon did not differ from the structure of soilborne populations. In contrast, the structure of F. oxysporum populations associated with roots of wheat or tomato differed from the structure of soilborne populations. High frequencies were found for IGS type 4 among wheat isolates at both T0 and T1 and for IGS type 11 among tomato isolates at T1. Moreover, a high level of genetic divergence was obtained between IGS types 4 and 11. Our results suggest that tomato and wheat have a selective effect on soilborne populations of F. oxysporum and that this effect seems to be plant specific.     

Recovery of Mutants Impaired in Pathogenicity After Transposition of Impala in Fusarium oxysporum f. sp. melonis

ABSTRACT The ability of transposon impala to inactivate genes involved in pathogenicity was tested in Fusarium oxysporum f. sp. melonis. Somatic excision of an impala copy inserted in the nitrate reductase-encoding niaD gene was positively selected through a phenotypic assay based on the restoration of nitrate reductase activity. Independent excision events were analyzed molecularly and shown to carry reinsertedimpala in more than 70% of the cases. Mapping of reinserted impala elements on large NotI-restriction fragments showed that impala transposes randomly. By screening 746 revertants on plants, a high proportion (3.5%) of mutants impaired in their pathogenic potential was recovered. According to the kinetics of wilt symptom development, the strains that were impaired in pathogenicity were clustered in three classes: class 1 grouped two strains that never induced Fusarium wilt symptoms on the host plant; class 2 and class 3 grouped 15 and 9 revertants which caused symptoms more than 50 and 30 days after inoculation, respectively. The first results demonstrate the efficiency of transposition in generating mutants affected in pathogenicity, which are usually difficult to obtain by classical mutagenesis, and open the possibility to clone the altered genes with impala as a tag.     

Cause and duration of mustard incorporation effects on soil-borne plant pathogenic fungi

Two fungal plant pathogens, Rhizoctonia solani AG 2-2 and Fusarium oxysporum f.sp. lini, were studied in relation to general responses of soil fungi and bacteria following incorporation of Brassica juncea. Our aim was to understand to what extent the changes in the biological and physicochemical characteristics of the soil could explain the effects on the studied pathogens and diseases, and to determine the temporal nature of the responses. Short-term effects of mustard incorporation (up to 4 months) were investigated in a microcosm experiment, and compared with a treatment where composted plant material was incorporated. In a field experiment, the responses were followed up to 11 months after removal or incorporation of a mustard crop. In general, responses in the variables measured changed more after incorporation of fresh mustard material than after addition of similar amounts of composted plant material (microcosms) or after removal of the mustard crop (field). The soil inoculum potential of R. solani AG 2-2 decreased directly after incorporation of mustard, but increased later to disease levels above those in the untreated soil. Neither of these effects could be explained by changes in the population density of R. solani AG 2-2. Fusarium spp. were less influenced, although an increase in the suppressiveness to Fusarium wilt was observed after mustard incorporation as compared with the treatment where mustard was removed. The microbial responses to mustard incorporation were more pronounced for bacteria than for fungi. After an initial substantial increase, the bacterial density decreased but remained above the levels in the control treatment throughout the experimental periods. The bacterial community structure was modified up to 8 months after mustard incorporation. We conclude that incorporation of fresh mustard influences soil microbial communities, especially the bacteria, and has a potential to control the pathogenic activity of R. solani 2-2 on a short-term perspective. The time dependency in microbial responses is important and should be taken into consideration for the evaluation of the potential of Brassicas to control plant disease on a field scale.     

Diversity of microorganisms associated with atypical superficial blemishes of potato tubers and pathogenicity assessment

Skin blemishes of potato (Solanum tuberosum L.) tubers can cause severe economical losses to production. Some blemishes are due to known pathogens and others whose causes are unknown are called atypical blemishes. The present work aims at determining the origin of superficial atypical blemishes on a set of 204 tubers coming from 12 different French regions producing potato. The diversity of fungi and Streptomyces bacteria associated with blemishes was investigated by systematic isolation followed by identification by sequencing the internal transcribed spacer of the ribosomal DNA for fungi and by sequencing the 16S ribosomal DNA for bacteria. We found a high microbial diversity represented by 349 fungal isolates belonging to at least 47 different species and 21 bacterial strains of Streptomyces sp. The most represented fungi belonged to the genera Fusarium, Rhizoctonia, Alternaria, Penicillium, and Clonostachys. The pathogenicity of representative isolates was assessed in three bioassays; two bioassays based on single inoculations in previously sterilized potting mixture, and one bioassay based on both single and double inoculations under hydroponic conditions. We fulfilled the Koch’s postulates for Rhizoctonia solani AG 3 producing sclerotia. For other fungal and bacterial strains, our results did not show any causality or relationship between a single isolate or a complex and the occurrence of the blemishes. Moreover, the observation of irregular polygonal sunken corky lesions (polygonal lesions)—the most frequent atypical blemish—on non-inoculated tubers, suggested that the atypical blemishes could as well be a reaction of the plant to stressful environmental conditions.     

Genetic diversity of Fusarium oxysporum and related species pathogenic on tomato in Algeria and other Mediterranean countries

In order to characterize the pathogen(s) responsible for the outbreak of fusarium diseases in Algeria, 48 Fusarium spp. isolates were collected from diseased tomato in Algeria and compared with 58 isolates of Fusarium oxysporum originating from seven other Mediterranean countries and 24 reference strains. Partial sequences of the translation elongation factor EF‐1α gene enabled identification of 27 isolates as F. oxysporum, 18 as F. commune and three as F. redolens among the Algerian isolates. Pathogenicity tests confirmed that all isolates were pathogenic on tomato, with disease incidence greater at 28°C than at 24°C. All isolates were characterized using intergenic spacer (IGS) DNA typing, vegetative compatibility group (VCG) and PCR detection of the SIX1 (secreted in xylem 1) gene specific to F. oxysporum f. sp. lycopersici (FOL). No DNA polymorphisms were detected in the isolates of F. redolens or F. commune. In contrast, the 27 Algerian isolates of F. oxysporum were shown to comprise nine IGS types and 13 VCGs, including several potentially new VCGs. As none of the isolates was scored as SIX1+, the 27 isolates could be assigned to F. oxysporum f. sp. radicis‐lycopersici (FORL). Isolates from Tunisia were also highly diverse but genetically distinct from the Algerian isolates. Several Tunisian isolates were identified as FOL by a PCR that detected the presence of SIX1. The results show that isolates from European countries were less diverse than those from Tunisia. Given the difference between Algerian populations and populations in other Mediterranean countries, newly emergent pathogenic forms could have evolved from local non‐pathogenic populations in Algeria.     

Biotic changes in relation to local decrease in soil conduciveness to disease caused by <Emphasis Type="Italic">Rhizoctonia solani</Emphasis>

The relationships between biotic changes and local decrease in soil conduciveness in disease patches towards the disease incited by Rhizoctonia solani AG 2-2 in a sugar beet field in France were investigated. Soil samples from healthy and diseased areas were analysed for bacterial and fungal densities, molecular and physiological microbial community structures, and antagonistic abilities of Trichoderma isolates collected from diseased and healthy areas. Although the inoculum density was higher inside the disease patches, the respective soil was less conducive towards disease incited by R. solani AG 2-2. It was concluded that the pathogen was present in healthy areas but did not incite disease in field conditions. Conversely, the response of the microflora to previous development of R. solani in diseased areas prevented further pathogenic activity. Indeed, genetic and physiological structures of the fungal communities and physiological structures of the bacterial communities were modified in disease patches compared to healthy areas. The terminal restriction fragment length polymorphism (T-RFLP) analysis revealed that the peaks corresponding to R. solani and Trichoderma spp. were higher inside the patches than in the healthy areas. Trichoderma isolates from the disease patches were more antagonistic than those from the healthy areas. These results suggest that disease caused by R. solani AG 2-2 induced changes in genetic and physiological structure of microbial populations and development of antagonists. The decreased conduciveness inside the patches may help explain patch mobility in the following season.