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.

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

Carbon use by microorganisms in the rhizosphere microbiome has been linked to plant pathogen suppression and increased mineralization of soil nutrients for plant uptake; however, factors that influence carbon use traits are poorly understood for most microbial groups. This work characterized the relationships of phylogeny, plant species, and plant diversity with carbon use among fungi in the genus Fusarium from rhizosphere soil. Eighty-four randomly collected Fusarium isolates were cultured from the rhizosphere of the perennial plants Lespedeza capitata and Andropogon gerardii, maintained as long-term monocultures or growing in 16-plant species polycultures. For each isolate, a portion of the RPB2 locus was sequenced for phylogenetic analyses and growth on 95 carbon substrates was measured using Biolog SF-P2 plates. Similarity in carbon use among isolates decreased with increasing genetic distance and there were differences in niche width (i.e., number of carbon substrates used) and growth on preferred su...

https://apsjournals.apsnet.org/doi/pdf/10.1094/PBIOMES-06-17-0028-R

Phylogeny, Plant Species, and Plant Diversity Influence Carbon Use Phenotypes Among Fusarium Populations in the Rhizosphere Microbiome

In the present work, a highly pathogenic isolate of Fusarium oxysporum f. sp. lini, which is the most harmful pathogen affecting flax (Linum usitatissimum L.), was sequenced for the first time. To achieve a high-quality genome assembly, we used the combination of two sequencing platforms - Oxford Nanopore Technologies (MinION system) with long noisy reads and Illumina (HiSeq 2500 instrument) with short accurate reads. Given the quality of DNA is crucial for Nanopore sequencing, we developed the protocol for extraction of pure high-molecular-weight DNA from fungi. Sequencing of DNA extracted using this protocol allowed us to obtain about 85x genome coverage with long (N50 = 29 kb) MinION reads and 30x coverage with 2 × 250 bp HiSeq reads. Several tools were developed for genome assembly; however, they provide different results depending on genome complexity, sequencing data volume, read length and quality. We benchmarked the most requested assemblers (Canu, Flye, Shasta, wtdbg2, and MaSuRCA), Nanopore polishers (Medaka and Racon), and Illumina polishers (Pilon and POLCA) on our sequencing data. The assembly performed with Canu and polished with Medaka and POLCA was considered the most full and accurate. After further elimination of redundant contigs using Purge Haplotigs, we achieved a high-quality genome of F. oxysporum f. sp. lini with a total length of 59 Mb, N50 of 3.3 Mb, and 99.5% completeness according to BUSCO. We also obtained a complete circular mitochondrial genome with a length of 38.7 kb. The achieved assembly expands studies on F. oxysporum and plant-pathogen interaction in flax.

/pdf/high-quality-genome-assembly-of-fusarium-oxysporum-f-sp-lini-2xo45wdafa.pdf

High-Quality Genome Assembly of Fusarium oxysporum f. sp. lini.

Endophytic fungi (EFs) are one of the important and quantifiable components of fungal biodiversity. In the study, 171 endophytic fungi were isolated from the roots of Aconitum carmichaelii, a traditional Chinese medicine, collected from six production sites of Yunnan Province in southwestern China. These EFs were categorized to belong to 28 taxa by molecular identification, and Chaetomium and Fusarium were the dominant genera with a relative frequency of 16.96% and 16.37% respectively. Cladosporium and Pochonia were found to be unique dominant genera from the roots of A. carmichaelii in Huize and Yulong counties, respectively. The Shannon index ranged from 1.68 to 2.05 and the Simpson’s diversity index ranged from 0.81 to 0.92 for the EFs of A. carmichaeli, indicating the rich diversity of EFs in A. carmichaelii. Preliminary screening of the growth inhibition of three severe fungal pathogens by the isolated EFs was conducted and 17 genera of EFs were found to inhibit the growth of the tested pathogens. For example, Acrostalagmus luteoalbus, Phoma sp., and Thielavia sp. each displayed good anti-fungal activity against Alternaria alternate, Fusarium oxysporum f. sp. cucumerinum, and Phytophthora drechleri. The investigation of the root-EFs diversity of A. carmichaelii provides additional fungal resources with the potential to biologically control pathogenic fungi.

Root-endophytic fungi diversity of fuzi (aconitum carmichaelii) and their anti-fungal activity

This study aimed to isolate, identify, and evaluate the pathogenicity of nodule-borne fungi of asymptomatic Vigna spp. plants, grown in soils from preserved tropical dry forests (Caatinga) areas and identify the occurrence of co-habiting bacteria from these plants, and which have potential to control the co-occurring pathogenic fungi. Fungi and bacteria were isolated from three Vigna species (V. unguiculata, V. radiata, and V. mungo), grown in soil samples collected in five preserved Caatinga areas (Northeastern, Brazil). All fungi and selected bacteria were phylogenetically characterized by the sequencing of ITS1-5.8S-ITS2, and the 16S rRNA gene, respectively. The pathogenicity of fungi in cowpea seeds germination was evaluated throughout the inoculation experiment in Petri dishes and pots containing sterile substrate. The potential of nodule-borne bacteria to control pathogenic fungi in cowpea was assessed in a pot experiment with a sterilized substrate by the co-inoculation of fungi and bacteria isolated from the respective individual plants and soils. The 23 fungal isolates recovered were classified within the genera Fusarium, Macrophomina, Aspergillus, Cladosporium, and Nigrospora. The inoculation of fungi in cowpea seeds reduced the emergence of seeds in Petri dishes and pots. Twenty-four bacteria (Agrobacterium sp., Bradyrhizobium sp., Bacillus sp., Enterobacter sp., Pseudomonas sp., Paraburkholderia sp., and Rhizobium sp.) inhibited the harmful effects of Macrophomina sp. and Fusarium sp., increasing the germination and emergency of potted cowpea plants, highlighting the strains Agrobacterium sp. ESA 686 and Pseudomonas sp. ESA 732 that controlled, respectively, the Fusarium sp. ESA 771 and Macrophomina sp. ESA 786 by 100 and 84.6% of efficiency.

Vigna spp. Root-Nodules Harbor Potentially Pathogenic Fungi Controlled By Co-habiting Bacteria.

In this review, we tried to present Fusarium oxysporum in an ecological context rather than to confine it in the too classic double play of the nonpathogenic fungus that protects the plant against the corresponding forma specialis. Moreover, F. oxysporum is sometimes one, sometimes the other, and only the fungus can reveal its hidden face, according to it is or not in front of the target plant. Despite the quality and richness of the studies conducted to date, molecular approaches highlight some of the evolutionary mechanisms that explain the polyphyletic nature of this species, but still they do not identify a nonpathogenic F. oxysporum.

Charline Lecomte

Papers

Root Interactions with Nonpathogenic Fusarium oxysporum