First Report of Fusarium proliferatum Causing Root Rot on Soybean (Glycine max) in the United States

The Host Range of Fusarium proliferatum in Western Canada

Fusarium proliferatum is associated with the root rot of many plant species, but knowledge of its impact on western Canadian field crops is limited. This study assessed the host range of this fungus and its effect on plant emergence, plant height, and shoot and root dry weights in repeated greenhouse experiments with wheat, barley, faba beans, peas, lentils, canola, lupine, and soybeans. Infection was confirmed via PCR, and principal component analysis determined the utility of different parameters in assessing host responses. All crops were at least partly susceptible, developing mild to severe disease at the seedling and adult stages, and showing significant reductions in growth. In general, the barley and wheat demonstrated higher tolerances to infection, followed by the faba bean and the pea. The soybean, canola, lupine, and lentil were most susceptible. The canola and the soybean were particularly vulnerable to F. proliferatum at the pre-emergence stage, while infection greatly reduced the lentil's biomass. Reductions in the barley's emergence and other growth parameters, however, occurred only under a high inoculum concentration. Variability in root rot severity among cultivars of the same crop indicated some diversity in host reactions within species. Nonetheless, the absence of fully-resistant crops may pose challenges in managing F. proliferatum in western Canadian cropping systems.

Characterization of Fusarium species causing soybean root rot in Heilongjiang, China, and mechanism underlying the differences in sensitivity to DMI fungicides

Soybean root rot is a worldwide soil-borne disease threatening soybean production, causing large losses in soybean yield and quality. Fusarium species are the most detrimental pathogens of soybean root rot worldwide, causing large production losses. Fusarium root rot has been frequently reported in Heilongjiang Province of China, but the predominant Fusarium species and the sensitivity of these pathogens to different fungicides remain unclear. In this study, diseased soybean roots were collected from 14 regions of Heilongjiang province in 2021 and 2022. A total of 144 isolates of Fusarium spp. were isolated and identified as seven distinct species: F. scirpi, F. oxysporum, F. graminearum, F. clavum, F. acuminatum, F. avenaceum, and F. sporotrichioide. F. scirpi and F. oxysporum had high separation frequency and strong pathogenicity. The sensitivity of Fusarium spp. to five different fungicides was determined. Mefentrifluconazole and fludioxonil showed good inhibitory effects, and the sensitivity to pydiflumetofen and phenamacril varied between Fusarium species. In particular, the activity of DMI fungicide prothioconazole was lower than that of mefentrifluconazole. Molecular docking showed that mefentrifluconazole mainly bound to CYP51C, but prothioconazole mainly bound to CYP51B. Furthermore, the sensitivity to prothioconazole only significantly decreased in ΔFgCYP51B mutant, and the sensitivity to mefentrifluconazole changed in ΔFgCYP51C and ΔFgCYP51A mutants. The results demonstrated that the predominant Fusarium species causing soybean root rot in Heilongjiang province were F. scirpi and F. oxysporum and DMI fungicides had differences in binding cavity due to the diversity of CYP51 proteins in Fusarium.

Whole-genome sequencing of Fusarium spp. causing sugarcane root rot on both chewing cane and sugar-making cane

Previously we isolated three Fusarium strains (a F. sacchari strain namely GXUF-1, and another two F. commune strains namely GXUF-2 and GXUF-3), and we verified that GXUF-3 was able to cause sugarcane root rot to the chewing cane cultivar Badila. Considering that Fusarium spp. are a group of widely distributed fungal pathogens, we tested whether these three Fusarium isolates were able to cause root rot to Badila as well as sugar-making cane cultivar (Guitang42), using a suitable inoculation method established based on infection assays using Badila. We found that the three Fusarium strains were able to cause root rot symptoms to both Badila and Guitang42, to different extents. To better investigate the potential pathogenicity mechanisms, we performed Illumina high-throughput sequencing and analyzed the whole genomic sequence data of these three Fusarium strains. The results reveal that the assembly sizes of the three Fusarium strains were in a range of 44.7-48.2 Mb, with G + C contents of 48.0-48.5%, and 14,154-15,175 coding genes. The coding genes were annotated by multiple public databases, and potential pathogenic genes were predicted using proprietary databases (such as PHI, DFVF, CAZy, etc.). Furthermore, based on evolutionary analysis of the coding sequence, we found that contraction and expansion of gene families occurred in the three Fusarium strains. Overall, our results suggest a potential risk that the root rot disease may occur to the sugar-making canes although it was initially spotted from fruit cane, and provide clues to understand the pathogenic mechanisms of Fusarium spp. causing sugarcane root rot.

Shift in the rhizosphere soil fungal community associated with root rot infection of Plukenetia volubilis Linneo caused by Fusarium and Rhizopus species

BACKGROUND

Plukenetia volubilis Linneo is an oleaginous plant belonging to the family Euphorbiaceae. Due to its seeds containing a high content of edible oil and rich in vitamins, P. volubilis is cultivated as an economical plant worldwide. However, the cultivation and growth of P. volubilis is challenged by phytopathogen invasion leading to production loss.

METHODS

In the current study, we tested the pathogenicity of fungal pathogens isolated from root rot infected P. volubilis plant tissues by inoculating them into healthy P. volubilis seedlings. Metagenomic sequencing was used to assess the shift in the fungal community of P. volubilis rhizosphere soil after root rot infection.

RESULTS

Four Fusarium isolates and two Rhizopus isolates were found to be root rot causative agents of P. volubilis as they induced typical root rot symptoms in healthy seedlings. The metagenomic sequencing data showed that root rot infection altered the rhizosphere fungal community. In root rot infected soil, the richness and diversity indices increased or decreased depending on pathogens. The four most abundant phyla across all samples were Ascomycota, Glomeromycota, Basidiomycota, and Mortierellomycota. In infected soil, the relative abundance of each phylum increased or decreased depending on the pathogen and functional taxonomic classification.

CONCLUSIONS

Based on our results, we concluded that Fusarium and Rhizopus species cause root rot infection of P. volubilis. In root rot infected P. volubilis, the shift in the rhizosphere fungal community was pathogen-dependent. These findings may serve as a key point for a future study on the biocontrol of root rot of P. volubilis.

Identification of Quantitative Trait Loci Associated With Partial Resistance to Fusarium Root Rot and Wilt Caused by Fusarium graminearum in Field Pea

Fusarium root rot, caused by a complex of Fusarium spp., is a major disease of field pea (Pisum sativum). The development of genetic resistance is the most promising approach to manage the disease, but no pea germplasm has been identified that is completely resistant to root rot. The aim of this study was to detect quantitative trait loci (QTL) conferring partial resistance to root rot and wilting, caused by five fungal isolates representing Fusarium solani, F. avenaceum, F. acuminatum, F. proliferatum, and F. graminearum. Evaluation of the root rot-tolerant cultivar "00-2067" and susceptible cultivar "Reward" was carried out with the five species. There was a significant difference (p < 0.001) between the mean root rot values of the two cultivars inoculated with the F. avenaceum (F4A) and F. graminearum (FG2) isolates. Therefore, in the QTL study, the F8 recombinant inbred line (RIL) population derived from "Reward" × "00-2067" was inoculated in the greenhouse (4 ×) with only F4A and FG2. The parents and F8 population were genotyped using 13.2K single nucleotide polymorphisms (SNPs) and 222 simple sequence repeat (SSR) markers. A significant genotypic effect (p < 0.05) and high heritability (79% to 92.1%) were observed for disease severity, vigor, and plant height following inoculation with F4A and FG2. Significant correlation coefficients were detected among and within all traits. This suggested that a high proportion of the genetic variance was transmitted from the parents to the progeny. However, no significant QTL (LOD > 3) were detected for the RILs inoculated with F4A. In the case of the RILs inoculated with FG2, 5 QTL for root rot severity and 3 QTL each for vigor and plant height were detected. The most stable QTL for plant height (Hgt-Ps3.1) was detected on Chrom5/LGIII. The two most stable QTL for partial resistance to FG2, Fg-Ps4.1, and Fg-Ps4.2 were located in a 15.1-cM and 11.2-cM genomic region, respectively, on Chrom4/LGIV. The most stable QTL for vigor (Vig-Ps4.1) was found in the same region. Twenty-five major and moderate effect digenic epistatic interactions were detected. The identified region on chrom4/LGIV could be important for resistance breeding and marker development.

Effects of Spore Density and Interaction With Heterodera glycines on Soybean Root Rot Caused by Fusarium solani and F. tricinctum

Fusarium root rot, caused by Fusarium solani and F. tricinctum, is a major soybean disease in the North Central United States. This study investigated the effects of the macroconidia density and the additive effects of soybean cyst nematode (SCN), Heterodera glycines, on the severity of Fusarium root rot. To determine the effect of spore density on severity, experiments were conducted in La Prairie silt loam soil in a greenhouse using conidial suspensions ranging from 101 to 106 macroconidia/ml soil. Root discoloration and lesion lengths on taproots increased as spore numbers increased, with significant effects of spore densities starting at 104 and 105 macroconidia/ml soil for F. solani and F. tricinctum, respectively. A nonlinear sigmoid model was fitted to root discoloration against density, whereas a linear regression model was fitted to root lesion length against density. The interaction between the nematode at different egg densities with the two Fusarium spp. at 105 macroconidia/ml soil was investigated. In the greenhouse, root discoloration and lesion length were significantly greater in plants inoculated with Fusarium spp. and H. glycines at 10 eggs/ml soil or greater, compared with Fusarium spp. alone. In field trials, coinfestation of soil with the two Fusarium spp. and H. glycines significantly increased root rot severity at an egg density of 16.7 eggs/ml soil. The results indicated that the presence of SCN can increase severity of root rot caused by F. solani and F. tricinctum and egg density in the soil is an important factor in the interaction.

Fungal Endophytes Promote Tomato Growth and Enhance Drought and Salt Tolerance

In a search for efficient fungal endophytes that can promote crop production and/or increase crop tolerance to abiotic stress, we isolated and tested various species harbored by wild plants. Sixty-seven endophytic fungal isolates were obtained from drought stressed, poor soil habitats, and inland high salt areas. We extensively tested the roles of Ampelomyces sp. and Penicillium sp. isolates in improving tomato growth and yield. Under greenhouse and field trails, Ampelomyces sp. and Penicillium sp. endophytes proved effective in conferring positive benefits to tomatoes placed under stress as well as under normal growing conditions. Ampelomyces sp. conferred tolerance to tomatoes placed under drought stress in addition to enhancing overall plant growth and fruit yield in comparison to non-symbiotic plants under drought stress. Penicillium sp. conferred tolerance to tomatoes placed under 300 mM salinity stress in addition to enhancing root biomass in comparison to non-symbiotic plants. Both endophytes proved efficient in enhancing plant growth, stress tolerance, recovery, and fruit yield under optimal experimental conditions in comparison to non-symbiotic plants. Field testing of tomato yield showed increased yield of symbiotic tomatoes compared to non-symbiotic ones. This data suggests that both Ampelomyces sp. and Penicillium sp. share a promising potential for improving future agricultural production, particularly with the projected changes in climate in the future.

Maize/Soybean Relay Strip Intercropping Reduces the Occurrence of Fusarium Root Rot and Changes the Diversity of the Pathogenic Fusarium Species

Fusarium species are the most detrimental pathogens of soybean root rot worldwide, causing large loss in soybean production. Maize/soybean relay strip intercropping has significant advantages on the increase of crop yields and efficient use of agricultural resources, but its effects on the occurrence and pathogen population of soybean root rot are rarely known. In this study, root rot was investigated in the fields of the continuous maize/soybean strip relay intercropping and soybean monoculture. Fusarium species were isolated from diseased soybean roots and identified based on sequence analysis of translation elongation factor 1α (EF-1α) and RNA polymerase II second largest subunit (RPB2), and the diversity and pathogenicity of these species were also analyzed. Our results showed that intercropping significantly decreased soybean root rot over monoculture. A more diverse Fusarium population including Fusarium solani species complex (FSSC), F. incarnatum-equiseti species complex (FIESC), F. oxysporum, F. fujikuroi, F. proliferatum and F. verticillioides, F. graminearum and F. asiaticum was identified from intercropping while FSSC, FIESC, F. oxysporum, F. commune, F. asiaticum and F. meridionale were found from monoculture. All Fusarium species caused soybean root infection but exhibited distinct aggressiveness. The most aggressive F. oxysporum was more frequently isolated in monoculture than intercropping. FSSC and FIESC were the dominant species complex and differed in their aggressiveness. Additionally, F. fujikuroi, F. proliferatum and F. verticillioides were specifically identified from intercropping with weak or middle aggressiveness. Except for F. graminearum, F. meridionale and F. asiaticum were firstly reported to cause soybean root rot in China. This study indicates maize/soybean relay strip intercropping can reduce soybean root rot, change the diversity and aggressiveness of Fusarium species, which provides an important reference for effective management of this disease.

Characterization and Pathogenicity of Fusarium Species Associated with Soybean Pods in Maize/Soybean Strip Intercropping

Intercropping has been considered as a kind of a sustainable agricultural cropping system. In southwest China, maize/soybean strip intercropping has commonly been practised under local limited agricultural land resources. However, heavy rainfall in combination with high humidity and low temperatures cause severe pod and seed deterioration in the maturity and pre-harvesting stages of intercropped soybean. Numerous Fusarium species have been reported as the dominant pathogens of soybean root rot, seedling blight, as well as pod field mold in this area. However, the diversity and pathogenicity of Fusarium species on soybean pods remain unclear. In the current study, diseased soybean pods were collected during the cropping season of 2018 from five different intercropped soybean producing areas. A total of 83 Fusarium isolates were isolated and identified as F. fujikuroi, F. graminearum, F. proliferatum, and F. incarnatum-equiseti species complex based on morphological characteristics and phylogenetic analysis of the nucleotide sequence of EF1-α and RPB2 genes. Pathogenicity tests demonstrated that all Fusarium species were pathogenic to seeds of the intercropped soybean cultivar Nandou12. Fusarium fujikuroi had the maximum disease severity, with a significant reduction of seed germination rate, root length, and seed weight, followed by F. equiseti, F. graminearum, F. proliferatum, and F. incarnatum. Additionally, the diversity of Fusarium species on soybean pods was also considerably distinct according to the geographical origin and soybean varieties. Thus, the findings of the current study will be helpful for the management and resistance breeding of soybean pod decay in the maize/soybean intercropping system.

Fungal Endophyte Diversity and Bioactivity in the Indian Medicinal Plant Ocimum sanctum Linn

Endophytic mycopopulation isolated from India's Queen of herbs Tulsi (Ocimum sanctum) were explored and investigated for their diversity and antiphytopathogenic activity against widespread plant pathogens Botrytis cinerea, Sclerotinia sclerotiorum, Rhizoctonia solani and Fusarium oxysporum. 90 fungal isolates, representing 17 genera were recovered from 313 disease-free and surface sterilised plant segments (leaf and stem tissues) from three different geographic locations (Delhi, Hyderabad and Mukteshwar) during distinct sampling times in consequent years 2010 and 2011 in India. Fungal endophytes were subjected to molecular identification based on rDNA ITS sequence analysis. Plant pathogens such as F. verticillioides, B. maydis, C. coarctatum, R. bataticola, Hypoxylon sp., Diaporthe phaseolorum, Alternaria tenuissima and A. alternata have occurred as endophyte only during second sampling (second sampling in 2011) in the present study. Bi-plot generated by principal component analysis suggested tissue specificity of certain fungal endophytes. Dendrogram revealed species abundance as a function of mean temperature of the location at the time of sampling. Shannon diversity in the first collection is highest in Hyderabad leaf tissues (H' = 1.907) whereas in second collection it was highest from leaf tissues of Delhi (H' = 1.846). Mukteshwar (altitude: 7500 feet) reported least isolation rate in second collection. Nearly 23% of the total fungal isolates were considered as potent biocontrol agent. Hexane extract of M. phaseolina recovered from Hyderabad in first collection demonstrated highest activity against S. sclerotiorum with IC50 value of 0.38 mg/ml. Additionally, its components 2H-pyran-2-one, 5,6-dihydro-6-pentyl and palmitic acid, methyl ester as reported by GC-MS Chromatogram upon evaluation for their antiphytopathogenic activity exhibited IC50 value of 1.002 and 0.662 against respectively S. sclerotiorum indicating their significant role in antiphytopathogenic activity of hexane extract. The production of 2H-pyran-2-one, 5,6-dihydro-6-pentyl from M. phaseolina, an endophytic fungus is being reported for the first time.

Identification and mapping of quantitative trait loci (QTL) conferring resistance to Fusarium graminearum from soybean PI 567301B

KEY MESSAGE

A major novel QTL was identified in a recombinant inbred line population derived from a cross of 'Wyandot' × PI 567301B for Fusarium graminearum, a seed and seedling pathogen of soybean. Fusarium graminearum is now recognized as a primary pathogen of soybean, causing root, seed rot and seedling damping-off in North America. In a preliminary screen, 'Wyandot' and PI 567301B were identified with medium and high levels of partial resistance to F. graminearum, respectively. The objective of this study was to characterise resistance towards F. graminearum using 184 recombinant inbred lines (RILs) derived from a cross of 'Wyandot' × PI 567301B. The parents and the RILs of the mapping population were evaluated for resistance towards F. graminearum using the rolled towel assay in a randomized incomplete block design. A genetic map was constructed from 2545 SNP markers and 2 SSR markers by composite interval mapping. One major and one minor QTL were identified on chromosomes 8 and 6, respectively, which explained 38.5 and 8.1 % of the phenotypic variance. The major QTL on chromosome 8 was mapped to a 300 kb size genomic region of the Williams 82 sequence. Annotation of this region indicates that there are 39 genes including the Rhg4 locus for soybean cyst nematode (SCN) resistance. Based on previous screens, PI 567301B is susceptible to SCN. Fine mapping of this locus will assist in cloning these candidate genes as well as identifying DNA markers flanking the QTL that can be used in marker-assisted breeding to develop cultivars with high levels of resistance to F. graminearum.

Distribution and Frequency of Fusarium Species Associated with Soybean Roots in Iowa

A 3-year survey was conducted in Iowa to characterize the distribution and frequency of species of Fusarium associated with soybean roots. Ten plants were collected from each of 40 to 57 fields each year at V2 to V5 and R3 to R4 soybean growth stages. Fusarium colonies were isolated from symptomatic and symptomless roots and identified to species based on cultural and morphological characteristics. Species identification was confirmed by amplification and sequencing of the translation elongation factor (EF1-α) gene. Fifteen species were identified; Fusarium oxysporum was isolated most frequently, accounting for more than 30% of all isolates. F. acuminatum, F. graminearum, and F. solani were also among the most frequent and widespread species. Eleven other species were recovered from few fields, accounting for less than 10% of all isolates in a given year. No consistent trends were observed in geographic distribution of species. Variability in species frequency was found between soybean growth stages. Fusarium oxysporum was recovered at higher frequency during vegetative stages (40%) than reproductive stages (22%). Conversely, species such as F. acuminatum, F. graminearum, and F. solani were recovered more often from reproductive-stage plants. No significant differences in species composition were observed among fields differing in tillage practices and row spacing.

Aggressiveness of Fusarium species and impact of root infection on growth and yield of soybeans

Fusarium spp. are commonly isolated from soybean roots but the pathogenic activity of most species is poorly documented. Aggressiveness and yield impact of nine species of Fusarium were determined on soybean in greenhouse (50 isolates) and field microplot (19 isolates) experiments. Root rot severity and shoot and root dry weights were compared at growth stages V3 or R1. Root systems were scanned and digital image analysis was conducted; yield was measured in microplots. Disease severity and root morphology impacts varied among and within species. Fusarium graminearum was highly aggressive (root rot severity >90%), followed by F. proliferatum and F. virguliforme. Significant variation in damping-off (20 to 75%) and root rot severity (<20 to >60%) was observed among F. oxysporum isolates. In artificially-infested microplots, root rot severity was low (<25%) and mean yield was not significantly reduced. However, there were significant linear relationships between yield and root symptoms for some isolates. Root morphological characteristics were more consistent indicators of yield loss than root rot severity. This study provides the first characterization of aggressiveness and yield impact of Fusarium root rot species on soybean at different plant stages and introduces root image analysis to assess the impact of root pathogens on soybean.