Roots of symptom-free leguminous cover crop and living mulch species harbor diverse Fusarium communities that show highly variable aggressiveness on pea (Pisum sativum)

Didymella pinodella: An Important Pea Root Rot Pathogen in France to Watch Out For?

Root rot pathogens restrict pea and wheat production globally. In the EU, pea and pea-based cereal mixtures are being promoted; however, root rot pathogen dynamics in such mixtures are poorly understood. Winter pea and wheat were grown either in pure stands or in mixtures in the field in western France, and the severity of root rot in pea, wheat, and their mixtures, as well as the key pathogens associated with these crops, were assessed. Disease severity was moderate in pea and low in wheat, with no effect of sowing pattern. Didymella pinodella, a previously unreported pathogen in the pea-root rot complex in France, emerged as the most dominant pathogen in pea. It also occurred in low frequencies in wheat. Subsequent greenhouse aggressiveness tests showed that ten of the commonly grown pea cultivars in France lack resistance to D. pinodella. Among the Fusarium spp. isolated, F. avenaceum was the most frequent, occurring at similar frequencies in pea and wheat. In conclusion, D. pinodella may be an important pea root rot pathogen in France and there is a lack of resistance in the tested pea cultivars. In addition, F. avenaceum is a shared pathogen of wheat and pea.

Farming system effects on root rot pathogen complex and yield of faba bean (vicia faba) in Germany

A survey across Germany was undertaken from 2016-2019 to evaluate effects of management system (organic vs conventional), pedo-climatic conditions and crop rotation history on faba bean root health status, diversity of major root rot pathogens and yield. Root rot incidence was generally low and there was no effect of the management system on the spectrum of pathogens isolated. Among the most common fungal species identified, frequencies of Fusarium redolens and Didymella pinodella were significantly higher in roots from organic fields compared with conventional and lower was observed for F. avenaceum, F. tricinctum and F. culmorum. Faba bean roots were colonized at similar rates by F. equiseti and the members of the F. oxysporum (FOSC) and F. solani (FSSC) species complexes in both management systems. Almost no legumes had been grown in the 5-11 years preceding the conventional faba beans surveyed while legumes had almost always been present during this period in the organic fields. This difference in rotational histories between the farming systems led to apparent cropping systems effects on the isolation frequencies of several species. For example, D. pinodella was ubiquitous in organic fields with a high frequency of legumes in the rotations but much rarer and often absent in conventional fields. Pedo-climatic conditions, particularly cool conditions at sowing and plant emergence and/or during the vegetative season favored most of the most prevalent Fusarium species identified in this study. In organic systems, yields correlated negatively with D. pinodella and F. redolens frequencies whereas higher levels of F. tricintum in faba bean roots had a positive correlation with yield. In conventional systems, faba bean yields depended more on the total precipitation before sowing and during the main growing season but were also negatively correlated with the frequencies of FOSC and F. culmorum. Phylogenetic analysis based on the TEF1 alpha locus indicated that the FSSC isolates mainly belonged to the F. pisi lineage. In contrast, the FOSC isolates were placed in 9 different lineages, with a conspicuous dominance of F. libertatis that has until now not been associated with any leguminous host.

A Novel Real Time PCR Method for the Detection and Quantification of Didymella pinodella in Symptomatic and Asymptomatic Plant Hosts

Didymella pinodella is the major pathogen of the pea root rot complex in Europe. This wide host range pathogen often asymptomatically colonizes its hosts, making the control strategies challenging. We developed a real-time PCR assay for the detection and quantification of D. pinodella based on the TEF-1 alpha gene sequence alignments. The assay was tested for specificity on a 54-isolate panel representing 35 fungal species and further validated in symptomatic and asymptomatic pea and wheat roots from greenhouse tests. The assay was highly consistent across separate qPCR reactions and had a quantification/detection limit of 3.1 pg of target DNA per reaction in plant tissue. Cross-reactions were observed with DNA extracts of five Didymella species. The risk of cross contamination, however, is low as the non-targets have not been associated with pea previously and they were amplified with at least 1000-fold lower sensitivity. Greenhouse inoculation tests revealed a high correlation between the pathogen DNA quantities in pea roots and pea root rot severity and biomass reduction. The assay also detected D. pinodella in asymptomatic wheat roots, which, despite the absence of visible root rot symptoms, caused wheat biomass reduction. This study provides new insights into the complex life style of D. pinodella and can assist in better understanding the pathogen survival and spread in the environment.

Untangling the Pea Root Rot Complex Reveals Microbial Markers for Plant Health

Plant health is recognised as a key element to ensure global food security. While plant breeding has substantially improved crop resistance against individual pathogens, it showed limited success for diseases caused by the interaction of multiple pathogens such as root rot in pea (Pisum sativum L.). To untangle the causal agents of the pea root rot complex and determine the role of the plant genotype in shaping its own detrimental or beneficial microbiome, fungal and oomycete root rot pathogens, as well as previously identified beneficials, i.e., arbuscular mycorrhizal fungi (AMF) and Clonostachys rosea, were qPCR quantified in diseased roots of eight differently resistant pea genotypes grown in four agricultural soils under controlled conditions. We found that soil and pea genotype significantly determined the microbial compositions in diseased pea roots. Despite significant genotype x soil interactions and distinct soil-dependent pathogen complexes, our data revealed key microbial taxa that were associated with plant fitness. Our study indicates the potential of fungal and oomycete markers for plant health and serves as a precedent for other complex plant pathosystems. Such microbial markers can be used to complement plant phenotype- and genotype-based selection strategies to improve disease resistance in one of the world's most important pulse crops of the world.

Fusarium spp. Associated With Root Rot of Pulse Crops and Their Cross-Pathogenicity to Cereal Crops in Montana

Root rot caused by Fusarium species is a major problem in the pulse growing regions of Montana. Fusarium isolates (n = 112) were obtained from seeds and roots of chickpea, dry pea, and lentil. Isolates were identified by comparing the sequences of the internal transcribed spacer region and the translation elongation factor 1-α in Fusarium-ID database. Fusarium avenaceum was the most abundant species (28%), followed by F. acuminatum (21%), F. poae (13%), F. oxysporum (8%), F. culmorum (6%), F. redolens (6%), F. sporotrichioides (6%), F. solani (4%), F. graminearum (2%), F. torulosum (2%), and F. tricinctum (0.9%). The aggressiveness of a subset of 50 isolates that represent various sources of isolation was tested on three pulse crops and two cereal crops. Nonparametric analysis of variance conducted on ranks of disease severity indicated that F. avenaceum and F. solani isolates were highly aggressive on pea and chickpea. In lentil, F. avenaceum and F. culmorum were highly aggressive. In barley, F. avenaceum, F. solani, F. culmorum, and F. graminearum were highly aggressive. In wheat, F. avenaceum, F. graminearum, and F. culmorum were highly aggressive. Two F. avenaceum isolates were highly aggressive across all the crops tested and found to be cross-pathogenic. One isolate of F. culmorum and an isolate of F. graminearum obtained from chickpea and lentil seed were highly aggressive on barley and wheat. The results indicate that multiple Fusarium spp. from seeds and roots can cause root rot on both pulse and cereal crops. Rotating these crops may still lead to an increase in inoculum levels, making crop rotation limited in efficacy as a disease management strategy.

First Report of Fusarium venenatum causing foot and root rot of wheat (Triticum aestivum) in Germany

Field experiments were established in the 2018/19 and 2019/20 growing seasons at the experimental station in Neu-Eichenberg, Hessen, Germany to examine the suitability of multiple wheat cultivars for intercropping with pea and the effect of mixtures on diseases. Approximately 600 wheat tillers (BBCH 49-61, depending on the year and cultivar) were sampled in each year and assessed for severity of foot (lower stem) rot symptoms. Fungi from plants with Fusarium-like symptoms exhibiting reddish-brown discolorations on the stems were isolated following the methods described in Šišić et al. (2018). Surface disinfected (3% NaOCl for 10s) wheat stems and roots were cut into three 1 cm long pieces and placed on COONS agar (Coons, 1916). Following 7 - 12 days of incubation under constant blacklight blue fluorescent light, pure cultures were generated on potato dextrose and synthetic nutrient-poor agar (Nirenberg, 1976) using the hyphal tip transfer technique, and the resulting colonies examined microscopically. Based on morphology ca 15% of all Fusarium isolates recovered belonged to a distinct taxonomic unit and were initially identified as F. sambucinum-like (Leslie and Summerell, 2006). The identity of 16 randomly selected isolates (GenBank accession numbers MW085924 - MW085939) was confirmed by sequencing a portion of the translation elongation factor 1-alpha gene region (O'Donnell et al., 1998). Blast analysis in the FUSARIUM-ID (Geiser et al., 2004) and the NCBI databases revealed >99 to 100% identity match with the Fusarium venenatum accession numbers NRRL 22196, FRC R-09186 and MRC 2394. Pathogenicity tests were conducted on wheat cultivar Torborzo using six F. venenatum isolates. Inoculum was prepared using a sterile sand-millet mix infested with six agar plugs of each of the isolates. Once fully colonized, the inoculum was mixed with sterilized sand in a 1:7 ratio (by volume), transferred to 300 ml pots and 4 surface sterilized wheat seeds (5 min 70% alcohol) were sown in each pot. Non-inoculated controls were amended with sterilized inoculum. The experiment was conducted in a greenhouse in a completely randomized design with 5 replicates. Disease symptoms were assessed after four weeks. All isolates induced reddish-brown discolorations on the lower stems similar to those observed in the field grown plants. In addition, the infected plants developed dark brown to black discolorations on the crowns and roots and showed clear signs of stunted root growth. These symptoms were further accompanied by chlorosis (yellowing) of the lower leaves starting from the leaf tip. All isolates were successfully reisolated from the infected wheat plants but not from the controls. To the best of our knowledge, this is the first report of F. venenatum causing foot and root rot of wheat in Germany. Results from field and greenhouse inoculation experiments indicate that F. venenatum may be an important pathogen of wheat in Germany. Further studies on distribution and relative abundance of the species in the Fusarium foot and root rot complex of wheat in Germany are warranted. In addition, it is important to note that our results contrast the results from previous studies (Farr and Rossman, 2021) which reported F. venenatum primarily as a soil saprophyte and presumably non-pathogenic fungus in its nature. Our findings thus, also warrant the need to further investigate pathogenic potential of this species and the role it may play on other common rotational crops in Germany.

Heritable Variation in Pea for Resistance Against a Root Rot Complex and Its Characterization by Amplicon Sequencing

Soil-borne pathogens cause severe root rot of pea (Pisum sativum L.) and are a major constraint to pea cultivation worldwide. Resistance against individual pathogen species is often ineffective in the field where multiple pathogens form a pea root rot complex (PRRC) and conjointly infect pea plants. On the other hand, various beneficial plant-microbe interactions are known that offer opportunities to strengthen plant health. To account for the whole rhizosphere microbiome in the assessment of root rot resistance in pea, an infested soil-based resistance screening assay was established. The infested soil originated from a field that showed severe pea root rot in the past. Initially, amplicon sequencing was employed to characterize the fungal microbiome of diseased pea roots grown in the infested soil. The amplicon sequencing evidenced a diverse fungal community in the roots including pea pathogens Fusarium oxysporum, F. solani, Didymella sp., and Rhizoctonia solani and antagonists such as Clonostachys rosea and several mycorrhizal species. The screening system allowed for a reproducible assessment of disease parameters among 261 pea cultivars, breeding lines, and landraces grown for 21 days under controlled conditions. A sterile soil control treatment was used to calculate relative shoot and root biomass in order to compare growth performance of pea lines with highly different growth morphologies. Broad sense heritability was calculated from linear mixed model estimated variance components for all traits. Emergence on the infested soil showed high (H 2 = 0.89), root rot index (H 2 = 0.43), and relative shoot dry weight (H 2 = 0.51) medium heritability. The resistance screening allowed for a reproducible distinction between PRRC susceptible and resistant pea lines. The combined assessment of root rot index and relative shoot dry weight allowed to identify resistant (low root rot index) and tolerant pea lines (low relative shoot dry weight at moderate to high root rot index). We conclude that relative shoot dry weight is a valuable trait to select disease tolerant pea lines. Subsequently, the resistance ranking was verified in an on-farm experiment with a subset of pea lines. We found a significant correlation (r s = 0.73, p = 0.03) between the controlled conditions and the resistance ranking in a field with high PRRC infestation. The screening system allows to predict PRRC resistance for a given field site and offers a tool for selection at the seedling stage in breeding nurseries. Using the complexity of the infested field soil, the screening system provides opportunities to study plant resistance in the light of diverse plant-microbe interactions occurring in the rhizosphere.

Bacterivorous Nematodes Correlate with Soil Fertility and Improved Crop Production in an Organic Minimum Tillage System

Reduced nutrient mineralization rates under minimum tillage are usually compensated by mineral fertilizer application. These, however, cannot be applied in organic farming systems. We hypothesized that an organic minimum tillage system based on frequent cover cropping and application of dead mulch would improve soil fertility and compensate for the potential negative effects of minimum tillage. Two long-term field experiments were set up in 2010 and 2011 to compare plowing versus minimum tillage including the application of transferred mulch. A second factor, the application of compost versus mineral potassium and phosphorus, was also compared. In 2019, soils were analyzed for soil pH, organic carbon, macro- and micronutrients, microbial biomass, microbial activity, and total nematode abundance. In addition, performance of pea in the same soils was determined under greenhouse conditions. Across both experiments, macronutrients (+52%), micronutrients (+11%), microbial biomass (+51%), microbial activity (+86%), and bacterivorous nematodes (+112%) increased in minimum tillage compared to the plow-based system. In the greenhouse, pea biomass was 45% higher in the soil that had been subjected to minimum tillage compared to the plow. In conclusion, soil fertility can be improved in organic minimum tillage systems, which include intensive cover cropping and the application of dead mulch, over plow-based systems.

Screening of Different Physalis Genotypes as Potential Rootstocks or Parents Against Vascular Wilt Using Physiological Markers

Cape gooseberry (Physalis peruviana L.) is one of the most exported Andean fruits in Colombia. Vascular wilt caused by Fusarium oxysporum f. sp. physali (FOph) has led to a reduction in crop areas in recent years. Therefore, the aim of this study was to select genotypes with resistance to vascular wilt that can be useful as rootstocks from a group of six Physalis genotypes (Physalis ixocarpa, Physalis floridana, and Physalis peruviana genotypes Colombia, Sudafrica, Peru, and Accession 62) using physiological variables such as maximum quantum efficiency of Photosystem II (Fv/Fm), leaf gas exchange properties [net photosynthesis rate (Pn) and stomatal conductance (g s )], and leaf water potential. An experiment was carried out under greenhouse conditions in which plants of the different Physalis materials were inoculated with the F. oxysporum f. sp. physali strain Map5 at a concentration of 1 × 106 conidia mL-1. Physiological and disease development variables were measured at 15, 23, and 31 days after inoculation (DAI). The results obtained showed that P. peruviana genotypes Colombia and Sudafrica showed greater susceptibility to the disease (disease severity index 3.8 and 3.6, respectively). Net photosynthesis rate (Pn), stomatal conductance (g s ), water potential (Ψ fw ), and Fv/Fm ratio were lower compared to non-inoculated plants. P. floridana and P. ixocarpa plants inoculated with F. oxysporum showed similar behavior to non-inoculated plants for the evaluated variables. In conclusion, the results obtained suggest that these two genotypes can be considered in breeding programs or as rootstock for the establishment of cape gooseberry crops in soils with the presence of the pathogen.

Confirmation of Fusarium root rot resistance QTL Fsp-Ps 2.1 of pea under controlled conditions

BACKGROUND

Dry pea production has increased substantially in North America over the last few decades. With this expansion, significant yield losses have been attributed to an escalation in Fusarium root rots in pea fields. Among the most significant rot rotting pathogenic fungal species, Fusarium solani fsp. pisi (Fsp) is one of the main causal agents of root rot of pea. High levels of partial resistance to Fsp has been identified in plant genetic resources. Genetic resistance offers one of the best solutions to control this root rotting fungus. A recombinant inbred population segregating for high levels of partial resistance, previously single nucleotide polymorphism (SNP) genotyped using genotyping-by-sequencing, was phenotyped for disease reaction in replicated and repeated greenhouse trials. Composite interval mapping was deployed to identify resistance-associated quantitative trait loci (QTL).

RESULTS

Three QTL were identified using three disease reaction criteria: root disease severity, ratios of diseased vs. healthy shoot heights and dry plant weights under controlled conditions using pure cultures of Fusarium solani fsp. pisi. One QTL Fsp-Ps 2.1 explains 44.4-53.4% of the variance with a narrow confidence interval of 1.2 cM. The second and third QTL Fsp-Ps3.2 and Fsp-Ps3.3 are closely linked and explain only 3.6-4.6% of the variance. All of the alleles are contributed by the resistant parent PI 180693.

CONCLUSION

With the confirmation of Fsp-Ps 2.1 now in two RIL populations, SNPs associated with this region make a good target for marker-assisted selection in pea breeding programs to obtain high levels of partial resistance to Fusarium root rot caused by Fusarium solani fsp. pisi.

Two new species of the Fusarium solani species complex isolated from compost and hibiscus (Hibiscus sp.)

Two new species in the Fusarium solani species complex (FSSC) are described and introduced. The new taxa are represented by German isolates CBS 142481 and CBS 142480 collected from commercial yard waste compost and vascular tissue of a wilting branch of hibiscus, respectively. The phylogenetic relationships of the collected strains to one another and within the FSSC were evaluated based on DNA sequences of 6 gene loci. Due to the limited sequence data available for reference strains in GenBank, however, a multi-gene phylogenetic analysis included partial sequences for the internal transcribed spacer region and intervening 5.8S nrRNA gene (ITS), translation elongation factor 1-alpha (tef1) and the RNA polymerase II second largest subunit (rpb2). Morphological and molecular phylogenetic data independently showed that these strains are distinct populations of the FSSC, nested within Clade 3. Thus, we introduce Fusarium stercicola and Fusarium witzenhausenense as novel species in the complex. In addition, 19 plant species of 7 legume genera were evaluated for their potential to host the newly described taxa. Eighteen plant species were successfully colonized, with 6 and 9 of these being symptomatic hosts for F. stercicola and F. witzenhausenense, respectively. As plants of the family Fabaceae are very distant to the originally sourced material from which the new taxa were recovered, our results suggest that F. stercicola and F. witzenhausenense are not host-specific and are ecologically fit to sustain stable populations in variety of habitats.