Evaluating the Importance of Stem Canker of Soybean in Iowa

Exploring Endophytic Fungi as Natural Antagonists against Fungal Pathogens of Food Crops

The yield and quality of cultivated food crops are frequently compromised by the prevalent threat from fungal pathogens that can cause widespread damage in both the pre-harvest and post-harvest stages. This paper investigates the challenges posed by fungal pathogens to the sustainability and yield of essential food crops, leading to significant economic and food security repercussions. The paper critiques the long-standing reliance on synthetic fungicides, emphasizing the environmental and health concerns arising from their widespread and occasionally inappropriate use. In response, the paper explores the potential of biological control agents, specifically endophytic fungi in advancing sustainable agricultural practices. Through their diverse symbiotic relationships with host plants, these fungi exhibit strong antagonistic capabilities against phytopathogenic fungi by producing various bioactive compounds and promoting plant growth. The review elaborates on the direct and indirect mechanisms of endophytic antagonism, such as antibiosis, mycoparasitism, induction of host resistance, and competition for resources, which collectively contribute to inhibiting pathogenic fungal growth. This paper consolidates the crucial role of endophytic fungi, i.e., Acremonium, Alternaria, Arthrinium, Aspergillus, Botryosphaeria, Chaetomium, Cladosporium, Cevidencealdinia, Epicoccum, Fusarium, Gliocladium, Muscodor, Nigrospora, Paecilomyces, Penicillium, Phomopsis, Pichia, Pochonia, Pythium, Ramichloridium, Rosellinia, Talaromyces, Trichoderma, Verticillium, Wickerhamomyces, and Xylaria, in biological control, supported by the evidence drawn from more than 200 research publications. The paper pays particular attention to Muscodor, Penicillium, and Trichoderma as prominent antagonists. It also emphasizes the need for future genetic-level research to enhance the application of endophytes in biocontrol strategies aiming to highlight the importance of endophytic fungi in facilitating the transition towards more sustainable and environmentally friendly agricultural systems.

Rapid and sensitive detection of two fungal pathogens in soybeans using the recombinase polymerase amplification/CRISPR-Cas12a method for potential on-site disease diagnosis

BACKGROUND

Diaporthe aspalathi and Diaporthe caulivora are two of the fungal pathogens causing soybean stem canker (SSC) in soybean, which is one of the most widespread diseases in soybean growing regions and can cause 100% loss of yield. Current methods for the detection of fungal pathogens, including morphological identification and molecular detection, are mostly limited by the need for professional laboratories and staff. To develop a detection method for potential on-site diagnosis for two of the fungal pathogens causing SSC, we designed a rapid assay combining recombinase polymerase amplification (RPA) and CRISPR-Cas12a-based diagnostics to specifically detect D. aspalathi and D. caulivora.

RESULTS

The translation elongation factor 1-alpha gene was employed as the target gene to evaluate the specificity and sensitivity of this assay. The RPA/CRISPR-Cas12a system has excellent specificity to distinguish D. aspalathi and D. caulivora from closely related species. The sensitivities of RPA/CRISPR-Cas12a-based fluorescence detection and lateral flow assay for D. aspalathi and D. caulivora are 14.5 copies and 24.6 copies, respectively. This assay can detect hyphae in inoculated soybean stems at 12 days after inoculation and has a recovery as high as 86% for hyphae-spiked soybean seed powder. The total time from DNA extraction to detection was not more than 60 min.

CONCLUSION

The method developed for rapid detection of plant pathogens includes DNA extraction with magnetic beads or rapid DNA extraction, isothermal nucleic acid amplification at 39 °C, CRISPR-Cas12a cleavage reaction at 37 °C, and lateral flow assay or endpoint fluorescence visualization at room temperature. The RPA and CRISPR-Cas12a reagents can be preloaded in the microcentrifuge tube to simplify the procedures in the field. Both RPA and CRISPR-Cas12a reaction can be realized on a portable incubator, and the results are visualized using lateral flow strips or portable flashlight. This method requires minimal equipment and operator training, and has promising applications for rapid on-site disease screening, port inspection, or controlling fungal pathogen transmission in crop. © 2023 Society of Chemical Industry.

The genome of a Far Eastern isolate of Diaporthe caulivora, a soybean fungal pathogen

Diaporthe caulivora is an economically important fungal pathogen and a causal agent of soybean stem canker and seed decay. Here, the genome of a Russian Far Eastern isolate of D. caulivora was sequenced, assembled, and announced. Assembly quality was enough for advanced annotation, including prediction of potential disease-related genes encoding virulence factors and molecular determinants contributing to pathogen-host selection, interactions, and adaptation. Comparative analysis of 15 Diaporthe species was conducted regarding general genome properties, collinearity, and proteomes, and included detailed investigation of interspersed repeats. A notable feature of this analysis is a high recombinant variability of Diaporthe genomes, determined by the number and distribution of interspersed repeats, which also proved to be responsible for the diversity of GC content and genome size. This variability is assumed the main determinant of the divergence of Diaporthe genomes. A Bayesian multi-gene phylogeny was inferred for the 15 Diaporthe species on the basis of twenty thousand polymorphic sites of > 100 orthologous genes using independently adjusted evolutionary models. This allowed for the most accurate determination of evolutionary relationships and species boundaries for effective reporting about these plant pathogens. The evidence, obtained by different genome analysis techniques, implies the host-independent evolution of Diaporthe species. KEY POINTS: • The genome of a Far Eastern isolate of D. caulivora was announced. • A high degree of recombinant variability determines genomic divergence in Diaporthe genus. • The multi-gene phylogeny implies host-independent evolution of Diaporthe species.

Inoculation Method Impacts Symptom Development Associated with Diaporthe aspalathi, D. caulivora, and D. longicolla on Soybean (Glycine max)

One hundred fifty-two Diaporthe isolates were recovered from symptomatic soybean (Glycine max) stems sampled from the U.S. states of Iowa, Indiana, Kentucky, Michigan, and South Dakota. Using morphology and DNA sequencing, isolates were identified as D. aspalathi (8.6%), D. caulivora (24.3%), and D. longicolla (67.1%). Aggressiveness of five isolates each of the three pathogens was studied on cultivars Hawkeye (D. caulivora and D. longicolla) and Bragg (D. aspalathi) using toothpick, stem-wound, mycelium contact, and spore injection inoculation methods in the greenhouse. For D. aspalathi, methods significantly affected disease severity (P < 0.001) and pathogen recovery (P < 0.001). The relative treatment effects (RTE) of stem-wound and toothpick methods were significantly greater than for the other methods. For D. caulivora and D. longicolla, a significant isolate × method interaction affected disease severity (P < 0.05) and pathogen recovery (P < 0.001). Significant differences in RTEs were observed among D. caulivora and D. longicolla isolates only when the stem-wound and toothpick methods were used. Our study has determined that the stem-wound and toothpick methods are reliable to evaluate the three pathogens; however, the significant isolate × method interactions for D. caulivora and D. longicolla indicate that multiple isolates should also be considered for future pathogenicity studies.

Optimization and Application of a Quantitative Polymerase Chain Reaction Assay to Detect Diaporthe Species in Soybean Plant Tissue

Diaporthe caulivora and D. longicolla are the causal agents of stem canker of soybean (Glycine max L.). Accurate identification of stem canker pathogens upon isolation from infected soybean plants is difficult and unreliable based on morphology. In this study, two TaqMan probe-based quantitative polymerase chain reaction (qPCR) assays were optimized for detection of D. caulivora and D. longicolla in soybean plants. The assays used previously reported D. caulivora-specific (DPC-3) and D. longicolla-specific (PL-3) probe/primer sets. The sensitivity limit of the two assays was determined to be over a range of 100 pg to 10 fg of pure D. caulivora and D. longicolla genomic DNA. The qPCR assays were validated with plant samples collected from commercial soybean fields. The PL-3 set detected D. longicolla in soybean plants collected from the fields (quantification cycle value <35), which was confirmed by isolation on potato dextrose agar (PDA). D. caulivora was detected only in low levels (quantification cycle value <40) by DPC-3 set in a few of the symptomatic field samples, although the pathogen was not isolated on PDA. The qPCR assays were also useful in quantitatively phenotyping soybean plants for resistance to D. caulivora and D. longicolla under greenhouse conditions.

Geospatial and temporal analyses of Bean pod mottle virus epidemics in soybean at three spatial scales

A statewide survey was carried out from 2005 through 2007 to quantify, map, and analyze the spatial dynamics and seasonal patterns of Bean pod mottle virus (BPMV) prevalence and incidence within Iowa. In all, 8 to 16 soybean fields were arbitrarily sampled from 96 counties in 2005 and all 99 counties in 2006 and 2007. Field- and county-scale BPMV prevalence and incidence data were mapped using geographic information systems software. BPMV prevalence was highest in the 2006 soybean growing season, when BPMV was detected in 38.7% of all soybean fields, 91.9% of all counties, and 100% of the agricultural climate districts. BPMV incidence at the field scale was highest in 2006, when mean statewide end-of-season incidence was 24.4%. Spatial analyses indicated that BPMV incidence was spatially clustered at the county scale in all three growing seasons. Prevalence at the county scale was clustered in 2005 and 2007 but not in 2006. Semivariogram analyses at the field scale indicated the presence of significant (P ≤ 0.05) spatial dependence (clustering) at distances ≤23.4 km in 2005, 297.7 km in 2006, and 45.2 km in 2007. Data for county-scale incidence displayed a north (low incidence) to south (high incidence) BPMV gradient in each year of the survey. High county-scale BPMV prevalence and incidence levels in 2006 were significantly associated with BPMV prevalence and incidence in 2007 (P ≤ 0.05). Soybean fields with narrow row spacings (≤38 cm) were associated with higher levels of BPMV incidence. Soybean fields infected with BPMV had a higher probability of infection by Phomopsis pod and stem blight than did non-BPMV-infected fields. This study provides new quantitative tools and information to better understand the seasonal, temporal, and geographical distribution of BPMV disease risk at several spatial scales.

Effects of Virus Infection on Susceptibility of Soybean Plants to Phomopsis longicolla

Infection of soybean by Bean pod mottle virus (BPMV) or Soybean mosaic virus (SMV) has been reported to increase susceptibility to seed infection by Phomopsis spp., but the mechanism is unclear. Effects of virus infection on susceptibility to Phomopsis longicolla were studied in greenhouse experiments. Three soybean cultivars were inoculated with BPMV at growth stage V2 to V3, and with P. longicolla at R3, R5, or R7. Inoculation with BPMV did not increase the incidence of stem infection by P. longicolla, but it increased susceptibility to seed infection of cultivars Spansoy 201 at R5, and Pioneer brand 92M02 at R3, R5, and R7. A delay in maturity was observed only in 92M02. Thus, BPMV predisposed soybean plants to seed infection by P. longicolla, but this predisposition was not due solely to prolonging maturation. In separate experiments, two soybean cultivars were inoculated with SMV (V2 to V3) and P. longicolla (R3 and R5). Inoculation with SMV did not increase the incidence of stem or seed infection by P. longicolla. The SMV-Phomopsis spp. relationship may be cultivar and strain dependent. Results suggest that the risk of soybean seed infection by P. longicolla may be higher when BPMV vector populations are high and BPMV infection is widespread.