Potential Inoculum Sources and Incidence of Strawberry Soilborne Pathogens in Spain

Applying an NMR-based metabolomic workflow to unveil strawberry molecular mechanisms in vernalization

Nuclear Magnetic Resonance (NMR) is a mature technique in metabolomics due to its non-invasive, highly reproducible, and inherently quantitative nature. However, difficulties in data analysis hinder its standardization in research. Herein, we propose an NMR-based metabolomic workflow that comprises data preprocessing, metabolite annotation, and data analysis. In this work, we apply such workflow to study vernalization, which is a critical process for crop development with largely unknown molecular mechanisms. Our findings suggest that sugar mobility, accessibility, and increased photosynthetic activity support plant viability post-vernalization. In other words, these processes ensure successful transplanting of the plant, highlighting the importance of sufficient cold exposure for flowering, fruiting, and ripening. This study demonstrates that the proposed workflow is suitable to capture metabolic changes in plant development. Such methodology underscores the potential of NMR-based metabolomics as a powerful tool for crop monitoring, aiding in improved agricultural practices and yield optimization.

Characterization and Fungicide Sensitivity of Gnomoniopsis fructicola Causing Gnomonia Leaf Blotch of Strawberry in the Carolinas

Emerging fungal pathogens have always been an issue of concern in southeastern U.S. strawberry production. In 2023, an unusual outbreak of Gnomonia leaf blotch occurred at one North Carolina and multiple South Carolina (SC) strawberry farms and marked the first reports of its occurrence in SC. Molecular identification and phylogenetic analysis of isolates from multiple locations identified the fungus Gnomoniopsis fructicola as the causal agent. In vitro germination of G. fructicola progressed slowly and remained less than 40% even after 24 h of incubation. Similarly, germ tube growth was slow compared with other pathogens. Slow symptom development on strawberry leaves of young strawberry plants grown in the greenhouse started 5 weeks after inoculation. Once the pathogen established on greenhouse plants, leaf necrosis forming blotches was observed. The baseline sensitivity of G. fructicola isolates to commonly used chemical classes of fungicides was assessed. Propiconazole, cyprodinil, pyraclostrobin, and fludioxonil were highly effective in mycelial growth assays with effective concentration of fungicide required for 50% growth inhibition (EC50) values ≤0.01 μg/ml. Iprodione and thiophanate-methyl were also effective, with EC50 values ranging from 0.05 to 1.38 and 2.01 to 23.96 μg/ml, respectively. Fluopyram and fenhexamid were ineffective. with EC50 values >100 μg/ml. Based on conversations with the producers, the disease outbreak was linked to transplants from the same nursery source. This study reports for the first time the presence of Gnomonia leaf blotch in SC and provides valuable insights into chemical management options for G. fructicola.

Host Range of Phytophthora spp. from Berry Crops in Huelva, Spain

Crop declines have been observed in raspberry and blueberry farms in the southwest region of Spain, which is the most important berry-producing area in the country. This study aimed to identify and characterize the pathogens associated with these diseases using molecular and morphological methods. Additionally, pathogenicity tests were performed on different raspberry, blueberry, and strawberry cultivars to determine possible susceptible hosts in the area. An isolate of Phytophthora cactorum was obtained from a symptomatic strawberry plant, an isolate of P. cinnamomi was obtained from a symptomatic blueberry plant, and isolates identified as P. rosacearum, P. rubi, and a previously unknown species named P. balkanensis were recovered from symptomatic raspberry plants. Results from the pathogenicity tests reported, for the first time, P. rubi causing root rot and wilting complex in Spanish raspberry crops. Additionally, P. cinnamomi was found to affect highbush blueberry production in Spain. Thus, this study provides valuable insights into the identification and characterization of Phytophthora spp. associated with the decline of blueberry and raspberry crops in Huelva. It also provides essential recommendations regarding the potential risks associated with the use of other types of berries as rotational crops and emphasizes the necessity for effective management strategies to mitigate crop losses. This is particularly critical given the limited soil disinfection alternatives available in Spain.

Optimization of the Use of Industrial Wastes in Anaerobic Soil Disinfestation for the Control of Fusarium Wilt in Strawberry

Anaerobic soil disinfestation (ASD) is proposed as an alternative to the use of chemical fumigants against Fusarium wilt in strawberry crops. Different residual wastes (rice bran, fishmeal, and residual strawberry extrudate) were assessed as amendments for ASD. Two different concentrations and two incubation durations were tested in growth chamber trials. The abundance of several microbial groups was noted before and after the treatments. Strawberry plants were grown in the treated soils to record Fusarium wilt disease severity. The population density of F. oxysporum increased after ASD in most amendments with rice bran and residual strawberry extrudate. Changes in Trichoderma spp., copiotrophic bacteria, and Streptomyces spp. populations were observed after anaerobiosis treatments and plant trials. A reduction in the disease severity was achieved in ASD-treated soils with 20 t/ha of rice bran at both 25 and 60 days of incubation, but not when using a 13.5 t/ha dose. Similarly, treatments using 19.3 t/ha of fishmeal for both incubation durations were able to reduce disease severity. In contrast, a severity reduction was only obtained in soils treated with 25.02 t/ha of the residual strawberry extrudate and incubated for 60 days in anaerobic conditions. Two of the three by-products tested were able to reduce Fusarium wilt symptoms in strawberry plants after an ASD-treatment period of only 25 days. Accordingly, the technique seems promising for strawberry growers in Huelva, Spain, and highly sustainable by giving value to residues produced in surrounding areas.

An Improved Method for Quantification of Viable Fusarium Cells in Infected Soil Products by Propidium Monoazide Coupled with Real-Time PCR

Fusarium is a soil-borne pathogen that causes root rot disease in cucumber. To date, quantitative real-time PCR (qPCR) is a common tool to detect the content of Fusarium in soil. However, qPCR cannot distinguish between viable and nonviable cells. The aim of this study was to develop a detection technique to pretreat tissue fluid with propidium monoazide (PMA) followed by extract DNA, and then to quantify viable Fusarium cells in contaminated soil. In this work, the specific primer pair F8-1/F8-2 was designed based on the translation elongation factor (EF) gene and a PMA-qPCR assay was established to amplify and quantify soils of viable Fusarium cells. The PMA pretreatment test was optimized, which indicated that the optimal PMA concentration and light exposure time were 50 mmol L⁻¹ and 15 min, respectively. The lowest limit of viable cells in suspension detected and soil by PMA-qPCR were 82 spore mL⁻¹ and 91.24 spore g⁻¹, respectively. For naturally contaminated soil, viable Fusarium cells were detected in eight of the 18 samples, and the Fusarium amount ranged from 10⁴ to 10⁶ spore g⁻¹. In conclusion, the PMA-qPCR method has the characteristics of high sensitivity, efficiency, and time saving, which could support nursery plants to avoid Fusarium infection and agro-industry losses.

"Shining a LAMP" (Loop-Mediated Isothermal Amplification) on the Molecular Detection of Phytopathogens Phytophthora spp. and Phytophthora cactorum in Strawberry Fields

Phytopathogenic microorganisms belonging to the genus Phytophthora have been recognized many times as causal agents of diseases that lower the yield of many plants important for agriculture. Meanwhile, Phytophthora cactorum causes crown rot and leather rot of berry fruits, mainly strawberries. However, widely-applied culture-based methods used for the detection of pathogens are time-consuming and often inaccurate. What is more, molecular techniques require costly equipment. Here we show a rapid and effective detection method for the aforementioned targets, deploying a simple molecular biology technique, Loop-Mediated Isothermal Amplification (LAMP). We optimized assays to amplify the translation elongation factor 1-α (EF1a) gene for two targets: Phytophthora spp. And Phytophthora cactorum. We optimized the LAMP on pure strains of the pathogens, isolated from organic plantations of strawberry, and successfully validated the assay on biological material from the environment including soil samples, rhizosphere, shoots and roots of strawberry, and with SYBR Green. Our results demonstrate that a simple and reliable molecular detection method, that requires only a thermoblock and simple DNA isolation kit, can be successfully applied to detect pathogens that are difficult to separate from the field. We anticipate our findings to be a starting point for developing easier and faster modifications of the isothermal detection methods and which can be applied directly in the plantation, in particular with the use of freeze-dried reagents and chemistry, allowing observation of the results with the naked eye.

Increase of Productivity and Neutralization of Pathological Processes in Plants of Grain and Fruit Crops with the Help of Aqueous Solutions Activated by Plasma of High-Frequency Glow Discharge

In this work, we, for the first time, manufactured a plasma-chemical reactor operating at a frequency of 0.11 MHz. The reactor allows for the activation of large volumes of liquids in a short time. The physicochemical properties of activated liquids (concentration of hydrogen peroxide, nitrate anions, redox potential, electrical conductivity, pH, concentration of dissolved gases) are characterized in detail. Antifungal activity of aqueous solutions activated by a glow discharge has been investigated. It was shown that aqueous solutions activated by a glow discharge significantly reduce the degree of presence of phytopathogens and their effect on the germination of such seeds. Seeds of cereals (sorghum and barley) and fruit (strawberries) crops were studied. The greatest positive effect was found in the treatment of sorghum seeds. Moreover, laboratory tests have shown a significant increase in sorghum drought tolerance. The effectiveness of the use of glow-discharge-activated aqueous solutions was shown during a field experiment, which was set up in the saline semi-desert of the Northern Caspian region. Thus, the technology developed by us makes it possible to carry out the activation of aqueous solutions on an industrial scale. Water activated by a glow discharge exhibits antifungicidal activity and significantly accelerates the development of the grain and fruit crops we studied. In the case of sorghum culture, glow-discharge-activated water significantly increases drought resistance.

Potential inoculum sources of Fusarium species involved in asparagus decline syndrome and evaluation of soil disinfestation methods by qPCR protocols

BACKGROUND

Asparagus decline syndrome (ADS), one of the most important diseases affecting asparagus crops, causes important yield losses worldwide. Fusarium proliferatum, F. oxysporum and F. redolens are among the main species associated with ADS. To explore their potential inoculum sources and the effectiveness of soil disinfestation practices for ADS management, molecular methods based on a quantitative real-time polymerase chain reaction (qPCR) were developed. qPCR-based molecular tools demonstrated advantages in the sensitive and specific detection and quantification of fungal pathogens in comparison with less-accurate and time-consuming traditional culture methods.

RESULTS

F. proliferatum, F. oxysporum and F. redolens could be specifically detected and accurately quantified in asparagus plants, soil and irrigation water collected from asparagus fields with ADS symptoms by means of the designed TaqMan qPCR protocols. Furthermore, these molecular tools were successfully applied for evaluation of the efficacy of diverse soil disinfestation treatments. Chemical fumigation with dazomet and biosolarization with pellets of Brassica carinata contributed to a significant reduction in the inoculum densities of the three Fusarium species in treated soils, which was correlated with production increases.

CONCLUSIONS

The capability to accurately detect and quantify the main Fusarium species involved in ADS in plants, soil and water samples by means of qPCR will allow identification of high-risk fields that can be avoided or managed to reduce yield losses. Quantification of pathogen densities in the soil may also provide essential insights into the effectiveness of soil disinfestation methods for ADS management. © 2021 Society of Chemical Industry.

The rhizosphere microbiome plays a role in the resistance to soil-borne pathogens and nutrient uptake of strawberry cultivars under field conditions

Microbial-root associations are important to help plants cope with abiotic and biotic stressors. Managing these interactions offers an opportunity for improving the efficiency and sustainability of agricultural production. By characterizing the bacterial and archaeal community (via 16S rRNA sequencing) associated with bulk and rhizosphere soil of sixteen strawberry cultivars in two controlled field studies, we explored the relationships between the soil microbiome and plant resistance to two soil-borne fungal pathogens (Verticillium dahliae and Macrophomina phaseolina). Overall, the plants had a distinctive and genotype-dependent rhizosphere microbiome with higher abundances of known beneficial bacteria such as Pseudomonads and Rhizobium. The rhizosphere microbiome played a significant role in the resistance to the two soil-borne pathogens as shown by the differences in microbiome between high and low resistance cultivars. Resistant cultivars were characterized by higher abundances of known biocontrol microorganisms including actinobacteria (Arthrobacter, Nocardioides and Gaiella) and unclassified acidobacteria (Gp6, Gp16 and Gp4), in both pathogen trials. Additionally, cultivars that were resistant to V. dahliae had higher rhizosphere abundances of Burkholderia and cultivars resistant to M. phaseolina had higher abundances of Pseudomonas. The mechanisms involved in these beneficial plant-microbial interactions and their plasticity in different environments should be studied further for the design of low-input disease management strategies.

Effect of chemical alternatives to methyl bromide on soil-borne disease incidence and fungal populations in Spanish strawberry nurseries: A long-term study

BACKGROUND

Chloropicrin (PIC) mixtures of 1,3-dichloropropene and chloropicrin (DD:PIC), dazomet, and metam sodium (MS) have been applied as chemical alternatives to methyl bromide (MB) in Spanish strawberry nurseries since MB was banned as a soil fumigant in 2005. These chemical alternatives were applied to soil in two Spanish strawberry nurseries between 2003 and 2017 to test their efficacy against the main crown and root disease and soil fungal populations in comparison with the use of MB and PIC (MB:PIC). These chemicals were applied at several doses with different application methods under plastic films. Crown and root disease incidence was calculated as the percentage of plants with symptoms caused by soil-borne pathogens. Soil fungal populations were estimated as colony forming units per gram of dry soil.

RESULTS

All chemicals significantly reduced soil-borne fungal disease incidence and fungal population in both nurseries over the years. Phytophthora cactorum and Fusarium spp. were the main pathogens causing soil-borne diseases, followed by Verticillium spp. MB:PIC remained the treatment that best controlled P. cactorum. MS and DD:PIC controlled Fusarium disease to a lesser extent than MB:PIC and dazomet in both nurseries. MB:PIC and PIC were the two treatments that most reduced Verticillium spp. The population of Verticillium spp. declined and the presence of other species such as Colletotrichum spp. and Rhizoctonia spp. was minimal during the study.

CONCLUSION

Chemicals are necessary to obtain healthy strawberry plants. The use of chemical alternatives to MB has resulted in changes in the incidence of soil-borne diseases and soil fungal populations in strawberry nurseries. Dazomet was an effective alternative to MB as a soil-borne disease control, except against Verticillium spp. MB alternatives in strawberry nursery soils have caused Fusarium spp. to displace Verticillium spp.

Species Composition and Toxigenic Potential of Fusarium Isolates Causing Fruit Rot of Sweet Pepper in China

Apart from causing serious yield losses, various kinds of mycotoxins may be accumulated in plant tissues infected by Fusarium strains. Fusarium mycotoxin contamination is one of the most important concerns in the food safety field nowadays. However, limited information on the causal agents, etiology, and mycotoxin production of this disease is available on pepper in China. This research was conducted to identify the Fusarium species causing pepper fruit rot and analyze their toxigenic potential in China. Forty-two Fusarium strains obtained from diseased pepper from six provinces were identified as F. equiseti (27 strains), F. solani (10 strains), F. fujikuroi (five strains). This is the first report of F. equiseti, F. solani and F. fujikuroi associated with pepper fruit rot in China, which revealed that the population structure of Fusarium species in this study was quite different from those surveyed in other countries, such as Canada and Belgium. The mycotoxin production capabilities were assessed using a well-established liquid chromatography mass spectrometry method. Out of the thirty-six target mycotoxins, fumonisins B₁ and B₂, fusaric acid, beauvericin, moniliformin, and nivalenol were detected in pepper tissues. Furthermore, some mycotoxins were found in non-colonized parts of sweet pepper fruit, implying migration from colonized to non-colonized parts of pepper tissues, which implied the risk of mycotoxin contamination in non-infected parts of food products.

Alternative Molecular-Based Diagnostic Methods of Plant Pathogenic Fungi Affecting Berry Crops-A Review

Increasing consumer awareness of potentially harmful pesticides used in conventional agriculture has prompted organic farming to become notably more prevalent in recent decades. Central European countries are some of the most important producers of blueberries, raspberries and strawberries in the world and organic cultivation methods for these fruits have a significant market share. Fungal pathogens are considered to be the most significant threat to organic crops of berries, causing serious economic losses and reducing yields. In order to ameliorate the harmful effects of pathogenic fungi on cultivations, the application of rapid and effective identification methods is essential. At present, various molecular methods are applied for fungal species recognition, such as PCR, qPCR, LAMP and NGS.