A pipeline for rapidly evaluating activity and inferring mechanisms of action of prospective antifungal compounds

BACKGROUND

Fungal phytopathogens are a significant threat to crops and food security, and there is a constant need to develop safe and effective compounds that antagonize them. In-planta assays are complex and tedious and are thus not suitable for initial high-throughput screening of new candidate antifungal compounds. We propose an in vitro screening pipeline that integrates five rapid quantitative and qualitative methods to estimate the efficacy and mode of action of prospective antifungal compounds.

RESULTS

The pipeline was evaluated using five documented antifungal compounds (benomyl, catechol, cycloheximide, 2,4-diacetylphloroglucinol, and phenylacetic acid) that have different modes of action and efficacy, against the model soilborne fungal pathogen Fusarium oxysporum f. sp. radicis cucumerinum. We initially evaluated the five compounds' ability to inhibit fungal growth and metabolic activity using green fluorescent protein (GFP)-labeled F. oxysporum and PrestoBlue staining, respectively, in multiwell plate assays. We tested the compounds' inhibition of both conidial germination and hyphal elongation. We then employed FUN-1 and SYTO9/propidium iodide staining, coupled to confocal microscopy, to differentiate between fungal growth inhibition and death at the cellular level. Finally, using a reactive oxygen species (ROS)-detection assay, we were able to quantify ROS production in response to compound application.

CONCLUSIONS

Collectively, the proposed pipeline provides a wide array of quantitative and qualitative data on the tested compounds that can help pinpoint promising novel compounds; these can then be evaluated more vigorously using in planta screening assays. © 2024 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Characterization of Coniella granati Isolates Causing Pomegranate Decline in Italy

Coniella granati, the causal agent of pomegranate crown rot, twig blight, and fruit decay, is an emerging worldwide pathogen with a heavy impact on pomegranate cultivation. In this study, we report the rapid spread of the fungus in Italian pomegranate orchards associated with crown rot symptoms and provide new results on fungal development, baseline sensitivity to different fungicides, and intraspecific variability by analyzing 11 isolates, representative of populations of the pathogen from comparable pomegranate orchards in different regions of Italy. In vitro assays showed that 25 to 30°C was the optimal range for both colony growth and conidial germination, corroborating the results previously obtained for Californian and Greek isolates. According to the baseline sensitivity assay on the response of colony growth and conidial germination to 10 fungicides, fludioxonil, thiophanate-methyl, tebuconazole, and cyprodinil were the most effective. Random amplified polymorphic DNA (RAPD) analysis, carried out using fourteen 10-mer primers, showed very low intraspecific variability (similarity coefficient >0.95), probably as a result of the recent spread of the pathogen in Italy and the uncommon occurrence of the sexual process as a source of genetic variability. In summary, this study provides new knowledge on C. granati that will be helpful for improving pomegranate crown rot management.

The devastating oomycete phytopathogen Phytophthora cactorum: Insights into its biology and molecular features

Phytophthora cactorum is one of the most economically important soilborne oomycete pathogens in the world. It infects more than 200 plant species spanning 54 families, most of which are herbaceous and woody species. Although traditionally considered to be a generalist, marked differences of P. cactorum isolates occur in degree of pathogenicity to different hosts. As the impact of crop loss caused by this species has increased recently, there has been a tremendous increase in the development of new tools, resources, and management strategies to study and combat this devastating pathogen. This review aims to integrate recent molecular biology analyses of P. cactorum with the current knowledge of the cellular and genetic basis of its growth, development, and host infection. The goal is to provide a framework for further studies of P. cactorum by highlighting important biological and molecular features, shedding light on the functions of pathogenicity factors, and developing effective control measures.

TAXONOMY

P. cactorum (Leb. & Cohn) Schröeter: kingdom Chromista; phylum Oomycota; class Oomycetes; order Peronosporales; family Peronosporaceae; genus Phytophthora.

HOST RANGE

Infects about 200 plant species in 154 genera representing 54 families. Economically important host plants include strawberry, apple, pear, Panax spp., and walnut.

DISEASE SYMPTOMS

The soilborne pathogen often causes root, stem, collar, crown, and fruit rots, as well as foliar infection, stem canker, and seedling damping off.

Establishment of the Recombinase Polymerase Amplification-Lateral Flow Dipstick Detection Technique for Fusarium oxysporum

Fusarium oxysporum causes crown rot, wilt, root rot, and many other major plant diseases worldwide. During the progression of strawberry crown rot disease, the pathogen is transmitted from the mother plant to the seedling through the stolon, with obvious characteristics of latent infection. Therefore, rapid and timely detection of F. oxysporum is important for efficient disease management. In this study, a recombinase polymerase amplification-lateral flow dipstick (RPA-LFD) detection technique was developed for the rapid detection of F. oxysporum on strawberry plants by targeting the CYP51C gene, which is unique to Fusarium spp. Because this RPA-LFD detection technique was highly specific to F. oxysporum, other Fusarium and non-Fusarium fungi were not detected. The optimal reaction temperature and time for this technique were 39°C and 8 min, respectively. The detection limit was 1 pg of F. oxysporum genomic DNA in a 50-μl reaction system. A total of 46 strawberry plants with or without crown rot symptoms collected from Jiande, Changxing, and Haining in Zhejiang Province were further assessed for F. oxysporum infection using both RPA-LFD and traditional tissue isolation techniques. The RPA-LFD test showed that 32 of the 46 strawberry plants tested were positive for F. oxysporum, while in the traditional isolation technique, F. oxysporum was isolated from 30 of the 46 strawberry plants. These results suggest that our established RPA-LFD method is rapid, sensitive, and highly specific in detecting F. oxysporum infection in strawberry plants.

Comparative Transcriptome Analysis Reveals Novel Candidate Resistance Genes Involved in Defence against Phytophthora cactorum in Strawberry

Crown rot, caused by Phytophthora cactorum, is a devastating disease of strawberry. While most commercial octoploid strawberry cultivars (Fragaria × ananassa Duch) are generally susceptible, the diploid species Fragaria vesca is a potential source of resistance genes to P. cactorum. We previously reported several F. vesca genotypes with varying degrees of resistance to P. cactorum. To gain insights into the strawberry defence mechanisms, comparative transcriptome profiles of two resistant genotypes (NCGR1603 and Bukammen) and a susceptible genotype (NCGR1218) of F. vesca were analysed by RNA-Seq after wounding and subsequent inoculation with P. cactorum. Differential gene expression analysis identified several defence-related genes that are highly expressed in the resistant genotypes relative to the susceptible genotype in response to P. cactorum after wounding. These included putative disease resistance (R) genes encoding receptor-like proteins, receptor-like kinases, nucleotide-binding sites, leucine-rich repeat proteins, RPW8-type disease resistance proteins, and 'pathogenesis-related protein 1'. Seven of these R-genes were expressed only in the resistant genotypes and not in the susceptible genotype, and these appeared to be present only in the genomes of the resistant genotypes, as confirmed by PCR analysis. We previously reported a single major gene locus RPc-1 (Resistance to Phytophthora cactorum 1) in F. vesca that contributed resistance to P. cactorum. Here, we report that 4-5% of the genes (35-38 of ca 800 genes) in the RPc-1 locus are differentially expressed in the resistant genotypes compared to the susceptible genotype after inoculation with P. cactorum. In particular, we identified three defence-related genes encoding wall-associated receptor-like kinase 3, receptor-like protein 12, and non-specific lipid-transfer protein 1-like that were highly expressed in the resistant genotypes compared to the susceptible one. The present study reports several novel candidate disease resistance genes that warrant further investigation for their role in plant defence against P. cactorum.

nicotianae

Phytophthora crown rot (PhCR) and leather rot (LR) caused by Phytophthora spp. are major threats to strawberry production worldwide. In the United States, these diseases are mainly caused by Phytophthora cactorum; however, P. nicotianae has also been recently reported causing PhCR. Growers have relied on three different chemical products (i.e., mefenoxam and phosphites for PhCR and LR, and azoxystrobin for LR). Because resistance to mefenoxam and azoxystrobin has been reported, this study aimed to assess the in vitro sensitivity of Phytophthora spp. isolates from strawberry to phosphites and investigate its efficacy on in vivo assays. In vitro sensitivity of P. cactorum (n = 128) and P. nicotianae (n = 24) isolates collected from 1997 to 2018 was assessed for phosphite at 10, 50, 100, 150, and 300 µg/ml. Regardless of the Phytophthora sp. and isolation organ, most of the isolates (75% for P. cactorum and 54.2% for P. nicotianae) had effective concentration that inhibits pathogen growth by 50% (EC₅₀) values ranging from 50 to 100 µg/ml. In vivo tests with strawberry fruit and plants revealed that commercial formulations of phosphite applied at the highest field rate controlled P. cactorum isolates but failed to control PhCR and LR caused by some isolates of P. nicotianae. In this study, EC₅₀ results from in vitro assay did not truly translate the efficacy of phosphites on controlling LR and PhCR caused by P. cactorum and P. nicotianae. Our findings support the hypothesis that the product acts in a dual way: direct on the pathogen and stimulating the plant immune system. Moreover, this has important implications for disease management, highlighting the importance of a correct diagnosis before phosphite recommendations, because its efficacy varies within Phytophthora spp.

First report of Fusarium equiseti causing root and crown rot in tomato in Mexico

Tomato (Solanum lycopersicum L.) is one of the most important crops in Mexico due to its economic and nutritional value. Among the main diseases in tomato production is Fusarium wilt, which can cause 60% production losses (Ascencio et al, 2008). Mixed infections of Fusarium species or other fungi genera, would increase disease severity. During April to May of 2021, tomato plants with more than 60 days old, were collected from the main production areas of Aguascalientes (22°03'46.5"N 102°05'17.4"W and 22°04'53.64"N 101°58'55.81"W) and Zacatecas (23°05'59.2"N 102°41'07.3"W and 22°16'52.1"N 102°00'11.8"W) Mexico states. Plants showed main root rot, vascular bundles necrosis with corky appearance, stem crown rot, and ascending yellowing. The main root and stem crown were cut in 0.25 cm2 pieces and disinfested in 2% NaClO for one minute, rinsed with distilled water two times, placed on acidified potato dextrose agar (PDA) medium, and incubated at 25 ± 2°C for 7 days. Characteristic Fusarium growths were purified by hyphal tip on PDA, subsequently pure strains were obtained by single-spore isolation method. Several fungi colonies were obtained, but we focused on the colonies that showed abundant aerial mycelium of white color and irregular growth, which turned yellowish to golden and brown color as it ages. Carnation leaf agar (CLA) medium were used for conidia and sporodochium development. Chains of terminal, intercalary and agglomerated chlamydospores with thick, rough brown walls of 18.9 (7.46) µm in diameter (n=120) were observed in the mycelium. Macroconidia with 5 to 7 septa were 30 to 75 (28.32) µm in long and 1.2 to 4.8 (3.2) µm in wide (n=72). Basal cell developed in foot-shape, apical cell was elongated and slightly curved, and some macroconidia had swollen midd-cell. Sporodochium was orange to brown in color and microconidia were absent (Figure 1). Two representative strains from each state, LCA-3.1 and EMA-1 from Aguascalientes and ECZ-4 and LRZ-6 from Zacatecas, were selected for DNA amplification of ITS, TEF-1α and RPB2 regions, with universal primers ITS1/ITS4, EF1/EF2 and 2-5F2/7cR (White et al.1990; O'Donnell et al. 1998, 2013). PCR products were sequenced by Psomagen, Inc. (USA). The sequences obtained showed 100% of similarity among themselves and within species of the Fusarium incarnatum-equiseti species complex (FIESC) with nucleotide NCBI accessions NR_121457 (Type material) for ITS and MW362069 for TEF-1α; and 99.28% with MN170399 for RPB2 in FUSARIOID-ID database. According to morphological (Leslie and Summerell, 2006) and molecular characteristics, isolates were identified as Fusarium equiseti (FIESC 14). The LCA-3.1 sequences were selected to be deposited in GenBank with accession numbers OM812801 (ITS), OM937108 (TEF-1α) and ON653596 (RPB2). Pathogenicity tests were performed twice, under greenhouse conditions in tomato seedlings of cv. Rio Grande. Five tomato seedlings were inoculated by root immersion method (Lopez et al, 2018) in a 1x106 spores/mL solution for 8 min, and transplanted to 1L pots with sterile peat. Five controls plants were immersed in sterile water. At 14 days after inoculation, a general plant decline and slower growth compared to the control plants were observed. Subsequently, plants showed root rot, vascular necrosis, and a brown ring in stem crown. Controls were symptomless. The fungi were re-isolated from symptomatic plants and were morphologically similar to the inoculated strains. Patel et al. (2017) described the pathogenic and toxic effects of F. equiseti on tomato, causing low seed germination, and low root and shoot growth. This is the first report of F. equiseti causing root and stem rot in tomato plants in Mexico.

Diversity Between Leaf Anthracnose and Crown Rot From the Same Strawberry Plant

Leaf anthracnose (LA) and anthracnose crown rot (ACR) represent serious fungal diseases that pose significant threats to strawberry production. To characterize the pathogen diversity associated with above diseases, 100 strawberry plants, including varieties of "Hongjia," "Zhangji," and "Tianxianzui," were sampled from Jiande and Zhoushan, the primary plantation regions of Zhejiang province, China. A total of 309 Colletotrichum isolates were isolated from crown (150 isolates) and leaves (159 isolates) of affected samples. Among these, 100 isolates obtained from the plants showing both LA and CR symptoms were selected randomly for further characterization. Based on the morphological observations combined with phylogenetic analysis of multiple genes (ACT, ITS, CAL, GAPDH, and CHS), all the 100 tested isolates were identified as C. gloeosporioides species complex, including 91 isolates of C. siamense, 8 isolates of C. fructicola causing both LA and ACR, and one isolate of C. aenigma causing ACR. The phenotypic characteristics of these isolated species were investigated using the BIOLOG phenotype MicroArray (PM) and a total of 950 different metabolic phenotype were tested, showing the characteristics among these isolates and providing the theoretical basis for pathogenic biochemistry and metabolism. The pathogenicity tests showed that even the same Colletotrichum species isolated from different diseased tissues (leaves or crowns) had significantly different pathogenicity toward strawberry leaves and crown. C. siamense isolated from diseased leaves (CSLA) was more aggressive than C. siamense isolated from rotted crown (CSCR) during the infection on "Zhangji" leaves. Additionally, C. fructicola isolated from affected leaf (CFLA) caused more severe symptoms on the leaves of four strawberry varieties compared to C. fructicola isolated from diseased crown (CFCR). For crown rot, the pathogenicity of CSCR was higher than that of CSLA.

Comparative Analysis of Host-Associated Variation in Phytophthora cactorum

Phytophthora cactorum is often described as a generalist pathogen, with isolates causing disease in a range of plant species. It is the causative agent of two diseases in the cultivated strawberry, crown rot (CR; causing whole plant collapse) and leather rot (LR; affecting the fruit). In the cultivated apple, P. cactorum causes girdling bark rots on the scion (collar rot) and rootstock (crown rot), as well as necrosis of the fine root system (root rot) and fruit rots. We investigated evidence for host specialisation within P. cactorum through comparative genomic analysis of 18 isolates. Whole genome phylogenetic analysis provided genomic support for discrete lineages within P. cactorum, with well-supported non-recombining clades for strawberry CR and apple infecting isolates specialised to strawberry crowns and apple tissue. Isolates of strawberry CR are genetically similar globally, while there is more diversity in apple-infecting isolates. We sought to identify the genetic basis of host specialisation, demonstrating gain and loss of effector complements within the P. cactorum phylogeny, representing putative determinants of host boundaries. Transcriptomic analysis highlighted that those effectors found to be specific to a single host or expanded in the strawberry lineage are amongst those most highly expressed during infection of strawberry and give a wider insight into the key effectors active during strawberry infection. Many effectors that had homologues in other Phytophthoras that have been characterised as avirulence genes were present but not expressed in our tested isolate. Our results highlight several RxLR-containing effectors that warrant further investigation to determine whether they are indeed virulence factors and host-specificity determinants for strawberry and apple. Furthermore, additional work is required to determine whether these effectors are suitable targets to focus attention on for future resistance breeding efforts.

Calcium oxide, potassium phosphite and a Trichoderma enriched compost water suspension protect Capsicum annuum against Phytophthora capsici by priming the immune system

BACKGROUND

Proper management of Phytophthora capsici in pepper cultivation is extremely important, since Phytophthora blight is the main disease of this crop worldwide. In the past, the main strategy adopted had been the use of fungicides, causing, in some cases, the development of P. capsici resistant strains. In this work three different treatments selected from previous studies (potassium phosphite, calcium oxide and a water suspension from Trichoderma sp. TW2 enriched compost) were tested to prove their ability to activate the systemic acquired resistance (SAR) in pepper against P. capsici; acibenzolar-s-methyl was used as positive control. Two independent growth chamber pot experiments were performed, spatially dividing the site of treatments application (as radical drench) and the site of inoculation (as agar plug on the third leaf).

RESULTS

Leaf lesions were measured, showing a significant reduction on all treated plants compared to the untreated control. To further confirm this hypothesis, the expression levels of three SAR key genes (CaPBR1, CaPO1 and CaDEF1) were evaluated though RT-Real Time PCR at the three end-point times: T0, T6 and T24. A significant increase of target genes expression at least in one end-point time in each treated plant was observed. Eventually, statistical overaccumulation of salicylic acid was observed in the upper leaves at the same end-point times, through HPLC-MS/MS analysis.

CONCLUSION

This work confirmed the hypothesis that the three treatments tested have the ability to prime the plant immune system, leading pepper to an alert status able to confer a better defence against P. capsici. © 2021 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Developing Actinobacterial Endophytes as Biocontrol Products for Fusarium pseudograminearum in Wheat

Crown rot of wheat, caused by Fusarium pseudograminearum, results in millions of dollars of yield losses globally each year. Management strategies to control crown rot are limited and there are concerns about development of fungicide resistance so novel treatment strategies are desirable. A collection of endophytic Actinobacteria was screened for their ability to suppress the growth of F. pseudograminearum and the development of crown rot symptoms in wheat with the aim of identifying candidates that can be developed into biocontrol products. The ability of the Actinobacteria isolates to suppress the growth of three different F. pseudograminearum strains in vitro was assessed using agar-plate competition assays. Soil-free seedling assays were used to screen for suppression of development of early disease symptoms in the susceptible wheat (Triticum aestivum) cv. Tamaroi. Four of the isolates were tested in a glasshouse pot experiment to assess their ability to decrease disease symptoms and prevent yield losses in wheat cv. Tamaroi grown to maturity in an unsterilized soil. The screening of 53 isolates identified two Streptomyces isolates, MH71 and MH243, with very strong antifungal activity against F. pseudograminearum strains in agar-plate competition and seedling assays. In the glasshouse pot trial, plants treated with seed coatings of either MH71 or MH243 had > 24% lower disease severity than control plants infected with F. pseudograminearum. These two cultures show potential for development as biocontrol products because they are easy to culture, grow on relatively inexpensive media, produce highly durable spores and can be delivered to plants as a seed coat.

First report of Fusarium commune causing root and crown rot on maize in Italy

Maize (Zea mays L.) is a cereal crop of great economic importance in Italy; production is currently of 62,587,469 t, with an area that covers 628,801 ha, concentrated in northern Italy (ISTAT 2020). Fusarium species are associated with root and crown rot causing failures in crop establishment under high soil moisture. In 2019 maize seedlings collected in a farm located in San Zenone degli Ezzelini (VI, Italy) showed root and crown rot symptoms with browning of the stem tissues, wilting of the seedling, and collapsing due to the rotting tissues at the base of the stem. The incidence of diseased plants was approximately 15%. Seedlings were cleaned thoroughly from soil residues under tap water. Portions (about 3-5 mm) of tissue from roots and crowns of the diseased plants were cut and surface disinfected with a water solution of NaClO at 0.5% for 2 minutes and rinsed in sterile H20. The tissue fragments were plated on Potato Dextrose Agar (PDA) amended with 50 mg/l of streptomycin sulfate and incubated for 48-72 hours at 25oC. Over the 80 tissue fragments plated, 5% were identified as Fusarium verticillioides, 60% as Fusarium spp., 35% developed saprophytes. Fusarium spp. isolates that showed morphological characteristics not belonging to known pathogenic species on maize were selected and used for further investigation while species belonging to F. oxysporum were discarded. Single conidia of the Fusarium spp. colonies were cultured on PDA and Carnation Leaf Agar (CLA) for pathogenicity tests, morphological and molecular identification. The colonies showed white to pink, abundant, densely floccose to fluffy aerial mycelium. Colony reverse showed light violet pigmentation, in rings on PDA. On CLA the isolates produced slightly curved macronidia with 3 septa 28.1 - 65.5 µm long and 2.8-6.3 µm wide (n=50). Microconidia were cylindrical, aseptate, 4.5 -14.0 µm long and 1.5-3.9 µm wide (n=50). Spherical clamydospores were 8.8 ± 2.5 µm size (n=30), produced singly or in pairs on the mycelium, according to the description by Skovgaard et al. (2003) for F. commune. The identity of two single-conidia strains was confirmed by sequence comparison of the translation elongation factor-1α (tef-1α), and RNA polymerase II subunit (rpb2) gene fragments (O'Donnell et al. 2010). BLASTn searches of GenBank, and Fusarium-ID database, using the partial tef-1α (MW419921, MW419922) and rpb2 (MW419923, MW419924) sequences of representative isolate DB19lug07 and DB19lug20, revealed 99% identity for tef-1α and 100% identity to F. commune NRRL 28387(AF246832, AF250560). Pathogenicity tests were carried out by suspending conidia from a 10-days old culture on PDA in sterile H2O to 5×104 CFU/ml. Fifty seeds were immersed in 50 ml of the conidial suspension of each isolate for 24 hours and in sterile water (Koch et al. 2020). The seeds were drained, dried at room temperature, and sown in trays filled with a steamed mix of white peat and perlite, 80:20 v/v, and maintained at 25°C and RH of 80-85% for 14 days with 12 hours photoperiod. Seedlings were extracted from the substrate, washed under tap water, and observed for the presence of root and crown rots like the symptoms observed on the seedlings collected in the field. Control seedlings were healthy and F. commune was reisolated from the symptomatic ones and identified by resequencing of tef-1α gene. F. commune has been already reported on maize (Xi et al. 2019) and other plant species, like soybean (Ellis et al. 2013), sugarcane (Wang et al. 2018), potato (Osawa et al. 2020), indicating that some attention must be paid in crop rotation and residue management strategies. To our knowledge this is the first report of F. commune as a pathogen of maize in Italy. References Ellis M L et al. 2013. Plant Disease, 97, doi: 10.1094/PDIS-07-12-0644-PDN. ISTAT. 2020. http://dati.istat.it/Index.aspx?QueryId=33702. Accessed December 28, 2020. Koch, E. et al. 2020. Journal of Plant Diseases and Protection. 127, 883-893 doi: 10.1007/s41348-020-00350-w O'Donnell K et al. 2010. J. Clin. Microbiol. 48:3708. https://doi.org/10.1128/JCM.00989-10 Osawa H et al. 2020. Journal of General Plant Pathology, doi.org/10.1007/s10327-020-00969-5. Skovgaard K 2003. Mycologia, 95:4, 630-636, DOI: 10.1080/15572536.2004.11833067. Wang J et al. 2018. Plant Disease, 102, doi/10.1094/PDIS-07-17-1011-PDN Xi K et al. 2019. Plant Disease, 103, doi/10.1094/PDIS-09-18-1674-PDN.

Evidence for the plant recruitment of beneficial microbes to suppress soil-borne pathogens

An emerging experimental framework suggests that plants under biotic stress may actively seek help from soil microbes, but empirical evidence underlying such a 'cry for help' strategy is limited. We used integrated microbial community profiling, pathogen and plant transcriptive gene quantification and culture-based methods to systematically investigate a three-way interaction between the wheat plant, wheat-associated microbiomes and Fusarium pseudograminearum (Fp). A clear enrichment of a dominant bacterium, Stenotrophomonas rhizophila (SR80), was observed in both the rhizosphere and root endosphere of Fp-infected wheat. SR80 reached 3.7 × 10⁷ cells g^-1 in the rhizosphere and accounted for up to 11.4% of the microbes in the root endosphere. Its abundance had a positive linear correlation with the pathogen load at base stems and expression of multiple defence genes in top leaves. Upon re-introduction in soils, SR80 enhanced plant growth, both the below-ground and above-ground, and induced strong disease resistance by boosting plant defence in the above-ground plant parts, but only when the pathogen was present. Together, the bacterium SR80 seems to have acted as an early warning system for plant defence. This work provides novel evidence for the potential protection of plants against pathogens by an enriched beneficial microbe via modulation of the plant immune system.

An Emerging Strawberry Fungal Disease Associated with Root Rot, Crown Rot and Leaf Spot Caused by Neopestalotiopsis rosae in Mexico

In the 2017 strawberry season, several transplant losses reaching 50% were observed in Zamora, Michoacán Valley, Mexico, due to a new fungal disease associated with root rot, crown rot, and leaf spot. In this year the disease appeared consistently and increased in the following seasons, becoming a concern among strawberry growers. Thus, the aim of this research was to determine the etiology of the disease and to determine the in vitro effect of fungicides on mycelial growth of the pathogen. Fungal isolates were obtained from symptomatic strawberry plants of the cultivars 'Albion' and 'Festival' and were processed to obtain monoconidial isolates. Detailed morphological analysis was conducted. Concatenated phylogenetic reconstruction was conducted by amplifying and sequencing the translation elongation factor 1 α, β-tubulin partial gene, and the internal transcribed spacer region of rDNA. Pathogenicity tests involving inoculation of leaves and crowns reproduced the same symptoms as those observed in the field, fulfilling Koch's postulates. Morphology and phylogenetic reconstruction indicated that the causal agent of the described symptoms was Neopestalotiopsis rosae, marking the first report anywhere in the world of this species infecting strawberry. N. rosae was sensitive to cyprodinil + fludioxonil, captan, iprodione, difenoconazole, and prochloraz.

Identification of New Sources of Resistance to Crown Rot and Fusarium Head Blight in Wheat

Crown rot (CR) and Fusarium head blight (FHB) are two serious wheat diseases caused by Fusarium pathogens in China. To identify new resistant sources for CR and FHB, 205 Chinese wheat cultivars collected from Huang-Huai wheat-growing region in China were screened for resistance. Cunmai633, LS4607, Pubing01, and Hongyun2 showed seedling resistance to CR with disease index (DI) less than 0.25. Sixteen cultivars showed adult-plant resistance to CR with DI lower than 0.10. Twenty-six cultivars showed moderate resistance to CR at seedling stage with DI from 0.26 to 0.35, and 63 cultivars showed moderate adult-plant resistance with DI from 0.11 to 0.20. Among them, Cunmai633, LS4607, Pubing01, Xinong916, Zhengda161, Xumai14017, Zhengpinmai30, Bainong8822, Jimai216, Huacheng865, Fengyumai5, and Tianmin319 showed resistance or moderate resistance to CR at both seedling and adult plant stages, with Cunmai633 showing the best resistance. Most of the cultivars (>76%) were susceptible to FHB in both the 2017 and 2018 experiments with DI > 0.40. However, some cultivars demonstrated excellent FHB resistance. For example, Zhongyu1526, Tianminxiaoyan369, and Yangao168 were resistant (DI ≤ 0.25) in 2017 and moderately resistant (0.26 ≤ DI ≤ 0.40) in 2018; Zhongwo9 was moderately resistant in 2017 (DI = 0.38) and resistant in 2018 (DI = 0.25). Eight cultivars (Cunmai608, Zhengmai162, Minfeng266, Junda159, LS4607, Deyan1603, Pumai1165, and Fengmai12) showed moderate FHB resistance with DI lower than 0.40 in both experiments. LS4607 showed moderate resistance to both diseases. The resistant cultivars identified in this study can be used for mapping the resistance genes and improving resistance to CR and/or FHB.

Macrophomina Crown and Root Rot of Pistachio in California

In this study, declining pistachio rootstocks were detected in newly planted commercial pistachio orchards in Kern County, California. Symptoms were characterized by wilted foliage combined with crown rot in the rootstock. From diseased trees, 42 isolates were obtained, and all had similar cultural and morphological characteristics of Macrophomina phaseolina. Analyses of nucleotide sequences of three gene fragments, the internal transcribed spacer region (ITS1-5.8S-ITS2), partial sequences of β-tubulin, and translation elongation factor 1-α (TEF1) confirmed this identification, and 20 representative isolates are presented in the phylogenetic study. Testing of Koch's postulates showed that M. phaseolina, when inoculated to stems and roots of the pistachio rootstocks using mycelial plugs or a microsclerotial suspension, is indeed pathogenic to this host. The widely used clonal University of California Berkeley I (UCBI) rootstock appeared highly susceptible to M. phaseolina, suggesting that this pathogen is an emerging threat to the production of pistachio in California. This study confirmed the association of M. phaseolina with the decline of pistachio trees and represents the first description of this fungus as a crown rot-causing agent of pistachio in California.

Trichoderma Counteracts the Challenge of Phytophthora nicotianae Infections on Tomato by Modulating Plant Defense Mechanisms and the Expression of Crinkler, Necrosis-Inducing Phytophthora Protein 1, and Cellulose-Binding Elicitor Lectin Pathogenic Effectors

Decoding the mechanisms of plant defense against plant pathogens in a scenario where antagonistic activity and the plant growth-promoting effects of useful organisms intervene simultaneously is a new frontier of plant pathology. Here, we demonstrated that (i) two selected strains of Trichoderma asperellum and Trichoderma atroviride promoted tomato (Solanum lycopersicum) growth and reduced the severity of disease caused by the oomycete Phytophthora nicotianae and (ii) the genetic patterns of the components of the experimental model system tomato-Trichoderma spp.-P. nicotianae were differentially expressed. The beneficial effects in both the promotion of the growth of host plant and the biological control of the pathogen by two selected strains of different Trichoderma species were tested both in planta and in vitro. In both respects, T. atroviride demonstrated to be more effective than T. asperellum. Additionally, the simultaneous transcriptional reprogramming of several plant defense-related genes, pathogen effectors, and mycoparasitism-related genes in tomato, P. nicotianae, and Trichoderma spp., respectively, was evaluated during the three-component interaction. Results support the hypothesis that Trichoderma spp. elicit the expression of plant defense-related genes. As expected, a mycoparasitism-related gene was significantly up-regulated in Trichoderma-colonizing tomato plants infected by P. nicotianae. Finally, a marked up-regulation of the genes encoding two necrosis-inducing effectors was observed in P. nicotianae infecting tomato plants colonized by Trichoderma. In conclusion, this study is a contribution toward understanding the genetic pathways related with the ability of Trichoderma spp. to counteract the challenge of P. nicotianae infections on tomato. Additionally, the experiments revealed the beneficial effects in the tomato growth promotion of a new T. atroviride strain and its good antagonistic effectiveness in the biological control of root and crown rot incited by P. nicotianae, confirming that Trichoderma spp. can be a powerful tool in integrated pest management strategies of Phytophthora diseases of horticultural crops.

Causing Crown Rot of Winter Wheat in Serbia

Investigations related with factors influencing root and crown rot are rare and mainly related to farming practice and soil management. The main objective of this study was to examine broader range of factors influencing stem-base infestation of winter wheat in the field conditions. The effect of spatial distribution of infected plants on disease index (DIs) assessments was also investigated. Analysis of factors influencing DIs of crown rot of wheat demonstrated significant influence of the growing seasons (P < 0.001) and extreme fluctuations in winter temperatures (P < 0.001). In addition to that, localities together with their interaction with the growing season also significantly influenced DIs (P < 0.001). Aggregation of infected plants influenced variability of DI estimations, and it was pointed out that more extensive investigation should be conducted on broad range of DI in order to establish sampling method giving uniform sampling precision. Fusarium graminearum was shown to be predominant Fusarium species in Serbia (72.6%) using sequence-characterized amplified region analysis. Interestingly F. oxysporum was isolated in higher frequencies (27.4%) than it was reported in the literature. Given that there were no reports on the diversity of Fusarium species causing crown rot of wheat in Serbia, this study presents first report on this important subject. It also indicated that more attention should be focused on combined effects of abiotic and biotic factors influencing stem-base infestation of winter wheat. This knowledge will contribute to better understanding of factors influencing root and crown rot of wheat which would ensure sustainable disease management in the future.

Differential Metabolic Reprogramming in Paenibacillus alvei-Primed Sorghum bicolor Seedlings in Response to Fusarium pseudograminearum Infection

Metabolic changes in sorghum seedlings in response to Paenibacillus alvei (NAS-6G6)-induced systemic resistance against Fusarium pseudograminearum crown rot were investigated by means of untargeted ultra-high performance liquid chromatography-high definition mass spectrometry (UHPLC-HDMS). Treatment of seedlings with the plant growth-promoting rhizobacterium P. alvei at a concentration of 1 × 108 colony forming units mL-1 prior to inoculation with F. pseudograminearum lowered crown rot disease severity significantly at the highest inoculum dose of 1 × 106 spores mL-1. Intracellular metabolites were subsequently methanol-extracted from treated and untreated sorghum roots, stems and leaves at 1, 4 and 7 days post inoculation (d.p.i.) with F. pseudograminearum. The extracts were analysed on an UHPLC-HDMS platform, and the data chemometrically processed to determine metabolic profiles and signatures related to priming and induced resistance. Significant treatment-related differences in primary and secondary metabolism post inoculation with F. pseudograminearum were observed between P. alvei-primed versus naïve S. bicolor seedlings. The differential metabolic reprogramming in primed plants comprised of a quicker and/or enhanced upregulation of amino acid-, phytohormone-, phenylpropanoid-, flavonoid- and lipid metabolites in response to inoculation with F. pseudograminearum.

Potential of UVC germicidal irradiation in suppressing crown rot disease, retaining postharvest quality and antioxidant capacity of Musa AAA "Berangan" during fruit ripening

Crown rot caused by fungal pathogen is the most prevalent postharvest disease in banana fruit that results significant economic losses during transportation, storage, and ripening period. Antifungal effects of ultraviolet C (UVC) irradiation at doses varied from 0.01 to 0.30 kJ m-2 were investigated in controlling postharvest crown rot disease, maintenance of fruit quality, and the effects on antioxidant capacity of Berangan banana fruit during ripening days at 25 ± 2°C and 85% RH. Fruits irradiated with 0.30 kJ m-2 exhibited the highest (i.e., 62.51%) reduction in disease severity. However, the application of UVC at all doses caused significant browning damages on fruit peel except the dose of 0.01 kJ m-2. This dose synergistically reduced 46.25% development of postharvest crown and did not give adverse effects on respiration rate, ethylene production, weight loss, firmness, color changes, soluble solids concentration, titratable acidity, and pH in banana as compared to the other treatments and control. Meanwhile, the dose also enhanced a significant higher level of total phenolic content, FRAP, and DPPH values than in control fruits indicating the beneficial impact of UVC in fruit nutritional quality. The results of scanning electron micrographs confirmed that UVC irradiation retarded the losses of wall compartments, thereby maintained the cell wall integrity in the crown tissue of banana fruit. The results suggest that using 0.01 kJ m-2 UVC irradiation dose as postharvest physical treatment, the crown rot disease has potential to be controlled effectively together with maintaining quality and antioxidant of banana fruit.

Degradation of the benzoxazolinone class of phytoalexins is important for virulence of Fusarium pseudograminearum towards wheat

Wheat, maize, rye and certain other agriculturally important species in the Poaceae family produce the benzoxazolinone class of phytoalexins on pest and pathogen attack. Benzoxazolinones can inhibit the growth of pathogens. However, certain fungi can actively detoxify these compounds. Despite this, a clear link between the ability to detoxify benzoxazolinones and pathogen virulence has not been shown. Here, through comparative genome analysis of several Fusarium species, we have identified a conserved genomic region around the FDB2 gene encoding an N-malonyltransferase enzyme known to be involved in benzoxazolinone degradation in the maize pathogen Fusarium verticillioides. Expression analyses demonstrated that a cluster of nine genes was responsive to exogenous benzoxazolinone in the important wheat pathogen Fusarium pseudograminearum. The analysis of independent F. pseudograminearum FDB2 knockouts and complementation of the knockout with FDB2 homologues from F. graminearum and F. verticillioides confirmed that the N-malonyltransferase enzyme encoded by this gene is central to the detoxification of benzoxazolinones, and that Fdb2 contributes quantitatively to virulence towards wheat in head blight inoculation assays. This contrasts with previous observations in F. verticillioides, where no effect of FDB2 mutations on pathogen virulence towards maize was observed. Overall, our results demonstrate that the detoxification of benzoxazolinones is a strategy adopted by wheat-infecting F. pseudograminearum to overcome host-derived chemical defences.

Predicting Cereal Root Disease in Western Australia Using Soil DNA and Environmental Parameters

Root diseases have long been prevalent in Australian grain-growing regions, and most management decisions to reduce the risk of yield loss need to be implemented before the crop is sown. The levels of pathogens that cause the major root diseases can be measured using DNA-based services such as PreDicta B. Although these pathogens are often studied individually, in the field they often occur as mixed populations and their combined effect on crop production is likely to vary across diverse cropping environments. A 3-year survey was conducted covering most cropping regions in Western Australia, utilizing PreDicta B to determine soilborne pathogen levels and visual assessments to score root health and incidence of individual crop root diseases caused by the major root pathogens, including Rhizoctonia solani (anastomosis group [AG]-8), Gaeumannomyces graminis var. tritici (take-all), Fusarium pseudograminearum, and Pratylenchus spp. (root-lesion nematodes) on wheat roots for 115, 50, and 94 fields during 2010, 2011, and 2012, respectively. A predictive model was developed for root health utilizing autumn and summer rainfall and soil temperature parameters. The model showed that pathogen DNA explained 16, 5, and 2% of the variation in root health whereas environmental parameters explained 22, 11, and 1% of the variation in 2010, 2011, and 2012, respectively. Results showed that R. solani AG-8 soil pathogen DNA, environmental soil temperature, and rainfall parameters explained most of the variation in the root health. This research shows that interactions between environment and pathogen levels before seeding can be utilized in predictive models to improve assessment of risk from root diseases to assist growers to plan more profitable cropping programs.

Changing fitness of a necrotrophic plant pathogen under increasing temperature

Warmer temperatures associated with climate change are expected to have a direct impact on plant pathogens, challenging crops and altering plant disease profiles in the future. In this study, we have investigated the effect of increasing temperature on the pathogenic fitness of Fusarium pseudograminearum, an important necrotrophic plant pathogen associated with crown rot disease of wheat in Australia. Eleven wheat lines with different levels of crown rot resistance were artificially inoculated with F. pseudograminearum and maintained at four diurnal temperatures 15/15°C, 20/15°C, 25/15°C and 28/15°C in a controlled glasshouse. To quantify the success of F. pseudograminearum three fitness measures, these being disease severity, pathogen biomass in stem base and flag leaf node, and deoxynivalenol (DON) in stem base and flag leaf node of mature plants were used. F. pseudograminearum showed superior overall fitness at 15/15°C, and this was reduced with increasing temperature. Pathogen fitness was significantly influenced by the level of crown rot resistance of wheat lines, but the influence of line declined with increasing temperature. Lines that exhibited superior crown rot resistance in the field were generally associated with reduced overall pathogen fitness. However, the relative performance of the wheat lines was dependent on the measure of pathogen fitness, and lines that were associated with one reduced measure of pathogen fitness did not always reduce another. There was a strong correlation between DON in stem base tissue and disease severity, but length of browning was not a good predictor of Fusarium biomass in the stem base. We report that a combination of host resistance and rising temperature will reduce pathogen fitness under increasing temperature, but further studies combining the effect of rising CO2 are essential for more realistic assessments.

Fusarium dactylidis sp. nov., a novel nivalenol toxin-producing species sister to F. pseudograminearum isolated from orchard grass (Dactylis glomerata) in Oregon and New Zealand

The B trichothecene toxin-producing clade (B clade) of Fusarium includes the etiological agents of Fusarium head blight, crown rot of wheat and barley and stem and ear rot of maize. B clade isolates also have been recovered from several wild and cultivated grasses, including Dactylis glomerata (orchard grass or cock's foot), one of the world's most important forage grasses. Two isolates from the latter host are formally described here as F. dactylidis. Phenotypically F. dactylidis most closely resembles F. ussurianum from the Russian Far East. Both species produce symmetrical sporodochial conidia that are similar in size and curved toward both ends. However, conidia of F. ussurianum typically end in a narrow apical beak while the apical cell of F. dactylidis is acute. Fusarium dactylidis produced nivalenol mycotoxin in planta as well as low but detectable amounts of the estrogenic mycotoxin zearalenone in vitro. Results of a pathogenicity test revealed that F. dactylidis induced mild head blight on wheat.

Effects of Phosphonate and Mefenoxam Treatments on Development of Perennial Cankers Caused by Two Phytophthora spp. on Almond

Orchard experiments were conducted to evaluate chemical treatments for management of perennial cankers caused by Phytophthora cactorum and P. citricola on almond (Prunus dulcis) in the San Joaquin Valley of California. Single preventive foliar sprays with phosphonate were tested by wounding and inoculating tree trunks and branches with either pathogen at time intervals from 15 days to 5 months after spraying. One to 3 months after inoculation, resulting cankers were measured. Preventive foliar sprays with phosphonate in the fall or spring suppressed development of cankers for up to 5 months after treatment; mean canker lengths on the trees sprayed with phosphonate before inoculation were 22 to 98% smaller than those on trees that received no phosphonate. In subsequent tests, preventive chemigation with phosphonate in spring or summer also inhibited canker expansion. A curative topical treatment with either fosetyl-Al or mefenoxam on cankers caused by P. cactorum or P. citricola reduced canker expansion by 36 to 88%. Neither preventive nor therapeutic treatments eradicated the pathogens from the diseased tissues, but disease ratings made 1 year after the treatments indicated extended disease suppression. Phosphonate and mefenoxam treatments can effectively manage almond scion cankers caused by P. cactorum or P. citricola.

Influence of Late Season Harvesting, Fall Grazing, and Fungicide Treatment on Verticillium Wilt Incidence, Plant Density, and Forage Yield of Alfalfa

Studies were conducted in the presence of Verticillium wilt (Verticillium albo-atrum) to determine the effect of fall harvesting and grazing over time on plant stand and forage yield of alfalfa (Medicago sativa). Resistant and susceptible cultivars were tested on established and newly seeded fields. In the fall (experiments 1 and 2), cultivars were either: (i) cut (third time); (ii) grazed; (iii) cut and grazed; or (iv) left uncut and ungrazed. Although Verticillium was present, test sites for experiments 2 and 3 were sprayed with a spore suspension of V. albo-atrum immediately following the first cutting of each experiment to standardize disease pressure. In experiment 1, the moderately resistant cultivar Apollo II, harvested twice without a late third cutting or fall grazing, produced the highest forage yield the following year. Fall grazing reduced subsequent yields in both the 2- and 3-cut treatments. In experiment 2, a third cutting decreased plant density and forage yield in both resistant and susceptible cultivars, while grazing had no effect. Neither fall treatment affected incidence of Verticillium wilt. In experiment 3, application of the fungicide benomyl to plant stubble following each harvest decreased Verticillium wilt in Apollo but not in Arrow. Overall, with the resistant cultivar Arrow, harvesting twice annually and grazing after a killing frost in lieu of late fall cutting slowed disease development, prolonged stand life, and maximized forage yield and quality.

Evaluation of Resistance of Winter Wheat to Fusarium acuminatum by Inoculation of Seedling Roots with Single, Germinated Macroconidia

Fusarium acuminatum is one of the causal agents of dryland root rot of winter wheat in Colorado. The effect of F. acuminatum seedling root infection, recorded at heading, on winter wheat cultivars Sandy and CO84 was investigated in the greenhouse. Winter wheat seeds were surface disinfested, germinated, and vernalized. Vernalized seedling roots were inoculated by placing a single, germinated macroconidium of F. acuminatum on the largest root. Inoculated and non-inoculated vernalized seedlings were transplanted to pots and half the plants subjected to water stress. Inoculated plants had significantly lower survival rates and, at maturity, lower relative leaf water content, fewer tillers, shorter plant height, and higher cell ion leakage than non-inoculated plants. Wheat cultivars differed significantly for most traits studied. CO84 was susceptible whereas Sandy was more tolerant of the pathogen, particularly under water stress conditions. These results suggest that relative leaf water content, cell ion leakage, and to some extent seedling survival may be useful attributes for evaluation of resistance to the root rot pathogen.