Fusarium spp. associated with rice Bakanae: ecology, genetic diversity, pathogenicity and toxigenicity

A diverse Fusarium community is responsible for contamination of rice with a variety of Fusarium toxins

Rice plays an important role in the daily diet in China and therefore its quality and safety have been of great concern. However, few systematic studies have investigated Fusarium community and toxins in rice grains. Here, we collected 1381 rice samples from Jiangsu Province in eastern China and found a higher frequency of zearalenone (ZEN), deoxynivalenol (DON), fumonisins (FBs), and beauvericin (BEA). The positive samples were individually contaminated with a minimum of one and a maximum of ten toxins. Fusarium was isolated and identified as the major fungus, which exhibited temporal and geographical distribution. The most prevalent species complexes within this genus were Fusarium incarnatum-equiseti species complex (FIESC), Fusarium fujikuroi species complex (FFSC), and Fusarium sambucinum species complex (FSAMSC). Nevertheless, the amplicon sequence analysis revealed a low relative abundance of Fusarium in the rice panicles, and the fungal community exhibited an irregular change along with the symptom's emergence. In vitro toxigenic profiles of Fusarium strains showed significant complexity and specificity depending on the type and content. FIESC strains were non-pathogenic to wheat heads and weakly pathogenic to maize ears, respectively, accumulating lower amounts of toxins than F. asiaticum and F. fujikuroi. There was no significant variation in the ability to cause panicle blight in rice among the various species tested. Our study provides detailed information about the contamination of Fusarium toxins and community in rice after harvest. This information is valuable for understanding the relationship between Fusarium and rice and for developing effective control strategies.

Early surveillance of rice bakanae disease using deep learning and hyperspectral imaging

Bakanae disease, caused by Fusarium fujikuroi, poses a significant threat to rice production and has been observed in most rice-growing regions. The disease symptoms caused by different pathogens may vary, including elongated and weak stems, slender and yellow leaves, and dwarfism, as example. Bakanae disease is likely to cause necrosis of diseased seedlings, and it may cause a large area of infection in the field through the transmission of conidia. Therefore, early disease surveillance plays a crucial role in securing rice production. Traditional monitoring methods are both time-consuming and labor-intensive and cannot be broadly applied. In this study, a combination of hyperspectral imaging technology and deep learning algorithms were used to achieve in situ detection of rice seedlings infected with bakanae disease. Phenotypic data were obtained on the 9th, 15th, and 21st day after rice infection to explore the physiological and biochemical performance, which helps to deepen the research on the disease mechanism. Hyperspectral data were obtained over these same periods of infection, and a deep learning model, named Rice Bakanae Disease-Visual Geometry Group (RBD-VGG), was established by leveraging hyperspectral imaging technology and deep learning algorithms. Based on this model, an average accuracy of 92.2% was achieved on the 21st day of infection. It also achieved an accuracy of 79.4% as early as the 9th day. Universal characteristic wavelengths were extracted to increase the feasibility of using portable spectral equipment for field surveillance. Collectively, the model offers an efficient and non-destructive surveillance methodology for monitoring bakanae disease, thereby providing an efficient avenue for disease prevention and control.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42994-024-00169-1.

Ultrasensitive and on-site diagnosis of rice bakanae disease based on CRISPR-LbCas12a coupled with LAMP

BACKGROUND

Rice bakanae disease (RBD) has longstanding challenges impacted rice production, which is predominantly induced by Fusarium fujikuroi Nirenberg. Early diagnosis of F. fujikuroi is important to control RBD and improve quality and quantity of rice production. This study presents a novel on-site diagnosis platform combined with CRISPR/LbCas12a and LAMP to detect F. fujikuroi.

RESULTS

LAMP amplification of TEF1-α, a characteristic gene of F. fujikuroi were performed, followed with trans-cleavage reaction of LbCas12a, cleaving the single-stranded DNA reporter, which is modified by the terminal fluorophore and quencher groups, producing fluorescence signal. The platform was confirmed with high specificity and sensitivity (LOD <1 aM). Furthermore, we designed a lateral flow strip experiment based on the trans-cleavage activity of LbCas12a, which was identified with similar sensitivity and specificity to the fluorescence detection method.

CONCLUSION

In summary, this study achieved a platform with remarkable sensitivity and specificity for F. fujikuroi detection and provide potential for on-site and ultrasensitive diagnostic tools for RBD. © 2024 Society of Chemical Industry.

Bioprocess of Gibberellic Acid by Fusarium fujikuroi: The Challenge of Regulation, Raw Materials, and Product Yields

Gibberellic acid (GA3) is a tetracyclic diterpenoid carboxylic acid synthesized by the secondary metabolism of Fusarium fujikuroi. This phytohormone is widely studied due to the advantages it offers as a plant growth regulator, such as growth stimulation, senescence delay, flowering induction, increased fruit size, and defense against abiotic or biotic stress, which improve the quality and yield of crops. Therefore, GA3 has been considered as an innovative strategy to improve agricultural production. However, the yields obtained at large scale are insufficient for the current market demand. This low productivity is attributed to the lack of adequate parameters to optimize the fermentation process, as well as the complexity of its regulation. Therefore, this article describes the latest advances for potentializing the GA3 production process, including an analysis of its origins from crops, the benefits of its application, the related biosynthetic metabolism, the maximum yields achieved from production processes, and their association with genetic engineering techniques for GA3 producers. This work provides a new perspective on the critical points of the production process, in order to overcome the limits surrounding this modern line of bioengineering.

Development and application of a novel suspension concentrate for seed coating of rice for controlling bakanae disease and seedling rot disease

The main rice planting areas in the middle and lower reaches of the Yangtze River are primarily affected by two types of rice seedling diseases: bakanae disease and seedling rot disease. These diseases lead to considerable losses. Seed coating technology effectively protects rice from these diseases and mitigates environmental pollution. We determined the antifungal activity of six fungicides, including phenamacril, azoxystrobin, fludioxonil, metconazole, thifluzamide and prothioconazole against Fusarium moniliforme Sheldon and Curvularia lunata in this study. In addition, the impact of fungicides and surfactants on rice seed germination were determined. Furthermore, phenamacril and fludioxonil were selected as the active components of suspension concentrate for seed coating. The antifungal activity of phenamacril against F. moniliforme Sheldon was 0.139 mg/L and fludioxonil against C. lunata was 0.110 mg/L. PEG-2000 was selected as the surfactant due to its promoting effect on rice seedling. Based on the above findings, 6% phenamacril fludioxonil FS was developed via the wet sand grinding method. The toxicity of 6% phenamacril fludioxonil FS to zebrafish was verified, and field experiments were conducted in five different regions of the Yangtze River Basin. The results indicated minimal toxicity of 6% phenamacril fludioxonil FS to zebrafish. Relative to the control agent consisting of 6.25% phenamacril metalaxyl-M FS, 6% phenamacril fludioxonil FS showed better control effect and exhibited superior efficacy in promoting growth and increasing yield in all five regions. Specifically, the control effect of 6% phenamacril fludioxonil FS on bakanae exceeded 84.83% with the highest yield increasing value recorded at 30.48%. Currently, the market offers a limited selection of suspension concentrate for seed coating of rice. The findings of this study may offer a viable alternative formulation and directions for further research concerning the application of suspension concentrate for seed coating of rice.

Map-Based Cloning and Characterization of a Major QTL Gene, FfR1, Which Confers Resistance to Rice Bakanae Disease

Bakanae disease (BD), caused by the fungal pathogen Fusarium fujikuroi, is a serious threat to rice production worldwide. Breeding elite rice varieties resistant to BD requires the identification of resistance genes. Previously, we discovered a resistant quantitative trait locus (QTL), qFfR1, in a Korean japonica rice variety, Nampyeong. In this study, we fine-mapped qFfR1 with a Junam*4/Nampyeong BC3F3 population and delimited its location to a 37.1 kb region on chromosome 1. Complementation experiments with seven candidate genes in this region revealed that OsI_02728 is the gene for qFfR1. This gene encodes a protein with a typical leucine-rich repeat (LRR) receptor-like protein structure. RNA-sequencing-based transcriptomic analysis revealed that FfR1 induces the transcription of defense genes, including lignin and terpenoid biosynthesis genes, pathogenesis-related genes, and thionin genes. These results may facilitate investigations into the molecular mechanisms underlying BD resistance, including molecular patterns of Fusarium fujikuroi interacting with FfR1 and players working in signal transduction pathways downstream of FfR1, and the breeding of new BD-resistant varieties by providing a BD resistance gene with its precise selection marker. This will contribute to efficient control of BD, which is becoming more prevalent according to temperature rises due to climate change.

Rapid and accurate identification of bakanae pathogens carried by rice seeds based on hyperspectral imaging and deep transfer learning

Bakanae disease is a common seed-borne disease of rice. Rapid and accurate detection of bakanae pathogens carried by rice seeds is essential for the health of rice germplasm resources and the safety of rice production. This study aims to propose a general framework for species identification of major bakanae pathogens carried by rice seeds based on hyperspectral imaging and deep transfer learning. Seven varieties of rice seeds and four kinds of bakanae pathogens were analyzed. One-dimensional deep convolution neural networks (DCNNs) were first constructed using complete datasets. They achieved accuracies larger than 96.5% on the testing sets of most datasets, exceeding the conventional SVM and PLS-DA models. Then the developed DCNNs were transferred to detect other complete training sets. Most of the deep transferred models achieved comparable or even better performance than the original DCNNs. Two smaller target training sets were further constructed by randomly selecting spectra from the complete training sets. As the size of the target training sets reduced, the accuracies of all models on the corresponding testing sets also decreased gradually. Visualization analysis were conducted using the t-distribution stochastic neighbor embedding (t-SNE) algorithm and a proposed gradient-weighted activation wavelength (Grad-AW) method. They all showed that deep transfer learning could utilize the representation patterns in the source datasets to improve the target tasks. The overall results indicated that the bakanae pathogens were all identified accurately under our proposed framework. Hyperspectral imaging combined with deep transfer learning provided a new idea for the quality detection of large-scale seeds in modern seed industry.

Ashikuzzaman, Md. Shamim Reja, Rahman MM, Khaton A, Tang MAK, Rahman MS, Hossain Md. Faruquee, Lee SJ, Rahman AM. Optimization of green silver nanoparticles as nanofungicides for management of rice bakanae disease

Rice bakanae, a devastating seed-borne disease caused by Fusarium species requires a more attractive and eco-friendly management strategy. The optimization of plant-mediated silver nanoparticles (AgNPs) as nanofungicides by targeting Fusarium species may be a rational approach. In this study, Azadirachta indica leaf aqueous extract-based AgNPs (AiLAE-AgNPs) were synthesized through the optimization of three reaction parameters: A. indica leaf amount, plant extract-to-AgNO3 ratio (reactant ratio), and incubation time. The optimized green AgNPs were characterized using ultraviolet-visible light (UV-Vis) spectroscopy, field emission scanning electron microscopy (FESEM) with energy dispersive X-ray (EDX) spectroscopy, transmission electron microscopy (TEM), dynamic light scattering (DLS), and powder X-ray diffraction (XRD) techniques. The optimal conditions for producing spherical, unique, and diminutive-sized AgNPs ranging from 4 to 27 nm, with an average size of 15 nm, were 2 g AiLAE at a 1:19 ratio (extract-to-AgNO3) and incubated for 4 h. Fusarium isolates collected from infected soils and identified as F. fujikuroi (40) and F. proliferatum (58 and 65) by PCR were used for seed infestation. The AgNPs exhibited concentration-dependent mycelial growth inhibition with EC50 values ranging from 2.95 to 5.50 μg/mL. The AgNPs displayed exposure time-dependent seed disinfectant potential (complete CFU reduction in F. fujikuroi (40) and F. proliferatum (58) was observed at a concentration of 17.24 μg/mL). The optimized green AgNPs were non-toxic to germinating seeds, and completely cured bakanae under net-house conditions, suggesting their great nano-fungicidal potency for food security and sustainable agriculture.

Diversity and Pathogenicity of Fusarium Species Associated with Stalk and Crown Rot in Maize in Northern Italy

The genus Fusarium includes several agronomically important and toxin-producing species that are distributed worldwide and can cause a wide range of diseases. Crown and stalk rot and grain infections are among the most severe symptoms that Fusarium spp. can cause in maize. Disease development usually occurs during germination, but it may also affect the later phases of plant growth. The purpose of this study was to investigate the diversity and pathogenicity of 41 isolates recovered from symptomatic seedlings collected in Northern Italy and seeds of five different geographical origins in 2019 and 2020. The pathogenicity was tested and confirmed in 23 isolates causing rotting in maize seedlings, with disease indexes from 20% to 90%. A multilocus phylogeny analysis based on four genomic loci (tef1-α, rpb2, calm and tub2) was performed on 23 representative isolates. Representative isolates were identified as species belonging to three species complexes (SC), including Fusarium verticillioides and F. annulatum in the F. fujikuroi SC. Fusarium commune was identified in the F. nisikadoi SC, and three different lineages were found in the Fusarium oxysporum SC. This study reports F. annulatum and two lineages of the Fusarium oxysporum SC as maize pathogens for the first time in Italy.

G, Bashyal BM, Bhowmick PK, Vinod KK, Bollinedi H, Singh NK, Singh AK. Fine mapping of qBK1.2, a major QTL governing resistance to bakanae disease in rice

Bakanae disease caused by Fusarium fujikuroi is an emerging disease of rice causing losses in all rice-growing regions around the world. A BC2F2 population was developed by backcrossing the recurrent parent Pusa Basmati 1121 (PB1121) with the recombinant inbred line RIL28, which harbors a major quantitative trait locus (QTL) governing resistance to bakanae, qBK1.2. MassARRAY-based single-nucleotide polymorphism (SNP) assays targeting the genomic region of qBK1.2 helped in fine mapping the QTL to a region of 130 kb between the SNP markers rs3164311 and rs3295562 using 24 recombinants. In-silico mining of the fine-mapped region identified 11 putative candidate genes with functions related to defense. The expression analysis identified two significantly differentially expressed genes, that is, LOC_Os01g06750 and LOC_Os01g06870, between the susceptible genotype PB1121 and the resistant genotypes Pusa1342 and R-NIL4. Furthermore, the SNPs identified in LOC_Os01g06750 produced minor substitutions of amino acids with no major effect on the resistance-related functional motifs. However, LOC_Os01g06870 had 21 amino acid substitutions, which led to the creation of the leucine-rich repeat (LRR) domain in the resistant genotype Pusa1342, thereby making it a potential candidate underlying the major bakanae-resistant QTL qBK1.2. The markers used in the fine mapping program are of immense utility in marker-assisted breeding for bakanae resistance in rice.

Current Studies on Bakanae Disease in Rice: Host Range, Molecular Identification, and Disease Management

The seed borne disease such as bakanae is difficult to control. Crop yield loss caused by bakanae depending on the regions and varieties grown, ranging from 3.0% to 95.4%. Bakanae is an important disease of rice worldwide and the pathogen was identified as Fusarium fujikuroi Nirenberg (teleomorph: Gibberella fujikuroi Sawada). Currently, four Fusaria (F. fujikuroi, F. proliferatum, F. verticillioides and F. andiyazi) belonging to F. fujikuroi species complex are generally known as the pathogens of bakanae. The infection occurs through both seed and soil-borne transmission. When infection occurs during the heading stage, rice seeds become contaminated. Molecular detection of pathogens of bakanae is important because identification based on morphological and biological characters could lead to incorrect species designation and time-consuming. Seed disinfection has been studied for a long time in Korea for the management of the bakanae disease of rice. As seed disinfectants have been studied to control bakanae, resistance studies to chemicals have been also conducted. Presently biological control and resistant varieties are not widely used. The detection of this pathogen is critical for seed certification and for preventing field infections. In South Korea, bakanae is designated as a regulated pathogen. To provide highly qualified rice seeds to farms, Korea Seed & Variety Service (KSVS) has been producing and distributing certified rice seeds for producing healthy rice in fields. Therefore, the objective of the study is to summarize the recent progress in molecular identification, fungicide resistance, and the management strategy of bakanae.

Integrated transcriptome and metabolome analysis unveil the response mechanism in wild rice (Zizania latifolia griseb.) against sheath rot infection

Sheath rot disease (SRD) is one of the most devastating diseases of Manchurian wild rice (MWR) (Zizania latifolia Griseb). Pilot experiments in our laboratory have shown that an MWR cultivar "Zhejiao NO.7"exhibits signs of SRD tolerance. To explore the responses of Zhejiao No. 7 to SRD infection, we used a combined transcriptome and metabolome analysis approach. A total of 136 differentially accumulated metabolites (DAMs, 114 up- and 22 down-accumulated in FA compared to CK) were detected. These up-accumulated metabolites were enriched in tryptophan metabolism, amino acid biosynthesis, flavonoids, and phytohormone signaling. Transcriptome sequencing results showed the differential expression of 11,280 genes (DEGs, 5,933 up-, and 5,347 downregulated in FA compared to CK). The genes expressed in tryptophan metabolism, amino acid biosynthesis, phytohormone biosynthesis and signaling, and reactive oxygen species homeostasis confirmed the metabolite results. In addition, genes related to the cell wall, carbohydrate metabolism, and plant-pathogen interaction (especially hypersensitive response) showed changes in expression in response to SRD infection. These results provide a basis for understanding the response mechanisms in MWR to FA attack that can be used for breeding SRD-tolerant MWR.

Multiple Mutations in SDHB and SDHC2 Subunits Confer Resistance to the Succinate Dehydrogenase Inhibitor Cyclobutrifluram in Fusarium fujikuroi

Fusarium fujikuroi is one of the dominant phytopathogenic fungi causing rice bakanae disease worldwide. Cyclobutrifluram is a novel succinate dehydrogenase inhibitor (SDHI), which shows strong inhibitory activity against F. fujikuroi. The baseline sensitivity of 112 F. fujikuroi to cyclobutrifluram was determinated with a mean EC₅₀ value of 0.025 μg/mL. A total of 17 resistant mutants were obtained by fungicide adaptation and displayed equal or slightly weaker fitness than parental isolates, which suggests that the resistance risk of F. fujikuroi to cyclobutrifluram is medium. A positive cross-resistance was detected between cyclobutrifluram and fluopyram. The amino acid substitutions H248L/Y of FfSdhB and G80R or A83V of FfSdhC₂ conferred cyclobutrifluram resistance in F. fujikuroi, which was validated by molecular docking and protoplast transformation. The results indicate that the affinity between cyclobutrifluram and FfSdhs obviously decreased after point mutations, causing the resistance of F. fujikuroi.

Past and Future Epidemiological Perspectives and Integrated Management of Rice Bakanae in Korea

In the past, rice bakanae was considered an endemic disease that did not cause significant losses in Korea; however, the disease has recently become a serious threat due to climate change, changes in farming practices, and the emergence of fungicide-resistant strains. Since the bakanae outbreak in 2006, its incidence has gradually decreased due to the application of effective control measures such as hot water immersion methods and seed disinfectants. However, in 2013, a marked increase in bakanae incidence was observed, causing problems for rice farmers. Therefore, in this review, we present the potential risks from climate change based on an epidemiological understanding of the pathogen, host plant, and environment, which are the key elements influencing the incidence of bakanae. In addition, disease management options to reduce the disease pressure of bakanae below the economic threshold level are investigated, with a specific focus on resistant varieties, as well as chemical, biological, cultural, and physical control methods. Lastly, as more effective countermeasures to bakanae, we propose an integrated disease management option that combines different control methods, including advanced imaging technologies such as remote sensing. In this review, we revisit and examine bakanae, a traditional seed-borne fungal disease that has not gained considerable attention in the agricultural history of Korea. Based on the understanding of the present significance and anticipated risks of the disease, the findings of this study are expected to provide useful information for the establishment of an effective response strategy to bakanae in the era of climate change.

An explanation of the mystifying bakanae disease narrative for tomorrow's rice

Rice production is severely hampered by the bakanae disease (Fusarium fujikuroi), formerly recognized as Fusarium moniliforme. F. moniliforme was called the F. fujikuroi species complex (FFSC) because it was later discovered that it had some separate species. The FFSC's constituents are also well recognized for producing phytohormones, which include auxins, cytokinin, and gibberellins (GAs). The normal symptoms of bakanae disease in rice are exacerbated by GAs. The members of the FFSC are responsible for the production of fumonisin (FUM), fusarins, fusaric acid, moniliformin, and beauvericin. These are harmful to both human and animal health. This disease is common around the world and causes significant yield losses. Numerous secondary metabolites, including the plant hormone gibberellin, which causes classic bakanae symptoms, are produced by F. fujikuroi. The strategies for managing bakanae, including the utilization of host resistance, chemical compounds, biocontrol agents, natural goods, and physical approaches, have been reviewed in this study. Bakanae disease is still not entirely preventable, despite the adoption of many different tactics that have been used to manage it. The benefits and drawbacks of these diverse approaches are discussed by the authors. The mechanisms of action of the main fungicides as well as the strategies for resistance to them are outlined. The information compiled in this study will contribute to a better understanding of the bakanae disease and the development of a more effective management plan for it.

Transcriptomic analysis of bakanae disease resistant and susceptible rice genotypes in response to infection by Fusarium fujikuroi

BACKGROUND

Fusarium fujikuroi causing bakanae is one of the most significant pathogens of rice and much responsible for yield losses thereby emerging as a major risk to food security.

METHODS

In the present study transcriptomic analysis was conducted between two contrasting resistant (C101A51) and susceptible (Rasi) genotypes of rice with the combinations of C101A51 control (CC) vs. C101A51 inoculated (CI); Rasi control (RC) vs. Rasi inoculated (RI) and C101A51 inoculated (CI) vs. Rasi inoculated (RI).

RESULTS

In CC vs. CI commonly expressed genes were 12,764. Out of them 567 (4%) were significantly upregulated and 1399 (9%) genes were downregulated. For the RC vs. RI 14, 333 (79%) genes were commonly expressed. For CI vs. RI 13,662 (72%) genes were commonly expressed. Genes related to cysteine proteinase inhibitor 10, disease resistance protein TAO1-like, oleosin 16 kDa-like, pathogenesis-related protein (PR1), (PR4), BTB/POZ and MATH domain-containing protein 5-like, alpha-amylase isozyme were upregulated in resistant genotype C101A51. Whereas, genes related to GDSL esterase/lipase, serine glyoxylate aminotransferase, CASP-like protein 2C1, WAT1-related protein, Cytoplasmic linker associated proteins, xyloglucan endotransglucosylase/hydrolase protein and β-D xylosidase 7 were upregulated in susceptible genotype Rasi. Gene ontology analysis showed functions related to defence response (GO:0006952), regulation of plant hypersensitive type response (GO:0010363), Potassium ion transmembrane activity (GO:0015079), chloroplast (GO:0009507), response to wounding (GO:0009611), xylan biosynthetic process (GO:0045492) were upregulated in resistant genotype C101A51 under inoculated conditions.

CONCLUSION

Real time PCR based validation of the selected DEGs showed that the qRT-PCR was consistent with the RNA-Seq results. This is the first transcriptomic study against bakanae disease of rice in Indian genotypes. Further, functional studies on identified genes and their utilization through different methodology will be helpful for the development of bakanae disease management strategies.

Identification of Fusarium andiyazi Associated with the Bakanae Disease of Rice in Turkey

Rice is an important nutrient staple for much of the Turkish population. In this study, field surveys were carried out to collect isolates of Fusarium andiyazi, a member of the Fusarium fujikuroi species complex (FFSC) associated with Bakanae disease. As part of the study, morphological and microscopic features of Fusarium andiyazi isolates recovered from infected rice plants were determined. The molecular detection of F. andiyazi was carried out through PCR analysis of partial translation elongation factor 1-alpha (TEF-1α) gene and the internal transcribed spacer (ITS) region. Gib2 and Fgc primers were used for specific detection of strain of FFSC. In the phylogenetic analysis, using the sequences of the partial TEF-1α gene, F. andiyazi were clustered in the same branch with the reference isolates. The pathogenicity tests revealed that the isolates of F. andiyazi were pathogen on susceptible Baldo cultivar under room climate conditions. The disease severity ranged from 3.27% to 86.30%. The pathogen causes typical disease symptoms associated with Bakanae and mostly inhibited seed germination, while most of the isolates caused abnormal elongation compared to the control plants. This is the first report of presence of F. andiyazi causing Bakanae disease on rice in Turkey.

In Vitro Determination of Sensitivity of Fusarium fujikuroi to Fungicide Azoxystrobin and Investigation of Resistance Mechanism

Rice bakanae disease (RBD) caused by Fusarium fujikuroi is a widespread and destructive disease of rice. It is urgent to introduce a new class of fungicide to manage the fungicidal resistance problem and effectively control the disease. Azoxystrobin (AZO) is an active fungicide with a broad antifungal spectrum, while its activity against F. fujikuroi is not well investigated. In this study, the baseline sensitivity of F. fujikuroi to AZO was established by testing the sensitivity of 100 isolates, collected from Anhui Province of China. The mechanism of resistance to AZO was also investigated. AZO exhibited a strong activity against the 100 F. fujikuroi isolates with EC₅₀ values of 0.822 ± 0.285 and 0.762 ± 0.283 μg/mL for mycelial growth and conidial germination, respectively, and both of the baseline sensitivity curves were validated as unimodal curves. To investigate the resistance mechanism, six mutants with resistance factor (RF) values >50 were generated from wild-type sensitive strains through UV mutagenesis, and sequence analysis showed that mutation G143A in cyt b conferred the resistance to AZO. Mycelial growth, conidia production, pathogenicity, and ATP production were decreased in all six resistant mutants as compared to the parental strains, indicating the fitness penalties in this phenotype of resistance mutation. In addition, the cross-resistance assay showed that there was no cross-resistance between AZO and carbendazim, prochloraz, phenamacril, or pydiflumetofen. AZO can be an efficient candidate to control RBD in China with moderate to low fungal resistance risk, but continuous resistance monitoring should be performed during the application of this fungicide.

Genetic Diversity and Population Structure of Head Blight Disease Causing Fungus Fusarium graminearum in Northern Wheat Belt of India

Head blight or scab caused by Fusarium graminearum (FG), once ranked as a minor disease in wheat, is now emerging as one of the economically important diseases in India. The present study represents the first in-depth population genetic analysis of the FG from the northern wheat belt of India. In this study, multiple conserved gene sequences comprised of β-tubulin (TUB), translation elongation factor 1-α (TEF), and histone-3 (HIS) regions were used for multi-locus phylogenetic analysis of 123 geographically distinct F. graminearum isolates collected from four different states (Haryana (HR), Punjab (PB), Rajasthan (RJ) and West Bengal (WB)) of India. The phylogenetic and haplotype analysis showed the presence of thirty haplotypes in all the analyzed populations. The haplotypic diversity in the RJ population (Hd = 0.981) was higher than in the HR (Hd = 0.972), PB (Hd = 0.965) and WB population (Hd = 0.962). Recombination events (Rm = 12) and mutation events (485) were also detected. Analysis of molecular variance (AMOVA) indicated that genetic diversity was exclusively due to the differences within populations. The haplotype network was widely dispersed and not associated with specific populations, as a single common haplotype was not detected. The PB population contained both unique (H9, H10 and H11) and shared haplotypes (27 haplotypes) in a higher number in comparison to other geographical locations. Except for haplotype H22 (contains highly aggressive isolates), there was no specific linkage noticed between the isolate aggressiveness and haplotype. The concatenated sequences of all the three genes demonstrated a low level of genetic differentiation (Fst = −0.014 to 0.02) in the analyzed population. Positive values for the neutrality tests in PB, HR and RJ reveal a balancing selection mechanism behind the FG population structure. The WB population showed both positive and negative values of neutrality indices, indicating the role of both population expansion as well as balancing selection in structuring the FG population.

Preinoculation with Endophytic fungus Phomopsis liquidambaris reduced rice bakanae disease caused by Fusarium proliferatum via enhanced plant resistance

AIMS

This study evaluated the control effect of the endophytic fungus Phomopsis liquidambaris B3 against rice bakanae disease (RBD) caused by Fusarium proliferatum and the disease control result of different inoculation times of beneficial micro-organisms.

METHODS AND RESULTS

Rice seedlings preinoculated, coinoculated and noninoculated with B3 were exposed to F. proliferatum stress and grown under controlled conditions. Greenhouse experimental results showed that rice preinoculation with B3 significantly reduced rice bakanae disease by 21.45%, inhibited the colonization of F. proliferatum, increased defence-related enzyme activities, upregulated the expression of defence genes and promoted plant photosynthesis. However, bakanae disease in rice coinoculation with B3 increased by 11.45%, resulted in excessive reactive oxygen species (ROS) bursts and plant cell death.

CONCLUSIONS

Preinoculation with the endophytic fungus P. liquidambaris B3 significantly reduced rice bakanae disease by triggering the SA-dependent defence pathways of plants, and promoted plant growth. However, coinoculatiton with P. liquidambaris B3 activated excessive defence responses, resulting in plants cell death and aggravation of bakanae disease.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study indicated that P. liquidambaris B3 was an effective method for agricultural control against rice bakanae disease caused by F. proliferatum, and provides an experimental basis for the development of sustainable endophytic fungal resources to effectively control plant diseases caused by pathogenic fungi, and suggests that precise application of beneficial micro-organisms may be become a key factor in farmland crop disease management.

Diversity of Fusarium associated banana wilt in northern Viet Nam

Fusarium is one of the most important fungal genera of plant pathogens that affect the cultivation of a wide range of crops. Agricultural losses caused by Fusariumoxysporumf.sp.cubense (Foc) directly affect the income, subsistence, and nourishment of thousands of farmers worldwide. For Viet Nam, predictions on the impact of Foc for the future are dramatic, with an estimated loss in the banana production area of 8% within the next five years and up to 71% within the next 25 years. In the current study, we applied a combined morphological-molecular approach to assess the taxonomic identity and phylogenetic position of the different Foc isolates collected in northern Viet Nam. In addition, we aimed to estimate the proportion of the different Fusarium races infecting bananas in northern Viet Nam. The morphology of the isolates was investigated by growing the collected Fusarium isolates on four distinct nutritious media (PDA, SNA, CLA, and OMA). Molecular phylogenetic relationships were inferred by sequencing partial rpb1, rpb2, and tef1a genes and adding the obtained sequences into a phylogenetic framework. Molecular characterization shows that c. 74% of the Fusarium isolates obtained from infected banana pseudostem tissue belong to F.tardichlamydosporum. Compared to F.tardichlamydosporum, F.odoratissimum accounts for c.10% of the Fusarium wilt in northern Viet Nam, demonstrating that Foc TR4 is not yet a dominant strain in the region. Fusariumcugenangense – considered to cause Race 2 infections among bananas – is only found in c. 10% of the tissue material that was obtained from infected Vietnamese bananas. Additionally, one of the isolates cultured from diseased bananas was phylogenetically not positioned within the F.oxysporum species complex (FOSC), but in contrast, fell within the Fusariumfujikuroi species complex (FFSC). As a result, a possible new pathogen for bananas may have been found. Besides being present on several ABB ‘Tay banana’, F.tardichlamydosporum was also derived from infected tissue of a wild Musalutea, showing the importance of wild bananas as a possible sink for Foc.

Characterization of Prochloraz Resistance in Fusarium fujikuroi from Heilongjiang Province in China

Prochloraz is widely used to control rice bakanae disease caused by Fusarium fujikuroi. The current study was aimed at monitoring the development of F. fujikuroi resistance to prochloraz in the Heilongjiang Province and analyzing the fitness of F. fujikuroi strains with different resistance levels. The results indicated that most of the 89 F. fujikuroi strains collected from the Heilongjiang Province were resistant to prochloraz, with resistance frequency reaching 92.1%. To assess the field resistance risk of prochloraz, 21 F. fujikuroi strains with different resistance levels were selected to investigate their biological characteristics and assess their fitness. Mycelial growth, sporulation, and germination rates were significantly different among the tested strains. However, when grouped into two subpopulations, no significant difference was tested between prochloraz-resistant and prochloraz-sensitive strains. Pathogenicity assays revealed that the disease severity index of prochloraz-resistant strains was higher than that of prochloraz-sensitive strains. Cross-resistance assays showed no cross-resistance between prochloraz and five other fungicides, namely phenamacril, ipconazole, tebuconazole, carbendazim, and fluopyram. Ffcyp51A gene overexpression was observed in the prochloraz-resistant F. fujikuroi strains after exposure to prochloraz. Collectively, these results indicated that F. fujikuroi resistance against prochloraz was severe. Furthermore, prochloraz-resistant strains were highly fit and could potentially become a dominant population in rice fields, consequently resulting in yield loss.

Activity of a SDHI fungicide penflufen and the characterization of natural-resistance in Fusarium fujikuroi

The occurrence of bakanae disease of rice caused by the fungus Fusarium fujikuroi in Zhejiang Province has become increasingly aggravated in recent years, concomitant with the development of resistance to the widely applied fungicides, prochloraz and phenamacril. In this study, the activity of a novel succinate dehydrogenase inhibitor (SDHI) fungicide, penflufen, against different fungi was evaluated in addition to the potential of penflufen in controlling F. fujikuroi infections. Penflufen exhibited good bioactivity against F. fujikuroi, but weak activity against Fusarium spp. and other investigated plant-pathogenic fungi including Colletotrichum spp. In addition to inhibiting mycelial growth, penflufen effectively inhibited F. fujikuroi conidium production. For germination, penflufen could effectively inhibit that of small conidia, but only delay the germination of large conidia. In addition, the sensitivity to penflufen among 100 F. fujikuroi isolates that were collected in areas that were never exposed to SDHIs was determined based on mycelium growth. Sensitivities surprisingly exhibited bimodal distributions, indicating the presence of natural resistance. Cross-resistance was not observed between penflufen in F. fujikuroi and two fungicides that have been extensively applied in field including prochloraz (a DMI) and phenamacril (a 2-cyanoacrylate fungicide), nor with the three SDHIs, fluopyram, benzovindiflupyr, and pydiflumetofen. Additional analysis identified five different point mutations in SDH-A (i.e., at residues 46, 225, 283, 430, and 586) of naturally resistant isolates. These results inform the potential application of the new SDHI fungicide penflufen for managing crop diseases and understanding possible resistance mechanisms among pathogens.

Identification and First Report of Fusarium andiyazi Causing Sheath Rot of Zizania latifolia in China

Zizania latifolia is a perennial plant native to East Asia. The swollen culm of Z. latifolia is a popular vegetable and traditional herbal medicine consumed in China and some other Asian countries. From 2019 to 2021, a sheath rot disease was found in Zhejiang Province of China. Symptoms mainly occurred in the leaf sheath showing as brown necrotic lesions surrounded by yellow halos. The pathogen fungal isolates were isolated from the affected sheaths. Ten representative isolates were selected for morphological and molecular identification by phylogenetic analyses of the translation elongation factor 1-α (TEF1) and the RNA polymerase II subunit beta (RPB2) gene regions. Based on the combined datasets, the fungal isolates were identified as Fusarium andiyazi. Koch’s postulates were confirmed by pathogenicity test, re-isolation and re-identification of the fungal isolates. To the best of our knowledge, this is the first report of sheath rot caused by F. andiyazi in Z. latifolia in China.

In Vitro Evaluation of the Inhibitory Activity of Different Selenium Chemical Forms on the Growth of a Fusarium proliferatum Strain Isolated from Rice Seedlings

In this study, the in vitro effects of different Se concentrations (5, 10, 15, 20, and 100 mg kg−1) from different Se forms (sodium selenite, sodium selenate, selenomethionine, and selenocystine) on the development of a Fusarium proliferatum strain isolated from rice were investigated. A concentration-dependent effect was detected. Se reduced fungal growth starting from 10 mg kg−1 and increasing the concentration (15, 20, and 100 mg kg−1) enhanced the inhibitory effect. Se bioactivity was also chemical form dependent. Selenocystine was found to be the most effective at the lowest concentration (5 mg kg−1). Complete growth inhibition was observed at 20 mg kg−1 of Se from selenite, selenomethionine, and selenocystine. Se speciation analysis revealed that fungus was able to change the Se speciation when the lowest Se concentration was applied. Scanning Electron Microscopy showed an alteration of the fungal morphology induced by Se. Considering that the inorganic forms have a higher solubility in water and are cheaper than organic forms, 20 mg kg−1 of Se from selenite can be suggested as the best combination suitable to inhibit F. proliferatum strain. The addition of low concentrations of Se from selenite to conventional fungicides may be a promising alternative approach for the control of Fusarium species.

Molecular phylogeny, pathogenic variability and phytohormone production of Fusarium species associated with bakanae disease of rice in temperate agro-ecosystems

Bakanae is the emerging disease threating the rice cultivation globally. Yield reduction of 4-70% is recorded in different parts of the world. A total of 119 Fusarium isolates were collected from rice plants at different geographical locations and seeds of different rice cultivars. The isolates were evaluated for morphological, biochemical and pathogenic diversity. The amplification of TEF-1α gene was carried out for exploring the species spectrum associated with the cultivated and pre-released rice varieties. The production of gibberellin varied from 0.53 to 2.26 µg/25 ml, while as that of Indole acetic acid varied from 0.60 to 3.15 µg/25 ml among the Fusarium isolates. The phylogenetic analysis identified 5 different species of the genus Fusarium viz. Fusarium fujikuroi, F. proliferatum, F. equiseti, F.oxysporum and F. persicinum after nucleotide blasting in NCBI. Only two Fusarium spp. F. fujikuroi and F. proliferatum were found to be pathogenic under virulence assays of the isolates. The isolates showed a considerable variation in morphological and pathogenic characters. The isolates were divided into different groups based on morphology and pathogenicity tests. The isolates showed a considerable variation in morphology, phytohormone profile and virulence indicative of population diversity. Three species F. equiseti, F.oxysporum and F. persicinum which have not been reported as pathogens of rice in India were found to be associated with bakanae disease of rice, however their pathogenicity could not be established.

The effects of different potato dextrose agar media on secondary metabolite production in Fusarium

Potatoes contain several nutrients essential for fungal growth, making them an excellent component of media such as the popular Potato Dextrose Agar (PDA) medium. Commercially, PDA is available from multiple retailers offering virtually the same product. These media, however, could contain small differences in composition of nutrients affecting the expression of secondary metabolites. This study aims to investigate the use of four PDA media from different manufacturers (Fluka, Oxoid, Sigma, and VWR) and their effect on the metabolite profile of four species of Fusarium (F. fujikuroi, F. graminearum, F. pseudograminearum and F. avenaceum). Secondary metabolites were analysed using HPLC-HRMS, from which statistically significant differences in intensities were observed for 9 out of 10 metabolites.

Mapping of a Major QTL, qBK1Z, for Bakanae Disease Resistance in Rice

Bakanae disease is a fungal disease of rice (Oryza sativa L.) caused by the pathogen Gibberella fujikuroi (also known as Fusarium fujikuroi). This study was carried out to identify novel quantitative trait loci (QTLs) from an indica variety Zenith. We performed a QTL mapping using 180 F_2:9 recombinant inbred lines (RILs) derived from a cross between the resistant variety, Zenith, and the susceptible variety, Ilpum. A primary QTL study using the genotypes and phenotypes of the RILs indicated that the locus qBK1^z conferring bakanae disease resistance from the Zenith was located in a 2.8 Mb region bordered by the two RM (Rice Microsatellite) markers, RM1331 and RM3530 on chromosome 1. The log of odds (LOD) score of qBK1^z was 13.43, accounting for 30.9% of the total phenotypic variation. A finer localization of qBK1^z was delimited at an approximate 730 kb interval in the physical map between Chr01_1435908 (1.43 Mbp) and RM10116 (2.16 Mbp). Introducing qBK1^z or pyramiding with other previously identified QTLs could provide effective genetic control of bakanae disease in rice.

Hormones as go-betweens in plant microbiome assembly

The interaction of plants with complex microbial communities is the result of co-evolution over millions of years and contributed to plant transition and adaptation to land. The ability of plants to be an essential part of complex and highly dynamic ecosystems is dependent on their interaction with diverse microbial communities. Plant microbiota can support, and even enable, the diverse functions of plants and are crucial in sustaining plant fitness under often rapidly changing environments. The composition and diversity of microbiota differs between plant and soil compartments. It indicates that microbial communities in these compartments are not static but are adjusted by the environment as well as inter-microbial and plant-microbe communication. Hormones take a crucial role in contributing to the assembly of plant microbiomes, and plants and microbes often employ the same hormones with completely different intentions. Here, the function of hormones as go-betweens between plants and microbes to influence the shape of plant microbial communities is discussed. The versatility of plant and microbe-derived hormones essentially contributes to the creation of habitats that are the origin of diversity and, thus, multifunctionality of plants, their microbiota and ultimately ecosystems.

Identification of Rice Seed-Derived Fusarium Spp. and Development of LAMP Assay against Fusarium Fujikuroi

Fusarium species are important seedborne pathogens that cause rice bakanae disease (RBD). In this study, 421 strains were isolated from 25 rice samples collected from Zhejiang, Anhui, and Jiangxi provinces of China. Furthermore, 407 isolates were identified as F. fujikuroi (80.05% isolation frequency), F. proliferatum (8.31%), F. equiseti (5.94%), F. incarnatum (2.61%), F. andiyazi (0.95%), and F. asiaticum (0.48%) based on morphology and translation elongation factor 1-alpha (TEF1-α) gene. Phylogenetic analysis of combined sequences of the RNA polymerase II largest subunit (RPB1), RNA polymerase II second largest subunit (RPB2), TEF1-α gene, and ribosomal DNA (rDNA) internal transcribed spacer (ITS) showed that 17 representative strains were attributed to six species. Pathogenicity tests showed that representative isolates possessed varying ability to cause symptoms of bakanae on rice seedlings. Moreover, the seed germination assay revealed that six isolates had different effects, such as inhibition of seed germination, as well as seed and bud rot. The loop mediated isothermal amplification (LAMP)-based assay were developed for the detection of F. fujikuroi. According to sequences of desaturase-coding gene promoter, a species-specific marker desM231 was developed for the detection of F. fujikuroi. The LAMP assay using seeds collected from field was validated, and diagnostics developed are efficient, rapid, and sensitive.

Auxin, Abscisic Acid and Jasmonate Are the Central Players in Rice Sheath Rot Caused by Sarocladium oryzae and Pseudomonas fuscovaginae

Sheath rot is an emerging rice disease that causes severe yield losses worldwide. The main causal agents are the toxin producers Sarocladium oryzae and Pseudomonas fuscovaginae. The fungus S. oryzae produces helvolic acid and cerulenin and the bacterium P. fuscovaginae produces cyclic lipopeptides. Helvolic acid and the lipopeptide, fuscopeptin, inhibit membrane-bound H⁺-ATPase pumps in the rice plant. To manage rice sheath rot, a better understanding of the host response and virulence strategies of the pathogens is required. This study investigated the interaction of the sheath rot pathogens with their host and the role of their toxins herein. Japonica rice was inoculated with high- and low-helvolic acid-producing S. oryzae isolates or with P. fuscovaginae wild type and fuscopeptin mutant strains. During infection, cerulenin, helvolic acid and the phytohormones abscisic acid, jasmonate, auxin and salicylic acid were quantified in the sheath. In addition, disease severity and grain yield parameters were assessed. Rice plants responded to high-toxin-producing S. oryzae and P. fuscovaginae strains with an increase in abscisic acid, jasmonate and auxin levels. We conclude that, for both pathogens, toxins play a core role during sheath rot infection. S. oryzae and P. fuscovaginae interact with their host in a similar way. This may explain why both sheath rot pathogens cause very similar symptoms despite their different nature.

Phytohormone production by the arbuscular mycorrhizal fungus Rhizophagus irregularis

Arbuscular mycorrhizal symbiosis is a mutualistic interaction between most land plants and fungi of the glomeromycotina subphylum. The initiation, development and regulation of this symbiosis involve numerous signalling events between and within the symbiotic partners. Among other signals, phytohormones are known to play important roles at various stages of the interaction. During presymbiotic steps, plant roots exude strigolactones which stimulate fungal spore germination and hyphal branching, and promote the initiation of symbiosis. At later stages, different plant hormone classes can act as positive or negative regulators of the interaction. Although the fungus is known to reciprocally emit regulatory signals, its potential contribution to the phytohormonal pool has received little attention, and has so far only been addressed by indirect assays. In this study, using mass spectrometry, we analyzed phytohormones released into the medium by germinated spores of the arbuscular mycorrhizal fungus Rhizophagus irregularis. We detected the presence of a cytokinin (isopentenyl adenosine) and an auxin (indole-acetic acid). In addition, we identified a gibberellin (gibberellin A₄) in spore extracts. We also used gas chromatography to show that R. irregularis produces ethylene from methionine and the α-keto γ-methylthio butyric acid pathway. These results highlight the possibility for AM fungi to use phytohormones to interact with their host plants, or to regulate their own development.

Fusarium fujikuroi Species Complex Associated With Rice, Maize, and Soybean From Jiangsu Province, China: Phylogenetic, Pathogenic, and Toxigenic Analysis

Species belonging to the Fusarium fujikuroi species complex (FFSC) are of vital importance and are a major concern for food quantity and quality worldwide, as they not only cause serious diseases in crops but also produce various mycotoxins. To characterize the population structure and evaluate the risk of poisonous secondary metabolites, a total of 237 candidate strains were isolated from rice, maize, and soybean samples in Jiangsu Province, China. Species identification of the individual strain was accomplished by sequencing the translation elongation factor 1α gene (TEF-1α) and the fumonisin (FB) synthetic gene (FUM1). The distribution of Fusarium species among the different crops was observed. The maize seeds were dominated by F. proliferatum (teleomorph, Gibberella intermedia) and F. verticillioides (teleomorph, G. moniliformis), whereas F. fujikuroi (teleomorph, G. fujikuroi) was the most frequently isolated species from rice and soybean samples. In addition, phylogenetic analyses of these strains were performed, and the results suggested clear groups showing no obvious relationship with the origin source. FFSC species pathogenicity and toxigenicity were studied. All of the species reduced the rice seed germination rate, with no significant differences. F. fujikuroi showed two distinct patterns of influencing the length of rice seedlings, which were correlated with FBs and gibberellic acid synthesis. FBs were mainly produced by F. verticillioides and F. proliferatum. F. proliferatum and F. fujikuroi also produced moniliformin and beauvericin. The toxigenicity of F. andiyazi (teleomorph, G. andiyazi) was extremely low. Further analysis indicated that the sequence variations in TEF-1α and the differences in the expression levels of the toxin synthesis genes were associated with the diversity of secondary metabolites in F. fujikuroi strains. These findings provide insight into the population-level characterization of the FFSC and might be helpful in the development of strategies for the management of diseases and mycotoxins.

Fusarium fujikuroi species complex in Brazilian rice: Unveiling increased phylogenetic diversity and toxigenic potential

Fusarium fujikuroi species complex (FFSC) species are commonly encountered infecting rice, but knowledge of the diversity and toxigenic potential of the species is lacking in Brazil, the largest rice-producing country outside Asia. One hundred FFSC isolates obtained from national rice were identified using morphology and phylogeny of TEF, CAL and TUB genes. Eight previously known and one novel Fusarium species were identified. Three species accounted for around 60% of the strains: F. fujikuroi (n = 23), F. proliferatum (n = 22) and F. verticillioides (n = 16). The less frequent species were F. volatile (n = 8), F. anthophilum (n = 6), F. pseudocircinatum (n = 4), F. sterilihyphosum (n = 2) and F. begoniae (n = 1). The novel Fusarium species was represented by 18 isolates. All species produced at least one of the analyzed mycotoxins [beauvericin (BEA), fumonisins (FBs), moniliformin (MON) and enniatins (ENNs)]. BEA was produced by all species but F. verticillioides. The FBs (mainly FB1) were produced mostly by F. fujikuroi, F. proliferatum and F. verticillioides. F. begoniae and F. verticillioides did not produce ENNs and F. sterilihyphosum and F. begoniae did not produce MON, while the other species produced MON and ENNs. Our results add new knowledge of the diversity, geographical distribution and host range of FFSC species.

A New Mutation Genotype of K218T in Myosin-5 Confers Resistance to Phenamacril in Rice Bakanae Disease in the Field

In 2017 and 2018, a total of 294 Fusarium fujikuroi isolates were collected from bakanae-diseased rice plants in Jinhua, Shaoxing, and Jiaxing in Zhejiang Province, China. Phenamacril sensitivity of these isolates was determined by the 50% effective concentration value or minimum inhibitory concentration methods. Our results indicated that the phenamacril resistance frequency of F. fujikuroi increased from 18% in 2017 to 47% in 2018, and rice plants infected with F. fujikuroi-resistant isolates could not be protected effectively with 50 mg/liter of phenamacril. Phenamacril-resistant F. fujikuroi isolates obtained from rice fields showed stable resistance, because their fitness levels (i.e., mycelial growth, sporulation, and pathogenicity) were similar to the phenamacril-sensitive isolates. In addition to the point mutation at codon 219 in the myosin-5 gene that conferred resistance to phenamacril, our results also showed another point mutation at codon 218 (AAG→ACG) in myosin-5 that also conferred resistance to phenamacril. In this study, we found rapid development and persistence of diversified genotypes of phenamacril resistance, highlighting the importance of proper use of phenamacril in rice fields. Our results may also help researchers develop new fungicides or new control strategies using combinations of different fungicides in the control of phenamacril-resistant F. fujikuroi isolates.

Occurrence of Fusarium mycotoxins and toxigenic Fusarium species in freshly harvested rice in Jiangsu, China

In 2017, 236 rice samples were collected from 42 counties in Jiangsu province, China, and analysed for Fusarium mycotoxins. Mycotoxin analyses showed that deoxynivalenol (DON), 3-acetyldeoxynivalenol (3-ADON), 15-acetyldeoxynivalenol (15-ADON), nivalenol (NIV), fusarenone X (FUS-X), zearalenone (ZEA), fumonisins (including FB1, FB2, and FB3), and beauvericin (BEA) were present in unhusked rice samples. Regional differences in mycotoxin contamination of unhusked rice were attributed to differences in precipitation during rice anthesis and agricultural practices among the three study regions. Importantly, the mean concentrations of DON, NIV, ZEA, and fumonisins in white rice were significantly lower than those in unhusked rice, and the relative proportion of the toxins in rice by-products exceeded 84%. Fusarium isolates were then obtained from the unhusked rice samples; Fusarium asiaticum was the most common, followed by Fusarium fujikuroi, Fusarium proliferatum, Fusarium verticillioides, and Fusarium commune. Genotype and chemical analyses of mycotoxins showed that most F. asiaticum isolates (71%) were 3-ADON chemotypes; the remainder were NIV producers. All of the F. proliferatum and F. verticillioides isolates, and most of the F. fujikuroi isolates produce fumonisins, and most of the three species coproduced BEA. The present study is the first to evaluate Fusarium mycotoxins and toxigenic Fusarium species from rice freshly harvested in Jiangsu province, China. The results of this study improve our understanding the population dynamics of Fusarium species in rice and the development of effective control measures.

Different Phenotypes, Similar Genomes: Three Newly Sequenced Fusarium fujikuroi Strains Induce Different Symptoms in Rice Depending on Temperature

Bakanae, caused by the hemibiotrophic fungus Fusarium fujikuroi, is one of the most important diseases of rice and is attributed to up to 75% of losses, depending on the strain and environmental conditions. Some strains cause elongation and thin leaves, whereas others induce stunting and chlorotic seedlings. Differences in symptoms are attributed to genetic differences in the strains. F. fujikuroi strains Augusto2, CSV1, and I1.3 were sequenced with Illumina MiSeq, and pathogenicity trials were conducted on rice cultivar Galileo, which is susceptible to bakanae. By performing gene prediction, single nucleotide polymorphism (SNP) calling, and structural variant analysis with a reference genome, we show how an extremely limited number of polymorphisms in genes not commonly associated with bakanae disease can cause strong differences in phenotype. CSV1 and Augusto2 were particularly close, with only 21,887 SNPs between them, but they differed in virulence, reaction to temperature, induced symptoms, colony morphology and color, growth speed, fumonisin, and gibberellin production. Genes potentially involved in the shift in phenotype were identified. Furthermore, we show how temperature variation may result in different symptoms even in rice plants inoculated with the same F. fujikuroi strain. Moreover, all of the F. fujikuroi strains became more virulent at higher temperatures. Significant differences were likewise observed in gibberellic acid production and in the expression of both fungal and plant gibberellin biosynthetic genes.

Phytohormone production by the arbuscular mycorrhizal fungus Rhizophagus irregularis

Arbuscular mycorrhizal symbiosis is a mutualistic interaction between most land plants and fungi of the glomeromycotina subphylum. The initiation, development and regulation of this symbiosis involve numerous signalling events between and within the symbiotic partners. Among other signals, phytohormones are known to play important roles at various stages of the interaction. During presymbiotic steps, plant roots exude strigolactones which stimulate fungal spore germination and hyphal branching, and promote the initiation of symbiosis. At later stages, different plant hormone classes can act as positive or negative regulators of the interaction. Although the fungus is known to reciprocally emit regulatory signals, its potential contribution to the phytohormonal pool has received little attention, and has so far only been addressed by indirect assays. In this study, using mass spectrometry, we analyzed phytohormones released into the medium by germinated spores of the arbuscular mycorrhizal fungus Rhizophagus irregularis. We detected the presence of a cytokinin (isopentenyl adenosine) and an auxin (indole-acetic acid). In addition, we identified a gibberellin (gibberellin A4) in spore extracts. We also used gas chromatography to show that R. irregularis produces ethylene from methionine and the α-keto γ-methylthio butyric acid pathway. These results highlight the possibility for AM fungi to use phytohormones to interact with their host plants, or to regulate their own development.

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.

Fine mapping of qBK1, a major QTL for bakanae disease resistance in rice

BACKGROUND

Bakanae disease is an important fungal disease caused by Gibberella fujikuroi. Incidence of rice bakanae disease creates serious problems in the foremost rice growing countries, and no rice variety has been found to be completely resistant to this disease. However, breeding rice varieties resistant to bakanae disease may be a cost-saving solution preferable to the application of fungicides. In this study, we aimed to determine the exact position and the candidate gene for qBK1, a major resistant quantitative trait locus (QTLs) for bakanae disease.

RESULTS

The genotypes/phenotypes of recombinants selected from backcrossed recombinant inbred lines of two rice varieties, Shingwang (resistant) and Ilpum (susceptible), indicated that the locus qBK1, conferring resistance to bakanae disease in Shingwang, was delimited to a 35-kb interval delimited by InDel 18 (23.637 Mbp) and InDel 19-14 (23.672 Mbp). Sequence analysis of this 35-kb region revealed four candidate genes, LOC_Os01g41770, LOC_Os01g41780, LOC_Os01g41790, and LOC_Os01g41800. There were many non-synonymous SNPs in LOC_Os01g41770 and the transcript of LOC_Os01g41790 was early terminated in Shingwang, whereas there were no differences in both LOC_Os01g41780 and LOC_Os01g41800 sequences between Ilpum and Shingwang. Expression profiling of the four candidate genes showed the up-regulation of LOC_Os01g41770, LOC_Os01g41780, and LOC_Os01g41790 in Ilpum and of LOC_Os01g41800 in Shingwang after inoculation of G. fujikuroi.

CONCLUSION

Utilization of marker-assisted selection (MAS) with a precise molecular marker on qBK1 could provide an effective tool for breeding rice varieties resistant to bakanae disease. To our knowledge, this is the first report on fine mapping and candidate gene approaches for identifying the gene for qBK1.

Pre- and Postharvest Strategies to Minimize Mycotoxin Contamination in the Rice Food Chain

Rice is part of many people's diet around the world, being the main energy source in some regions. Although fewer reports exist on the occurrence of mycotoxins in rice compared to other cereals, fungal contamination and the associated production of toxic metabolites, even at lower occurrence levels compared to other crops, are of concern because of the high consumption of rice in many countries. Due to the diversity of fungi that may contaminate the rice food chain, the co-occurrence of mycotoxins is frequent. Specific strategies to overcome these problems may be applied at the preharvest part of the crop chain, while assuring good practices at harvest and postharvest stages, since different fungi may find suitable conditions to grow at the various stages of the production chain. Therefore, the aim of this review is to present the state-of-the-art knowledge on such strategies in an integrated way, from the field to the final products, to reduce mycotoxin contamination in rice.

Investigation of the Metabolic Profile and Toxigenic Variability of Fungal Species Occurring in Fermented Foods and Beverage from Nigeria and South Africa Using UPLC-MS/MS

Fungal species recovered from fermented foods and beverage from Nigeria and South Africa were studied to establish their toxigenic potential in producing an array of secondary metabolites including mycotoxins (n = 49) that could compromise human and animal safety. In total, 385 fungal isolates were grown on solidified yeast extract sucrose agar. Their metabolites were extracted and analyzed via ultra-performance liquid chromatography tandem mass spectrometry. To examine the grouping of isolates and co-occurrence of metabolites, hierarchal clustering and pairwise association analysis was performed. Of the 385 fungal strains tested, over 41% were toxigenic producing different mycotoxins. A. flavus and A. parasiticus strains were the principal producers of aflatoxin B₁ (27⁻7406 µg/kg). Aflatoxin B₁ and cyclopiazonic acid had a positive association. Ochratoxin A was produced by 67% of the A. niger strains in the range of 28⁻1302 µg/kg. The sterigmatocystin producers found were A. versicolor (n = 12), A. amstelodami (n = 4), and A. sydowii (n = 6). Apart from P. chrysogenum, none of the Penicillium spp. produced roquefortine C. Amongst the Fusarium strains tested, F. verticillioides produced fumonisin B₁ (range: 77⁻218 µg/kg) meanwhile low levels of deoxynivalenol were observed. The production of multiple metabolites by single fungal species was also evident.

OsDCL1a activation impairs phytoalexin biosynthesis and compromises disease resistance in rice

BACKGROUND AND AIMS

MicroRNAs (miRNAs) are small non-coding RNAs that act as post-transcriptional regulators of gene expression via sequence-specific cleavage or translational repression of target transcripts. They are transcribed as long single-stranded RNA precursors with unique stem-loop structures that are processed by a DICER-Like (DCL) ribonuclease, typically DCL1, to produce mature miRNAs. Although a plethora of miRNAs have been found to be regulated by pathogen infection in plants, the biological function of most miRNAs remains largely unknown. Here, the contribution of OsDCL1 to rice immunity was investigated.

METHODS

Activation-tagged Osdcl1a (Osdcl1a-Ac) rice mutants were examined for resistance to pathogen infection. mRNA and small RNA deep sequencing, quantitative real-time PCR (RT-qPCR) and stem-loop reverse tanscripion-PCR (RT-PCR) were used to examine DCL1a-mediated alterations in the rice transcriptome. Rice diterpene phytoalexins were quantified by liquid chromatography-tandem mass spectrometry (LC-MSMS). Accumulation of O2·- was determined by nitroblue tetrazolium (NBT) staining.

KEY RESULTS

dcl1a-Ac mutants exhibit enhanced susceptibility to infection by fungal pathogens which was associated with a weaker induction of defence gene expression. Comparison of the mRNA and miRNA transcriptomes of dcl1a-Ac and wild-type plants revealed misregulation of genes involved in detoxification of reactive oxygen species. Consequently, dcl1a-Ac plants accumulated O2·- in their leaves and were more sensitive to methyl viologen-induced oxidative stress. Furthermore, dcl1a-Ac plants showed downregulation of diterpenoid phytoalexin biosynthetic genes, these genes also being weakly induced during pathogen infection. Upon pathogen challenge, dcl1a-Ac plants failed to accumulate major diterpenoid phytoalexins. OsDCL1a activation resulted in marked alterations in the rice miRNAome, including both upregulation and downregulation of miRNAs.

CONCLUSIONS

OsDCL1a activation enhances susceptibility to infection by fungal pathogens in rice. Activation of OsDCL1a represses the pathogen-inducible host defence response and negatively regulates diterpenoid phytoalexin production. These findings provide a basis to understand the molecular mechanisms through which OsDCL1a mediates rice immunity.

Manipulation of Phytohormone Pathways by Effectors of Filamentous Plant Pathogens

Phytohormones regulate a large variety of physiological processes in plants. In addition, salicylic acid (SA), jasmonic acid (JA), and ethylene (ET) are responsible for primary defense responses against abiotic and biotic stresses, while plant growth regulators, such as auxins, brassinosteroids (BRs), cytokinins (CKs), abscisic acid (ABA), and gibberellins (GAs), also contribute to plant immunity. To successfully colonize plants, filamentous pathogens like fungi and oomycetes have evolved diverse strategies to interfere with phytohormone pathways with the help of secreted effectors. These include proteins, toxins, polysaccharides as well as phytohormones or phytohormone mimics. Such pathogen effectors manipulate phytohormone pathways by directly altering hormone levels, by interfering with phytohormone biosynthesis, or by altering or blocking important components of phytohormone signaling pathways. In this review, we outline the various strategies used by filamentous phytopathogens to manipulate phytohormone pathways to cause disease.

Genetic Differentiation Associated with Fumonisin and Gibberellin Production in Japanese Fusarium fujikuroi

Fusarium fujikuroi is a pathogenic fungus that infects rice. It produces several important mycotoxins, such as fumonisins. Fumonisin production has been detected in strains of maize, strawberry, and wheat, whereas it has not been detected in strains from rice seedlings infested with bakanae disease in Japan. We investigated the genetic relationships, pathogenicity, and resistance to a fungicide, thiophanate-methyl (TM), in 51 fumonisin-producing strains and 44 nonproducing strains. Phylogenetic analyses based on amplified fragment length polymorphism (AFLP) markers and two specific genes (a combined sequence of translation elongation factor 1α [TEF1α] and RNA polymerase II second-largest subunit [RPB2]) indicated differential clustering between the fumonisin-producing and -nonproducing strains. One of the AFLP markers, EATMCAY107, was specifically present in the fumonisin-producing strains. A specific single nucleotide polymorphism (SNP) between the fumonisin-producing and nonproducing strains was also detected in RPB2, in addition to an SNP previously found in TEF1α. Gibberellin production was higher in the nonproducing than in the producing strains according to an in vitro assay, and the nonproducing strains had the strongest pathogenicity with regard to rice seedlings. TM resistance was closely correlated with the cluster of fumonisin-nonproducing strains. The results indicate that intraspecific evolution in Japanese F. fujikuroi is associated with fumonisin production and pathogenicity. Two subgroups of Japanese F. fujikuroi, designated G group and F group, were distinguished based on phylogenetic differences and the high production of gibberellin and fumonisin, respectively.IMPORTANCE Fusarium fujikuroi is a pathogenic fungus that causes rice bakanae disease. Historically, this pathogen has been known as Fusarium moniliforme, along with many other species based on a broad species concept. Gibberellin, which is currently known as a plant hormone, is a virulence factor of F. fujikuroi Fumonisin is a carcinogenic mycotoxin posing a serious threat to food and feed safety. Although it has been confirmed that F. fujikuroi produces gibberellin and fumonisin, production varies among strains, and individual production has been obscured by the traditional appellation of F. moniliforme, difficulties in species identification, and variation in the assays used to determine the production of these secondary metabolites. In this study, we discovered two phylogenetic subgroups associated with fumonisin and gibberellin production in Japanese F. fujikuroi.

Evaluation of Phenamacril and Ipconazole for Control of Rice Bakanae Disease Caused by Fusarium fujikuroi

This study evaluated the use of phenamacril and ipconazole, alone and in mixtures, for the control of rice bakanae disease caused by Fusarium fujikuroi. Mixtures were studied with the goal of reducing the selection of fungicide-resistant field isolates of the fungus. When tested alone, both phenamacril and ipconazole exhibited high antifungal activity against F. fujikuroi mycelial growth; the average EC₅₀ value for 19 field isolates was 0.1544 μg/ml for phenamacril and 0.0472 μg/ml for ipconazole. A 2:1 mixture of phenamacril and ipconazole caused a slightly synergistic (greater than additive) inhibition of mycelial growth. Inhibition of F. fujikuroi sporulation was highest for ipconazole alone, intermediate with the 2:1 mixture, and lowest for phenamacril alone. Inhibition by phenamacril and ipconazole alone or by the 2:1 mixture was substantially lower for spore germination than for mycelial growth or sporulation. When the total fungicide concentration was <24 g of a.i./100 kg of treated rice seeds, the fungicides, whether alone or in the 2:1 mixture, were not phytotoxic to seeds or seedlings of two rice cultivars. In a greenhouse experiment, the 2:1 mixture of phenamacril and ipconazole at 6 g of a.i./100 kg of treated seeds provided 100% control of rice bakanae disease on two cultivars. Overall, the results indicate that the use of a 2:1 mixture of phenamacril and ipconazole should control rice bakanae disease while reducing the occurrence of fungicide resistance in F. fujikuroi.