Identification of miRNA-Target Gene Pairs Responsive to Fusarium Wilt of Cucumber via an Integrated Analysis of miRNA and Transcriptome Profiles.
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ABSTRACT:
SUBMITTER: Xu J
PROVIDER: S-EPMC8615934 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BACKGROUND:Myxobacteria are micropredators in the soil ecosystem with the capacity to move and feed cooperatively. Some myxobacterial strains have been used to control soil-borne fungal phytopathogens. However, interactions among myxobacteria, plant pathogens, and the soil microbiome are largely unexplored. In this study, we aimed to investigate the behaviors of the myxobacterium Corallococcus sp. strain EGB in the soil and its effect on the soil microbiome after inoculation for controlling cucumber Fusarium wilt caused by Fusarium oxysporum f. sp. cucumerinum (FOC). RESULTS:A greenhouse and a 2-year field experiment demonstrated that the solid-state fermented strain EGB significantly reduced the cucumber Fusarium wilt by 79.6% (greenhouse), 66.0% (2015, field), and 53.9% (2016, field). Strain EGB adapted to the soil environment well and decreased the abundance of soil-borne FOC efficiently. Spatiotemporal analysis of the soil microbial community showed that strain EGB migrated towards the roots and root exudates of the cucumber plants via chemotaxis. Cooccurrence network analysis of the soil microbiome indicated a decreased modularity and community number but an increased connection number per node after the application of strain EGB. Several predatory bacteria, such as Lysobacter, Microvirga, and Cupriavidus, appearing as hubs or indicators, showed intensive connections with other bacteria. CONCLUSION:The predatory myxobacterium Corallococcus sp. strain EGB controlled cucumber Fusarium wilt by migrating to the plant root and regulating the soil microbial community. This strain has the potential to be developed as a novel biological control agent of soil-borne Fusarium wilt. Video abstract.
| S-EPMC7137222 | biostudies-literature
Project description:Cucumber Fusarium wilt, caused by Fusarium oxysporum, is a devastating disease of cucumber and leads to enormous economic losses worldwide. The antagonistic bacterium Bacillus velezensis NH-1 suppresses F. oxysporum For a higher biological control effect, control-released microcapsules of NH-1 were prepared using cell immobilization technology. NH-1 cells were embedded in combinations of the biodegradable wall materials sodium alginate, chitosan, and cassava-modified starch to prepare control-released microbiological microcapsules. For the preparation of alginate single-layer microcapsules, the highest embedding rate of 72.60% was obtained by applying 3% sodium alginate and 2% calcium chloride. After the application of monolayer alginate microcapsules in soil, the number of bacterial cells corresponded to a sustained release curve, and the survival rate of NH-1 was higher than the control in which soil was directly irrigated with NH-1 broth. The use of 0.8% chitosan (pH 3.0) and 0.5% cassava-modified starch in the preparation of double-layer and triple-layer microcapsules changed the performance of the microcapsules and increased the embedding rate. After dry storage for 65 days, the number of NH-1 cells was at the highest level in the monolayer microcapsules. In the field experiment, the control efficiency of alginate-coated monolayer microcapsules on Fusarium wilt was 100%, which was significantly higher than for the NH-1 culture and double-layer and triple-layer microcapsules. Collectively, sodium alginate is an ideal wall material for preparing slow-release bacterial microcapsules to control cucumber Fusarium wilt. Monolayer alginate microcapsules retard the release of B. velezensis NH-1 in soils and significantly improve its biocontrol efficiency on cucumber Fusarium wilt.IMPORTANCEBacillus species are often used for the biocontrol of various plant pathogens, but the control efficiency of Bacillus is usually unstable in field experiments. To improve the control efficiency of Bacillus, in this study, microcapsules of Bacillus velezensis strain NH-1 were prepared using different wall materials (sodium alginate, chitosan, and cassava-modified starch). It was found that the control efficiency of alginate-coated monolayer microcapsules on Fusarium wilt was 100% in field experiments, which was higher than for NH-1 culture and double-layer and triple-layer microcapsules. This study provides a new approach for preparing a biocontrol agent against Fusarium wilt with high biocontrol efficiency.
| S-EPMC6495769 | biostudies-literature
Project description:Cucumber plants subjected to consecutive monoculture for 9 years were found to suffer from severe Fusarium wilt disease, caused by the soil-borne fungus Fusarium oxysporum f. sp. Cucumerinum J. H. Owen. In the present study, greenhouse experiments were performed to evaluate the influence of ammonia gas fumigation on Fusarium wilt suppression, fungal abundance and fungal community composition. Results showed that ammonia gas fumigation remarkably reduced disease incidence from 80% to 27%, resulting in a four-fold increase in yield, compared to the control. Total fungal abundance declined dramatically after fumigation and reached the lowest level at day 32, at 243 times lower than the control. Moreover, fumigation significantly increased soil fungal diversity, though it also decreased considerably coinciding with cucumber growth. Fumigation also significantly altered soil fungal community composition, relative to the control. Fusarium was strongly inhibited by fumigation in both relative abundance (3.8 times lower) and targeted quantification (a decrease of 167 fold). Collectively, the application of ammonia gas fumigation to control Fusarium wilt of cucumber resulted in a re-assembly of the fungal community to resemble that of a non-disease conducive consortium. Additional strategies, such as bioorganic fertilizer application, may still be required to develop sustainable disease suppression following fumigation.
| S-EPMC5322401 | biostudies-literature
Project description:BACKGROUND:Cucumber Fusarium wilt, caused by Fusarium oxysporum f. sp. cucumerinum (Foc), is one of the most notorious diseases in cucumber production. Our previous research showed the virulence of Foc significantly increases over consecutive rounds of infection in a resistant cultivar. To understand the virulence variation of Foc under host pressure, the mildly virulent strain foc-3b (WT) and its virulence-enhanced variant Ra-4 (InVir) were selected and their transcriptome profiles in infected cucumber roots were analyzed at 24?h after inoculation (hai) and 120?hai. RESULTS:A series of differentially expressed genes (DEGs) potentially involved in fungal pathogenicity and pathogenicity variation were identified and prove mainly involved in metabolic, transport, oxidation-reduction, cell wall degradation, macromolecules modification, and stress and defense. Among these DEGs, 190 up- and 360 down-regulated genes were expressed in both strains, indicating their importance in Foc infection. Besides, 286 and 366 DEGs showed up-regulated expression, while 492 and 214 showed down-regulated expression in InVir at 24 and 120?hai, respectively. These DEGs may be involved in increased virulence. Notably, transposases were more active in InVir than WT, indicating transposons may contribute to adaptive evolution. CONCLUSIONS:By a comparative transcriptome analysis of the mildly and highly virulent strains of Foc during infection of cucumber, a series of DEGs were identified that may be associated with virulence. Hence, this study provides new insight into the transcriptomic profile underlying pathogenicity and virulence differentiation of Foc.
| S-EPMC6622004 | biostudies-literature
Project description:Fusarium wilt (FW) is a very serious soil-borne disease worldwide, which usually results in huge yield losses in cucumber production. However, the inheritance and molecular mechanism of the response to FW are still unknown in cucumber (Cucumis sativus L.). In this study, two inbred cucumber lines Superina (P1) and Rijiecheng (P2) were used as the sensitive and resistant lines, respectively. A mixed major gene plus polygene inheritance model was used to analyze the resistance to FW in different generations of cucumber, namely, P1, P2, F1 (P1×P2), B1, and B2, obtained by backcrossing F1 plants with Superina (B1) or Rijiecheng (B2), and F2, obtained by self-crossing the F1 plants. After screening 18 genetic models, we chose the E-1 model, which included two pairs of additive-dominance-epistatic major genes and additive-dominance polygenes, as the optimal model for resistance to FW on the basis of fitness tests. The major effect quantitative trait locus (QTL) fw2.1 was detected in a 1.91-Mb-long region of chromosome 2 by bulked-segregant analysis. We used five insertion/deletion markers to fine-map the fw2.1 to a 0.60 Mb interval from 1,248,093 to 1,817,308 bp on chromosome 2 that contained 80 candidate genes. We also used the transcriptome data of Rijiecheng inoculated with Fusarium oxysporum f. sp. cucumerinum (Foc) to screen the candidate genes. Twelve differentially expressed genes were detected in fw2.1, and five of them were significantly induced by FW. The expression levels of the five genes were higher in FW-resistant Rijiecheng inoculated with Foc than in the control inoculated with water. Our results will contribute to a better understanding of the genetic basis of FW resistance in cucumber, which may help in breeding FW-resistant cucumber lines in the future.
| S-EPMC6900741 | biostudies-literature
Project description:Cucumber is an important vegetable crop in China. Fusarium wilt is a soil-borne disease that can significantly reduce cucumber yields. Paenibacillus polymyxa WLY78 can strongly inhibit Fusarium oxysporum f. sp. Cucumerium, which causes Fusarium wilt disease. In this study, we screened the genome of WLY78 and found eight potential antibiotic biosynthesis gene clusters. Mutation analysis showed that among the eight clusters, the fusaricidin synthesis (fus) gene cluster is involved in inhibiting the Fusarium genus, Verticillium albo-atrum, Monilia persoon, Alternaria mali, Botrytis cinereal, and Aspergillus niger. Further mutation analysis revealed that with the exception of fusTE, the seven genes fusG, fusF, fusE, fusD, fusC, fusB, and fusA within the fus cluster were all involved in inhibiting fungi. This is the first time that demonstrated that fusTE was not essential. We first report the inhibitory mode of fusaricidin to inhibit spore germination and disrupt hyphal membranes. A biocontrol assay demonstrated that fusaricidin played a major role in controlling Fusarium wilt disease. Additionally, qRT-PCR demonstrated that fusaricidin could induce systemic resistance via salicylic acid (SA) signal against Fusarium wilt of cucumber. WLY78 is the first reported strain to both produce fusaricidin and fix nitrogen. Therefore, our results demonstrate that WLY78 will have great potential as a biocontrol agent in agriculture.
| S-EPMC6829208 | biostudies-literature
Project description:Exogenous silicates can enhance plant resistance to pathogens and change soil microbial communities. However, the relationship between changes in soil microbial communities and enhanced plant resistance remains unclear. Here, effects of exogenous sodium silicate on cucumber (Cucumis sativus L.) seedling resistance to Fusarium wilt caused by the soil-borne pathogen Fusarium oxysporum f.sp. cucumerinum Owen (FOC) were investigated by drenching soil with 2 mM sodium silicate. Soil bacterial and fungal community abundances and compositions were estimated by real-time PCR and high-throughput amplicon sequencing; then, feedback effects of changes in soil biota on cucumber seedling resistance to FOC were assessed. Moreover, effects of sodium silicate on the growth of FOC and Streptomyces DHV3-2, an antagonistic bacterium to FOC, were investigated both in vitro and in the soil environment. Results showed that exogenous sodium silicate enhanced cucumber seedling growth and resistance to FOC. In bare soil, sodium silicate increased bacterial and fungal community abundances and diversities. In cucumber-cultivated soil, sodium silicate increased bacterial community abundances, but decreased fungal community abundances and diversities. Sodium silicate also changed soil bacterial and fungal communality compositions, and especially, decreased the relative abundances of microbial taxa containing plant pathogens but increased these with plant-beneficial potentials. Moreover, sodium silicate increased the abundance of Streptomyces DHV3-2 in soil. Soil biota from cucumber-cultivated soil treated with sodium silicate decreased cucumber seedling Fusarium wilt disease index, and enhanced cucumber seedling growth and defense-related enzyme activities in roots. Sodium silicate at pH 9.85 inhibited FOC abundance in vitro, but did not affect FOC abundance in soil. Overall, our results suggested that, in cucumber-cultivated soil, sodium silicate increased cucumber seedling resistance to Fusarium wilt by changing soil microbial communities rather than by directly inhibiting the growth of FOC.
| S-EPMC5958222 | biostudies-literature
Project description:Fusarium wilt disease is one of the most problematic and destructive disease in cucumber production. The causative agents are Fusarium oxysporum and F. solani. These pathogens are soil borne and transmitted through infested soil and water. A field survey was conducted to study the disease prevalence in the major growing areas of cucumber in Peninsular Malaysia. Field study revealed that the disease was highly prevalence in the field with the disease incidence was in the range of 10%-60%. The morphological properties of F. oxysporum are microconidia (3.8-15.7 ?m × 2.9-4.9 ?m), macroconidia (14.8-38.5 ?m × 2.4-5.7 ?m) and number of septate was 1-4. While for F. solani are microconidia (3.39-14.63 ?m × 2.36-4.44 ?m), macroconidia (7.22-50.46 ?m × 2.43-6.14 ?m) and number of septate was 1-5. Based on molecular identification had confirmed that the disease is caused by F. oxysporum and F. solani with similarity index of 99%-100% based on internal transcribed spacer (ITS) gene sequences. The pathogenicity test showed that the symptoms of Fusarium wilt disease was firstly appeared as yellowing of old leaves. Progressively, the infected plant will be wilted and finally died. The outputs of this study are highly important to establish an effective disease management programme to reduce disease prevalence and yield loss in the field.
| S-EPMC7652250 | biostudies-literature
Project description:Kaposi's sarcoma associated herpesvirus (KSHV) causes several tumors, including primary effusion lymphoma (PEL) and Kaposi's sarcoma (KS). Cellular and viral microRNAs (miRNAs) have been shown to play important roles in regulating gene expression. A better knowledge of the miRNA-mediated pathways affected by KSHV infection is therefore important for understanding viral infection and tumor pathogenesis. In this study, we used deep sequencing to analyze miRNA and cellular mRNA expression in a cell line with latent KSHV infection (SLKK) as compared to the uninfected SLK line. This approach revealed 153 differentially expressed human miRNAs, eight of which were independently confirmed by qRT-PCR. KSHV infection led to the dysregulation of ~15% of the human miRNA pool and most of these cellular miRNAs were down-regulated, including nearly all members of the 14q32 miRNA cluster, a genomic locus linked to cancer and that is deleted in a number of PEL cell lines. Furthermore, we identified 48 miRNAs that were associated with a total of 1,117 predicted or experimentally validated target mRNAs; of these mRNAs, a majority (73%) were inversely correlated to expression changes of their respective miRNAs, suggesting miRNA-mediated silencing mechanisms were involved in a number of these alterations. Several dysregulated miRNA-mRNA pairs may facilitate KSHV infection or tumor formation, such as up-regulated miR-708-5p, associated with a decrease in pro-apoptotic caspase-2 and leukemia inhibitory factor LIF, or down-regulated miR-409-5p, associated with an increase in the p53-inhibitor MDM2. Transfection of miRNA mimics provided further evidence that changes in miRNAs are driving some observed mRNA changes. Using filtered datasets, we also identified several canonical pathways that were significantly enriched in differentially expressed miRNA-mRNA pairs, such as the epithelial-to-mesenchymal transition and the interleukin-8 signaling pathways. Overall, our data provide a more detailed understanding of KSHV latency and guide further studies of the biological significance of these changes.
| S-EPMC4420468 | biostudies-literature
Project description:IntroductionBiofungicides with low toxicity and high efficiency are a global priority for sustainable agricultural development. Phytohormone salicylic acid (SA) is an ancient medicine against various diseases in humans and activates the immune system in plants, but little is known of its function as a biofungicide.ObjectivesHere, Fusarium oxysporum, the causal agent of devastating Fusarium wilt and immunodepressed patients, was used as a model system to explore whether SA can enter the pathogen cells and suppress key targets of the pathogen.MethodsOxford Nanopore MinION sequencing and high-throughput chromosome conformation capture (Hi-C) sequencing were used to analyzed the genome of F. oxysporum. In addition, RNA-seq, qRT-PCR, and western blotting were conducted to detect gene and protein expression levels.ResultsWe isolated and sequenced the genome of F. oxysporum from potato dry rot, and the F. oxysporum included 12 chromosomes and 52.3 Mb genomic length. Pharmacological assays showed that exogenous application of SA can efficiently arrest hyphal growth, spore production, and pathogenicity of F. oxysporum, whereas endogenous salicylate hydroxylases significantly detoxify SA. The synergistic growth inhibition of F. oxysporum was observed when SA was combined with rapamycin. Kinase assays showed that SA inhibits FoTOR complex 1 (FoTORC1) by activating FoSNF1 in vivo. Transgenic potato plants with the interference of FoTOR1 and FoSAH1 genes inhibited the invasive growth of hyphae and significantly prevented the occurrence of Fusarium wilt.ConclusionThis study revealed the underlying mechanisms of SA against F. oxysporum and provided insights into SA in controlling various fungal diseases by targeting the SNF1-TORC1 pathway of pathogens.
| S-EPMC9263656 | biostudies-literature