Ecological Dynamics and Microbial Treatments against Oomycete Plant Pathogens.
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ABSTRACT:
SUBMITTER: Sullam KE
PROVIDER: S-EPMC8707103 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Seedling root rot of soybeans caused by the host-specific pathogen Phytophthora sojae, and a large number of Pythium species, is an economically important disease across the Midwest United States that negatively impacts soybean yields. Research on biocontrol strategies for crop pathogens has focused on compounds produced by microbes from soil, however, recent studies suggest that aquatic bacteria express distinct compounds that efficiently inhibit a wide range of pathogens. Based on these observations, we hypothesized that freshwater strains of pseudomonads might be producing novel antagonistic compounds that inhibit the growth of oomycetes. To test this prediction, we utilized a collection of 330 Pseudomonas strains isolated from soil and freshwater habitats, and determined their activity against a panel of five oomycetes: Phytophthora sojae, Pythium heterothalicum, Pythium irregulare, Pythium sylvaticum, and Pythium ultimum, all of which are pathogenic on soybeans. Among the bacterial strains, 118 exhibited antagonistic activity against at least one oomycete species, and 16 strains were inhibitory to all pathogens. Antagonistic activity toward oomycetes was significantly more common for aquatic isolates than for soil isolates. One water-derived strain, 06C 126, was predicted to express a siderophore and exhibited diverse antagonistic profiles when tested on nutrient rich and iron depleted media suggesting that more than one compound was produced that effectively inhibited oomycetes. These results support the concept that aquatic strains are an efficient source of compounds that inhibit pathogens. We outline a strategy to identify other strains that express unique compounds that may be useful biocontrol agents.
| S-EPMC5986895 | biostudies-literature
Project description:Genomics of oomycete downy mildew plant pathogens
| PRJNA396554 | ENA
Project description:Plant health is of utmost importance for optimal agricultural production and sustainability. Unfortunately, biotic and abiotic factors put a major constraint on crop safety and productivity. Plant diseases caused by oomycetes inflict serious damage to various crops. Moreover, the injudicious use of chemical pesticides poses threats related to pesticide resistance development in pathogens and environmental pollution. Biocontrol offers an effective solution for disease control; however, research on biocontrol of oomycete-related diseases is scarce. Thus, this study undertakes the screening of biocontrol resources for the effective management of oomycete-related plant diseases. In this regard, 86 isolates of Trichoderma spp. were assessed against Phytophthora nicotianae, P. capsici, Pythium vexans, P. ultimum, and P. dissotocum through dual culture assay. Furthermore, the antagonistic effect of selected isolates was studied against tobacco black shank disease and damping-off of cucumber seedlings in the greenhouse. The relative control effect of the three antagonistic Trichoderma strains AR-4, Tv-1, and ST4-1 on tobacco black shank was more than 60%, which was not significantly different from 6.88 gl-1 fluopicolide-propamocarb. Whereas, the relative control effect of Trichoderma AR-4 and ST4-1 on damping-off of cucumber seedlings was 80.33% and 82.67%, respectively, which were significantly higher than Trichoderma Tv-1 (35.49%) and fluopicolide-propamocarb (47.82%). According to the morphological and molecular characterization, the fungal strains AR-4, Tv-1, and ST4-1 were identified as Trichoderma koningiopsis, T. asperellum, and T. gamsii, respectively. In conclusion, the strains exhibited a strong antagonistic effect against oomycete pathogens and can be integrated into disease management strategies.
| S-EPMC9487998 | biostudies-literature
Project description:IntroductionOomycetes cause several damaging diseases of plants and animals, and some species also act as biocontrol agents on insects, fungi, and other oomycetes. RNA silencing is increasingly being shown to play a role in the pathogenicity of Phytophthora species, either through trans-boundary movement of small RNAs (sRNAs) or through expression regulation of infection promoting effectors.MethodsTo gain a wider understanding of RNA silencing in oomycete species with more diverse hosts, we mined genome assemblies for Dicer-like (DCL), Argonaute (AGO), and RNA dependent RNA polymerase (RDRP) proteins from Phytophthora plurivora, Ph. cactorum, Ph. colocasiae, Pythium oligandrum, Py. periplocum, and Lagenidium giganteum. Moreover, we sequenced small RNAs from the mycelium stage in each of these species.Results and discussionEach of the species possessed a single DCL protein, but they differed in the number and sequence of AGOs and RDRPs. SRNAs of 21nt, 25nt, and 26nt were prevalent in all oomycetes analyzed, but the relative abundance and 5' base preference of these classes differed markedly between genera. Most sRNAs mapped to transposons and other repeats, signifying that the major role for RNA silencing in oomycetes is to limit the expansion of these elements. We also found that sRNAs may act to regulate the expression of duplicated genes. Other sRNAs mapped to several gene families, and this number was higher in Pythium spp., suggesting a role of RNA silencing in regulating gene expression. Genes for most effector classes were the source of sRNAs of variable size, but some gene families showed a preference for specific classes of sRNAs, such as 25/26 nt sRNAs targeting RxLR effector genes in Phytophthora species. Novel miRNA-like RNAs (milRNAs) were discovered in all species, and two were predicted to target transcripts for RxLR effectors in Ph. plurivora and Ph. cactorum, indicating a putative role in regulating infection. Moreover, milRNAs from the biocontrol Pythium species had matches in the predicted transcriptome of Phytophthora infestans and Botrytis cinerea, and L. giganteum milRNAs matched candidate genes in the mosquito Aedes aegypti. This suggests that trans-boundary RNA silencing may have a role in the biocontrol action of these oomycetes.
| S-EPMC10080066 | biostudies-literature
Project description:BACKGROUND:Genomic studies demonstrate that components of virulence mechanisms in filamentous eukaryotic pathogens (FEPs, fungi and oomycetes) of plants are often highly conserved, or found in gene families that include secreted hydrolytic enzymes (e.g., cellulases and proteases) and secondary metabolites (e.g., toxins), central to the pathogenicity process. However, very few large-scale genomic comparisons have utilized complete proteomes from dozens of FEPs to reveal lifestyle-associated virulence mechanisms. Providing a powerful means for exploration, and the discovery of trends in large-scale datasets, network analysis has been used to identify core functions of the primordial cyanobacteria, and ancient evolutionary signatures in oxidoreductases. RESULTS:We used a sequence-similarity network to study components of virulence mechanisms of major pathogenic lifestyles (necrotroph (ic), N; biotroph (ic), B; hemibiotroph (ic), H) in complete pan-proteomes of 65 FEPs and 17 saprobes. Our comparative analysis highlights approximately 190 core functions found in 70% of the genomes of these pathogenic lifestyles. Core functions were found mainly in: transport (in H, N, B cores); carbohydrate metabolism, secondary metabolite synthesis, and protease (H and N cores); nucleic acid metabolism and signal transduction (B core); and amino acid metabolism (H core). Taken together, the necrotrophic core contains functions such as cell wall-associated degrading enzymes, toxin metabolism, and transport, which are likely to support their lifestyle of killing prior to feeding. The biotrophic stealth growth on living tissues is potentially controlled by a core of regulatory functions, such as: small G-protein family of GTPases, RNA modification, and cryptochrome-based light sensing. Regulatory mechanisms found in the hemibiotrophic core contain light- and CO2-sensing functions that could mediate important roles of this group, such as transition between lifestyles. CONCLUSIONS:The selected set of enriched core functions identified in our work can facilitate future studies aimed at controlling FEPs. One interesting example would be to facilitate the identification of the pathogenic potential of samples analyzed by metagenomics. Finally, our analysis offers potential evolutionary scenarios, suggesting that an early-branching saprobe (identified in previous studies) has probably evolved a necrotrophic lifestyle as illustrated by the highest number of shared gene families between saprobes and necrotrophs.
| S-EPMC6933724 | biostudies-literature
Project description:Effectors are essential virulence proteins produced by a broad range of parasites, including viruses, bacteria, fungi, oomycetes, protozoa, insects and nematodes. Upon entry into host cells, pathogen effectors manipulate specific physiological processes or signaling pathways to subvert host immunity. Most effectors, especially those of eukaryotic pathogens, remain functionally uncharacterized. Here, we show that two effectors from the oomycete plant pathogen Phytophthora sojae suppress RNA silencing in plants by inhibiting the biogenesis of small RNAs. Ectopic expression of these Phytophthora suppressors of RNA silencing enhances plant susceptibility to both a virus and Phytophthora, showing that some eukaryotic pathogens have evolved virulence proteins that target host RNA silencing processes to promote infection. These findings identify RNA silencing suppression as a common strategy used by pathogens across kingdoms to cause disease and are consistent with RNA silencing having key roles in host defense.
| S-EPMC4049077 | biostudies-literature
Project description:Microorganisms provide both beneficial and harmful effects to human beings. Beneficial effects come from the symbiotic relationship that exists between humans and microbiota, but then several human illnesses have turned some friendly microbes into opportunistic pathogens, causing several microbial-related diseases. Various efforts have been made to create and utilize antimicrobial agents in the treatment and prevention of these infections, but such efforts have been hampered by the emergence of antimicrobial resistance. Despite extensive studies on drug discovery to alleviate this problem, issues with the toxicity and tolerance of certain compounds and continuous microbial evolution have forced researchers to focus on screening various phytochemical dietary compounds for antimicrobial activity. Linolenic acid and its derivatives (eicosapentaenoic acid and docosahexaenoic acid) are omega-3 fatty acids that have been studied due to their role in human health, being important for the brain, the eye, the cardiovascular system, and general human growth. However, their utilization as antimicrobial agents has not been widely appreciated, perhaps due to a lack of understanding of antimicrobial mechanisms, toxicity, and route of administration. Therefore, this review focuses on the efficacy, mechanism, and toxicity of omega-3 fatty acids as alternative therapeutic agents for treating and preventing diseases associated with pathogenic microorganisms.
| S-EPMC5964344 | biostudies-other
Project description:Nitrogen is a major constituent of proteins, chlorophyll, nucleotides, and hormones and has profound effects on plant growth and productivity. RWP-RK family transcription factors (TFs) are key regulators that bind to cis-acting elements in the promoter regions of nitrogen use efficiency-related genes and genes responsible for gametogenesis and embryogenesis. The proteins share a conserved RWPxRK motif; have been found in all vascular plants, green algae, and slime molds; and are considered to be a plant-specific TF family. In this study, we show that RWP-RK proteins are also widely present in the Stramenopila kingdom, particularly among the oomycetes, with 12-15 members per species. These proteins form three distinct phylogenetic subgroups, two of which are relatively closely related to the nodule inception (NIN)-like protein (NLP) or the RWP-RK domain protein (RKD) subfamilies of plant RWP-RK proteins. The donor for horizontal gene transfer of RWP-RK domains to slime molds is likely to have been among the Stramenopila, predating the divide between brown algae and oomycetes. The RWP-RK domain has secondary structures that are conserved across plants and oomycetes, but several amino acids that may affect DNA-binding affinity differ. The transcriptional activities of orthologous RWP-RK genes were found to be conserved in oomycetes. Our results demonstrate that RWP-RK family TF genes are present in the oomycetes and form specific subgroups with functions that are likely conserved. Our results provide new insights for further understanding the evolution and function of this TF family in specific eukaryotic organisms.
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