RESUMEN
Seeds are important microbial vectors, and seed-associated pathogens can be introduced into a country through trade, resulting in yield and quality losses in agriculture. The aim of this study was to characterize the microbial communities associated with barley seeds, and based on which, to develop technical approaches to trace their geographical origins, and to inspect and identify quarantine pathogens. Our analysis defined the core microbiota of barley seed and revealed significant differences in the barley seed-associated microbial communities among different continents, suggesting a strong geographic specificity of the barley seed microbiota. By implementing a machine learning model, we achieved over 95% accuracy in tracing the origin of barley seeds. Furthermore, the analysis of co-occurrence and exclusion patterns provided important insights into the identification of candidate biocontrol agents or microbial inoculants that could be useful in improving barley yield and quality. A core pathogen database was developed, and a procedure for inspecting potential quarantine species associated with barley seed was established. These approaches proved effective in detecting four fungal and three bacterial quarantine species for the first time in the port of China. This study not only characterized the core microbiota of barley seeds but also provided practical approaches for tracing the regional origin of barley and identifying potential quarantine pathogens.
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Bacterias , Hongos , Hordeum , Microbiota , Enfermedades de las Plantas , Semillas , Hordeum/microbiología , Semillas/microbiología , Bacterias/aislamiento & purificación , Bacterias/clasificación , Bacterias/genética , Enfermedades de las Plantas/microbiología , Enfermedades de las Plantas/prevención & control , Hongos/aislamiento & purificación , Hongos/clasificación , Hongos/genética , China , CuarentenaRESUMEN
Expanding and intensifying agriculture has led to a loss of soil carbon. As agroecosystems cover over 40% of Earth's land surface, they must be part of the solution put in action to mitigate climate change. Development of efficient management practices to maximize soil carbon retention is currently limited, in part, by a poor understanding of how plants, which input carbon to soil, and microbes, which determine its fate there, interact. Here we implement a diversity gradient by intercropping undersown species with barley in a large field trial, ranging from one to eight undersown species. We find that increasing plant diversity strengthens positive associations within the rhizosphere soil microbial community in relation to negative associations. These associations, in turn, enhance community carbon use efficiency. Jointly, our results highlight how increasing plant diversity in agriculture can be used as a management strategy to enhance carbon retention potential in agricultural soils.
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Agricultura , Biodiversidad , Carbono , Rizosfera , Microbiología del Suelo , Suelo , Carbono/metabolismo , Agricultura/métodos , Suelo/química , Hordeum/microbiología , Hordeum/metabolismo , Plantas/metabolismo , Plantas/microbiología , Microbiota , Raíces de Plantas/microbiología , Raíces de Plantas/metabolismoRESUMEN
Fusarium head blight (FHB) is a major disease of wheat and barley worldwide and is caused by different species in the genus Fusarium, Fusarium graminearum being the most important. We conducted population genomics analyses using SNPs obtained through genotyping by sequencing of over 500 isolates of F. graminearum from the US Upper Midwest, New York, Louisiana, and Uruguay. PCA and STRUCTURE analyses group our isolates into four previously described populations: NA1, NA2, Southern Louisiana (SLA) and Gulf Coast (GC). Some isolates were not assigned to populations because of mixed ancestry. Population structure was associated with toxin genotype and geographic origin. The NA1, NA2, and SLA populations are differentiated (FST 0.385 - 0.551) but the presence of admixed isolates indicates that the populations are not reproductively isolated. Patterns of linkage disequilibrium (LD) decay suggest frequent recombination within populations. Fusarium graminearum populations from the US have great evolutionary potential given the high recombination rate and a large proportion of admixed isolates. The NA1, NA2, and Southern Louisiana (SLA) populations separated from their common ancestral population roughly at the same time in the past and are evolving with moderate levels of subsequent gene flow between them. Genome-wide selection scans in all three populations revealed outlier regions with the strongest signatures of recent positive natural selection. These outlier regions include many genes with unknown function and some genes with known roles in plant-microbe interaction, fungicide/drug resistance, cellular transport and genes that are related to cellular organelles. Only a very small proportion of outlier regions are shared as outliers among the three populations, suggesting unique host-pathogen interactions and environmental adaptation.
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Fusarium , Desequilibrio de Ligamiento , Enfermedades de las Plantas , Polimorfismo de Nucleótido Simple , Fusarium/genética , Fusarium/clasificación , Fusarium/aislamiento & purificación , Enfermedades de las Plantas/microbiología , Polimorfismo de Nucleótido Simple/genética , Triticum/microbiología , Genoma Fúngico/genética , Américas , Genotipo , Genómica , Metagenómica , Hordeum/microbiología , UruguayRESUMEN
Mitigating the negative impacts of polycyclic aromatic hydrocarbons (PAHs) is an urgent need due to their toxicity and persistence in the environment. This study investigated the use of Pseudomonas aeruginosa ASU-B6 to detoxify pyrene (PY). The bacterium P. aeruginosa ASU-B6 is capable of degrading PY by 92% as a sole carbon source after 15 days of incubation with phthalate being the major metabolic product. In this regard, the impact of pyrene (PY), P. aeruginosa ASU-B6 (ASU-B6), the bacterial strain combined with pyrene (ASU-B6/PY) and the metabolites produced after pyrene degradation (PY-metabolites) on the germination and physiological attributes of Hordeum vulgare and Vicia faba seedlings were studied. A single application of PY or ASU-B6 showed a toxic effect on the germination of both tested seeds. Interestingly, broad bean seedlings exhibited less sensitivity to PY stress in terms of growth and metabolism compared to barley. Notably, ASU-B6 inhibited fresh and dry weight of shoots and roots of barley and, to a lesser extent, reduced the germination of broad beans compared to the control. However, the combined PY-metabolites and ASU-B6/PY showed a mutual ameliorative effect on seedlings growth, alleviating the phytotoxic impact of each component. Pyrene reduced the virulence of ASU-B6 by inhibiting the production of pyocyanin pigment, while bacteria ameliorated pyrene toxicity through its degradation. Heatmap and principal component analyses highlighted that increasing the contents of hydrogen peroxide, superoxide anion, hydroxyl radical, and lipid peroxidation positively correlated to the toxicity of PY or ASU-B6. However, improving the antioxidant system which buffers the oxidative stress induced by different combinations of PY and ASU-B6 enhanced the growth of germinated seedlings corresponding to PY or ASU-B6. This study reflected the role of ASU-B6 in ameliorating PY-phytotoxicity. In addition, the application of ASU-B6 strain is recommended as a prospective candidate for remediation of PAHs-contaminated environment with a positive impact on the plant growth and metabolic products.
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Germinación , Hordeum , Pseudomonas aeruginosa , Pirenos , Vicia faba , Hordeum/efectos de los fármacos , Hordeum/microbiología , Hordeum/metabolismo , Hordeum/crecimiento & desarrollo , Vicia faba/efectos de los fármacos , Vicia faba/microbiología , Vicia faba/metabolismo , Vicia faba/crecimiento & desarrollo , Pirenos/toxicidad , Pirenos/metabolismo , Pseudomonas aeruginosa/efectos de los fármacos , Pseudomonas aeruginosa/metabolismo , Germinación/efectos de los fármacos , Plantones/efectos de los fármacos , Plantones/microbiología , Plantones/crecimiento & desarrollo , Plantones/metabolismo , Hidrocarburos Policíclicos Aromáticos/toxicidad , Hidrocarburos Policíclicos Aromáticos/metabolismo , Biodegradación AmbientalRESUMEN
BACKGROUND: Wheat stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is an important disease of barley and wheat. A diverse sexual Pgt population from the Pacific Northwest (PNW) region of the US contains a high proportion of individuals with virulence on the barley stem rust resistance (R) gene, Rpg1. However, the evolutionary mechanisms of this virulence on Rpg1 are mysterious considering that Rpg1 had not been deployed in the region and the gene had remained remarkably durable in the Midwestern US and prairie provinces of Canada. METHODS AND RESULTS: To identify AvrRpg1 effectors, genome wide association studies (GWAS) were performed using 113 Pgt isolates collected from the PNW (n = 89 isolates) and Midwest (n = 24 isolates) regions of the US. Disease phenotype data were generated on two barley lines Morex and the Golden Promise transgenic (H228.2c) that carry the Rpg1 gene. Genotype data was generated by whole genome sequencing (WGS) of 96 isolates (PNW = 89 isolates and Midwest = 7 isolates) and RNA sequencing (RNAseq) data from 17 Midwestern isolates. Utilizing ~1.2 million SNPs generated from WGS and phenotype data (n = 96 isolates) on the transgenic line H228.2c, 53 marker trait associations (MTAs) were identified. Utilizing ~140 K common SNPs generated from combined analysis of WGS and RNAseq data, two significant MTAs were identified using the cv Morex phenotyping data. The 55 MTAs defined two distinct avirulence loci, on supercontig 2.30 and supercontig 2.11 of the Pgt reference genome of Pgt isolate CRL 75-36-700-3. The major avirulence locus designated AvrRpg1A was identified with the GWAS using both barley lines and was delimited to a 35 kb interval on supercontig 2.30 containing four candidate genes (PGTG_10878, PGTG_10884, PGTG_10885, and PGTG_10886). The minor avirulence locus designated AvrRpg1B identified with cv Morex contained a single candidate gene (PGTG_05433). AvrRpg1A haplotype analysis provided strong evidence that a dominant avirulence gene underlies the locus. CONCLUSIONS: The association analysis identified strong candidate AvrRpg1 genes. Further analysis to validate the AvrRpg1 genes will fill knowledge gaps in our understanding of rust effector biology and the evolution and mechanism/s of Pgt virulence on Rpg1.
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Resistencia a la Enfermedad , Estudio de Asociación del Genoma Completo , Hordeum , Enfermedades de las Plantas , Puccinia , Hordeum/microbiología , Hordeum/genética , Enfermedades de las Plantas/microbiología , Enfermedades de las Plantas/genética , Resistencia a la Enfermedad/genética , Puccinia/patogenicidad , Puccinia/genética , Virulencia/genética , Mapeo Cromosómico , Polimorfismo de Nucleótido Simple , Sitios de Carácter Cuantitativo , Genes de Plantas , FenotipoRESUMEN
Leaf rust (LR) caused by Puccinia hordei is a serious disease of barley worldwide, causing significant yield losses and reduced grain quality. Discovery and incorporation of new sources of resistance from gene bank accessions into barley breeding programs is essential for the development of leaf rust resistant varieties. To identify Quantitative Trait Loci (QTL) conferring LR resistance in the two barley subsets, the Generation Challenge Program (GCP) reference set of 142 accessions and the leaf rust subset constructed using the Focused Identification of Germplasm Strategy (FIGS) of 76 barley accessions, were genotyped to conduct a genome-wide association study (GWAS). The results revealed a total of 59 QTL in the 218 accessions phenotyped against barley leaf rust at the seedling stage using two P. hordei isolates (ISO-SAT and ISO-MRC), and at the adult plant stage in four environments in Morocco. Out of these 59 QTL, 10 QTL were associated with the seedling resistance (SR) and 49 QTL were associated with the adult plant resistance (APR). Four QTL showed stable effects in at least two environments for APR, whereas two common QTL associated with SR and APR were detected on chromosomes 2H and 7H. Furthermore, 39 QTL identified in this study were potentially novel. Interestingly, the sequences of 27 SNP markers encoded the candidate genes (CGs) with predicted protein functions in plant disease resistance. These results will provide new perspectives on the diversity of leaf rust resistance loci for fine mapping, isolation of resistance genes, and for marker-assisted selection for the LR resistance in barley breeding programs worldwide.
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Resistencia a la Enfermedad , Estudio de Asociación del Genoma Completo , Hordeum , Enfermedades de las Plantas , Sitios de Carácter Cuantitativo , Plantones , Hordeum/genética , Hordeum/microbiología , Enfermedades de las Plantas/microbiología , Enfermedades de las Plantas/genética , Plantones/genética , Plantones/microbiología , Resistencia a la Enfermedad/genética , Puccinia/patogenicidad , Genotipo , Polimorfismo de Nucleótido Simple , Fenotipo , Basidiomycota , Mapeo Cromosómico , FitomejoramientoRESUMEN
Hybrid genotypes can provide significant yield gains over conventional inbred varieties due to heterosis or hybrid vigor. However, hybrids can also display unintended negative attributes or phenotypes such as extreme pathogen susceptibility. The necrotrophic pathogen Pyrenophora teres f. maculata (Ptm) causes spot form net blotch, which has caused significant yield losses to barley worldwide. Here, we report on a non-transgressive hybrid susceptibility locus in barley identified between the three parental lines CI5791, Tifang and Golden Promise that are resistant to Ptm isolate 13IM.3. However, F2 progeny from CI5791 × Tifang and CI5791 × Golden Promise crosses exhibited extreme susceptibility. The susceptible phenotype segregated in a ratio of 1 resistant:1 susceptible representing a genetic segregation ratio of 1 parental (res):2 heterozygous (sus):1 parental (res) suggesting a single hybrid susceptibility locus. Genetic mapping using a total of 715 CI5791 × Tifang F2 individuals (1430 recombinant gametes) and 149 targeted SNPs delimited the hybrid susceptibility locus designated Susceptibility to Pyrenophora teres 2 (Spt2) to an ~ 198 kb region on chromosome 5H of the Morex V3 reference assembly. This single locus was independently mapped with 83 CI5791 × Golden Promise F2 individuals (166 recombinant gametes) and 180 genome wide SNPs that colocalized to the same Spt2 locus. The CI5791 genome was sequenced using PacBio Continuous Long Read technology and comparative analysis between CI5791 and the publicly available Golden Promise genome assembly determined that the delimited region contained a single high confidence Spt2 candidate gene predicted to encode a pentatricopeptide repeat-containing protein.
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Ascomicetos , Mapeo Cromosómico , Hordeum , Enfermedades de las Plantas , Hordeum/genética , Hordeum/microbiología , Enfermedades de las Plantas/microbiología , Enfermedades de las Plantas/genética , Ascomicetos/fisiología , Resistencia a la Enfermedad/genética , Fenotipo , Polimorfismo de Nucleótido Simple , Hibridación Genética , Vigor Híbrido/genética , GenotipoRESUMEN
Plant immunity is a multilayered process that includes recognition of patterns or effectors from pathogens to elicit defense responses. These include the induction of a cocktail of defense metabolites that typically restrict pathogen virulence. Here, we investigate the interaction between barley roots and the fungal pathogens Bipolaris sorokiniana (Bs) and Fusarium graminearum (Fg) at the metabolite level. We identify hordedanes, a previously undescribed set of labdane-related diterpenoids with antimicrobial properties, as critical players in these interactions. Infection of barley roots by Bs and Fg elicits hordedane synthesis from a 600-kb gene cluster. Heterologous reconstruction of the biosynthesis pathway in yeast and Nicotiana benthamiana produced several hordedanes, including one of the most functionally decorated products 19-ß-hydroxy-hordetrienoic acid (19-OH-HTA). Barley mutants in the diterpene synthase genes of this cluster are unable to produce hordedanes but, unexpectedly, show reduced Bs colonization. By contrast, colonization by Fusarium graminearum, another fungal pathogen of barley and wheat, is 4-fold higher in the mutants completely lacking hordedanes. Accordingly, 19-OH-HTA enhances both germination and growth of Bs, whereas it inhibits other pathogenic fungi, including Fg. Analysis of microscopy and transcriptomics data suggest that hordedanes delay the necrotrophic phase of Bs. Taken together, these results show that adapted pathogens such as Bs can subvert plant metabolic defenses to facilitate root colonization.
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Bipolaris , Diterpenos , Fusarium , Hordeum , Fitoalexinas , Enfermedades de las Plantas , Raíces de Plantas , Sesquiterpenos , Fusarium/patogenicidad , Fusarium/fisiología , Hordeum/microbiología , Diterpenos/farmacología , Diterpenos/metabolismo , Raíces de Plantas/microbiología , Enfermedades de las Plantas/microbiología , Bipolaris/metabolismo , Sesquiterpenos/metabolismo , Sesquiterpenos/farmacologíaRESUMEN
A polyphasic taxonomic approach was used to characterize the three bacterial strains (FP830T, FP2034, and FP2262) isolated from the rhizosphere soil of rice, corn, and highland barley in Beijing, Heilongjiang, and Tibet, respectively, in PR China. These strains were Gram-negative, rod-shaped, and have one or two polar flagella. They exhibited optimal growth at 28 °C and pH 7.0 in the presence of 1â% (w/v) NaCl and showed fluorescence under ultraviolet light when cultivated on King's B plates. The FP830T genome size is 6.4 Mbp with a G+C content of 61.0 mol%. FP830T has the potential to promote plant growth by producing various metabolites such as fengycin, pyoverdin, indole-3-acetic acid, and the volatile substance 2,3-butanediol. Phylogenetic analysis indicated that three isolates formed an independent branch, which most closely related to type strains Pseudomonas thivervalensis DSM 13194T and Pseudomonas zanjanensis SWRI12T. The values of average nucleotide identity and digital DNA-DNA hybridization between three isolates and closest relatives were not higher than 93.7 and 52.3â%, respectively. The dominant cellular fatty acids were C16â:â0, summed feature 3 (C16â:â1 ω7c/C16â:â1 ω6c), and summed feature 8 (C18â:â1 ω7c/C18â:â1 ω6c). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, and aminophospholipid. The predominant respiratory quinone was ubiquinone (Q-9). Based on polyphasic taxonomic analysis, it was concluded that strains FP830T, FP2034, and FP2262 represented a novel species within the genus Pseudomonas, and Pseudomonas beijingensis sp. nov. was proposed for the name of novel species. The type strain is FP830T (=ACCC 62448T=JCM 35689T).
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Técnicas de Tipificación Bacteriana , Composición de Base , ADN Bacteriano , Ácidos Grasos , Hibridación de Ácido Nucleico , Oryza , Filogenia , Pseudomonas , ARN Ribosómico 16S , Rizosfera , Análisis de Secuencia de ADN , Microbiología del Suelo , Pseudomonas/genética , Pseudomonas/clasificación , Pseudomonas/aislamiento & purificación , ARN Ribosómico 16S/genética , ADN Bacteriano/genética , China , Ácidos Grasos/análisis , Oryza/microbiología , Hordeum/microbiología , Zea mays/microbiología , TibetRESUMEN
Background: Anthropogenic mediations contribute a significant role in stimulating positive reactions in soil-plant interactions; however, methodical reports on how anthropogenic activities impact soil microorganism-induced properties and soil health are still inadequate. In this study, we evaluated the influence of anthropogenic fertilization of farmland soil on barley rhizosphere microbial community structure and diversity, and the significant impacts on agro-ecosystem productivity. This will help validate the premise that soil amendment with prolonged synthetic fertilizers can lead to a significant reduction in bacterial abundance and diversity, while soils amended with organic fertilizers elicit the succession of the native soil microbial community and favor the growth of copiotrophic bacteria. Methods: The total metagenomic DNA was extracted from soils obtained from the barley rhizosphere under chemical fertilization (CB), organic fertilization (OB), and bulk soil (NB). Subsequently, these samples were sequenced using an amplicon-based sequencing approach, and the raw sequence dataset was examined using a metagenomic rast server (MG-RAST). Results: Our findings showed that all environments (CB, OB, and NB) shared numerous soil bacterial phyla but with different compositions. However, Bacteroidetes, Proteobacteria, and Actinobacteria predominated in the barley rhizosphere under chemical fertilization, organic fertilization, and bulk soils, respectively. Alpha and beta diversity analysis showed that the diversity of bacteria under organic barley rhizosphere was significantly higher and more evenly distributed than bacteria under chemical fertilization and bulk soil. Conclusion: Understanding the impact of conventional and organic fertilizers on the structure, composition, and diversity of the rhizosphere microbiome will assist in soil engineering to enhance microbial diversity in the agroecosystem.
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Fertilizantes , Hordeum , Rizosfera , Microbiología del Suelo , Hordeum/microbiología , Fertilizantes/análisis , Microbiota , Bacterias/genética , Bacterias/clasificación , Suelo/químicaRESUMEN
Fusarium crown rot (FCR) caused by Fusarium pseudograminearum poses a significant threat to wheat production in the Huang-Huai-Hai region of China. However, the pathogenic mechanism of F. pseudograminearum is still poorly understood. Zn2Cys6 transcription factors, which are exclusive to fungi, play pivotal roles in regulating fungal development, drug resistance, pathogenicity, and secondary metabolism. In this study, we present the functional characterization of a Zn2Cys6 transcription factor F. pseudograminearum, designated Fp487. In F. pseudograminearum, Fp487 is shown to be required for mycelial growth through gene knockout and phenotypic analyses. Compared with wild-type CF14047, the ∆Fp487 mutant displayed a slight reduction in growth rate but a significant decrease in conidiogenesis, pathogenicity and 3-acetyl-deoxynivalenol (3AcDON) production. Moreover, the mutant exhibited heightened sensitivity to oxidative and cytomembrane stress. Furthermore, we synthesized dsRNA from the Fp487 gene in vitro, resulting in a reduction in the growth rate of F. pseudograminearum and its virulence on barley leaves through spray-induced gene silencing (SIGS). Notably, this study makes the first instance of inducing the expression of abundant dsRNA from F. pseudograminearum by engineering the Escherichia coli strain HT115 (DE3) and utilizing the SIGS technique to evaluate the virulence effect of dsRNA on F. pseudograminearum. In conclusion, our findings revealed the crucial role of Fp487 in regulating pathogenicity, stress responses, DON production, and conidiogenesis in F. pseudograminearum. Furthermore, Fp487 is a potential RNAi-based target for FCR control.
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Proteínas Fúngicas , Fusarium , Regulación Fúngica de la Expresión Génica , Hordeum , Enfermedades de las Plantas , Factores de Transcripción , Fusarium/genética , Fusarium/patogenicidad , Fusarium/crecimiento & desarrollo , Fusarium/metabolismo , Enfermedades de las Plantas/microbiología , Virulencia , Proteínas Fúngicas/genética , Proteínas Fúngicas/metabolismo , Factores de Transcripción/genética , Factores de Transcripción/metabolismo , Hordeum/microbiología , Esporas Fúngicas/crecimiento & desarrollo , Esporas Fúngicas/genética , Triticum/microbiología , Hojas de la Planta/microbiología , Técnicas de Inactivación de Genes , China , Micelio/crecimiento & desarrollo , Silenciador del GenRESUMEN
Most of the research on the characterization of Fusarium species focused on wheat, barley, rice, and maize in China. However, there has been limited research in highland barley (qingke). Recently, Fusarium head blight (FHB) of qingke was recently observed in Tibet, China, especially around the Brahmaputra River. To gain a better understanding of the pathogens involver, 201 Fusarium isolates were obtained from qingke samples in 2020. Among these isolates, the most abundant species was F. avenaceum (45.3 %), followed by F. equiseti (27.8 %), F. verticillioides (13.9 %), F. acuminatum (9.0 %), F. flocciferum (3.5 %), and F. proliferatum (0.5 %). The distribution of Fusarium species varied along the Brahmaputra River, with F. avenaceum being predominant in the midstream and downstream regions, while F. equiseti was more common in the upstream region. Chemical analyses of all the isolates revealed the production of different mycotoxins by various Fusarium species. It was found that enniatins were produced by F. acuminatum, F. avenaceum, and F. flocciferum, beauvericin (BEA) and fumonisins were produced F. proliferatum and F. verticillioides, and zearalenone (ZEN) and nivalenol (NIV) were produced by F. equiseti. Pathogenicity test showed that F. avenaceum was more aggressive in causing FHB compared to F. acuminatum, F. equiseti, and F. flocciferum. The disease severity, measured by the area under the disease progress curve (AUDPC), was significantly positively (P < 0.01) correlated with the concentration of total toxins produced by each species. Furthermore, all the Fusarium strains which were used for pathogenicity test were susceptible to carbendazim, and the 50 % effective concentration (EC50) ranged from 0.406 µg/mL to 0.673 µg/mL with an average EC50 of 0.551 ± 0.012 µg/mL.
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Fusarium , Hordeum , Micotoxinas , Enfermedades de las Plantas , Fusarium/clasificación , Fusarium/aislamiento & purificación , Fusarium/genética , Fusarium/patogenicidad , Hordeum/microbiología , Tibet , Enfermedades de las Plantas/microbiología , Micotoxinas/metabolismoRESUMEN
The barley powdery mildew fungus, Blumeria hordei (Bh), secretes hundreds of candidate secreted effector proteins (CSEPs) to facilitate pathogen infection and colonization. One of these, CSEP0008, is directly recognized by the barley nucleotide-binding leucine-rich-repeat (NLR) receptor MLA1 and therefore is designated AVRA1. Here, we show that AVRA1 and the sequence-unrelated Bh effector BEC1016 (CSEP0491) suppress immunity in barley. We used yeast two-hybrid next-generation interaction screens (Y2H-NGIS), followed by binary Y2H and in planta protein-protein interactions studies, and identified a common barley target of AVRA1 and BEC1016, the endoplasmic reticulum (ER)-localized J-domain protein HvERdj3B. Silencing of this ER quality control (ERQC) protein increased Bh penetration. HvERdj3B is ER luminal, and we showed using split GFP that AVRA1 and BEC1016 translocate into the ER signal peptide-independently. Overexpression of the two effectors impeded trafficking of a vacuolar marker through the ER; silencing of HvERdj3B also exhibited this same cellular phenotype, coinciding with the effectors targeting this ERQC component. Together, these results suggest that the barley innate immunity, preventing Bh entry into epidermal cells, requires ERQC. Here, the J-domain protein HvERdj3B appears to be essential and can be regulated by AVRA1 and BEC1016. Plant disease resistance often occurs upon direct or indirect recognition of pathogen effectors by host NLR receptors. Previous work has shown that AVRA1 is directly recognized in the cytosol by the immune receptor MLA1. We speculate that the AVRA1 J-domain target being inside the ER, where it is inapproachable by NLRs, has forced the plant to evolve this challenging direct recognition.
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Ascomicetos , Retículo Endoplásmico , Hordeum , Enfermedades de las Plantas , Inmunidad de la Planta , Proteínas de Plantas , Hordeum/microbiología , Hordeum/genética , Hordeum/inmunología , Ascomicetos/patogenicidad , Proteínas de Plantas/metabolismo , Proteínas de Plantas/genética , Retículo Endoplásmico/metabolismo , Enfermedades de las Plantas/microbiología , Enfermedades de las Plantas/inmunología , Inmunidad de la Planta/genética , Proteínas Fúngicas/metabolismo , Proteínas Fúngicas/genética , Dominios ProteicosRESUMEN
Barley (Hordeum vulgare) is essential to global food systems and the brewing industry. Its physiological traits and microbial communities determine malt quality. Although microbes influence barley from seed health to fermentation, there is a gap in metagenomic insights during seed storage. Crucially, elucidating the changes in microbial composition associated with barley seeds is imperative for understanding how these fluctuations can impact seed health and ultimately, influence both agricultural yield and quality of barley-derived products. Whole metagenomes were sequenced from eight barley seed samples obtained at different storage time points from harvest to nine months. After binning, 82 metagenome-assembled genomes (MAGs) belonging to 26 distinct bacterial genera were assembled, with a substantial proportion of potential novel species. Most of our MAG dataset (61%) showed over 90% genome completeness. This pioneering barley seed microbial genome retrieval provides insights into species diversity and structure, laying the groundwork for understanding barley seed microbiome interactions at the genome level.
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Hordeum , Semillas , Hordeum/microbiología , Hordeum/genética , Semillas/microbiología , Metagenoma , Microbiota , Metagenómica , Genoma Microbiano , Genoma Bacteriano , Bacterias/genética , Bacterias/clasificaciónRESUMEN
Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) is a traditional non-culture technique that can provide a fingerprint of the microbial community. In the field of gut microbiota analysis, PCR-DGGE still holds potential for development. In the present study, we utilized an improved nested PCR-DGGE approach targeting the V3 region of 16S ribosomal DNA to investigate the impact of whole grain highland hull-less barley (WHLB), a cereal known for its significant hypocholesterolemic effect, on the gut microbiota profiles of high-fat diet rats. Seventy-two male Sprague-Dawley rats were divided into four groups and fed a normal control diet, a high-fat diet, or a high-fat diet supplemented with a low or high dose of WHLB for 4 or 8 weeks. The results revealed that the dominant bands varied among different dose groups and further changed with different treatment times. The compositions of bacterial communities in feces and cecal content were similar, but the dominant bacterial bands differed. After performing double DGGE, extracting the bands, sequencing the DNA, and aligning the sequences, a total of 19 bands were classified under the Firmicutes and Bacteroidetes phyla, while two bands were identified as unclassified uncultured bacteria. The relative abundance of Lactobacillus gasseri, Uncultured Prevotella sp., and Clostridium sp. increased following the administration of WHLB. Illumina-based sequencing was employed to assess the reliability of DGGE, demonstrating its reliability in analyzing the dominant taxonomic composition, although it may have limitations in accurately detecting the alpha diversity of bacterial species. IMPORTANCE: While next-generation sequencing has overshadowed polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), the latter still holds promise for advancing gut microbiota analysis due to its unique advantages. In this study, we used optimized nested PCR-DGGE to investigate the gut microbiota profile of high-fat diet rats after administering whole grain highland hull-less barley. High-throughput sequencing was employed to validate the DGGE results. Our results proved the reliability of PCR-DGGE for analyzing the dominant taxonomic composition while also providing visual evidence of a notable relationship between the composition of cecal and fecal microbial communities, highlighting substantial differences in both richness and abundance.
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Bacterias , Electroforesis en Gel de Gradiente Desnaturalizante , Dieta Alta en Grasa , Microbioma Gastrointestinal , Hordeum , ARN Ribosómico 16S , Ratas Sprague-Dawley , Granos Enteros , Animales , Hordeum/microbiología , Masculino , Ratas , Microbioma Gastrointestinal/genética , Bacterias/clasificación , Bacterias/genética , Bacterias/aislamiento & purificación , ARN Ribosómico 16S/genética , Heces/microbiología , ADN Bacteriano/genética , Reacción en Cadena de la Polimerasa/métodos , Ciego/microbiologíaRESUMEN
This research explored the impact of binary cereal blends [barley with durum wheat (DW) and soft wheat (CW)], four autochthonous yeast strains (9502, 9518, 14061 and 17290) and two refermentation sugar concentrations (6-9 g/L), on volatolomics (VOCs) and odour profiles of craft beers using unsupervised statistics. For the first time, we applied permutation test to select volatiles with higher significance in explaining variance among samples. The unsupervised approach on the 19 selected VOCs revealed cereal-yeast interaction to be the main source of variability and DW-9502-6/9, DW-17290-6, CW-17290-6 and CW-9518-6 being the best technological strategies. In particular, in samples DW-9502-6/9, concentrations of some of the selected volatiles were observed to be approximately three to more than seven times higher than the average. PLS-correlation between VOCs and odour profiles proved to be very useful in assessing the weight of each of the selected VOCs on the perception of odour notes.
Asunto(s)
Cerveza , Odorantes , Compuestos Orgánicos Volátiles , Cerveza/análisis , Odorantes/análisis , Compuestos Orgánicos Volátiles/química , Compuestos Orgánicos Volátiles/análisis , Análisis Multivariante , Triticum/química , Triticum/genética , Hordeum/química , Hordeum/genética , Hordeum/microbiología , Humanos , FermentaciónRESUMEN
Invasive fungal pathogens pose a substantial threat to widely cultivated crop species, owing to their capacity to adapt to new hosts and new environmental conditions. Gaining insights into the demographic history of these pathogens and unravelling the mechanisms driving coevolutionary processes are crucial for developing durably effective disease management programmes. Pyrenophora teres is a significant fungal pathogen of barley, consisting of two lineages, Ptt and Ptm, with global distributions and demographic histories reflecting barley domestication and spread. However, the factors influencing the population structure of P. teres remain poorly understood, despite the varietal and environmental heterogeneity of barley agrosystems. Here, we report on the population genomic structure of P. teres in France and globally. We used genotyping-by-sequencing to show that Ptt and Ptm can coexist in the same area in France, with Ptt predominating. Furthermore, we showed that differences in the vernalization requirement of barley varieties were associated with population differentiation within Ptt in France and at a global scale, with one population cluster found on spring barley and another population cluster found on winter barley. Our results demonstrate how cultivation conditions, possibly associated with genetic differences between host populations, can be associated with the maintenance of divergent invasive pathogen populations coexisting over large geographic areas. This study not only advances our understanding of the coevolutionary dynamics of the Pt-barley pathosystem but also prompts further research on the relative contributions of adaptation to the host versus adaptation to abiotic conditions in shaping Ptt populations.
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Ascomicetos , Hordeum , Enfermedades de las Plantas , Hordeum/microbiología , Enfermedades de las Plantas/microbiología , Francia , Ascomicetos/genética , Interacciones Huésped-Patógeno/genética , Filogenia , VernalizaciónRESUMEN
Plant-associated microbes play vital roles in promoting plant growth and health, with plants secreting root exudates into the rhizosphere to attract beneficial microbes. Exudate composition defines the nature of microbial recruitment, with different plant species attracting distinct microbiota to enable optimal adaptation to the soil environment. To more closely examine the relationship between plant genotype and microbial recruitment, we analysed the rhizosphere microbiomes of landrace (Chevallier) and modern (NFC Tipple) barley (Hordeum vulgare) cultivars. Distinct differences were observed between the plant-associated microbiomes of the 2 cultivars, with the plant-growth promoting rhizobacterial genus Pseudomonas substantially more abundant in the Tipple rhizosphere. Striking differences were also observed between the phenotypes of recruited Pseudomonas populations, alongside distinct genotypic clustering by cultivar. Cultivar-driven Pseudomonas selection was driven by root exudate composition, with the greater abundance of hexose sugars secreted from Tipple roots attracting microbes better adapted to growth on these metabolites and vice versa. Cultivar-driven selection also operates at the molecular level, with both gene expression and the abundance of ecologically relevant loci differing between Tipple and Chevallier Pseudomonas isolates. Finally, cultivar-driven selection is important for plant health, with both cultivars showing a distinct preference for microbes selected by their genetic siblings in rhizosphere transplantation assays.
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Genotipo , Hordeum , Microbiota , Raíces de Plantas , Pseudomonas , Rizosfera , Hordeum/microbiología , Hordeum/genética , Hordeum/metabolismo , Raíces de Plantas/microbiología , Raíces de Plantas/metabolismo , Microbiota/fisiología , Microbiota/genética , Pseudomonas/genética , Pseudomonas/metabolismo , Pseudomonas/fisiología , Microbiología del Suelo , Exudados de Plantas/metabolismoRESUMEN
Host genotype affects microbiome composition in many plants, but the mechanisms and implications of this phenomenon are understudied. New work in PLOS Biology illustrates how host genotype leads to differential gene expression and fitness in bacteria of the barley rhizosphere.
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Hordeum , Microbiota , Rizosfera , Microbiota/genética , Hordeum/microbiología , Hordeum/genética , Microbiología del Suelo , Genotipo , Bacterias/genética , Bacterias/clasificación , Raíces de Plantas/microbiología , Raíces de Plantas/genéticaRESUMEN
Despite many recent studies on non-alcoholic fatty liver disease (NAFLD) therapeutics, the optimal treatment has yet to be determined. In this unfinished project, we combined secondary metabolites (SMs) from the gut microbiota (GM) and Hordeum vulgare (HV) to investigate their combinatorial effects via network pharmacology (NP). Additionally, we analyzed GM or barley - signalling pathways - targets - metabolites (GBSTMs) in combinatorial perspectives (HV, and GM). A total of 31 key targets were analysed via a protein-protein interaction (PPI) network, and JUN was identified as the uppermost target in NAFLD. On a bubble plot, we revealed that apelin signalling pathway, which had the lowest enrichment factor antagonize NAFLD. Holistically, we scrutinized GBSTM to identify key components (GM, signalling pathways, targets, and metabolites) associated with the Apelin signalling pathway. Consequently, we found that the primary GMs (Eubacterium limosum, Eggerthella sp. SDG-2, Alistipes indistinctus YIT 12060, Odoribacter laneus YIT 12061, Paraprevotella clara YIT 11840, Paraprevotella xylaniphila YIT 11841) to ameliorate NAFLD. The molecular docking test (MDT) suggested that tryptanthrin-JUN is an agonist, conversely, dihydroglycitein-HDAC5, 1,3-diphenylpropan-2-ol-NOS1, and (10[(Acetyloxy)methyl]-9-anthryl)methyl acetate-NOS2, which are antagonistic conformers in the apelin signalling pathway. Overall, these results suggest that combination therapy could be an effective strategy for treating NAFLD.