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  • 1
    In: Phytopathology®, Scientific Societies
    Abstract: Fire blight, caused by Erwinia amylovora, is a destructive disease of pome fruit trees. In the United States, apple and pear growers rely on applications of copper and antibiotics during bloom to control fire blight, but such methods have already led to regional instances of resistance. In this study, we used transcriptome analyses and field trials to evaluate the effectiveness of three commercially available plant defense elicitors and one plant growth regulator for fire blight management. Our data indicated that foliar applications of acibenzolar-S-methyl (ASM; Actigard® 50WG) triggered a strong defense-related response in apple leaves whereas the applications of Bacillus mycoides isolate J (LifeGard® WG) or Reynoutria sachalinensis extract (Regalia®) did not. Genes upregulated by ASM were enriched in the biological processes associated with plant immunity, such as defense response and protein phosphorylation. The expression of several pathogenesis-related (PR) genes was induced by ASM as well. Surprisingly, many differentially expressed genes in ASM-treated apple leaves overlapped with those induced by treatment with prohexadione-calcium (ProCa; Apogee®), a plant growth regulator that suppresses shoot elongation. Further analysis suggested that ProCa likely acts similarly to ASM to stimulate plant immunity, since genes involved in plant defense were shared and significantly upregulated ( 〉 2-fold) by both treatments. Our field trials agreed with the transcriptome study, demonstrating that ASM and ProCa exhibit the best control performance relative to the other biopesticides. Taken together, these data are pivotal for the understanding of plant response and shed light on future improvements of strategies for fire blight management.
    Type of Medium: Online Resource
    ISSN: 0031-949X , 1943-7684
    Language: English
    Publisher: Scientific Societies
    Publication Date: 2023
    detail.hit.zdb_id: 2037027-1
    SSG: 12
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  • 2
    In: Phytopathology®, Scientific Societies
    Abstract: Fire blight, a disease of pome fruits caused by the bacterium Erwinia amylovora, has become increasingly difficult to manage after the emergence of streptomycin-resistant strains. Alternative antibiotics and copper are available; however, these chemicals have use restrictions in some countries and also can carry risks of phytotoxicity. Therefore, there is growing interest in biological-based management options, with bacteriophage (phages) showing promise, as these naturally occurring pathogens of bacteria are easy to isolate and grow. However, there are several technical challenges regarding the implementation of phage biocontrol in the field as the viral molecules suffer from ultraviolet radiation (UVR) degradation and can die off rapidly in the absence of the host bacterium. In this work we assessed the efficacy of Erwinia phages and a commercial phage product for blossom blight control in the field across multiple locations in the eastern United States. In these tests, disease control ranged from 0.0 to 82.7%, and addition of a UVR protectant only resulted in significantly increased disease control in 2 of 12 tests. We also analyzed microbial community population changes in response to phage application. Changes in bacterial community diversity metrics over time were not detected, however relative abundances of target taxa were temporarily reduced after phage applications, indicating that these phage applications did not have deleterious effects on the flower microbiome. We have demonstrated that biological control of fire blight with phages is achievable, but a better understanding of phage:pathogen dynamics is required to optimize disease control efficacy.
    Type of Medium: Online Resource
    ISSN: 0031-949X , 1943-7684
    Language: English
    Publisher: Scientific Societies
    Publication Date: 2023
    detail.hit.zdb_id: 2037027-1
    SSG: 12
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  • 3
    Online Resource
    Online Resource
    Scientific Societies ; 2017
    In:  Phytobiomes Journal Vol. 1, No. 3 ( 2017-01), p. 158-168
    In: Phytobiomes Journal, Scientific Societies, Vol. 1, No. 3 ( 2017-01), p. 158-168
    Abstract: Manipulating plant-associated microbes to reduce disease or improve crop yields requires a thorough understanding of interactions within the phytobiome. Plants were sampled from a wheat/maize/soybean crop rotation site that implements four different crop management strategies. We analyzed the fungal and bacterial communities of leaves, stems, and roots of wheat throughout the growing season using 16S and fungal internal transcribed spacer 2 rRNA gene amplicon sequencing. The most prevalent operational taxonomic units (OTUs) were shared across all samples, although levels of the low-abundance OTUs varied. Endophytes were isolated from plants, and tested for antagonistic activity toward the wheat pathogen Fusarium graminearum. Antagonistic strains were assessed for plant protective activity in seedling assays. Our results suggest that microbial communities were strongly affected by plant organ and plant age, and may be influenced by management strategy.
    Type of Medium: Online Resource
    ISSN: 2471-2906 , 2471-2906
    Language: English
    Publisher: Scientific Societies
    Publication Date: 2017
    detail.hit.zdb_id: 2897163-2
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  • 4
    Online Resource
    Online Resource
    Scientific Societies ; 2023
    In:  Molecular Plant-Microbe Interactions® Vol. 36, No. 7 ( 2023-07), p. 411-424
    In: Molecular Plant-Microbe Interactions®, Scientific Societies, Vol. 36, No. 7 ( 2023-07), p. 411-424
    Abstract: Tar spot is a devasting corn disease caused by the obligate fungal pathogen Phyllachora maydis. Since its initial identification in the United States in 2015, P. maydis has become an increasing threat to corn production. Despite this, P. maydis has remained largely understudied at the molecular level, due to difficulties surrounding its obligate lifestyle. Here, we generated a significantly improved P. maydis nuclear and mitochondrial genome, using a combination of long- and short-read technologies, and also provide the first transcriptomic analysis of primary tar spot lesions. Our results show that P. maydis is deficient in inorganic nitrogen utilization, is likely heterothallic, and encodes for significantly more protein-coding genes, including secreted enzymes and effectors, than previous determined. Furthermore, our expression analysis suggests that, following primary tar spot lesion formation, P. maydis might reroute carbon flux away from DNA replication and cell division pathways and towards pathways previously implicated in having significant roles in pathogenicity, such as autophagy and secretion. Together, our results identified several highly expressed unique secreted factors that likely contribute to host recognition and subsequent infection, greatly increasing our knowledge of the biological capacity of P. maydis, which have much broader implications for mitigating tar spot of corn. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
    Type of Medium: Online Resource
    ISSN: 0894-0282 , 1943-7706
    Language: English
    Publisher: Scientific Societies
    Publication Date: 2023
    detail.hit.zdb_id: 2037108-1
    SSG: 12
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  • 5
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2017
    In:  BMC Bioinformatics Vol. 18, No. 1 ( 2017-12)
    In: BMC Bioinformatics, Springer Science and Business Media LLC, Vol. 18, No. 1 ( 2017-12)
    Type of Medium: Online Resource
    ISSN: 1471-2105
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2017
    detail.hit.zdb_id: 2041484-5
    SSG: 12
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  • 6
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2023
    In:  Microbiome Vol. 11, No. 1 ( 2023-06-15)
    In: Microbiome, Springer Science and Business Media LLC, Vol. 11, No. 1 ( 2023-06-15)
    Abstract: Hydrogen gas (H 2 ) is a common product of carbohydrate fermentation in the human gut microbiome and its accumulation can modulate fermentation. Concentrations of colonic H 2 vary between individuals, raising the possibility that H 2 concentration may be an important factor differentiating individual microbiomes and their metabolites. Butyrate-producing bacteria (butyrogens) in the human gut usually produce some combination of butyrate, lactate, formate, acetate, and H 2 in branched fermentation pathways to manage reducing power generated during the oxidation of glucose to acetate and carbon dioxide. We predicted that a high concentration of intestinal H 2 would favor the production of butyrate, lactate, and formate by the butyrogens at the expense of acetate, H 2 , and CO 2 . Regulation of butyrate production in the human gut is of particular interest due to its role as a mediator of colonic health through anti-inflammatory and anti-carcinogenic properties. Results For butyrogens that contained a hydrogenase, growth under a high H 2 atmosphere or in the presence of the hydrogenase inhibitor CO stimulated production of organic fermentation products that accommodate reducing power generated during glycolysis, specifically butyrate, lactate, and formate. Also as expected, production of fermentation products in cultures of Faecalibacterium prausnitzii strain A2-165, which does not contain a hydrogenase, was unaffected by H 2 or CO. In a synthetic gut microbial community, addition of the H 2 -consuming human gut methanogen Methanobrevibacter smithii decreased butyrate production alongside H 2 concentration. Consistent with this observation, M. smithii metabolic activity in a large human cohort was associated with decreased fecal butyrate, but only during consumption of a resistant starch dietary supplement, suggesting the effect may be most prominent when H 2 production in the gut is especially high. Addition of M. smithii to the synthetic communities also facilitated the growth of E. rectale , resulting in decreased relative competitive fitness of F. prausnitzii. Conclusions H 2 is a regulator of fermentation in the human gut microbiome. In particular, high H 2 concentration stimulates production of the anti-inflammatory metabolite butyrate. By consuming H 2 , gut methanogenesis can decrease butyrate production. These shifts in butyrate production may also impact the competitive fitness of butyrate producers in the gut microbiome.
    Type of Medium: Online Resource
    ISSN: 2049-2618
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
    detail.hit.zdb_id: 2697425-3
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  • 7
    Online Resource
    Online Resource
    Scientific Societies ; 2021
    In:  Phytobiomes Journal Vol. 5, No. 2 ( 2021-01), p. 202-219
    In: Phytobiomes Journal, Scientific Societies, Vol. 5, No. 2 ( 2021-01), p. 202-219
    Abstract: Microbiomes from maize and soybean were characterized in a long-term three-crop rotation research site, under four different land management strategies, to begin unraveling the effects of common farming practices on microbial communities. The fungal and bacterial communities of leaves, stems, and roots in host species were characterized across the growing season using amplicon sequencing and compared with the results of a similar study on wheat. Communities differed across hosts and among plant growth stages and organs, and these effects were most pronounced in the bacterial communities of the wheat and maize phyllosphere. Roots consistently showed the highest number of bacterial operational taxonomic units compared with aboveground organs, whereas the α-diversity of fungi was similar between above- and belowground organs. Network analyses identified putatively influential members of the microbial communities of the three host plant species. The fungal taxa specific to roots, stems, or leaves were examined to determine whether the specificity reflected their life histories based on previous studies. The analysis suggests that fungal spore traits are drivers of organ specificity in the fungal community. Identification of influential taxa in the microbial community and understanding how community structure of specific crop organs is formed will provide a critical resource for manipulations of microbial communities. The ability to predict how organ-specific communities are influenced by spore traits will enhance our ability to introduce them sustainably.
    Type of Medium: Online Resource
    ISSN: 2471-2906
    Language: English
    Publisher: Scientific Societies
    Publication Date: 2021
    detail.hit.zdb_id: 2897163-2
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  • 8
    In: Molecular Plant Pathology, Wiley, Vol. 23, No. 6 ( 2022-06), p. 855-869
    Abstract: The enterobacterial pathogen Erwinia amylovora uses multiple virulence‐associated traits to cause fire blight, a devastating disease of apple and pear trees. Many virulence‐associated phenotypes have been studied that are critical for virulence and pathogenicity. Despite the in vitro testing that has revealed how these systems are transcriptionally regulated, information on when and where in infected tissues these genes are being expressed is lacking. Here, we used a high‐throughput sequencing approach to characterize the transcriptome of E. amylovora during disease progression on apple flowers under field infection conditions. We report that type III secretion system genes and flagellar genes are strongly co‐expressed. Likewise, genes involved in biosynthesis of the exopolysaccharide amylovoran and sorbitol utilization had similar expression patterns. We further identified a group of 16 genes whose expression is increased and maintained at high levels throughout disease progression across time and tissues. We chose five of these genes for mutational analysis and observed that deletion mutants lacking these genes all display reduced symptom development on apple shoots. Furthermore, these induced genes were over‐represented for genes involved in sulphur metabolism and cycling, suggesting the possibility of an important role for maintenance of oxidative homeostasis during apple flower infection.
    Type of Medium: Online Resource
    ISSN: 1464-6722 , 1364-3703
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2022
    detail.hit.zdb_id: 2020755-4
    SSG: 12
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  • 9
    In: Functional Ecology, Wiley, Vol. 34, No. 10 ( 2020-10), p. 2075-2086
    Abstract: Global climate change and shifting land‐use are increasing plant stress due to abiotic factors such as drought, heat, salinity and cold, as well as via the intensification of biotic stressors such as herbivores and pathogens. The ability of plants to tolerate such stresses is modulated by the bacteria and fungi that live on or inside of plant tissues and comprise the plant microbiome. However, the impacts of diverse classes of beneficial members of the microbiome and the contrasting stresses that impact plants are most commonly studied independently of each other. Our meta‐analysis of 288 experiments across 89 studies moves beyond previous studies in that we simultaneously compare the roles of bacterial versus fungal microbiome members that live within plant tissues and colonize plant surfaces in ameliorating biotic versus abiotic sources of plant stress. The magnitude of microbial stress amelioration can be measured as the greater proportional impact of beneficial microbes on plant performance in more stressful environments. In the plant experiments we examine, the magnitude of microbial stress amelioration is substantial: it is 23% of the effect size of the typical impact of stress and 56% of the effect size of beneficial microbiome members in the absence of stress. The amount of benefit microbiome members confer to plants differs among classes of microbes, depending on whether plants are grown in stressful or non‐stressful environments. In the absence of stress, beneficial bacteria tend to confer greater plant benefits than do fungi. However, symbiotic fungi, especially arbuscular mycorrhizal fungi, more strongly ameliorate plant stress than do bacteria. In particular, beneficial microbes ameliorate salinity, foliar herbivory and fungal pathogen stress. These results highlight the fact that the impacts of beneficial and antagonistic components of the microbiome on plant performance depend on biotic and abiotic environmental contexts. Furthermore, beneficial microbes are especially critical for plant health in stressful environments and thus present opportunities to mitigate negative consequences of global change. A free plain language summary can be found within the Supporting Information of this article.
    Type of Medium: Online Resource
    ISSN: 0269-8463 , 1365-2435
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 2020307-X
    detail.hit.zdb_id: 619313-4
    SSG: 12
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