Browsing by Author "Kinkel, Linda"

Now showing 1 - 5 of 5
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    Cedar Creek enemy removal experiment: 2013 - 2014 The effect of foliar fungicide on soil fungala microbiomes
    (2017-10-05) Song, Zewei; Schlatter, Daniel; Hanson, Lindsey; Kinkel, Linda; songzewei@outlook.com; Song, Zewei
    This archive contains the sequencing data we used to characterizing the soil fungal microbiomes in the University of Minnesota Cedar Creek BigBio enemy removal experiment. For this project, we sampled soil microbiomes from control and foliar fungicide plots in both monoculture and 16 species polyculture at 2013 and 2014.
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    Effort Versus Reward: Preparing samples for fungal community characterization in high-throughput sequencing surveys of soils
    (2015-03-25) Song, Zewei; Schlatter, Dan; Kennedy, Peter; Kinkel, Linda; Kistler, H.Corby; Nguyen, Nhu; Bates, Scott; songx208@umn.edu; Song, Zewei
    Next generation fungal amplicon sequencing is being used with increasing frequency to study fungal diversity in various ecosystems; however, the influence of sample preparation on the characterization of fungal community is poorly understood. We investigated the effects of four procedural modifications to library preparation for high-throughput sequencing (HTS). The following treatments were considered: 1) the amount of soil used in DNA extraction, 2) the inclusion of additional steps (freeze/thaw cycles, sonication, or hot water bath incubation) in the extraction procedure, 3) the amount of DNA template used in polymerase chain reaction (PCR), and 4) the effect of sample pooling, either physically or computationally. Soils from two different ecosystems in Minnesota, USA, one prairie and one forest site, were used to assess the generality of our results. The first three treatments did not significantly influence observed fungal operational taxonomic unit (OTU) richness or community structure at either site. Physical pooling captured more OTU richness compared to individual samples, but total OTU richness at each site was highest when individual samples were computationally combined. We conclude that standard extraction kit protocols are well optimized for fungal HTS surveys, but because sample pooling can significantly influence OTU richness estimates, it is important to carefully consider the study aims when planning sampling procedures.
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    IPM Control of White Mold in Irrigated White Beans
    (St. Paul, MN: University of Minnesota Extension Service, 1999) Meronuck, Richard A.; Duellman, Kasia; Kinkel, Linda; Wright, Jerry; Rehm, George; Wiens, Mel
    White mold continues to be a "pesky" yield limiting disease in dry beans everywhere the crop is grown. Refinements to three common production practices can help reduce white mold in irrigated dry edible beans grown on sandy soils by providing a more effective integrated pest management (IPM) program.
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    Plant Signaling Compounds Alter Secondary Metabolite Production Among Antagonistic Streptomyces
    (2009-10-07) Bakker, Matthew; Salomon, Christine; Kinkel, Linda
    Streptomycetes have been implicated in the control of soil-borne plant pathogens, and are known to produce an extensive array of antimicrobial secondary metabolites. We investigated the hypothesis that plants manipulate the production of secondary metabolites by streptomycetes. We tested a collection of diverse Streptomyces isolates for responses to potential signaling molecules produced by plants, including plant hormones, flavonoids, sesquiterpene lactones, and crude root exudates. Secondary metabolite production was investigated with the use of high performance liquid chromatography (HPLC) and bioassays for inhibitory activity. We found evidence that streptomycetes respond to plant-produced compounds with altered patterns of secondary metabolite production. Streptomyces isolates in our study had the ability to chemically modify and produce close analogs of plant-derived compounds. The production of similar chemical compounds may facilitate cross-kingdom communication. Our work suggests the potential for plants to manipulate the activities of soil microbial communities, which may confer a selective advantage in suppression of plant pathogens. These results concur with studies from many different systems showing that microbial activity is tightly linked with the health and functioning of higher organisms.
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    Special crop research grand (SCRG) - MnDRIVE potato biocontrol 2014 experiment
    (2017-10-05) Song, Zewei; Hanson, Lindsey; Kinkel, Linda; songzewei@outlook.com; Song, Zewei
    This is the sequencing data for characterizing the soil microbiomes (fungal and bacterial communties) following the application of bacterial inoculations as biocontrols of potato tuber disease. The archived files are raw sequencing data. The detailed processing pipeline will be included in the incoming peer reviewed paper.