Browsing by Author "Song, Zewei"

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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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    Fungal Endophytes as Priority Colonizers Initiating Wood Decomposition
    (2016-06-23) Song, Zewei; Kennedy, Peter; Liew, Feng Jin; Schilling, Jonathan; schillin@umn.edu; Schilling, Jonathan
    Priority effects among wood decomposers have been demonstrated by manipulating fungal assembly history via inoculations in dead wood and then tracking community development using DNA sequencing. Individual wood-degrading fungi have been shown, however, to initiate decay after having colonized living trees as endophytes. To track these ‘upstream’ colonizers across the endophyte­saprophyte transition, we coupled high throughput sequencing with wood physiochemical analyses in stem sections extracted from healthy birch trees (Betula papyrifera; 4-7 cm dia.). We incubated wood in microcosms, limiting communities as endophytes­only or challenging endophytes with Fomes fomentarius or Piptoporus betulinus at high exogenous inoculum potential. Initial fungal richness in birch stems averaged 143 OTUs, and decreased nearly three-fold after five months of decomposition. Although F. fomentarius successfully colonized some stem sections incubated at 25°C, decayed wood was generally dominated by saprophytic fungi that were present originally in lower abundances as endophytes. Among saprophytes, fungi in the brown rot functional guild consistently dominated, matching wood residues bearing the chemical hallmarks of brown rot. Despite this functionally redundant outcome, the taxa that rose to dominate in individual sections varied. Surprisingly, the brown rot taxa dominating wood decomposition were better known for lumber degradation rather than log decay in ground contact. Given the isolation from colonizers in our design, this redundancy of brown rot as the outcome suggests that these taxa and more generally brown rot fungi could have adapted to decompose wood where there is lower competitive pressure. Competitive avoidance would complement the diffuse depolymerization mechanisms of brown rot fungi, which are likely more prone to sugar pilfering by other organisms than the processive depolymerization mechanisms of white rot fungi. Overall, this guild-level predictability of fungal endophyte development and consequence is encouraging given the challenges of predicting wood decomposition, and it provides a base for testing these dynamics under increasing natural complexity.
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    Measuring warfare in wood: linking competition among wood-degrading fungi of northern forests to its ecological consequences
    (2014-08) Song, Zewei
    Competition between distinctive groups of fungi determines the pattern of wood decomposition in forests, but the outcome of these battles may shift in a changing climate. With more than 70% of Earth's biotic carbon stored in woody tissues, understanding the processes that unlock this carbon and release the greenhouse gas CO2 is critical. For my thesis research, I am addressing several key questions about how fungi colonize and dominate wood on the forest floor. Quantitative PCR was developed to measure biomass of specific fungi from a community in Chapter one. This technique was coupled with ergosterol, dilute alkali solubility, pH and carbon component analysis to measure biotic and abiotic dynamic during wood decomposition. With these comprehensive tools, factors that may influence fungal competition and decomposition outcomes were studied in the following chapters. In Chapter two, wood type was shown not to influence the competition between a brown rot fungus and a white rot fungus. It is contrary to the observations on wood preferences in nature, but reflected different foraging strategies by fungi. This led to the study of Chapter three on priority effect. By increasing the inoculum potential either inside or outside wood substrate, I have shown evidence that a weak competitor fungus can outcompete its more aggressive opponents, thus achieving co-existence. Another two factors, temperature and endophytes, along with priority effect were studied in Chapter four. Endophytes showed a much larger effect in influencing wood decomposition than temperature, mostly through antagonisms against soil fungi. Studies on these factors reveals potential for a more comprehensive model for wood decomposition. Emphasis on the role of microbial components, especially the often neglected endophytic communities, is possible to explain the variability in wood decomposition that can not be explained by abiotic factors, alone.
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    Origin and development of fungal communities in an engineered biofilter
    (2017-05-09) Oliver, Jason; Song, Zewei; Schilling, Jonathan S; schillin@umn.edu; Schilling, Jonathan
    Microbial communities underpin the performance of biofilters used for treating pollutants, but community ‘seeding’ and development is not well understood, particularly for fungi. Fungi have unique biocatalytic potential in biofilters, and identifying their inoculum sources and community succession can inform design and management strategies to improve biofilter operation. Our goal was to track fungal community development in a full-scale woodchip biofilter treating air exhaust from a swine barn facility. We sequenced fungal ITS-1 amplicons 1) from potential inoculum sources (fresh wood chip media; manure from pits below pig housing) and 2) from wood chip biofilms at the inlet and outlet of the biofilter, sampling annually over 3 years. Inlet and outlet fungal communities were distinct at the outset, but became increasingly similar by year 3. A shift from Basidiomycetes and yeasts to Ascomycetes and molds was associated with a loss of richness as the community became dominated by fungi that originated from the manure exhaust. Notably, dominant taxa were pig skin dermatophytes, likely seeded continuously from within the barn. These patterns differ from those in natural wood decomposition studies, and the results suggest that hygiene within the barn will affect the performance of biofilters located outside of the barn, an aspect of biofilter management that has not been exploited. These ‘upstream’ inoculum effects may complicate management, however, our results identify several candidate fungi and an avenue for increasing inoculum potential on a continuous basis that might be valuable for seeding biofilters, improving control, and reduce lag-times during biofilter development.
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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.