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Fungal Diversity and Community Shifts In Molecular Approaches to Estimating Soil Fungal Diversity and Community Shifts in Response to Land-Use Change by Jason Alexander Jackson Program in Ecology Duke University Date:_______________________ Approved: ___________________________ Daniel deB. Richter, Co-Chair ___________________________ Rytas J. Vilgalys, Co-Chair ___________________________ Emily S. Bernhardt ___________________________ Shuijin Hu ___________________________ Justin P. Wright Dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Program in Ecology in the Graduate School of Duke University 2010 i v ABSTRACT Molecular Approaches to Estimating Soil Fungal Diversity and Community Shifts in Response to Land-Use Change by Jason Alexander Jackson Program in Ecology Duke University Date:_______________________ Approved: ___________________________ Daniel deB. Richter, Co-Chair ___________________________ Rytas J. Vilgalys, Co-Chair ___________________________ Emily S. Bernhardt ___________________________ Shuijin Hu ___________________________ Justin P. Wright An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Program in Ecology in the Graduate School of Duke University 2010 i v Copyright by Jason Alexander Jackson 2010 Abstract The Piedmont region of the southeastern United States has undergone considerable land-use change since settlement by Europeans and Africans. Forests were cleared for agriculture, followed centuries later by land abandonment. Following abandonment, natural recruitment, plantings for erosion control, and plantation forestry have resulted in a large area of the region covered by loblolly pine, Pinus taeda. Today, the Piedmont is a mosaic of farm fields, pastures, pine forests, and relic woodlots. The Calhoun Experimental Forest, located in Union County, SC, has provided a unique history of land use change’s alteration of soil properties and processes, the ability of reforestation to restore or deplete soil fertility, and provided insights into the effects this change has on biological diversity. In this work, the diversity of fungi living in soil is examined in the context of land-use change and soil biogeochemical change in and around the Calhoun Forest. This study uses molecular tools to identify fungal species from soil and to identify mycorrhizal associates of loblolly pine in a bioassay of propagule diversity, and proposes a novel use of quantitative PCR to quantify the relative abundance of major fungal families affected by land-use change. Fungal diversity in soils is high in all land uses, but fungal communities shift from agricultural field communities largely comprised of unicellular ascomycetes and iv basal lineages to forest communities dominated by saprophytic and symbiotic basidiomycetes. In addition to this shift across a land use gradient, fungal communities are also responding to changes in carbon quantity and quality, biologically available nitrogen and phosphorus, pH, acidity and texture. ECM propagule communities also differ across a land use gradient of cultivated fields, grasslands, pine forests, and mixed hardwood stands. There are few ECM propagules able to associate with loblolly pine in cultivated and grassland soils. There is a trend towards higher ECM diversity in the hardwood and pine soils, and both of those soil communities are distinct from each other as well as from soils from field treatments. Quantitative PCR, coupled with a nested set of taxon-specific, fungal primers, is a potential way to estimate the abundance of the given taxon relative to all fungi in an environmental DNA. Primers specific to several taxonomic level of fungi were tested to confirm amplification in PCR, then were tested for taxonomic specificity by generating clone libraries with environmental DNA. Several of the successful primers were tested with soil DNA extracts in QPCR and the calculated ratios of fungal abundance varied widely by method of analysis. The results suggest that many repeated measurements and many replicates are required for a robust estimate of the relative abundance of a specific taxon. v Dedication To William and Luke. Be bold, my sons, but always compassionate and clever in your boldness. vi Contents Abstract ......................................................................................................................................... iv List of Tables ................................................................................................................................. xi List of Figures .............................................................................................................................xiv List of Abbreviations ............................................................................................................... xvii Acknowledgements ................................................................................................................ xviii 1. Introduction ............................................................................................................................... 1 1.1 An old issue in a new light .............................................................................................. 1 1.2 Fungi in forests ................................................................................................................. 3 1.3 Soils of the Piedmont ....................................................................................................... 5 1.4 Land use change ............................................................................................................... 6 1.5 Molecular methods ........................................................................................................... 7 1.6 Diversity and land use change ....................................................................................... 8 1.7 Study Outline .................................................................................................................... 9 2. Using DNA libraries to estimate diversity and change in eukaryotic and fungal communities ................................................................................................................................ 11 2.1 Introduction ..................................................................................................................... 12 2.2 Methods ........................................................................................................................... 13 2.2.1 Site description .......................................................................................................... 13 2.2.2 Soil collection ............................................................................................................. 14 2.2.3 Edaphic properties .................................................................................................... 14 vii 2.2.4 Clone library construction and sequencing ........................................................... 15 2.2.5 Data analysis .............................................................................................................. 16 2.2.5.1 Fungal ITS libraries ............................................................................................ 16 2.2.5.2 Eukaryotic SSU libraries ................................................................................... 17 2.3 Results .............................................................................................................................. 18 2.3.1 Soil properties ............................................................................................................ 18 2.3.2 Diversity of soil communities .................................................................................. 19 2.3.3 Ordination of soil communities ............................................................................... 32 2.4 Discussion ........................................................................................................................ 38 2.4.1 Land use and edaphic properties ............................................................................ 38 2.4.2 Communities and environmental gradients .......................................................... 39 2.4.3 Land use and taxonomic diversity .......................................................................... 42 2.4.4 Challenges for molecular microbial ecology ......................................................... 44 2.5 Summary .......................................................................................................................... 45 3. A seedling bioassay to measure diversity of ECM propagules ........................................ 47 3.1 Introduction ..................................................................................................................... 47 3.2 Methods ........................................................................................................................... 50 3.2.1 Soil collection and seedling plantings .................................................................... 50 3.2.2 Seedling harvest ......................................................................................................... 51 3.2.3 Root tip clone libraries .............................................................................................. 52 3.2.4 Data analysis .............................................................................................................
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