Species Diversity, Ecology and Laccase Gene Diversity of Saprotrophic Fungi Across Different Plant Community Types

This dissertation explores the diversity, ecology and functional diversity of saprotrophic fungal across different plant community types. Saprotrophic fungi are responsible for recycling the majority of carbon from dead organic matter and have the unique ability to break down and release nutrients that can then be readily available for other organisms. A number of different biotic and abiotic factors affect the structure of saprotrophic fungal communities. Here, we investigated the effects of nutrient addition, substrate availability, and dominant plant community type on the structure and diversity of saprotrophic fungal communities. In addition, we investigated the diversity and structure of functional diversity of saprotrophic fungal communities. The first chapter explores saprotrophic fungal diversity found in leaf litter in a diverse lowland tropical forest. We investigated the affect of nutrient addition on the saptrotrophic fungal community using a replicated factorial N, P, K, micronutrient fertilization experiment. We found that the control plots had the lowest alpha diversity compared to treatments that received fertilization. The long-term addition of nutrients increased species richness relative to controls and had an effect on taxonomic composition of the leaf litter fungal communities at lower taxonomic levels, but not at higher taxonomic levels.The second chapter characterizes saprotrophic fungal communities on straw and wood substrates across forest and grassland plant community types and characterized how these communities changed over time as substrate quality changed. The goal was to determine if substrate, space, time or plant community were the major determinants of fungal saprotrophic community composition. We found that the wood substrates collected in the grassland and forest had the highest richness, estimated richness and phylogenetic diversity. Overall, there was a decrease in richness on the substrates in both plant communities over time, and plant community type appears to have a greater influence on saprotrophic fungal community structure than substrate type or substrate quality. In the third chapter, we investigated the diversity of saprotrophic basidiomycete laccase genes in grassland and forest plant community types and on straw and wood substrates. Functional diversity was assessed by the functional gene encoding laccase. Laccases play an important role in soil organic matter turnover and are able to completely degrade lignin. We found that the wood substrates had significantly higher richness of estimated OTUs as compared to the straw substrates. Laccase gene diversity was compared to basidiomycete diversity. We also found that both the laccase genes and basidiomycete assemblages associated strongly with plant community type

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Utilizing novel diversity estimators to quantify multiple dimensions of microbial biodiversity across domains

Abstract Background Microbial ecologists often employ methods from classical community ecology to analyze microbial community diversity. However, these methods have limitations because microbial communities differ from macro-organismal communities in key ways. This study sought to quantify microbial diversity using methods that are better suited for data spanning multiple domains of life and dimensions of diversity. Diversity profiles are one novel, promising way to analyze microbial datasets. Diversity profiles encompass many other indices, provide effective numbers of diversity (mathematical generalizations of previous indices that better convey the magnitude of differences in diversity), and can incorporate taxa similarity information. To explore whether these profiles change interpretations of microbial datasets, diversity profiles were calculated for four microbial datasets from different environments spanning all domains of life as well as viruses. Both similarity-based profiles that incorporated phylogenetic relatedness and naïve (not similarity-based) profiles were calculated. Simulated datasets were used to examine the robustness of diversity profiles to varying phylogenetic topology and community composition. Results Diversity profiles provided insights into microbial datasets that were not detectable with classical univariate diversity metrics. For all datasets analyzed, there were key distinctions between calculations that incorporated phylogenetic diversity as a measure of taxa similarity and naïve calculations. The profiles also provided information about the effects of rare species on diversity calculations. Additionally, diversity profiles were used to examine thousands of simulated microbial communities, showing that similarity-based and naïve diversity profiles only agreed approximately 50% of the time in their classification of which sample was most diverse. This is a strong argument for incorporating similarity information and calculating diversity with a range of emphases on rare and abundant species when quantifying microbial community diversity. Conclusions For many datasets, diversity profiles provided a different view of microbial community diversity compared to analyses that did not take into account taxa similarity information, effective diversity, or multiple diversity metrics. These findings are a valuable contribution to data analysis methodology in microbial ecology

Nutrient and stress tolerance traits linked to fungal responses to global change: Four case studies

In this case study analysis, we identified fungal traits that were associated with the responses of taxa to 4 global change factors: elevated CO2, warming and drying, increased precipitation, and nitrogen (N) enrichment. We developed a trait-based framework predicting that as global change increases limitation of a given nutrient, fungal taxa with traits that target that nutrient will represent a larger proportion of the community (and vice versa). In addition, we expected that warming and drying and N enrichment would generate environmental stress for fungi and may select for stress tolerance traits. We tested the framework by analyzing fungal community data from previously published field manipulations and linking taxa to functional gene traits from the MycoCosm Fungal Portal. Altogether, fungal genera tended to respond similarly to 3 elements of global change: increased precipitation, N enrichment, and warming and drying. The genera that proliferated under these changes also tended to possess functional genes for stress tolerance, which suggests that these global changes-even increases in precipitation-could have caused environmental stress that selected for certain taxa. In addition, these genera did not exhibit a strong capacity for C breakdown or P acquisition, so soil C turnover may slow down or remain unchanged following shifts in fungal community composition under global change. Since we did not find strong evidence that changes in nutrient limitation select for taxa with traits that target the more limiting nutrient, we revised our trait-based framework. The new framework sorts fungal taxa into Stress Tolerating versus C and P Targeting groups, with the global change elements of increased precipitation, warming and drying, and N enrichment selecting for the stress tolerators