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Author ORCID Identifier



Open Access Dissertation

Document Type


Degree Name

Doctor of Philosophy (PhD)

Degree Program


Year Degree Awarded


Month Degree Awarded


First Advisor

Klaus Nüsslein

Subject Categories

Bioinformatics | Biology | Environmental Microbiology and Microbial Ecology | Other Ecology and Evolutionary Biology | Terrestrial and Aquatic Ecology


In this dissertation several research studies are discussed that characterize the effects of anthropogenic, or human-induced, stress on both ammonia-oxidizing and total bacterial soil microbial communities. The disturbances of land-use change in tropical, South American rainforests and artificial warming and nitrogen (N) fertilization in temperate, North American forests were investigated as these disturbances represent past and current disturbances caused by human landscape alteration and climate change. Initially, the response of soil ammonia-oxidizing microbial communities to land-use change from primary rainforest to pasture and, finally, back to secondary forest was determined. Next, these analyses of land-use change effects were expanded to the total bacterial community in these rainforest soils sampled annually for three years. Lastly, the effects of increasing soil temperature and N-deposition on ammonia-oxidizing microbial communities in temperate forests were characterized. Land-use change affected ammonia-oxidizing communities in tropical soils. Both the abundance of ammonia-oxidizer marker genes and their community structure shifted due to land-use changes. Interestingly, phylogenetic analyses showed that community structural changes in ammonia-oxidizing thaumarchaea are driven by a shift away from primary rainforest, old pasture, and secondary forest clusters to separate clusters for young pasture. Additionally, there was a nearly complete disappearance in young pasture, old pasture, and secondary forest sites of a thaumarchaeal ammonia-oxidizing genus, the Nitrosotalea. We found that many of the bacterial community responses to land-use change stayed consistent between land-use types across all three years, especially in regards to OTU richness and Faith's phylogenetic diversity. Bacterial community turnover, or distance-decay, was significantly greater (P < 0.05) in forests compared to pastures for two out of three years sampled. Lastly, two bacterial species, Rhodomicrobium udaipurense and Anaeromyxobacter dehalogens, were found to be exclusive indicator species for the pasture land-use type across all sampling time points. Finally, when investigating the effects of increasing soil temperatures and N-deposition rates on temperate forest soil N-cycling, potential N-mineralization and nitrification rates and chitinase enzyme activity showed no difference between treatments (P > 0.05). Bacterial, fungal, and archaeal rRNA genes and thaumarchaeal amoA genes showed no significant difference between treatments. There were significant differences in ammonia-oxidizer community structure between control and heated plus nitrogen treatments. The majority of archaeal ammonia-oxidizer species were most closely related to Nitrosotalea and Nitrososphaera spp. However, the organic horizon in the heated plus nitrogen treatment was dominated by sequences most closely related to Nitrosopumilus maritimus. Taken together, these results can provide a conceptual foundation as to how anthropogenic stressors can alter microbial communities in tropical and temperate forests soils. These communities are critical to global biogeochemical cycling and climate regulation. By charactering how these communities respond to various anthropogenic stressors, the scientific community can begin to use this information to develop more holistic biogeochemical models to predict shifts in nutrient flow and greenhouse gas production.