Controls of microbially mediated soil carbon cycling: An examination of the effects of land-use and life history strategy on soil bacterial diversity and activity

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Soil dwelling microorganisms are essential components of numerous ecosystem processes and biogeochemical cycles. In particular, they are important actors in terrestrial carbon cycling, producing and turning over soil organic matter. Microbially mediated soil carbon cycling can be influenced by environmental conditions, with soil organic matter dynamics and carbon fate varying across biomes. Drastic alterations to soil habitat conditions brought about through anthropogenic changes to land-use (e.g. agriculture) can greatly influence these processes. However, we are limited in our understanding of how land-use regimes and other environmental conditions control microbially mediated soil carbon cycling. I took three approaches to explore this relationship. First, I examined how bacterial community assembly and composition differed across cropland, old-field, and forest soils. I found that homogeneous selection, whereby selection pressure causes bacterial communities to be more phylogenetically similar to each other than expected by random assembly from a metacommunity, was the dominant bacterial community assembly process across all three land-use types. However, I also found that land-use interacted with soil pH to drive the balance between stochastic and deterministic assembly processes. This result indicates a mechanism by which microbial communities may develop differently across land-use regimes. Second, I examined the overall organic matter turnover across land-use regimes and the identity of the bacterial taxa actively involved in this carbon processing. I found that the dynamics of organic matter turnover and the active bacterial populations involved were distinct across land-use regimes. From these patterns I developed a conceptual model explaining how initial microbial biomass, which is impacted by land-use, may control bacterial activities in organic matter turnover. Finally, I examined the genomic basis of bacterial life history strategies, specifically the copiotroph-oligotroph continuum. Life history strategy can explain both bacterial activity in soil carbon cycling and bacterial response to environmental change. I found that the abundance of transcription factor genes and genes encoding a secretion signal peptide were both genomic signatures of the copiotroph-oligotroph continuum. These signatures can be used to classify diverse microbes based on their life history strategy and may further explain the biological drivers of these strategies. I also developed a toolkit, MetaSIPSim, that simulates metagenomic DNA-stable isotope probing datasets. Such datasets can be used to improve metagenomic DNA-stable isotope probing methodologies and analyses, which in turn can be used to link microbial genes and genomes to in situ carbon cycling activity. Overall, this work advances our knowledge of, and ability to study the ecological and biological controls of bacterially mediated soil carbon cycling.

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217 pages


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community assembly; life history; metagenomics; microbial ecology; soil; stable isotope probing


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Union Local


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Buckley, Daniel H.

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Yavitt, Joseph B.
Hewson, Ian

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Ph. D., Microbiology

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Doctor of Philosophy

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Government Document




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dissertation or thesis

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