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Author ORCID Identifier


Open Access Dissertation

Document Type


Degree Name

Doctor of Philosophy (PhD)

Degree Program

Organismic and Evolutionary Biology

Year Degree Awarded


Month Degree Awarded


First Advisor

Kristen M. DeAngelis

Subject Categories

Biodiversity | Computational Biology | Environmental Microbiology and Microbial Ecology | Genomics | Laboratory and Basic Science Research | Organismal Biological Physiology | Research Methods in Life Sciences | Systems Biology


Soils serve as massive carbon sinks, but their ability to continue this ecological service is contingent on how the resident soil microbial community will respond to the ongoing climate crisis. One key dimension of the microbial response to warming is its carbon use efficiency (CUE), or the fraction of carbon taken up by an organism which is allocated to growth rather than respiration. However, the scientific community is still in the early stages of understanding the drivers, consequences - and even accurate measurements of - CUE. In this dissertation, I first quantified the variability of CUE and its responsiveness to temperature and substrate for soil bacteria grown in the lab. I subsequently implemented this knowledge into a plant litter decomposition model to determine how including organism-level variation in CUE alters projected soil carbon stocks in a warmer world. Finally, I completed a series of numerical simulations to evaluate how robust a commonly-used method of measuring CUE in the field is to changes in the microbial community present. I found that CUE was highly variable and depended on both substrate and temperature in a bacteria-specific manner. No robust genetic or genomic markers of CUE or its temperature dependence emerged, indicative of the wide diversity of bacteria characterized in this study. Nonetheless, efficiency tended to decrease with warming more-so in taxa which were already characterized by high efficiency, causing a degree of homogenization in CUE at higher temperatures. Introducing variation in CUE temperature sensitivity to the litter decomposition model DEMENT caused additional litter carbon loss under warming, which indicates the possible importance of accounting for CUE as a niche dimension for species sorting to act upon in decomposition models. Finally, I found the 18O-H2O method of measuring CUE in mixed soil communities is particularly susceptible to misleading results when the assumption of extracellular water being the sole source of oxygen to DNA is violated. Overall, my results indicate that understanding microbial physiology is essential to both the accurate measurement and projection of CUE under the global climate crisis, but that explaining the genomic underpinning of this physiological variation remains a challenge.


Creative Commons License

Creative Commons Attribution-Noncommercial 4.0 License
This work is licensed under a Creative Commons Attribution-Noncommercial 4.0 License