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A multi-omics approach to assessing growth, stress, and disturbance in soil microbial communities

Chuckran, Peter (2022) A multi-omics approach to assessing growth, stress, and disturbance in soil microbial communities. Doctoral thesis, Northern Arizona University.

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Microbes in soil are well-known drivers of several ecosystem processes, yet our ability to study their genetic controls on a community level is relatively recent. The total DNA and RNA of a microbial community—referred to as the metagenome and metatranscriptome and collectively part of the field of study known as “omics”—can yield valuable insight into microbial physiology and function, community structure, and the evolutionary processes of microorganisms. This dissertation leverages metagenomics and metatranscriptomics to assess soil microbial communities with a particular focus on understanding how this approach can be used to better understand dimensions of growth, stress, and disturbance. The first chapter introduces this topic and reviews the current state of the literature and crucial knowledge gaps, as well as a brief description of the subsequent chapters. Chapter 2 describes an experiment where we observed the transcriptional controls of soil microbial communities in response to labile carbon inputs and found that inputs of glucose rapidly stimulated the transcription of nitrogen cycling genes. Chapter 3 is a broad-scale data analysis of genomic traits in bacterial communities from soil, marine, host-associated, and hot-spring microbial communities. We found that soil communities have relationships between genomic traits which are distinct from those in other ecosystems—indicating a unique set of selection pressures in soils. In Chapter 4 we follow-up on these results and examine the distribution of genomic traits in soils along multiple environmental parameters. This analysis showed that bacterial traits in soils are likely driven by carbon limitation and soil pH. In Chapter 5 we reexamine the transcriptional response described in Chapter 2, this time focusing on how genomic traits such as nucleotide and codon selection impact the short-term response of soil microbes during growth and stress. Together, these results highlight the numerous ways in which we can derive insights from multi-omics data and how these findings can enhance our understanding of microbial life in soils.

Item Type: Thesis (Doctoral)
Publisher’s Statement: © Copyright is held by the author. Digital access to this material is made possible by the Cline Library, Northern Arizona University. Further transmission, reproduction or presentation of protected items is prohibited except with permission of the author.
Keywords: carbon; metagenomics; metatranscriptomics; microbial ecology; nitrogen; soil; microbiotic communities
Subjects: Q Science > QR Microbiology
NAU Depositing Author Academic Status: Student
Department/Unit: Graduate College > Theses and Dissertations
College of the Environment, Forestry, and Natural Sciences > Biological Sciences
Date Deposited: 15 Jul 2022 17:25
Last Modified: 25 Nov 2022 08:30
URI: https://openknowledge.nau.edu/id/eprint/5858

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