The Taxonomic and Functional Nature of Plant-Associated Microbiomes
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Yourstone, Scott. The Taxonomic and Functional Nature of Plant-associated Microbiomes. 2017. https://doi.org/10.17615/gs34-t448APA
Yourstone, S. (2017). The Taxonomic and Functional Nature of Plant-Associated Microbiomes. https://doi.org/10.17615/gs34-t448Chicago
Yourstone, Scott. 2017. The Taxonomic and Functional Nature of Plant-Associated Microbiomes. https://doi.org/10.17615/gs34-t448- Last Modified
- March 20, 2019
- Creator
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Yourstone, Scott
- Affiliation: School of Medicine, Curriculum in Bioinformatics and Computational Biology
- Abstract
- Microbes live in close association with eukaryotes and have substantial impacts on fitness and well-being of their hosts. In plants, microbes can colonize soil adjacent to plant roots and can even survive inside of plant tissues. They can have either positive or negative effects on plant fitness and therefore show potential for use as an agricultural tool. However, our current understanding of how these microbial communities are formed and how they function is limited. The work described in this dissertation reports novel insights regarding plant-associated microbiomes along with new and improved methods for observing their associations with plants. Chapter 1 gives a brief introduction to plant associated microbiomes and the common methods used to study them. Chapter 2 outlines colonization patterns of Arabidopsis thaliana associated microbiomes. The taxa that colonize Arabidopsis roots endophytically are distinct from those colonizing the soil surrounding the roots (rhizosphere) and unplanted bulk soil. This suggests that plants modulate these communities and possibly select for microbes that provide specific fitness advantages. Endophytic communities of plants grown in different soils exemplify how soil type is the primary factor in determining the taxa found in these communities. However, there are core taxa that are consistently found in the endophyte compartment regardless of soil type and other factors. These core microbes are potential candidates that are actively selected by plants. Communities associated with different Arabidopsis ecotypes and ages have only minor differences. Chapter 3 presents improved methods for profiling taxa in plant-associated microbiomes by utilizing two techniques. First, PCR amplification clamps designed from peptide nucleic acids are used to reduce plant chloroplast contamination. Removing unwanted chloroplast contamination reduces the cost of sequencing by increasing the yield of usable, bacterial 16S reads. Second, 16S amplicons are tagged with a unique DNA oligo (i.e. molecule tag) prior to PCR amplification. After PCR amplification and sequencing, reads having the same molecule tag likely originated from the same DNA template. Therefore, discrepancies between these reads are presumably sequencing errors and can be corrected bioinformatically. Identifying and correcting these sequencing errors can be performed using the MTToolbox software described in Chapter 4. Correcting sequencing errors using molecule tagged reads and MTToolbox substantially reduces the number of spurious singleton OTUs. Chapter 5 compares the functional profiles of Arabidopsis rhizospheres against those in the bulk soil and also describes novel methods for comparing across metagenomes. These methods can report functional differences between microbiomes at a global level or for specific taxa. For example, transcription-related functions were identified as frequently enriched in the rhizosphere across a broad diversity of taxa. Alternatively, synthesis of cyclic beta-1,2-glucans were identified as rhizosphere enriched in multiple taxa among a small group of betaproteobacteria despite other betaproteobacteria having different enrichment patterns. Additionally, rare functions in these metagenomes were more likely to be classified as rhizosphere enriched suggesting that microbes are constantly evolving new mechanisms for rhizosphere colonization. Therefore, identifying taxa specific enrichments patterns is important for understanding mechanisms associated with rhizosphere colonization. Collectively, the methods and insights described in this document expand our understanding of plant microbiomes and generate important hypotheses for future examination.
- Date of publication
- December 2017
- Keyword
- DOI
- Resource type
- Rights statement
- In Copyright
- Advisor
- Mieczkowski, Piotr
- Jones, Corbin
- Prins, Jan
- Dangl, Jeffery L.
- Pardo-Manuel Pardo-Pardo-Manuel de Villena, Fernando
- Degree
- Doctor of Philosophy
- Degree granting institution
- University of North Carolina at Chapel Hill Graduate School
- Graduation year
- 2017
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