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Browsing by Author "Hall, Ed, committee member"

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    Exploring the role of planned and unplanned biodiversity in the soil health of agroecosystems
    (Colorado State University. Libraries, 2021) Kelly, Courtland, author; Fonte, Steven J., advisor; Schipanski, Meagan E., committee member; Wallenstein, Matthew, committee member; Hall, Ed, committee member
    To view the abstract, please see the full text of the document.
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    Inactivation of Mycobacterium tuberculosis for safe use outside of the BSL-3 laboratory
    (Colorado State University. Libraries, 2020) Watkins, Jackson, author; Dobos, Karen, advisor; Goodrich, Raymond, committee member; Slayden, Richard, committee member; Hall, Ed, committee member
    Techniques for pathogen inactivation have been long employed by research laboratories to help ease the financial, physical, and health strains associated with (A)BSL-3 work. While robust protocols exist for many of these techniques, there are many holes in research associated with characterization of damage to treated organisms, and standardized methods for comparative analysis of successful sterilization. The work in this thesis aimed to develop methods to better understand current techniques of inactivation. At the same time, it also aimed to characterize the limitations of both a novel approach to inactivation, as well as the pathogenic models we commonly use for infectious disease research. We accomplished this by first developing a D10 value and standardized curve to describe inactivation of Mycobacterium tuberculosis by traditional cesium irradiation techniques. D10 modeling is a stepping stone for comparative analysis of organisms to one another, and also maintains calibration potential to measure radioactive source decay over time. We then focused on the effect of riboflavin photochemistry on Mycobacterium smegmatis as a model for Mtb grown from large-scale culture. We demonstrated the potential for M. smegmatis to enter a viable but non-culturable state, as well as potential reluctance to readily uptake exogenous riboflavin, making it uniquely resistant to this specific method of photosensitizer damage. Characterization of damage to M. smegmatis through propidium iodide flow cytometry assays, and 8-oxoguanosine detection assays, also offered insight into the limitations of M. smegmatis as a model for Mtb.
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    Investigating experimental and environmental factors to provide a mechanistic understanding of benthic algal biomass accumulation in freshwater streams
    (Colorado State University. Libraries, 2019) Beck, Whitney S., author; Poff, N. LeRoy, advisor; Hall, Ed, committee member; Hoeting, Jennifer, committee member; Spaulding, Sarah, committee member
    To view the abstract, please see the full text of the document.
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    Reconfiguring discourse to attend to interrelation: a rhetorical analysis of kelp agency in scientific texts
    (Colorado State University. Libraries, 2020) Anderson, Jennifer, author; Szymanski, Erika, advisor; Amidon, Timothy, committee member; Hall, Ed, committee member
    The purpose of this thesis is to consider how thinking-with kelp ecologies in knowledge-making practices opens opportunities for attending to the co-becoming of species through interrelations. In this thesis, I consider how scientific discourse practices constitute relations with kelp forests and how constitutions can change to think-with kelp forests as actors in knowledge-building. I argue this reconstitution is important for changing asymmetries in power over and cognitive distance from kelp ecosystems. Using critical discourse analysis, this thesis considers how scientific discourse practices constitute power hierarchies between kelp ecosystems and humans. Then, this thesis reads the power hierarchies through an ecological approach to rhetoric to trace how kelp forests produce relations through interactions with environmental processes and a diverse range of species actors. Through the rhetorical analysis, this thesis considers how thinking-with kelp forests can open opportunities for research and discourse practices to attend to co-constituting webs of interrelations. Finally, this thesis considers how embodied experiences with kelp forests open opportunities for researchers to notice and to respond to—to think-with—what matters for a kelp forest. This thesis responds to the modernist bifurcation of language and materiality, subject and object, mind and body. It considers how communication and knowledge-building can make-with the world today by attending to how all planetary actors are of the world through interrelationships with it.
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    Tracking the impact of wildfire on the soil microbiome across temporal scales
    (Colorado State University. Libraries, 2024) Nelson, Amelia Rose, author; Wilkins, Michael J., advisor; Hall, Ed, committee member; Borch, Thomas, committee member; Rhoades, Charles, committee member; Wrighton, Kelly, committee member
    As climate change progresses, the western United States is experiencing shifting wildfire behavior to more frequent and severe wildfires. Wildfires reduce soil microbial biomass and alter the soil microbiome community composition, selecting for "pyrophilous" microbial taxa with encoded traits that enable them to persist during wildfire or thrive in the soil thereafter. The soil microbiome is a key player in ecosystem carbon (C) cycling through the mediation of soil organic matter decomposition and stabilization. In addition to post-fire shifts in the soil microbiome, wildfire decreases soil C pools through combustion and alters C quality via fire-induced transformations to aromatic pyrogenic C (PyC). The intricate interplay between wildfire-induced alterations to soil microbiome composition and function, and subsequent ecosystem C cycling, remains poorly understood across different temporal and spatial scales. Leveraging multi-omics data alongside soil chemistry information (e.g., mass spectrometry) can offer insights into how shifting wildfire behavior may influence microbially mediated C cycling in forest ecosystems across the western US. To address this knowledge gap, I developed an extensive multi-omic dataset from burned Colorado subalpine coniferous forest soils collected over time (spanning 1 to 60 years following burning) and disturbance severity (low and high fire severity). This dataset includes 108 metagenomes and 12 metatranscriptomes, resulting in 1651 metagenome-assembled genomes (MAGs) that represent many of the dominant putative pyrophilous taxa previously identified in compositional studies. This dissertation presents the key findings derived from this comprehensive dataset, with the primary goal of addressing how wildfire impacts the soil microbiome with a focus on microbial interactions with soil C. Chapter 1 serves as a comprehensive literature review, providing an overview of prior research relevant to the research presented thereafter. It underscores the timely relevance of this dissertation research by examining how wildfire behavior is shifting globally with climate change and anthropogenic forcing. Given the critical role of forest ecosystems as significant global C sinks, understanding the repercussions of wildfires on ecosystem biogeochemistry is imperative. I broadly summarize previous research regarding severe wildfire impacts to soils and the soil microbiome and focus on existing knowledge gaps regarding the function of the post-wildfire soil microbiome across differing burn severities and time since fire. In Chapter 2, I characterize how burn severity impacts the soil microbiome one year post-fire in Colorado (CO) subalpine coniferous forests using soil samples collected in July 2019 from within the 2018 Ryan and Badger Creek fire burn scars that represent a burn severity gradient (control, low, moderate, and high severity burned soils). I used a suite of tools to understand both the impacts to soil chemistry and the soil microbiome, including Fourier-transform ion cyclotron resonance mass spectrometry (FTICR-MS) to characterize dissolved soil organic matter, 16S rRNA gene and ITS amplicon sequencing for soil microbiome composition, and coupled metagenomics and metatranscriptomics to identify shifts in soil microbial functional potential. The combination of these tools allowed me to characterize the entire soil microbiome, including bacteria, fungi, and viruses. From metagenomic sequencing, I recovered 637 MAGs, 1982 unique DNA and RNA viral populations, and 2 fungal genomes from low and high severity burned soil samples. I broadly found that Actinobacteria dominated the fraction of enriched and active bacterial taxa within high severity surficial soils and exhibited traits (e.g., heat resistance, fast growth, expression of genes for degrading aromatic PyC) that enabled them to survive the soil heating and thrive after the disturbance. Ectomycorrhizal fungi (EMF), key symbionts of coniferous trees and other plant taxa, were depleted in severely burned soils. Lastly, there were abundant viruses targeting dominant Actinobacteria MAGs that likely played important roles in assembly of the post-wildfire soil microbiome and serve as top-down controls of C cycling within the system. Overall, this study served as a holistic and comprehensive snapshot of the post-wildfire soil microbiome at one point in time and laid the foundation for forming hypotheses and guiding the subsequent studies. Building upon the groundwork laid in Chapter 2, Chapter 3 broadly evaluates the relative importance of putative pyrophilous traits identified between one year and 11 years following wildfire. Additionally, I explored the applicability of other proposed conceptual life history strategy frameworks (e.g., Y-A-S framework) in defining post-wildfire soil microbial dynamics. I utilized a series of soil samples collected from a chronosequence of CO wildfire burn scars representing 1, 3, 5, and 11 years following low- and high-severity wildfire. Using genome-resolved metagenomic approaches and combining this newly generated MAG catalog with the MAGs reconstructed from sequencing in Chapter 1 resulted in a total of 825 bacterial MAGs. Again, this dataset was coupled to various soil chemistry datasets, microbial biomass measurements (via PLFA), and marker gene sequencing data. I found that the potential for fast growth was an important bacterial trait driving dominance in the post-wildfire soil microbiome for up to approximately 11 years post-fire. Moreover, I observed that MAGs investing in traits aimed at acquiring diverse resources from the external environment often dominated severely burned soils, aligning with the 'A' strategy outlined in the Y-A-S framework. These insights suggest that microbial trait profiles play a pivotal role in shaping post-wildfire soil microbial successional dynamics. Furthermore, the study marks a significant step towards unraveling how trait-based frameworks can offer valuable insights into post-disturbance microbial ecology. In Chapter 4, the focus shifts to investigating one of the most extreme scenarios that can occur in a terrestrial ecosystem with severe wildfire: a burning-induced aboveground vegetation shift. Pile burning is a common fuel reduction or site preparation practice wherein logging residue is burned on the forest floor and, because of the high soil temperatures often reached during pile burning, can serve as a surrogate for studying impacts to soil caused by severe wildfire. Following clear-cut harvesting, pile burning can lead to the creation of persistence openings dominated by herbaceous plants within successfully regenerating conifer forest. In this study, a paired 60-year chronosequence of burn scar openings and surrounding forests that regenerated after clear-cut harvesting provided a unique opportunity to study soil microbiome changes associated with two distinct ecosystem development trajectories (i.e., burning-induced aboveground vegetation shift, regenerating coniferous forest). The primary objective was to identify whether the belowground soil microbiome exhibited resilience to a disturbance-induced aboveground vegetation shift. I collected soils from the aforementioned chronosequence and interrogated soil microbiome composition (via marker gene sequencing), functional potential (via metagenomics), and function (via laboratory incubations). There were compositional shifts in the soil microbiome that mirrored the ongoing aboveground vegetation shifts, with short-term changes to microbial community composition and C cycling functionality closely resembling a post-wildfire soil microbiome (e.g., PyC degradation). However, over the six-decade chronosequence the soil microbiome composition and function both displayed resilience, converging with that of the surrounding regenerating forest. This final research chapter extended the findings from the previous studies by exploring the longevity of wildfire impact to the soil microbiome in the extreme case of a burning-induced aboveground vegetation shift. The final chapter (Chapter 5) summarizes the key findings of this doctoral research and discusses potential research implications and applications along with future research directions and remaining knowledge gaps. In summary, the aims of this dissertation research were to identify how burn severity influences the soil microbiome composition and function one year post-fire (Chapter 2), assess the longevity of these impacts and the applicability of conceptual traits-based frameworks to the post-fire soil microbiome (Chapter 3), and evaluate the resilience of the belowground soil microbiome to a burning-induced multidecadal aboveground vegetation shift (Chapter 4). This research significantly advances our understanding of the impacts of wildfires on crucial forest ecosystems, with a specific emphasis on ecosystem C cycling.
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    Trends and controls on lake color in the high elevation western United States
    (Colorado State University. Libraries, 2021) Austin, Miles T., author; Ross, Matthew R. V., advisor; Hall, Ed, committee member; Bailey, Ryan, committee member
    Lakes are perceived to be having an increase in algal blooms across the Western United States due to climate change driven and other anthropogenic drivers. Despite this perception, long-term records do not exist for many lakes, so looking at macroscale patterns is challenging. We present and discuss here our results from using a remote sensing dataset, LimnoSat-US. LimnoSat-US contains Landsat imagery from 1984 to 2020. In the intermountain west, our focus study region of Colorado, Wyoming, Idaho, Montana, New Mexico, and Utah, LimnoSat includes 1,200 lakes and over 150,000 summer observations of water color and reflectance. We used LimnoSat-US to examine what controls lake color and what, if any, changes are occurring lake color, which is a strong indicator of whether a lake is prone to algae blooms. A lake's mean depth and annual temperature were the strongest predictors of whether a lake was, on average, blue and clear or green and murky. Despite the perception of increased algae blooms, we found no consistent evidence of lakes 'greening' or shifting from mostly oligotrophic, blue, and clear to eutrophic, green, and murky. Instead, the vast majority of our lakes (> 80%) had no trend in lake color. Further, we found that our approach did not capture the dominant controls on whether not a lake was shifting from blue to green or green to blue, highlighting the need for additional work.