Scholarship & Research
Permanent URI for this communityhttps://scholarworks.montana.edu/handle/1/1
Browse
50 results
Search Results
Item Assessing the impact of citizen science on motivation, civic awareness, and understanding of the scientific process in a college microbiology synchronous classroom(Montana State University - Bozeman, College of Letters & Science, 2022) Andrews, April Marie; Chairperson, Graduate Committee: C. John GravesThe COVID-19 pandemic impacted education by removing science from physical classrooms. Adopting remote learning in the fall of 2021 brought new challenges for hands-on discovery and engagement in scientific experiences for my microbiology students. The goal of this study was to assess the impact participation in citizen science had on student motivation, epistemic beliefs toward science, understanding the process of science, as well as value of data contributed by peers. The traditional curriculum was modified to include online collaboration and discussions by students to solve a real-world problem related to a potential public health threat by integrating a series of inquiry-based exercises. The project, Discover the Microbes Within: The Wolbachia Project, allowed students to partner with Vanderbilt University and join researchers from all over the world to study and understand the prevalence of this naturally occurring intracellular parasite. Students spent time exploring their community and collected specimens of native arthropods in and around the Toledo campus of Owens Community College. Students worked in small strategic online breakout groups and took on one of three roles; microbiologist, epidemiologist, and reproductive specialist as part of their research to validate claims regarding health threats. Students prepared and reported back to the class their proposal and task force recommendation to submit to the CDC. Students conducted online activities exploring biotechnology techniques (i.e., polymerase chain reaction, gel electrophoresis, Sanger sequencing, bioinformatics etc.) that promoted scientific literacy and problem-based learning outside a traditional classroom setting. Pre- and post-Likert scales were utilized to compare science motivation, scientific literacy, and opinions toward science and technology. A WebQuest online group evaluation, interviews and written response to discussion board forums were used as data collection instruments. Data were processed using both quantitative and qualitative analysis strategies. Students reported that they felt they were learning the same if not more online compared to face-to-face instruction at the end of the semester. The results suggested that students took a more proactive role in their education, self-identified more as 'real' scientists, and made positive growth with respect to epistemic beliefs toward science when given meaningful examples that make local connections during remote instruction.Item Integrating livestock into small-scale vegetable farming systems(Montana State University - Bozeman, College of Agriculture, 2021) Benson-Feagler, Trestin Thea; Chairperson, Graduate Committee: Megan Van Emon; D.L. Regan, M.L. Van Emon and C.J. Yeoman were co-authors of the article, 'Effects of integrating livestock into small-scale vegetable farming systems' submitted to the journal 'Sustainable agriculture research' which is contained within this thesis.Since World War II, modern agriculture systems have shifted to low-diversity monoculture crops, specializing in a singular species and generally separating those crops from livestock. Such systems require high inputs including fertilizers, herbicides and tillage, all of which may reduce ecological potential of farmland. Small-scale farms are becoming more popular due to recent interest in local eating and sustainability. To improve their environmental sustainability, some small-scale farms have incorporated livestock back into cropping systems. Soil health measurements can be valuable in understanding the impacts livestock have on small- scale farming systems as soil is the growth medium for vegetation. The objectives of this study were to evaluate nutrient cycling, microbial communities and compaction in response to grazed versus un-grazed vegetable cropping systems and use this information to understand the interaction between soil biology, nutrient cycling and livestock when integrated in a variety of vegetable production systems. Soil and biomass samples were collected over three years (2017- 2020) before and after sheep grazing occurred on three farm locations in the Northern Great Plains. Soil samples were analyzed for soil microbial diversity, bulk density and soil nutrients. While I found no consistent differences in soil nutrients, bulk density or soil microbial diversity, my results indicate that integrating livestock into small-scale vegetable farming systems did not negatively impact soil quality. Results from this study may help demonstrate to farmers and livestock operators the importance of an integrated approach, for those that already practice this approach there is affirmation that integration is feasible and purposeful and also become the starting point for further research into a little studied topic.Item Analysis of complex samples by mass spectrometry leads to insights into system dynamics(Montana State University - Bozeman, College of Letters & Science, 2021) Peach, Jesse Thomas; Chairperson, Graduate Committee: Brian Bothner; James Larson, Sutton Kanta, Eric Boltinghouse, Rebecca Mueller, Ganesh Balasubramanian, Mohammed Refai, Brent Peyton and Brian Bothner were co-authors of the article, 'Optimization of thermal small molecule and protein mass spectrometry analysis' submitted to the journal 'Analytical biochemistry' which is contained within this dissertation.; Rebecca Mueller, Dana Skorupa, Margaux Mesle, Sutton Kanta, Eric Boltinghouse, Bailey Sharon, Valerie Copie, Brian Bothner and Brent Peyton were co-authors of the article, 'Longitudinal meta-analysis of the Five Sisters Hot Springs in Yellowstone National Park reveals a dynamic thermoalkaline environment' submitted to the journal 'Environmental microbiology' which is contained within this dissertation.; Stephanie M. Wilson, Logan D. Gunderson, Lizzi Frothingham, Tan Tran, Seth T. Walk, Carl J. Yeoman, Brian Bothner and Mary P. Miles were co-authors of the article, 'Temporal metabolic response yields a dynamic biosignature of inflammation' submitted to the journal 'iScience' which is contained within this dissertation.Systems biology offers a holistic approach to biological science. In its most complete form, systems biology requires comprehensive data encompassing all of the parts or molecules across a set of hierarchical networks. To obtain and analyze the comprehensive and large datasets required for systems biology analysis, biologists have taken advantage of new technology and computational tools. Over the last few decades, advances in computational modeling and analysis technology has dramatically increased the efficacy of systems biology and the understanding of the natural world. However, systems biology is still an emerging discipline. The overwhelming scale of potential biological data that has yet to be described, coupled with interpretation and application obstacles, leaves much work to be accomplished. One aspect of systems biology that needs development is the interpretation and analysis of temporal biological data. Temporal data reveals more about biological phenomena than static data as biology is inherently dynamic. This dissertation explores the benefits of temporal profiling of complex samples to make time-resolved conclusions about complicated biological questions. Three research projects are the backbone of this document, with a chapter being devoted to each. Chapter 2 describes the development of a comprehensive method for extraction and mass spectrometry analysis of several different fractions from hot spring sediment. Chapter 3 delves into a multi-omics analysis tracking changes over the course of three years in a thermoalkaline spring system in Yellowstone National Park. It defines how specific extracellular small molecules correlate with microbial fitness. Specifically, how unique nitrogen and sulfur containing molecules in the sediment drive archaeal abundance and diversity. The final chapter introduces the concept of a 'dynamic biosignature', a set of metabolites that have similar responses to known biomarkers, in this case pro-inflammatory cytokines. A cohort of metabolites was identified that provided mechanistic insight into the inflammatory response. Overall, this dissertation provides examples of systems biology analysis and provides evidence that static, single time-point datasets fail to capture that which is the essence of biology - change.Item Investigation of field relevant parameters for microbially enhanced coalbed methane scale up(Montana State University - Bozeman, College of Engineering, 2019) Platt, George Addison; Chairperson, Graduate Committee: Robin Gerlach; K. J. Davis, E. P. Barnhart, M. W. Fields and R. Gerlach were co-authors of the article, 'Optimization of 13C-algae amendment concentration for enhanced coal dependent methanogenesis' submitted to the journal 'International journal of coal geology' which is contained within this thesis.; K. J. Davis, H. D. Schweitzer, H. J. Smith, E. P. Barnhart, M. W. Fields, R. Gerlach were co-authors of the article, 'Algal amendment enhances biogenic methane production from coals of different thermal maturity' submitted to the journal 'International journal of coal geology' which is contained within this thesis.Energy production from coal is projected to decline significantly over the next 30 years, due to concerns over anthropogenic carbon emissions, climate change, and cost. As coal-based energy production decreases, the demand for natural gas is expected to increase. Coalbed methane (CBM), a biogenic natural gas resource found in subsurface coal beds, may aid in meeting the projected increase in demand. However, costs associated with traditional CBM extraction currently make utilizing this resource economically prohibitive due to slow coal-to-methane conversion rates and the necessity to treat co-produced water. Algae can be cultivated in co-produced formation water and the addition of very small amounts of this algal biomass can increase coal-to-methane conversion rates. The goal of this work was to determine the optimal algae amendment concentration for the enhancement of microbial coal-to-methane conversion to maximize return on investment. Concentrations of 13C-labeled algae amendment ranging from 0.01-0.50 g/L (equivalent to 0.0001-0.005 g per g of coal) were tested in coal-containing batch microcosms. Enhanced methane production was observed in all amended microcosms and maximum methane production occurred between 169-203 days earlier than in unamended microcosms. When as little as 0.01 g/L algae amendment was added, 13CH 4 and 12CH 4 tracking revealed that the improvement in coal-to-methane conversion kinetics was due to enhanced coal degradation. Increasing amendment concentrations to 0.05-0.50 g/L improved coal-to-methane conversion rates further, but improvements from amendment concentrations above 0.05 g/L were insignificant. The geologic scope of this CBM enhancement strategy was investigated by studying methane production from five coals ranging in thermal maturity. Biogenic methane was produced from all coals, with subbituminous coals generally producing more methane than thermally mature bituminous coals. The addition of algae amendment to thermally mature coal microcosms resulted in methane production that was comparable to production from unamended, thermally immature coals. This improvement was associated with an increased relative abundance of coal degrading microorganisms. Collectively, this work demonstrates that algae amendment concentrations can be reduced further (to 0.01-0.05 g/L) relative to the previously investigated concentrations (ranging from 0.1-0.5 g/L) and still improve coal-to-methane conversion rates for a range of coal sources.Item Spectral signs of life in ice(Montana State University - Bozeman, College of Engineering, 2020) Messmer, Mitch Wade; Chairperson, Graduate Committee: Christine ForemanIn astrobiology, new technologies are being implemented in the search for extraterrestrial life. Interpreting results from new analytical techniques requires additional information about microbial properties. A catalogue of identifying characteristics, called biosignatures was created for bacterial and algal isolates from Greenland and Antarctica by measuring substrate utilization, UV/Vis absorbance, Fourier-Transform Infrared Spectroscopy, and Raman spectroscopy. Organisms were chosen from environments analogous to Martian glacier systems. Spectral properties of these polar isolates could serve as a reference for interpreting results from NASA's Perseverance rover. Substrate utilization was evaluated using EcoPlates on an Omnilog plate reader (Biolog, California, U.S.A.). UV/Vis absorbance spectra indicated that nine of the twenty-five bacterial isolates contained carotenoid pigments, and one contained violacein. UV/Vis analysis was effective at identifying the presence of pigments, but was insufficient for distinguishing between the types of carotenoids. FTIR analysis identified general biological features such as lipids, proteins, and carbohydrates, but did not detect pigments. Raman analysis of isolates with a 532 nm laser identified both the presence of carotenoid and violacein pigments, and the general cell features observed with FTIR. The degree of saturation of membrane lipids was evaluated for the bacterial isolates by comparing the ratio of unsaturated and saturated fatty acid peaks in the Raman spectra. Results were similar for the polar isolates and mesophiles, excluding the Bacillus subtilis spores. A principal component analysis was conducted to determine the regions of the spectra that contributed the variability between samples. The spectra of the bacterial isolates were more closely related based on colony color than phylogeny. Analysis of the algal isolates indicated that chlorophyll A and B fluoresced under exposure to the 532 nm laser, creating definitive biosignatures for algae. These analytical techniques proved effective at identifying cell properties that could serve as biosignatures for identifying microbial life. Identification of the spectral features of these cellular components may aid in narrowing the search for extraterrestrial life by highlighting specific target regions within the Raman spectra. Characteristics of these polar microbes may provide the foundation for interpreting spectral data collected from future explorations of extraterrestrial environments in the search for astrobiology.Item Human gut phages in health and disease(Montana State University - Bozeman, College of Letters & Science, 2018) Manrique Ronquillo, Maria del Pilar; Chairperson, Graduate Committee: Mark J. Young; Michael S. Dills and Mark J. Young were co-authors of the article, 'The human gut phage community and its implications for health and disease' in the journal 'Viruses' which is contained within this dissertation.; Benjamin Bolduc, Seth T. Walk, John van der Oost, Willem M. de Vos and Mark J. Young were co-authors of the article, 'Healthy human gut phageome' in the journal 'Proceedings of the National Academy of Sciences of the United States of America' which is contained within this dissertation.; Mark J. Young was a co-author of the article, 'Interactions of the healthy gut phage community (HGP) with the core gut bacterial community' submitted to the journal 'PLOS computational biology' which is contained within this dissertation.; Yifan Zhu, John van der Oost, Willem M. de Vos and Mark J. Young were co-authors of the article, 'Gut bacteriophages and fecal microbial transplantation outcome in subjects with metabolic syndrome' which is contained within this dissertation.; Seth T. Walk and Mark J. Young were co-authors of the article, 'Bacteriophage-enriched filtrates: a potential tool to modify the structure of the gut-associated bacterial community' which is contained within this dissertation.The human body is colonized by a diverse microbial community known as the human microbiota. Most of these microbes, reside in the human intestinal tract. The gut microbiota has coevolved with humans and has become essential for multiple physiological functions that range from digestion, to development of the immune system, protection for pathogens, and even behavior. The gut microbial community is primarily dominated by Bacteria and their viruses- bacteriophages (or phages for short). Even though our knowledge of the contribution of the former to human health is extensive, the role of bacteriophages in human health and disease has been explored considerably less. Study of bacteriophages in other microbial environments has highlighted their importance in influencing the structure and function of their host community. Therefore, understanding the role of bacteriophages in the human gut ecosystem, and overall, in human health, has become a focus of current research. The main overarching hypothesis of this thesis is that human gut bacteriophages contribute to human health. To test this hypothesis, viral metagenomic surveys of healthy and disease individuals, together with experiments in a gnotobiotic mouse model system were performed. A group of bacteriophages shared among healthy individuals and significantly depleted in individuals with IBD was identified. Moreover, a host reservoir for these phages was identified in the core gut bacterial community of healthy subjects. Study of phage dynamics during an FMT treatment in patients with metabolic syndrome further highlighted the association of bacteriophages with human health. Patients that showed significant clinical improvement harbored a richer community, and a community more similar to healthy donors than patients that did not respond to the treatment. Moreover, a set of potential phage biomarkers associated with health and treatment outcome were identified. Lastly, experiments in gnotobiotic mice demonstrated the ability of bacteriophage-enriched filtrates to modify the microbial community structure. This result highlights the potential use of bacteriophages to manipulate the human gut microbiota, and potentially restore human health.Item Methane flux from recently exposed subglacial sediments, Robertson Glacier, Canada(Montana State University - Bozeman, College of Letters & Science, 2014) Spotts, Terra Marie; Chairperson, Graduate Committee: Mark L. SkidmoreMethane is over 20 times more effective than CO 2 as a greenhouse gas. Thus, its atmospheric concentration and the processes controlling it are important components of the global climate system. Recent research has shown methanogenesis in subglacial sediments. However, the net contribution from subglacial systems to the global methane budget is poorly understood due to a dearth of empirical data. Using measurements via the static chamber method, the flux of methane from recently exposed subglacial sediments at Robertson Glacier, Canadian Rockies was quantified. Methane concentrations were measured from surface gas flux chambers in transects both parallel and perpendicular to the glacier terminus. Over 300 measurements were made during the 2012 melt season (July to September) and used to determine both spatial and temporal variability in the gas fluxes. The chamber farthest from the glacier terminus, approximately 50 m down valley, had an average flux close to zero whereas the chambers nearest the terminus had the highest average fluxes. The average methane efflux from the sediment surface to atmosphere was 0.22 micromoles m -2 d -1. The highest methane efflux during the season, 11.0 micromoles m -2 d -1, was measured in close proximity to the glacier terminus. Shallow sediment cores were collected adjacent to the static chambers and vertical gas concentration profiles were measured from the cores. Within the profiles, methane concentrations were greater than atmospheric concentrations at all depths. Additionally, CO 2, CO and H 2 gas concentrations were analyzed in the cores to evaluate potential microbial metabolic pathways of methane production. Previous studies on methane fluxes from glacial sediments in Greenland and the Swiss Alps used single time point flux measurements during a melt season from multiple locations. This study concludes that such point measurements are unlikely representative for determining a net seasonal flux as they do not consider temporal variability. There was a two order of magnitude difference between the annual source contribution of methane based on the average melt season flux and the highest measured surface flux. This indicates that single sampling periods may significantly over or underestimate the net seasonal flux of methane from recently exposed glacial sediments to the atmosphere.Item Characterization of an Endophytic Gloeosporium sp. and Its Novel Bioactivity with “Synergistans”(2014-12) Schaible, George A.; Strobel, Gary A.; Mends, Morgan Tess; Geary, Brad; Sears, JoeGloeosporium sp. (OR-10) was isolated as an endophyte of Tsuga heterophylla (Western hemlock). Both ITS and 18S sequence analyses indicated that the organism best fits either Hypocrea spp. or Trichoderma spp., but neither of these organisms possess conidiophores associated with acervuli, in which case the endophytic isolate OR-10 does. Therefore, the preferred taxonomic assignment was primarily based on the morphological features of the organism as one belonging to the genus Gloeosporium sp. These taxonomic observations clearly point out that limited ITS and 18S sequence information can be misleading when solely used in making taxonomic assignments. The volatile phase of this endophyte was active against a number of plant pathogenic fungi including Phytophthora palmivora, Rhizoctonia solani, Ceratocystis ulmi, Botrytis cinerea, and Verticillium dahliae. Among several terpenes and furans, the most abundantly produced compound in the volatile phase was 6-pentyl-2H-pyran-2-one, a compound possessing antimicrobial activities. When used in conjunction with microliter amounts of any in a series of esters or isobutyric acid, an enhanced inhibitory response occurred with each test fungus that was greater than that exhibited by Gloeosporium sp. or the compounds tested individually. Compounds behaving in this manner are hereby designated “synergistans.” An expression of the “median synergistic effect,” under prescribed conditions, has been termed the mSE50. This value describes the amount of a potential synergistan that is required to yield an additional median 50 % inhibition of a target organism. In this report, the mSE50s are reported for a series of esters and isobutyric acid. The results indicated that isoamyl acetate, allyl acetate, and isobutyric acid generally possessed the lowest mSE50 values. The value and potential importance of these microbial synergistic effects to the microbial environment are also discussed.Item Inference of interactions in cyanobacterial-heterotrophic co-cultures via transcriptome sequencing(2014-04) Beliaev, Alexander S.; Romine, Margaret F.; Serres, Margrethe; Bernstein, Hans C.; Linggi, Bryan E.; Markillie, Lye M.; Isern, Nancy G.; Chrisler, William B.; Kucek, Leo A.; Hill, Eric A.; Pinchuk, Grigoriy E.; Bryant, Donald A.; Wiley, H. Steven; Fredrickson, Jim K.; Konopka, AllanWe used deep sequencing technology to identify transcriptional adaptation of the euryhaline unicellular cyanobacterium Synechococcus sp. PCC 7002 and the marine facultative aerobe Shewanella putrefaciens W3-18-1 to growth in a co-culture and infer the effect of carbon flux distributions on photoautotroph–heterotroph interactions. The overall transcriptome response of both organisms to co-cultivation was shaped by their respective physiologies and growth constraints. Carbon limitation resulted in the expansion of metabolic capacities, which was manifested through the transcriptional upregulation of transport and catabolic pathways. Although growth coupling occurred via lactate oxidation or secretion of photosynthetically fixed carbon, there was evidence of specific metabolic interactions between the two organisms. These hypothesized interactions were inferred from the excretion of specific amino acids (for example, alanine and methionine) by the cyanobacterium, which correlated with the downregulation of the corresponding biosynthetic machinery in Shewanella W3-18-1. In addition, the broad and consistent decrease of mRNA levels for many Fe-regulated Synechococcus 7002 genes during co-cultivation may indicate increased Fe availability as well as more facile and energy-efficient mechanisms for Fe acquisition by the cyanobacterium. Furthermore, evidence pointed at potentially novel interactions between oxygenic photoautotrophs and heterotrophs related to the oxidative stress response as transcriptional patterns suggested that Synechococcus 7002 rather than Shewanella W3-18-1 provided scavenging functions for reactive oxygen species under co-culture conditions. This study provides an initial insight into the complexity of photoautotrophic–heterotrophic interactions and brings new perspectives of their role in the robustness and stability of the association.Item IL-1alpha signaling is critical for leukocyte recruitment after pulmonary Aspergillus fumigatus challenge(2015-01) Caffrey, Alayna K.; Lehmann, Margaret M.; Zickovich, Julianne M.; Espinosa, Vanessa; Shepardson, Kelly M.; Watschke, Christopher P.; Hilmer, Kimberly M.; Thammahong, Arsa; Barker, Bridget M.; Rivera, Amariliz; Cramer, Robert A.; Obar, Joshua J.Aspergillus fumigatus is a mold that causes severe pulmonary infections. Our knowledge of how A. fumigatus growth is controlled in the respiratory tract is developing, but still limited. Alveolar macrophages, lung resident macrophages, and airway epithelial cells constitute the first lines of defense against inhaled A. fumigatus conidia. Subsequently, neutrophils and inflammatory CCR2+ monocytes are recruited to the respiratory tract to prevent fungal growth. However, the mechanism of neutrophil and macrophage recruitment to the respiratory tract after A. fumigatus exposure remains an area of ongoing investigation. Here we show that A. fumigatus pulmonary challenge induces expression of the inflammasome-dependent cytokines IL-1β and IL-18 within the first 12 hours, while IL-1α expression continually increases over at least the first 48 hours. Strikingly, Il1r1-deficient mice are highly susceptible to pulmonary A. fumigatus challenge exemplified by robust fungal proliferation in the lung parenchyma. Enhanced susceptibility of Il1r1-deficient mice correlated with defects in leukocyte recruitment and anti-fungal activity. Importantly, IL-1α rather than IL-1β was crucial for optimal leukocyte recruitment. IL-1α signaling enhanced the production of CXCL1. Moreover, CCR2+ monocytes are required for optimal early IL-1α and CXCL1 expression in the lungs, as selective depletion of these cells resulted in their diminished expression, which in turn regulated the early accumulation of neutrophils in the lung after A. fumigatus challenge. Enhancement of pulmonary neutrophil recruitment and anti-fungal activity by CXCL1 treatment could limit fungal growth in the absence of IL-1α signaling. In contrast to the role of IL-1α in neutrophil recruitment, the inflammasome and IL-1β were only essential for optimal activation of anti-fungal activity of macrophages. As such, Pycard-deficient mice are mildly susceptible to A. fumigatus infection. Taken together, our data reveal central, non-redundant roles for IL-1α and IL-1β in controlling A. fumigatus infection in the murine lung.