subject:(microbial ecology)

University of Texas – Austin

1. Glinka, Clare Blieszner. Fungi are a persistent legacy : drivers of fungal abundance and community composition over time.

Degree: MA, Plant Biology, 2011, University of Texas – Austin

URL: http://hdl.handle.net/2152/ETD-UT-2011-05-3651

► Plants are a major force shaping how ecosystems function, including non-native plants. The effects that non-native plants have on ecosystem properties and processes can be… (more)

▼ Plants are a major force shaping how ecosystems function, including non-native plants. The effects that non-native plants have on ecosystem properties and processes can be particularly important as invasive plants are associated with changes in nitrogen and carbon cycling Plants can also indirectly affect ecosystem processes through their influence on the soil microbial community and different plants are associated with different microbial communities. The legacies produced by invasive plants can be long-lasting and inhibit the restoration of damaged ecosystems. Because of the central role of soil fungi in ecosystem processes, I examined how fungal abundance and community composition were altered by non-native plants, and the persistence of these changes. Specifically, I examined how two different cases of invasion by non-native species affected soil fungi over three years compared to soil fungi in native, undisturbed sites. I further tested how the soil fungi responded to the removal of the non-native plants and to inoculation with local native microbial communities. Legacy effects of land use history on soil fungal abundance and community composition were found in these central Florida communities. There were substantial differences in soil fungal abundance and community composition in disturbed and pasture sites compared to native scrub, and these differences persisted for three years after non-native grasses were removed. Not only did the grass-dominated pasture and disturbed sites differ from the undisturbed native shrub-dominated ecosystem, they differed significantly from each other, indicating that the different non-native grasses and other specific changes associated with each land use played a role in soil fungal communities. The combined results of this study have implications for restoration ecology. The current dependence of the fungal community on land use and the associated non-native species invasions (along with other analyses done in this system) suggest that a different approach to restoration is required here to overcome the observed legacy effects. Advisors/Committee Members: Hawkes, Christine V. (advisor), Fowler, Norma L. (committee member).

Subjects/Keywords: Microbial ecology

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APA (6^th Edition):

Glinka, C. B. (2011). Fungi are a persistent legacy : drivers of fungal abundance and community composition over time. (Masters Thesis). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/ETD-UT-2011-05-3651

Chicago Manual of Style (16^th Edition):

Glinka, Clare Blieszner. “Fungi are a persistent legacy : drivers of fungal abundance and community composition over time.” 2011. Masters Thesis, University of Texas – Austin. Accessed January 27, 2021. http://hdl.handle.net/2152/ETD-UT-2011-05-3651.

MLA Handbook (7^th Edition):

Glinka, Clare Blieszner. “Fungi are a persistent legacy : drivers of fungal abundance and community composition over time.” 2011. Web. 27 Jan 2021.

Vancouver:

Glinka CB. Fungi are a persistent legacy : drivers of fungal abundance and community composition over time. [Internet] [Masters thesis]. University of Texas – Austin; 2011. [cited 2021 Jan 27]. Available from: http://hdl.handle.net/2152/ETD-UT-2011-05-3651.

Council of Science Editors:

Glinka CB. Fungi are a persistent legacy : drivers of fungal abundance and community composition over time. [Masters Thesis]. University of Texas – Austin; 2011. Available from: http://hdl.handle.net/2152/ETD-UT-2011-05-3651

University of Oklahoma

2. Bill, Brian. AN INVESTIGATION INTO THE DISTRIBUTION OF MYXOBACTERIA, THE EFFECT OF PREDATOR-PREY INTERACTIONS ON SECONDARY METABOLITE EXPRESSION, AND DRIVERS OF MICROBIAL COMMUNITY ASSEMBLY.

Degree: PhD, 2019, University of Oklahoma

URL: http://hdl.handle.net/11244/320185

► The myxobacteria are Deltaproteobacteria capable of growing on a wide range of bacterial and fungal prey. To kill their prey, myxobacteria produce diverse secondary metabolites,… (more)

▼ The myxobacteria are Deltaproteobacteria capable of growing on a wide range of bacterial and fungal prey. To kill their prey, myxobacteria produce diverse secondary metabolites, many of which have medically desirable activities, including anti-viral, anti-fungal, anti-cancer, and antibacterial properties; however, the myxobacteria are difficult to cultivate because they do not form readily identifiable colonies on agar, do not disperse well in liquid, and grow slowly. As a consequence, the myxobacteria are poorly represented in culture, and as such their natural distribution and the effect predator-prey interactions on secondary metabolite expression are poorly understood. The purpose of the first part of this dissertation is to expand our knowledge of the natural distribution of the myxobacteria using cultivation-independent techniques, study the effect of predator-prey interactions on secondary metabolite expression, and improve their cultivation by supplementing growth media inhibitory dyes. The natural distribution of the myxobacteria was described using cultivation independent techniques. This analysis identified terrestrial, halophillic/halotolerant, and generalist families of myxobacteria, highlighted the limitations of cultivation-based biogeography, and provided insights into the ecology of both cultivated and uncultivated clades of myxobacteria. To test the effect of predator-prey interactions on secondary metabolite production, cultures of Myxococcus fulvus were grown on media containing heat-killed prey biomass as the sole carbon and energy source. Myxococcus fulvus produced more diverse LC-MS profiles when growing on prey that supported better growth, suggesting a link between predation rates and secondary metabolite expression. Finally, we report that a concentration of 1 mg/L crystal violet in standard growth media is useful for the isolation and purification of myxobacteria. Applied correctly, the insights from this dissertation will both improve cultivation of novel myxobacteria by directing sample site selection, and help unlock products of silent secondary metabolite gene clusters in existing cultures by leveraging the effects of predator-prey interactions. The second half of this dissertation focuses on the effect of chemical and biological forces on bacterial diversity and community structure. In the last 50 years, world wide application of NPK fertilizers has increased ~500%, and the widespread use of fertilizers in agriculture has indirectly increased the input of inorganic nutrients into natural ecosystems. Because microbial communities are sensitive to changes in nitrogen, phosphorus, and potassium, we hypothesized that nutrient enrichment would suppress diversity and alter the structure of leaf litter bacterial communities by selecting for copiotrophic taxa. We demonstrated that bacterial communities in tropical rainforest leaf litter are more sensitive to changes in nitrogen compared to potassium, phosphorus, or micronutrients. In addition to chemical factors, macrobiotic plant-animal … Advisors/Committee Members: Stevenson, Bradley (advisor), Kaspari, Michael (committee member), McInerney, Michael (committee member), Callaghan, Amy (committee member), Lawson, Paul (committee member).

Subjects/Keywords: Microbial Ecology

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APA (6^th Edition):

Bill, B. (2019). AN INVESTIGATION INTO THE DISTRIBUTION OF MYXOBACTERIA, THE EFFECT OF PREDATOR-PREY INTERACTIONS ON SECONDARY METABOLITE EXPRESSION, AND DRIVERS OF MICROBIAL COMMUNITY ASSEMBLY. (Doctoral Dissertation). University of Oklahoma. Retrieved from http://hdl.handle.net/11244/320185

Chicago Manual of Style (16^th Edition):

Bill, Brian. “AN INVESTIGATION INTO THE DISTRIBUTION OF MYXOBACTERIA, THE EFFECT OF PREDATOR-PREY INTERACTIONS ON SECONDARY METABOLITE EXPRESSION, AND DRIVERS OF MICROBIAL COMMUNITY ASSEMBLY.” 2019. Doctoral Dissertation, University of Oklahoma. Accessed January 27, 2021. http://hdl.handle.net/11244/320185.

MLA Handbook (7^th Edition):

Bill, Brian. “AN INVESTIGATION INTO THE DISTRIBUTION OF MYXOBACTERIA, THE EFFECT OF PREDATOR-PREY INTERACTIONS ON SECONDARY METABOLITE EXPRESSION, AND DRIVERS OF MICROBIAL COMMUNITY ASSEMBLY.” 2019. Web. 27 Jan 2021.

Vancouver:

Bill B. AN INVESTIGATION INTO THE DISTRIBUTION OF MYXOBACTERIA, THE EFFECT OF PREDATOR-PREY INTERACTIONS ON SECONDARY METABOLITE EXPRESSION, AND DRIVERS OF MICROBIAL COMMUNITY ASSEMBLY. [Internet] [Doctoral dissertation]. University of Oklahoma; 2019. [cited 2021 Jan 27]. Available from: http://hdl.handle.net/11244/320185.

Council of Science Editors:

Bill B. AN INVESTIGATION INTO THE DISTRIBUTION OF MYXOBACTERIA, THE EFFECT OF PREDATOR-PREY INTERACTIONS ON SECONDARY METABOLITE EXPRESSION, AND DRIVERS OF MICROBIAL COMMUNITY ASSEMBLY. [Doctoral Dissertation]. University of Oklahoma; 2019. Available from: http://hdl.handle.net/11244/320185

Oregon State University

3. Bryson, Samuel. Linking Phylogenetic Identity and Biogeochemical Function of Uncultivated Marine Microbes with Novel Mass Spectrometry Techniques.

Degree: PhD, 2017, Oregon State University

URL: http://hdl.handle.net/1957/61763

► The combined activities of diverse heterotrophic marine microorganisms significantly shape global biogeochemical cycles, but models of these activities are currently limited to aggregate microbial community… (more)

▼ The combined activities of diverse heterotrophic marine microorganisms significantly shape global biogeochemical cycles, but models of these activities are currently limited to aggregate microbial community processes, and it remains unclear how community structure and the functional roles of specific microbial taxa should be integrated into these models. Therefore, understanding the contributions of specific microbial populations toward net community processes remains a critical step for determining the appropriate taxonomic resolution that should be employed in more complex models of ecosystem processes. The application of ‘omics’ methods, such as metagenomics and metaproteomics, has revealed the phylogenetic diversity of natural microbial communities and the functional potential of discrete populations. From the integration of these observations, an understanding of microbial community dynamics has emerged in which niche processes influence general patterns of community structure at broad taxonomic scales across spatial and temporal resource gradients. Within these dynamic microbial systems, the partitioning of specific resources is governed by resource preferences and competitive interactions that cannot be ascertained with ‘omics’ approaches alone. In order to link phylogenetic identity with ecological function, and characterize resource partitioning in coastal marine microbial communities, we applied novel mass spectrometry techniques to stable isotope probing (SIP) experiments conducted on microbes sampled from coastal North Pacific surface waters. Chapter 2 presents the first application of proteomic stable isotope probing (proteomic SIP) to track 13C-labeled substrates into the proteomes of planktonic marine microbial communities. We developed two metrics for describing observations of label incorporation into peptides. Label frequency is a measure of protein synthesis activity that is calculated as the ratio of labeled to total detected peptide mass spectra for a defined set of proteins. Average enrichment is a measure of substrate specialization, and is calculated from the average percent of stable isotope content measured for a set of labeled peptides. Using these metrics, we compared the assimilation of 13C-labeled amino acids by abundant microbial taxa over two time-points, 15 and 32 hours. The communities sampled from Newport, OR and Monterey Bay, CA exhibited similar behaviors. Alteromonadales and Rhodobacterales proteomes had significantly high label frequency at the first time-point but had diverging trajectories in the second time-point indicating that Rhodobacterales held a competitive advantage as the amended substrate became depleted. In Chapter 3, we examined the assimilation of six 13C-labeld substrates by microbial taxa sampled from Monterey Bay, CA. Comparisons between relative abundance shifts and substrate assimilation were inconsistent, emphasizing the need for caution when interpreting relative abundances shifts in microbial community experiments.… Advisors/Committee Members: Mueller, Ryan (advisor), Giovannoni, Stephen (committee member).

Subjects/Keywords: marine microbial ecology

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APA (6^th Edition):

Bryson, S. (2017). Linking Phylogenetic Identity and Biogeochemical Function of Uncultivated Marine Microbes with Novel Mass Spectrometry Techniques. (Doctoral Dissertation). Oregon State University. Retrieved from http://hdl.handle.net/1957/61763

Chicago Manual of Style (16^th Edition):

Bryson, Samuel. “Linking Phylogenetic Identity and Biogeochemical Function of Uncultivated Marine Microbes with Novel Mass Spectrometry Techniques.” 2017. Doctoral Dissertation, Oregon State University. Accessed January 27, 2021. http://hdl.handle.net/1957/61763.

MLA Handbook (7^th Edition):

Bryson, Samuel. “Linking Phylogenetic Identity and Biogeochemical Function of Uncultivated Marine Microbes with Novel Mass Spectrometry Techniques.” 2017. Web. 27 Jan 2021.

Vancouver:

Bryson S. Linking Phylogenetic Identity and Biogeochemical Function of Uncultivated Marine Microbes with Novel Mass Spectrometry Techniques. [Internet] [Doctoral dissertation]. Oregon State University; 2017. [cited 2021 Jan 27]. Available from: http://hdl.handle.net/1957/61763.

Council of Science Editors:

Bryson S. Linking Phylogenetic Identity and Biogeochemical Function of Uncultivated Marine Microbes with Novel Mass Spectrometry Techniques. [Doctoral Dissertation]. Oregon State University; 2017. Available from: http://hdl.handle.net/1957/61763

Oregon State University

4. Welsh, Rory M. Bacterial Predation in Host Microbiomes.

Degree: PhD, Microbiology, 2015, Oregon State University

URL: http://hdl.handle.net/1957/57956

► In host-associated microbiomes, the mechanisms that regulate community composition or the principles that govern dynamics remain far from clear. However, understanding how the structure of… (more)

▼ In host-associated microbiomes, the mechanisms that regulate community composition or the principles that govern dynamics remain far from clear. However, understanding how the structure of microbial communities shift as the system moves away from a healthy state is critical to assessing disease progression and to formulate any potential mitigation strategy. In this dissertation, I targeted a relatively understudied genus of predatory bacteria, Halobacteriovorax, capable of preying on known pathogens, and aimed to determine the ecological role of these unusual predators in the microbiome of their coral host. Halobacteriovorax are a genus of delta proteobacteria which exhibit a biphasic lifestyle. In attack phase they are small (1 to 2 μm in length and 0.35μm in width), highly motile, single flagellated vibriod shaped bacteria that must attach to other bacteria before penetrating their periplasm where they undergo filamentous growth and genome replication without competition. As nutrients become exhausted from the prey cell, the elongated Halobacteriovorax filament divides into multiple attack phase progeny that lyse the bdelloplast. The ecological role of these predators is still relatively understudied, but given their predatory lifestyle, high grazing rates, and broad prey range, Halobacteriovorax could play a major role in structuring microbial communities. In order to study how cell-cell interactions impact microbial community structure and function, I employed a wide range of methods and technologies utilizing culture dependent and independent techniques. Using high throughput sequencing I detailed shifts in community structure of the microbiome of the mucosal surface layer of multiple coral species in their natural environment by repeatedly sampling individuals over a two-year time scale. Halobacteriovorax were a core microbiome component detected in over 78 percent of the 198 samples. Using network analysis I was able to obtain the temporal and spatial dynamics of Halobacteriovorax, and show that despite their predatory nature they predominately co-occur with their potential prey in our networks. I also isolated and cultured novel Halobacteriovorax strains from multiple coral species, and characterized these coral-associated predatory bacterial isolates using full-length 16S rRNA sequencing of cultures, phylogenetic analysis of the full length reads, prey range evaluation, and microscopic documentation of unique predatory lifecycle stages. In order to study cell-cell interactions I employed microfluidic devices and high-resolution video microscopy, image analysis, and cell tracking to observe individual predator-prey interactions utilizing predatory Halobacteriovorax and a common pathogen to a variety of aquatic host organisms, Vibrio coralliilyticus, as the prey. In this co-culture system, I captured striking microscale observations that demonstrate Halobacteriovorax’s ability to effectively prey on and reduce pathogenic V. coralliilyticus populations. To illuminate the role of Halobacteriovorax on the… Advisors/Committee Members: Vega Thurber, Rebecca L. (advisor), Schuster, Martin (committee member).

Subjects/Keywords: Microbiome; Microbial ecology

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APA (6^th Edition):

Welsh, R. M. (2015). Bacterial Predation in Host Microbiomes. (Doctoral Dissertation). Oregon State University. Retrieved from http://hdl.handle.net/1957/57956

Chicago Manual of Style (16^th Edition):

Welsh, Rory M. “Bacterial Predation in Host Microbiomes.” 2015. Doctoral Dissertation, Oregon State University. Accessed January 27, 2021. http://hdl.handle.net/1957/57956.

MLA Handbook (7^th Edition):

Welsh, Rory M. “Bacterial Predation in Host Microbiomes.” 2015. Web. 27 Jan 2021.

Vancouver:

Welsh RM. Bacterial Predation in Host Microbiomes. [Internet] [Doctoral dissertation]. Oregon State University; 2015. [cited 2021 Jan 27]. Available from: http://hdl.handle.net/1957/57956.

Council of Science Editors:

Welsh RM. Bacterial Predation in Host Microbiomes. [Doctoral Dissertation]. Oregon State University; 2015. Available from: http://hdl.handle.net/1957/57956

Cornell University

5. Roco, Constance. Characterization Of Soil Denitrifier Diversity: From Isolate Phyiology To Community Metagenomics.

Degree: PhD, Microbiology, 2015, Cornell University

URL: http://hdl.handle.net/1813/40894

► Denitrification is a part of the global nitrogen cycle in which reactive nitrogen in the biosphere is returned to the atmosphere, and is mediated by… (more)

▼ Denitrification is a part of the global nitrogen cycle in which reactive nitrogen in the biosphere is returned to the atmosphere, and is mediated by diverse communities of microorganisms. The work in this thesis was undertaken to gain a greater understanding of the ecology of denitrifying microorganisms. A combination of bioinformatic analysis of denitrification genes in pure cultures and environmental samples, as well as experimental work with denitrifying bacterial cultures and soil microcosms was performed to understand the relationship between genes and ecosystems in denitrification. First, we examined the diversity of denitrifiers in soil through genome sequencing of microbial isolates coupled to denitrification gas kinetic measurements. The results suggest that partial denitrifiers are common among soil bacteria and it was demonstrated that nitrogen oxide production could not always be predicted by the genetic potential of the isolates. This reveals there are different regulatory effects on each step of the denitrification pathway, which dictate the accumulation of denitrification products. Secondly, the prevalence of dissimilatory reduction of nitrate under aerobic conditions in soil was assessed. Bacteria capable of aerobic nitrate reduction were easily isolated and found to reduce nitrate at oxygen concentrations greater than levels associated with the onset of nitrite reduction and the genomic analysis of the nitrate reductase genes revealed a wide diversity of physiological controls. Finally, a soil microcosm study was performed to determine the influence of oxygen on denitrification gas kinetics and denitrifier community structure. Comparison of soils exposed to oxic, short anoxic and long anoxic conditions revealed the oxic soils had fastest denitrification rates, indicating denitrifiers were not hindered by oxic conditions. The genetic community structure, characterized through metagenomic and metatranscriptomic analysis, was shown to be an important factor in determining denitrification rates and end product ratios. In conclusion, denitrification is a complex pathway of ecological importance that is controlled by the interaction between genes and environmental factors. In order to develop useful tools to mitigate reactive nitrogen and other climate-forcing nitrogen species, a comprehensive understanding of the regulatory network of denitrification with respect to microbial physiology and environmental interactions is needed. Advisors/Committee Members: Shapleigh,James P (chair), Yavitt,Joseph B (coChair), Nicholson,Linda K (committee member), Goodale,Christine L (committee member).

Subjects/Keywords: Denitrification; Microbial ecology

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APA (6^th Edition):

Roco, C. (2015). Characterization Of Soil Denitrifier Diversity: From Isolate Phyiology To Community Metagenomics. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/40894

Chicago Manual of Style (16^th Edition):

Roco, Constance. “Characterization Of Soil Denitrifier Diversity: From Isolate Phyiology To Community Metagenomics.” 2015. Doctoral Dissertation, Cornell University. Accessed January 27, 2021. http://hdl.handle.net/1813/40894.

MLA Handbook (7^th Edition):

Roco, Constance. “Characterization Of Soil Denitrifier Diversity: From Isolate Phyiology To Community Metagenomics.” 2015. Web. 27 Jan 2021.

Vancouver:

Roco C. Characterization Of Soil Denitrifier Diversity: From Isolate Phyiology To Community Metagenomics. [Internet] [Doctoral dissertation]. Cornell University; 2015. [cited 2021 Jan 27]. Available from: http://hdl.handle.net/1813/40894.

Council of Science Editors:

Roco C. Characterization Of Soil Denitrifier Diversity: From Isolate Phyiology To Community Metagenomics. [Doctoral Dissertation]. Cornell University; 2015. Available from: http://hdl.handle.net/1813/40894

University of North Carolina – Greensboro

6. Williams, William T. Biogeography: do microbes have it?.

Degree: 2011, University of North Carolina – Greensboro

URL: http://libres.uncg.edu/ir/listing.aspx?styp=ti&id=8328

► The purpose of this study was to use an empirical approach to assess microbial biogeography in freshwater lakes. The targeted, empirical approach was pursued in… (more)

Subjects/Keywords: Microbial ecology – Research

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APA (6^th Edition):

Williams, W. T. (2011). Biogeography: do microbes have it?. (Masters Thesis). University of North Carolina – Greensboro. Retrieved from http://libres.uncg.edu/ir/listing.aspx?styp=ti&id=8328

Chicago Manual of Style (16^th Edition):

Williams, William T. “Biogeography: do microbes have it?.” 2011. Masters Thesis, University of North Carolina – Greensboro. Accessed January 27, 2021. http://libres.uncg.edu/ir/listing.aspx?styp=ti&id=8328.

MLA Handbook (7^th Edition):

Williams, William T. “Biogeography: do microbes have it?.” 2011. Web. 27 Jan 2021.

Vancouver:

Williams WT. Biogeography: do microbes have it?. [Internet] [Masters thesis]. University of North Carolina – Greensboro; 2011. [cited 2021 Jan 27]. Available from: http://libres.uncg.edu/ir/listing.aspx?styp=ti&id=8328.

Council of Science Editors:

Williams WT. Biogeography: do microbes have it?. [Masters Thesis]. University of North Carolina – Greensboro; 2011. Available from: http://libres.uncg.edu/ir/listing.aspx?styp=ti&id=8328

Montana State University

7. Encarnacion, Gem Deangkinay. Microbial ecology of nitrifying simulated premises plumbing.

Degree: PhD, College of Letters & Science, 2012, Montana State University

URL: https://scholarworks.montana.edu/xmlui/handle/1/1228

► Because of the Stage 2 Disinfectants and Disinfection Rule limiting then concentration of disinfection by products in drinking water, the use of chloramine as an… (more)

▼ Because of the Stage 2 Disinfectants and Disinfection Rule limiting then concentration of disinfection by products in drinking water, the use of chloramine as an alternative to chlorine has been increasing. However, the ammonia introduced by chloramination can lead to nitrification which results in the production of nitrite and nitrate, leading to regulatory violations. Nitrification in reactors with copper and polyvinyl chloride (PVC) surfaces was established by indigenous organisms from Bozeman tap water and has been stably maintained for more than 6 years. Statistical analyses of polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) profiles determined that the active bacterial populations were different in the two systems. The assemblage of the organisms was also different from the starting population (BAC influent) suggesting both material and ammonia/carbon source affect the population. No known ammonia oxidizing bacteria were detected suggesting the role of different group for ammonia oxidation. Fluorescence in situ hybridization (FISH) detected archaea in the biofilm from both reactors. Archaeal 16S rRNA gene sequences were found to be phylogenetically affiliated with known archaeal ammonia oxidizers. Two archaeal amoA sequences were amplified from the system as determined by DGGE. We propose to provisionally classify a detected archaeon as Candidatus Nitrosotenuis bozemanii, based on its affinity to Nitrosotenuis uzonensis (Hatzenpichler et al., in preparation). Bacterial abundances were comparable in the two systems but archaeal abundances were higher in the PVC reactor suggesting material effect on the overall microbial population composition and density. Enrichment in modified synthetic Crenarchaeota medium yielded a culture of archaea and bacteria that consistently oxidizes ammonia to nitrate. Attempts to isolate the archaeal component using antibiotics failed, suggesting the disruption of a possible beneficial relationship between the archaea and bacteria. Genes involved in the transformation of nitrogen within the system were also investigated and hao distantly related to that of ammonia oxidizing bacteria was detected but its potential role remains unknown. This study provides evidence of archaea associated with biofilms in drinking water and while further analysis is needed to definitively elucidate their role, results of this study prompts the reevaluation of the current concept of nitrification in drinking water. Advisors/Committee Members: Chairperson, Graduate Committee: Anne Camper (advisor), Mark D. Burr and Anne K. Camper were co-authors of the article, 'Bacterial communities in nitrifying simulated premises plumbing' in the journal 'Water research' which is contained within this thesis. (other), Anne K. Camper was a co-author of the article, 'Detection and enrichment of a nitrifying community containing a novel archaeon from simulated premises plumbing' in the journal 'PLoS One' which is contained within this thesis. (other).

Subjects/Keywords: Nitrification.; Microbial ecology.

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APA (6^th Edition):

Encarnacion, G. D. (2012). Microbial ecology of nitrifying simulated premises plumbing. (Doctoral Dissertation). Montana State University. Retrieved from https://scholarworks.montana.edu/xmlui/handle/1/1228

Chicago Manual of Style (16^th Edition):

Encarnacion, Gem Deangkinay. “Microbial ecology of nitrifying simulated premises plumbing.” 2012. Doctoral Dissertation, Montana State University. Accessed January 27, 2021. https://scholarworks.montana.edu/xmlui/handle/1/1228.

MLA Handbook (7^th Edition):

Encarnacion, Gem Deangkinay. “Microbial ecology of nitrifying simulated premises plumbing.” 2012. Web. 27 Jan 2021.

Vancouver:

Encarnacion GD. Microbial ecology of nitrifying simulated premises plumbing. [Internet] [Doctoral dissertation]. Montana State University; 2012. [cited 2021 Jan 27]. Available from: https://scholarworks.montana.edu/xmlui/handle/1/1228.

Council of Science Editors:

Encarnacion GD. Microbial ecology of nitrifying simulated premises plumbing. [Doctoral Dissertation]. Montana State University; 2012. Available from: https://scholarworks.montana.edu/xmlui/handle/1/1228

University of Illinois – Urbana-Champaign

8. Li, Dongfang. Investigation of Miscanthus associated microbiome: effects of biotic and abiotic factors.

Degree: PhD, Natural Res & Env Sciences, 2015, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/88261

► Long-term sustainable production of biofuel feedstock crops like Miscanthus species requires minimum anthropogenic energy inputs as well as the maintenance of soil fertility. Beneficial microbes,… (more)

▼ Long-term sustainable production of biofuel feedstock crops like Miscanthus species requires minimum anthropogenic energy inputs as well as the maintenance of soil fertility. Beneficial microbes, such as nitrogen-fixing bacteria, contribute to plant yield and fitness, representing under-explored plant nutrient sources. Optimizing the positive interactions between Miscanthus species and associated bacteria has high potential to support sustainable crop production. Bacterial community functions are directly related to community structures, which rely on surrounding biotic and abiotic factors. Therefore, before Miscanthus-bacteria interactions can be optimized for better plant productivity, it is necessary to investigate the factors that regulate community assemblage of these microbes. The goal of this dissertation is to identify factors that significantly explain the Miscanthus-associated bacterial community variation. To achieve this goal, a combination of observational and experimental approaches was used. Miscanthus plants were collected from native, naturalized and cultivated habitats. These habitats represent a broad range of biotic and abiotic factors. Both Miscanthus endophytic compartment (rhizomes) and their surrounding rhizosphere soil were collected from each plant because both endophytes and rhizosphere bacteria are known to contribute to mutualistic plant-microbe interactions. Here, I accessed and compared both endophytic and rhizosphere bacterial communities, and evaluated whether plant genotypes and soil edaphic factors may influence them differently. As one of the most important beneficial bacteria groups, Miscanthus-associated diazotrophs assemblages were also examined in this work. I found endophytic and rhizosphere communities correlated differently with their surrounding environment. Overall, I found that endophytic communities were more likely to be genotype-specific than the rhizosphere bacteria while the rhizosphere communities tended to change when soil conditions changed. The effect of agricultural practices could be hard to maintain and not significantly change microbial communities. Therefore, the goal of optimizing rhizosphere communities by changing soil conditions cannot be achieved easily. Instead, Miscanthus-associated endophytes are relatively stable to environmental change, and I identified some key endophytic-enriched taxa were shared among Miscanthus sites at a global scale. Hence, facilitate beneficial taxa to colonize Miscanthus endophytic compartment during rhizome propagation or pre-treatment of Miscanthus seeds with beneficial strains may be effective strategies to enhance the mutualism between Miscanthus and bacteria. Even closely related Miscanthus genotypes tended to harbor very different endophytic N-fixing bacteria. On one hand, this result indicates the possibility of identifying plant genetic markers that control endophytic bacteria recruitment. On the other hand, the contribution of beneficial bacteria to Miscanthus must be evaluated on a genotype-by-genotype basis. I… Advisors/Committee Members: Kent, Angela D. (advisor), Heath, Katy D (Committee Chair), Davis, Adam S. (committee member), Sacks, Erik J. (committee member), Voigt, Thomas B. (committee member), Yannarell, Anthony C. (committee member).

Subjects/Keywords: Microbial ecology; Miscanthus

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APA (6^th Edition):

Li, D. (2015). Investigation of Miscanthus associated microbiome: effects of biotic and abiotic factors. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/88261

Chicago Manual of Style (16^th Edition):

Li, Dongfang. “Investigation of Miscanthus associated microbiome: effects of biotic and abiotic factors.” 2015. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed January 27, 2021. http://hdl.handle.net/2142/88261.

MLA Handbook (7^th Edition):

Li, Dongfang. “Investigation of Miscanthus associated microbiome: effects of biotic and abiotic factors.” 2015. Web. 27 Jan 2021.

Vancouver:

Li D. Investigation of Miscanthus associated microbiome: effects of biotic and abiotic factors. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2015. [cited 2021 Jan 27]. Available from: http://hdl.handle.net/2142/88261.

Council of Science Editors:

Li D. Investigation of Miscanthus associated microbiome: effects of biotic and abiotic factors. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2015. Available from: http://hdl.handle.net/2142/88261

University of California – Irvine

9. Hatosy, Stephen Mark. Phylogenetic and Functional Biogeography of Marine Bacteria.

Degree: Biological Sciences, 2015, University of California – Irvine

URL: http://www.escholarship.org/uc/item/3z64m8m8

► Communities vary across space and time. In addition, they may vary differently at different spatial and temporal scales. It is well established that marine bacterial… (more)

▼ Communities vary across space and time. In addition, they may vary differently at different spatial and temporal scales. It is well established that marine bacterial communities are temporally structured by seasons. However, there are other environmental changes that occur at different temporal scales. Here, we quantified the community variation at three temporal scales across three time series. We found that communities varied at the three time scales with the majority of community variation occurred within seasons. Additionally, we found that community variation correlated with different environmental variables at different temporal scales.Next I wanted to identify the effect phylogenetic scale has on biodiversity patterns. Most of bacterial ecology defines a taxon as a group that shares more than 97% similarity of the 16S rRNA. However, these groups are not independent of each other. They share evolutionary history charted by divergences into different niches. In order to identify the role of phylogentic resolution on population dynamics, I undertook a 4.5-year sampling project and analysed the variation in relative abundance at different taxonomic levels (genus level, clade level, and subgroup level). I found that the frequency of variation increased as I moved to finer phylogentic resolutions. In addition, the correlation with temperature also changed by changing phylogentic resolution. Finally, I wanted to identify antibiotic resistance genes in marine environments. Natural environments are quickly being discovered to harbor a number of antibiotic resistance genes. However, marine environments have been mostly overlooked even though they cover more than 70% of Earth's surface, and hold on the order of 1029 bacterial cells. As part of my dissertation, I wished to fill this knowledge gap. By using the culture independent method of functional metagenomics, I discovered genes that conferred antibiotic resistance. Of these genes, 28% were identified as previously known antibiotic resistance genes. The majority were unknown to confer resistance, but had activities similar to antibiotic resistance genes (e.g. transport pumps, enzymatic degradation, etc.). I also identified that the majority of these genes were found in marine bacteria, such as Pelagibacter, Roseobacter, and Prochlorococcus. Therefore, I have uncovered a potential global reservoir of antibiotic resistance genes.

Subjects/Keywords: Ecology; Metagenomics; Microbial ecology; Pyrosequencing

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APA (6^th Edition):

Hatosy, S. M. (2015). Phylogenetic and Functional Biogeography of Marine Bacteria. (Thesis). University of California – Irvine. Retrieved from http://www.escholarship.org/uc/item/3z64m8m8

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Hatosy, Stephen Mark. “Phylogenetic and Functional Biogeography of Marine Bacteria.” 2015. Thesis, University of California – Irvine. Accessed January 27, 2021. http://www.escholarship.org/uc/item/3z64m8m8.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Hatosy, Stephen Mark. “Phylogenetic and Functional Biogeography of Marine Bacteria.” 2015. Web. 27 Jan 2021.

Vancouver:

Hatosy SM. Phylogenetic and Functional Biogeography of Marine Bacteria. [Internet] [Thesis]. University of California – Irvine; 2015. [cited 2021 Jan 27]. Available from: http://www.escholarship.org/uc/item/3z64m8m8.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Hatosy SM. Phylogenetic and Functional Biogeography of Marine Bacteria. [Thesis]. University of California – Irvine; 2015. Available from: http://www.escholarship.org/uc/item/3z64m8m8

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Cornell University

10. Eggleston, Erin. Investigating Aquatic Microbial Community Dynamics From Rivers To Oceans Using Molecular Biological Techniques.

Degree: PhD, Microbiology, 2015, Cornell University

URL: http://hdl.handle.net/1813/41090

► Aquatic habitats are dominated by microbial life and these microbial communities are responsible for the major biogeochemical cycles within these environments. Using molecular biological techniques… (more)

▼ Aquatic habitats are dominated by microbial life and these microbial communities are responsible for the major biogeochemical cycles within these environments. Using molecular biological techniques we set out to examine the activity and diversity of these microbial communities within a variety of aquatic ecosystems. First, we examined the relative expression of key respiratory genes from plankton metatrancriptomic libraries prepared from samples over an oxygen gradient. These samples demonstrated changes consistent with energetically favorable terminal electron acceptor availability and we show that, rather than abrupt transitions between terminal electron acceptors, there is substantial overlap in time and space of these various anaerobic respiratory processes in Chesapeake Bay. Second, metatranscriptomes of four major Chesapeake Bay tributaries, the Choptank, James, Potomac and Susquehanna Rivers were annotated to characterize active microbial communities within these environments. Annotations for reads mapped to bacterial and archaeal transcripts were highly similar between rivers (~17 ±3% Archaeal and ~83 ± 3% Bacterial). Because nutrient loading from rivers is a major factor driving anoxia and general biological health within Chesapeake Bay, we also examined the relationship between the active microbial communities in the riverine samples to those within the bay. We found that although oxic waters within the Chesapeake Bay vary taxonomically from those within the rivers, functionally these communities are dominated by transcripts related to cell growth, transport and photosynthesis. Finally, we examined viral and bacterial dynamics along a latitudinal transect in the Atlantic Ocean from approximately 10N to 40S. Viral abundance decreased with depth and was highly correlated to bacterial abundance. Viral-size fraction DNA was used to quantify the abundance of two pelagiphages, using pelagiphage-specific primers along this transect. We found that HTVC010P, a member of a podoviridae sub-family, was most abundant in surface waters. HTVC008M, a T4-like myovirus, was present in the deep chlorophyll maximum, although it was not as highly abundant as HTVC010P in surface waters. Interestingly, HTVC008M was only present at a few of the most southern stations, suggesting latitudinal biogeography dynamics of SAR11 phages. Additionally, viral production experiments provide evidence that HTVC008M may be temperate. Advisors/Committee Members: Hewson,Ian (chair), Sparks,Jed P. (committee member), Buckley,Daniel H (committee member).

Subjects/Keywords: Transcriptomics; Microbial Ecology; Viral Ecology

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APA (6^th Edition):

Eggleston, E. (2015). Investigating Aquatic Microbial Community Dynamics From Rivers To Oceans Using Molecular Biological Techniques. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/41090

Chicago Manual of Style (16^th Edition):

Eggleston, Erin. “Investigating Aquatic Microbial Community Dynamics From Rivers To Oceans Using Molecular Biological Techniques.” 2015. Doctoral Dissertation, Cornell University. Accessed January 27, 2021. http://hdl.handle.net/1813/41090.

MLA Handbook (7^th Edition):

Eggleston, Erin. “Investigating Aquatic Microbial Community Dynamics From Rivers To Oceans Using Molecular Biological Techniques.” 2015. Web. 27 Jan 2021.

Vancouver:

Eggleston E. Investigating Aquatic Microbial Community Dynamics From Rivers To Oceans Using Molecular Biological Techniques. [Internet] [Doctoral dissertation]. Cornell University; 2015. [cited 2021 Jan 27]. Available from: http://hdl.handle.net/1813/41090.

Council of Science Editors:

Eggleston E. Investigating Aquatic Microbial Community Dynamics From Rivers To Oceans Using Molecular Biological Techniques. [Doctoral Dissertation]. Cornell University; 2015. Available from: http://hdl.handle.net/1813/41090

University of Tennessee – Knoxville

11. Gainer, Phillip Jackson. MICROBIAL INTERACTIONS IN THE NORTH PACIFIC OCEAN.

Degree: 2018, University of Tennessee – Knoxville

URL: https://trace.tennessee.edu/utk_graddiss/5012

► A majority of Earth’s surface is covered by the marine ecosystem. This ecosystem is characterized by the numerical dominance of microbes, both eukaryotic and prokaryotic… (more)

▼ A majority of Earth’s surface is covered by the marine ecosystem. This ecosystem is characterized by the numerical dominance of microbes, both eukaryotic and prokaryotic and their infecting viruses. As the basis of the food web in marine systems these members of the microbial community are vital to the function of the planet. Despite their noted importance, the microbial communities in many oceanic regions are largely uncharacterized due to geographic isolation, including the largest oceanic basin on the planet, the North Pacific Ocean. Basin scale studies of the North Pacific have primarily focused on characterization of abundance and diversity of bacteria and viruses. Interactions between these microbial constituents have been largely unexplored on a basin scale. As such, this body of work aims to generate hypotheses on the influence that biotic interactions have on microbial community structure and evolution on a basin scale. First, the role biotic interactions responsible for shaping virus abundances and production rates in the North Pacific Ocean were examined. We found that virus abundance and production rates correlated to bacterial taxa that are enriched in particle associated communities, indicating that particles may serve as sites of increased viral activity in the North Pacific Ocean. Secondly, we utilized network analysis to explore inferred bacterial co-occurrences within the North Pacific Basin. We found that diverse taxa participate in at least one significant co-occurrence with another microbe within this basin. Further, network topology parameters, such as high connectance and low modularity, proposed to be hallmarks of community stability differed regionally, indicating that the North Pacific Subtropical Gyre may be more robust to environmental changes. Finally, we developed an assay to screen for Synechococcus WH7803 transposon mutants that are resistant to a co-occurring cyanomyovirus, to identify genes necessary for lytic viral infection. Characterization of these genes will allow for a more holistic understanding of the interactions between this cyanobacterium and its infecting viruses in the natural environment. These findings highlight the importance of considering interactions between microbial entities in the marine system in understanding the functioning of microbial communities in the North Pacific basin.

Subjects/Keywords: Marine Microbial Ecology; Viruses; Microbial Interactions

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Gainer, P. J. (2018). MICROBIAL INTERACTIONS IN THE NORTH PACIFIC OCEAN. (Doctoral Dissertation). University of Tennessee – Knoxville. Retrieved from https://trace.tennessee.edu/utk_graddiss/5012

Chicago Manual of Style (16^th Edition):

Gainer, Phillip Jackson. “MICROBIAL INTERACTIONS IN THE NORTH PACIFIC OCEAN.” 2018. Doctoral Dissertation, University of Tennessee – Knoxville. Accessed January 27, 2021. https://trace.tennessee.edu/utk_graddiss/5012.

MLA Handbook (7^th Edition):

Gainer, Phillip Jackson. “MICROBIAL INTERACTIONS IN THE NORTH PACIFIC OCEAN.” 2018. Web. 27 Jan 2021.

Vancouver:

Gainer PJ. MICROBIAL INTERACTIONS IN THE NORTH PACIFIC OCEAN. [Internet] [Doctoral dissertation]. University of Tennessee – Knoxville; 2018. [cited 2021 Jan 27]. Available from: https://trace.tennessee.edu/utk_graddiss/5012.

Council of Science Editors:

Gainer PJ. MICROBIAL INTERACTIONS IN THE NORTH PACIFIC OCEAN. [Doctoral Dissertation]. University of Tennessee – Knoxville; 2018. Available from: https://trace.tennessee.edu/utk_graddiss/5012

Duke University

12. Larkin-Swartout, Alyse Anne. Ecological Controls on Prochlorococcus sp. Diversity, Composition, and Activity at High Taxonomic Resolution .

Degree: 2016, Duke University

URL: http://hdl.handle.net/10161/13359

► Although there are many examples of microbial biogeography, few microbes have been studied at high taxonomic resolution over large spatial scales. As a result,… (more)

▼ Although there are many examples of microbial biogeography, few microbes have been studied at high taxonomic resolution over large spatial scales. As a result, the environmental and ecological processes that drive niche partitioning, diversity, composition, and activity of microbial taxa are often poorly understood. To address this gap, I examine the most abundant phytoplankton in the global ocean, Prochlorococcus sp., a marine cyanobacterium. Using amplicon libraries of the Prochlorococcus internal transcribed spacer (ITS) region and 23S rRNA gene as markers, I demonstrate several key differences between the two major high light (HL) clades of Prochlorococcus. First, by examining ITS amplicon libraries at high taxonomic resolution it is revealed that “sub-ecotype” clades have unique, cohesive responses to environmental variables and distinct biogeographies, suggesting that presently defined ecotypes can be further partitioned into ecologically meaningful units. Whereas unique combinations of environmental traits drive the distribution of the HL-I sub-ecotype clades, the HL-II sub-ecotype clades appear ecologically coherent. Second, using 23S rRNA and rDNA libraries I show that activity (rRNA) and abundance (rDNA) are highly correlated for Prochlorococcus across all sites and operational taxonomic units (OTUs) in the surface ocean, demonstrating a tight coupling between activity and abundance. Finally, I investigate the associations between Prochlorococcus and the rest of the microbial community in the North Pacific and find region-specific trends in both strength and sign. Associations with other microbes are strongest for HL-I in the temperate region and strongest for HL-II in the sub-tropical gyre. This dissertation clarifies the relative importance of the environment, geography, community, and taxonomy in terms of their role in creating complex assemblages of Prochlorococcus and helps improve our understanding of how marine microbial communities are assembled in situ. Advisors/Committee Members: Johnson, Zackary I (advisor).

Subjects/Keywords: Biological oceanography; Ecology; Microbiology; Bacterioplankton; Microbial activity; Microbial diversity; Microbial ecology; Microbial interactions; Prochlorococcus

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APA (6^th Edition):

Larkin-Swartout, A. A. (2016). Ecological Controls on Prochlorococcus sp. Diversity, Composition, and Activity at High Taxonomic Resolution . (Thesis). Duke University. Retrieved from http://hdl.handle.net/10161/13359

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Larkin-Swartout, Alyse Anne. “Ecological Controls on Prochlorococcus sp. Diversity, Composition, and Activity at High Taxonomic Resolution .” 2016. Thesis, Duke University. Accessed January 27, 2021. http://hdl.handle.net/10161/13359.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Larkin-Swartout, Alyse Anne. “Ecological Controls on Prochlorococcus sp. Diversity, Composition, and Activity at High Taxonomic Resolution .” 2016. Web. 27 Jan 2021.

Vancouver:

Larkin-Swartout AA. Ecological Controls on Prochlorococcus sp. Diversity, Composition, and Activity at High Taxonomic Resolution . [Internet] [Thesis]. Duke University; 2016. [cited 2021 Jan 27]. Available from: http://hdl.handle.net/10161/13359.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Larkin-Swartout AA. Ecological Controls on Prochlorococcus sp. Diversity, Composition, and Activity at High Taxonomic Resolution . [Thesis]. Duke University; 2016. Available from: http://hdl.handle.net/10161/13359

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of California – Berkeley

13. Cruz Martinez, Karelyn. EFFECTS OF ALTERNATE PRECIPITATION PATTERNS ON SOIL MICROBIAL COMMUNITIES IN A CALIFORNIA GRASSLAND.

Degree: Microbiology, 2010, University of California – Berkeley

URL: http://www.escholarship.org/uc/item/2pg7k9w1

► Anthropogenic changes in climatic conditions, such as the timing and amount of rainfall, can have profound biotic and abiotic consequences on grassland ecosystems. Grassland's plant… (more)

▼ Anthropogenic changes in climatic conditions, such as the timing and amount of rainfall, can have profound biotic and abiotic consequences on grassland ecosystems. Grassland's plant and animal phenology are adapted to the ecosystem's wet and cold winters and hot and dry summers and changes to this pattern will have profound consequences in aboveground community structure. Changes in climatic conditions and aboveground communities will also affect the soil biogeochemistry and microbial communities. Soil microbes are an essential component in ecosystem functioning, as they are the key players in nutrient cycling. This thesis investigated the direct and indirect effects of climate change on the structure, composition and abundance of grassland soil microbial communities. The research used the high-throughput technique of 16S rRNA microarrays (Phylochip) to detect changes in the abundances and activities of soil bacterial and archaeal taxa in response to changes in precipitation patterns, aboveground plant communities, and soil environmental conditions. The research took advantage of alongterm climate change experiment that simulated both an increase and an extension of the current winter season in northern California. Five years into the experiment, soil samples and aboveground plant diversity were collected before and after each treatment for two consecutive years. The variability in soil microbial communities after natural wet-dry rainfall events was also investigated. Results showed that, at the community level, soil microbial communities are very robust and resilient to intensified or extended rainfalls during the winter but under extreme and unusual weather events their community structure can be altered. On the other hand, an increased in moss biomass in the plots that received additional water during the spring and fluctuations in soil moisture content (precipitation models and wet-dry patterns) caused changes in soil environmental conditions which in turn affected the activity and abundance of some microbial taxa/guilds. Soil organic carbon and inorganic nitrogen were among the environmental variables that correlated the most with these changes in microbial groups. Considering the great importance soil microbes have in ecosystem functioning, the approach developed here will find application for monitor responses of keystone microbial species/guilds to future changes in climatic conditions. These responses should be taken in consideration for future soil management and conservation practices, and the impacts included in future climate change models.

Subjects/Keywords: Microbiology; Environmental Microbiology; Microbial Ecology

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APA (6^th Edition):

Cruz Martinez, K. (2010). EFFECTS OF ALTERNATE PRECIPITATION PATTERNS ON SOIL MICROBIAL COMMUNITIES IN A CALIFORNIA GRASSLAND. (Thesis). University of California – Berkeley. Retrieved from http://www.escholarship.org/uc/item/2pg7k9w1

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Cruz Martinez, Karelyn. “EFFECTS OF ALTERNATE PRECIPITATION PATTERNS ON SOIL MICROBIAL COMMUNITIES IN A CALIFORNIA GRASSLAND.” 2010. Thesis, University of California – Berkeley. Accessed January 27, 2021. http://www.escholarship.org/uc/item/2pg7k9w1.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Cruz Martinez, Karelyn. “EFFECTS OF ALTERNATE PRECIPITATION PATTERNS ON SOIL MICROBIAL COMMUNITIES IN A CALIFORNIA GRASSLAND.” 2010. Web. 27 Jan 2021.

Vancouver:

Cruz Martinez K. EFFECTS OF ALTERNATE PRECIPITATION PATTERNS ON SOIL MICROBIAL COMMUNITIES IN A CALIFORNIA GRASSLAND. [Internet] [Thesis]. University of California – Berkeley; 2010. [cited 2021 Jan 27]. Available from: http://www.escholarship.org/uc/item/2pg7k9w1.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Cruz Martinez K. EFFECTS OF ALTERNATE PRECIPITATION PATTERNS ON SOIL MICROBIAL COMMUNITIES IN A CALIFORNIA GRASSLAND. [Thesis]. University of California – Berkeley; 2010. Available from: http://www.escholarship.org/uc/item/2pg7k9w1

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Alberta

14. Lin,Xiaoxi. Microbial ecology of food fermentations and intestinal ecosystems.

Degree: PhD, Department of Agricultural, Food, and Nutritional Science, 2014, University of Alberta

URL: https://era.library.ualberta.ca/files/6t053h01f

► Microbiota are ubiquitous in nature. Similarities as well as differences are present between microbiota in animals and fermentation systems. The aim of the PhD project… (more)

▼ Microbiota are ubiquitous in nature. Similarities as well as differences are present between microbiota in animals and fermentation systems. The aim of the PhD project was to investigate factors affects microbial ecology in rodent and sourdough models. To determine how compromised health of the host by tumor and CPT-11 therapies affects intestinal microbiota in tumor bearing rats, qualitative and quantitative taxonomic analyses were combined to characterize intestinal microbiota during CPT-11-based chemotherapy. Both tumor and CPT-11 chemotherapy increased cecal Clostridium cluster XI and Enterobacteriaceae. The effect of dietary fibre was evaluated in the same model. Cecal butyrate concentrations and feed intake were highly correlated. Moreover, a positive correlation of the host expression of MCT1 with body weight as well as a positive correlation of the abundance of bacterial butyryl-CoA gene with cecal butyrate concentrations were obeserved. These correlations support the interpretation that the influence of dietary fibre on CPT-11 toxicity is partially mediated by an increased cecal production of butyrate. Similar to intestinal microbiota, in sourdough, cereal substrates contain various compounds that may have selective effect on sourdough microbiota. The effect of growth rate and acid resistance on microbial competitiveness in sourdoughs was evaluated by assessing competitiveness of glycerol-dehydratase (gupCDE) positive and glutamate-decarboxylase (gadB) positive strains of L. reuteri relative to the corresponding null mutants. Both glycerol and glutamate metabolism determine the competitiveness of L. reuteri in sourdough fermentations. Besides competition over shared energy source, microbes also compete with each other by producing antimicrobial compounds. Reutericyclin is an antibiotic produced by sourdough-originated L. reuteri which is bactericidal against most gram-positive bacteria. A combination comparative genomics, bioinformatics analysis, and the characterization of null-mutants was used to determine the genetic determinants of reutericyclin biosynthesis. A gene cluster unique to reutericyclin producers was identified on a genomic island acquired through lateral gene transfer. It includes genes coding for a nonribosomal peptide synthetase (NRPS), a polyketide synthase (PKS), homologues of phlABC, and putative transport and regulatory proteins. The combination of PhlABC homologues with both a NRPS and PKS is exclusive to the lactic acid bacteria Streptococcus mutans, L. plantarum and L. reuteri, indicating that the genes in these organisms share a common evolutionary origin.

Subjects/Keywords: fermentation; ecology; sourdough; microbiota; microbial

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APA (6^th Edition):

Lin,Xiaoxi. (2014). Microbial ecology of food fermentations and intestinal ecosystems. (Doctoral Dissertation). University of Alberta. Retrieved from https://era.library.ualberta.ca/files/6t053h01f

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Chicago Manual of Style (16^th Edition):

Lin,Xiaoxi. “Microbial ecology of food fermentations and intestinal ecosystems.” 2014. Doctoral Dissertation, University of Alberta. Accessed January 27, 2021. https://era.library.ualberta.ca/files/6t053h01f.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

MLA Handbook (7^th Edition):

Lin,Xiaoxi. “Microbial ecology of food fermentations and intestinal ecosystems.” 2014. Web. 27 Jan 2021.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Vancouver:

Lin,Xiaoxi. Microbial ecology of food fermentations and intestinal ecosystems. [Internet] [Doctoral dissertation]. University of Alberta; 2014. [cited 2021 Jan 27]. Available from: https://era.library.ualberta.ca/files/6t053h01f.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Council of Science Editors:

Lin,Xiaoxi. Microbial ecology of food fermentations and intestinal ecosystems. [Doctoral Dissertation]. University of Alberta; 2014. Available from: https://era.library.ualberta.ca/files/6t053h01f

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

University of Georgia

15. Workman, John Barrett. A holistic approach to decreasing dollar spot severity and over-wintering inocula of Sclerotinia homoeocarpa.

Degree: 2014, University of Georgia

URL: http://hdl.handle.net/10724/28455

► A common fungal disease of warm- and cool-season turfgrasses is dollar spot, caused by Sclerotinia homoeocarpa. Epidemics occur when temperatures rise above 10°C, and continue… (more)

Subjects/Keywords: Biocontrol; compost; microbial ecology; turfgrass

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APA (6^th Edition):

Workman, J. B. (2014). A holistic approach to decreasing dollar spot severity and over-wintering inocula of Sclerotinia homoeocarpa. (Thesis). University of Georgia. Retrieved from http://hdl.handle.net/10724/28455

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Workman, John Barrett. “A holistic approach to decreasing dollar spot severity and over-wintering inocula of Sclerotinia homoeocarpa.” 2014. Thesis, University of Georgia. Accessed January 27, 2021. http://hdl.handle.net/10724/28455.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Workman, John Barrett. “A holistic approach to decreasing dollar spot severity and over-wintering inocula of Sclerotinia homoeocarpa.” 2014. Web. 27 Jan 2021.

Vancouver:

Workman JB. A holistic approach to decreasing dollar spot severity and over-wintering inocula of Sclerotinia homoeocarpa. [Internet] [Thesis]. University of Georgia; 2014. [cited 2021 Jan 27]. Available from: http://hdl.handle.net/10724/28455.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Workman JB. A holistic approach to decreasing dollar spot severity and over-wintering inocula of Sclerotinia homoeocarpa. [Thesis]. University of Georgia; 2014. Available from: http://hdl.handle.net/10724/28455

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Victoria University of Wellington

16. Cowie, Rebecca Olivia MacLennan. Bacterial Community Structure, Function and Diversity in Antarctic Sea Ice.

Degree: 2011, Victoria University of Wellington

URL: http://hdl.handle.net/10063/1852

► Antarctic sea ice is an important feature of the southern ocean where at its maximum it can cover 8 % of the Southern Hemisphere. It… (more)

▼ Antarctic sea ice is an important feature of the southern ocean where at its maximum it can cover 8 % of the Southern Hemisphere. It provides a stable environment for the colonisation of diverse and highly specialised microbes which play a central role in the assimilation and regulation of energy through the Antarctic food web. Polar environments are sensitive to changes in the environment. Small changes in temperature can have large effects on sea ice thickness and extent and Antarctic sea ice cover is expected to shrink by 25 % over the next century. It is unknown how the sea ice microbiota will respond. In order to understand the effects of climate change on the sea ice ecosystem it is necessary to obtain information about the community structure, function and diversity and their reactions with the environment. Studies have focused on algal diversity and physiology in Antarctic sea ice and in comparison studies on the prokaryotic community are few. Although prokaryotic diversity has been investigated using clone libraries and culture based methods, it is likely that certain species have still not been described. Almost nothing is known about the Antarctic sea ice bacterial community spatial and temporal dynamics under changing abiotic and biotic conditions or their role in biogeochemical cycles. This is the first study linking Antarctic bacterial communities to function by using statistics to investigate the relationships between environmental variables and community structure. Bacterial community structure was investigated by extracting both the DNA and RNA from the environment to understand both the metabolically active (RNA) and total (DNA) bacterial community. The thickness of the sea ice and nutrient concentrations were key factors regulating bacterial community composition in Antarctic sea ice. Sea ice thickness is likely to have an effect on the physiological responses of algae leading to changes in photosynthate concentrations and composition of dissolved organic matter (DOM). Further investigations into the relationships between enzymatic activity and community structure revealed that the composition of the DOM drove variation between bacterial communities. There was no relationship between bacterial abundance and chlorophyll-a (as a measure of algal biomass), suggesting a un-coupling of the microbial loop. However bacteria were actively involved in the hydrolysis of polymers throughout the sea ice core. Investigations using quantitative PCR (qPCR) found that the functional genes involved in denitrification and light energy utilisation were in low abundance therefore these processes are minor in Antarctic sea ice. These results confirm that sea ice bacteria are predominantly heterotrophs and have a major role in the cycling of carbon and nitrogen through the microbial loop ... Advisors/Committee Members: Ryan, Ken.

Subjects/Keywords: Microbial ecology; Prokaryotic diversity

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APA (6^th Edition):

Cowie, R. O. M. (2011). Bacterial Community Structure, Function and Diversity in Antarctic Sea Ice. (Doctoral Dissertation). Victoria University of Wellington. Retrieved from http://hdl.handle.net/10063/1852

Chicago Manual of Style (16^th Edition):

Cowie, Rebecca Olivia MacLennan. “Bacterial Community Structure, Function and Diversity in Antarctic Sea Ice.” 2011. Doctoral Dissertation, Victoria University of Wellington. Accessed January 27, 2021. http://hdl.handle.net/10063/1852.

MLA Handbook (7^th Edition):

Cowie, Rebecca Olivia MacLennan. “Bacterial Community Structure, Function and Diversity in Antarctic Sea Ice.” 2011. Web. 27 Jan 2021.

Vancouver:

Cowie ROM. Bacterial Community Structure, Function and Diversity in Antarctic Sea Ice. [Internet] [Doctoral dissertation]. Victoria University of Wellington; 2011. [cited 2021 Jan 27]. Available from: http://hdl.handle.net/10063/1852.

Council of Science Editors:

Cowie ROM. Bacterial Community Structure, Function and Diversity in Antarctic Sea Ice. [Doctoral Dissertation]. Victoria University of Wellington; 2011. Available from: http://hdl.handle.net/10063/1852

Northeastern University

17. Lynum, Christopher A. Microbial response to salt marsh restoration.

Degree: MS, Department of Marine and Environmental Sciences, 2018, Northeastern University

URL: http://hdl.handle.net/2047/D20289461

► Salt marshes offer a variety of ecosystem services such as carbon sequestration, storm buffering capacity, food web support, and nutrient filtration. Many of these ecosystem… (more)

Subjects/Keywords: microbial ecology; restoration; salt marsh

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APA (6^th Edition):

Lynum, C. A. (2018). Microbial response to salt marsh restoration. (Masters Thesis). Northeastern University. Retrieved from http://hdl.handle.net/2047/D20289461

Chicago Manual of Style (16^th Edition):

Lynum, Christopher A. “Microbial response to salt marsh restoration.” 2018. Masters Thesis, Northeastern University. Accessed January 27, 2021. http://hdl.handle.net/2047/D20289461.

MLA Handbook (7^th Edition):

Lynum, Christopher A. “Microbial response to salt marsh restoration.” 2018. Web. 27 Jan 2021.

Vancouver:

Lynum CA. Microbial response to salt marsh restoration. [Internet] [Masters thesis]. Northeastern University; 2018. [cited 2021 Jan 27]. Available from: http://hdl.handle.net/2047/D20289461.

Council of Science Editors:

Lynum CA. Microbial response to salt marsh restoration. [Masters Thesis]. Northeastern University; 2018. Available from: http://hdl.handle.net/2047/D20289461

18. Dewar, Meagan L. Gastrointestinal microbiota of seabirds.

Degree: School of Exercise and Nutrition Sciences, 2012, Deakin University

URL: http://hdl.handle.net/10536/DRO/DU:30056597

► This work provided novel insight into the previously uncharacterised microbial composition of Antarctic and temperate penguins and procellariiform seabirds. Using real time PCR and 16S… (more)

Subjects/Keywords: microbial ecology; seabirds; penguins

11 more images…

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APA (6^th Edition):

Dewar, M. L. (2012). Gastrointestinal microbiota of seabirds. (Thesis). Deakin University. Retrieved from http://hdl.handle.net/10536/DRO/DU:30056597

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Dewar, Meagan L. “Gastrointestinal microbiota of seabirds.” 2012. Thesis, Deakin University. Accessed January 27, 2021. http://hdl.handle.net/10536/DRO/DU:30056597.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Dewar, Meagan L. “Gastrointestinal microbiota of seabirds.” 2012. Web. 27 Jan 2021.

Vancouver:

Dewar ML. Gastrointestinal microbiota of seabirds. [Internet] [Thesis]. Deakin University; 2012. [cited 2021 Jan 27]. Available from: http://hdl.handle.net/10536/DRO/DU:30056597.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Dewar ML. Gastrointestinal microbiota of seabirds. [Thesis]. Deakin University; 2012. Available from: http://hdl.handle.net/10536/DRO/DU:30056597

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Oregon

19. Stephens, William. Bacterial Colonization Dynamics and Ecology of the Developing Zebrafish Intestine.

Degree: PhD, Department of Biology, 2013, University of Oregon

URL: http://hdl.handle.net/1794/13237

► Human intestinal microbiomes exhibit a large degree of interindividual compositional variation. Animal models, such as the zebrafish, facilitate the design of controlled and highly replicated… (more)

▼ Human intestinal microbiomes exhibit a large degree of interindividual compositional variation. Animal models, such as the zebrafish, facilitate the design of controlled and highly replicated studies that allow us to understand the normal variation in vertebrate intestinal composition and to study the rules guiding normal assembly of these complex communities. The smaller intestinal size and high fecundity of the zebrafish allow us to fully sample the intestinal contents of many animals, while the optical transparency allows direct in vivo observation of fluorescently labeled bacterial species within the intestine. The studies in this dissertation utilize these advantages to investigate the composition, colonization dynamics and functional requirements for colonization in the vertebrate intestine. We first describe the taxonomic composition and diversity of the zebrafish intestinal microbiota from wild-caught and domesticated zebrafish. In the process, we identify a set of core bacterial genera that are consistently present in zebrafish intestines. We then use species from two of these genera in subsequent studies to gain a detailed understanding of the colonization dynamics and genetic requirements of the two species. We initially describe the application of light sheet microscopy to imaging the zebrafish intestine and associated colonizing bacteria. We find that a single species, Aeromonas veronii, does not occupy the entire intestinal space and that competition within the same species appears to prevent further colonization. These results are extended to a zebrafish isolated Vibrio species as well as A. veronii by tagging bacteria with transposon insertions and tracking the changes in colonizing population sizes. These insertion libraries also identify genes in each bacterial species that are important in the process of colonization, highlighting the key role for motility and chemotaxis in this process. The descriptions and methods discussed in this dissertation advance the use of this important model organism towards the understanding of vertebrate host-microbial interactions. This dissertation includes previously published co-authored material as well as unpublished co-authored material. Advisors/Committee Members: Eisen, Judith (advisor).

Subjects/Keywords: Host-microbe; Microbial ecology; Transposon

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APA (6^th Edition):

Stephens, W. (2013). Bacterial Colonization Dynamics and Ecology of the Developing Zebrafish Intestine. (Doctoral Dissertation). University of Oregon. Retrieved from http://hdl.handle.net/1794/13237

Chicago Manual of Style (16^th Edition):

Stephens, William. “Bacterial Colonization Dynamics and Ecology of the Developing Zebrafish Intestine.” 2013. Doctoral Dissertation, University of Oregon. Accessed January 27, 2021. http://hdl.handle.net/1794/13237.

MLA Handbook (7^th Edition):

Stephens, William. “Bacterial Colonization Dynamics and Ecology of the Developing Zebrafish Intestine.” 2013. Web. 27 Jan 2021.

Vancouver:

Stephens W. Bacterial Colonization Dynamics and Ecology of the Developing Zebrafish Intestine. [Internet] [Doctoral dissertation]. University of Oregon; 2013. [cited 2021 Jan 27]. Available from: http://hdl.handle.net/1794/13237.

Council of Science Editors:

Stephens W. Bacterial Colonization Dynamics and Ecology of the Developing Zebrafish Intestine. [Doctoral Dissertation]. University of Oregon; 2013. Available from: http://hdl.handle.net/1794/13237

University of Nottingham

20. Mugampoza, Diriisa. Characterisation of the non-starter bacterial flora of Stilton cheese.

Degree: PhD, 2013, University of Nottingham

URL: http://eprints.nottingham.ac.uk/13833/ ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.594723

► This study characterised the bacterial flora of a commercially produced Stilton cheese in an effort to determine the contribution of non-starter lactic acid bacteria (NSLAB)… (more)

▼ This study characterised the bacterial flora of a commercially produced Stilton cheese in an effort to determine the contribution of non-starter lactic acid bacteria (NSLAB) to its aroma profile. A total of 123 microbial strains previously isolated from different sites (outer crust, blue veins and white core) of the cheese sample obtained at the end of ripening (~8 weeks) were recovered in MRS and BHI broths and preliminarily identified using conventional microbiological methods in order to establish population diversity and to screen out yeasts and moulds. Organisms identified with partial 16S rDNA sequence analysis were Lactobacillus plantarum, Lactobacillus brevis, Enterococcus faecalis, Staphylococcus aureus, Acinetobacter baumanii and Psychrobacter spp., with the genus Lactobacillus being the dominant (75%) group detected in all the sampled sites. Cluster analysis of pulse-field gel electrophoresis patterns associated the Lactobacillus isolates according to their site of isolation. Lb. plantarum isolates, two from each of the cheese sites, were evaluated for tolerance to heat stress and to different levels of salt, acid and relative humidity (RH) in order to ascertain whether the stress conditions associated with the isolation site could select the phenotype of microbial species recovered. The D72°C values revealed that isolates obtained from the outer crust were more heat sensitive suggesting they may have colonised the cheese post-pasteurisation. All the isolates were sensitive at pH range 3-4 but could grow at pH range 4.5-5. Similarly, isolates could grow at 3.5-5% (w/v) sodium chloride but were suppressed at 10%. Lactobacilli from the outer crust were the most halo-tolerant growing at 8% sodium chloride. For all strains, survival was low at 33-54% RH when cells were suspended in sterile de-ionised water but survived better at 33% RH in maximum recovery diluent (MRD) suggesting cellular protection by MRD. Lb. plantarum isolates from each site (outer crust=7; blue veins=19; white core=24) were tested for antimicrobial activity against Listeria monocytogenes, Escherichia coli, Pseudomonas aeruginosa, Staph. aureus, Salmonella Typhimurium, Clostridium sporogenes, Lb. pentosus and Lactococcus lactis using the plate agar overlay and paper disc diffusion assays. All the 59 Lactobacillus isolates were tested for plantaricin EF genes using PCR. The nature of antimicrobial activity was examined using cell-free supernatants treated to neutralise acids and/or hydrogen peroxide. Treatment with proteinase K was used to ascertain whether activity was due to bacteriocin (putative plantaricin) production. On solid medium, the isolates had antimicrobial activity against Gram-negative and Gram-positive bacteria, each isolate showing activity against more than one species. Lb. pentosus, Ps. aeruginosa, E. coli and L. monocytogenes were the most sensitive whereas Cl. sporogenes was the most resistant spp. Activity against these organisms was mainly attributed to acid, and to a less extent, hydrogen peroxide and plantaricin…

Subjects/Keywords: 637.3; QR100 Microbial ecology

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APA (6^th Edition):

Mugampoza, D. (2013). Characterisation of the non-starter bacterial flora of Stilton cheese. (Doctoral Dissertation). University of Nottingham. Retrieved from http://eprints.nottingham.ac.uk/13833/ ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.594723

Chicago Manual of Style (16^th Edition):

Mugampoza, Diriisa. “Characterisation of the non-starter bacterial flora of Stilton cheese.” 2013. Doctoral Dissertation, University of Nottingham. Accessed January 27, 2021. http://eprints.nottingham.ac.uk/13833/ ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.594723.

MLA Handbook (7^th Edition):

Mugampoza, Diriisa. “Characterisation of the non-starter bacterial flora of Stilton cheese.” 2013. Web. 27 Jan 2021.

Vancouver:

Mugampoza D. Characterisation of the non-starter bacterial flora of Stilton cheese. [Internet] [Doctoral dissertation]. University of Nottingham; 2013. [cited 2021 Jan 27]. Available from: http://eprints.nottingham.ac.uk/13833/ ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.594723.

Council of Science Editors:

Mugampoza D. Characterisation of the non-starter bacterial flora of Stilton cheese. [Doctoral Dissertation]. University of Nottingham; 2013. Available from: http://eprints.nottingham.ac.uk/13833/ ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.594723

Montana State University

21. Meadow, James Francis. Geothermal soil ecology in Yellowstone National Park.

Degree: PhD, College of Agriculture, 2012, Montana State University

URL: https://scholarworks.montana.edu/xmlui/handle/1/1849

► Microbial communities in soil are among the most diverse and species-rich of any habitat, but we know surprisingly little about the factors that structure them.… (more)

▼ Microbial communities in soil are among the most diverse and species-rich of any habitat, but we know surprisingly little about the factors that structure them. Geothermal soils present unique and relatively unexplored model systems in which to address ecological questions using soil microbial communities, since harsh conditions in these soils exert strong filters on most organisms. This work represents two very different approaches to studying soil ecology in geothermal soils in Yellowstone National Park: 1) Arbuscular mycorrhizal fungal (AMF) communities living in the roots of Mimulus gutattus in contrasting plant community types were compared to assess a link in community structure between plants and their AMF symbionts; and 2) soil microbial communities were surveyed across multiple spatial scales in an unstudied diatomaceous biological soil crust in alkaline siliceous geothermal soils, using bar-coded 454 pyrosequencing of 18S and 16S rDNA. Mycorrhizal communities living in plant roots from contrasting community types showed a striking difference in taxon richness and diversity that appears to transcend soil-chemical differences, though robust conclusions are difficult since plant and fungal communities are structured by some of the same confounding soil conditions. Cluster and discriminant analyses were employed to compare drivers of AMF community structure. Eukaryotic and prokaryotic communities in a diatomaceous biological soil crust differ significantly from that of an adjacent sinter soil, and along a photic depth gradient. Along with a description of this unique system, extensive multivariate community analyses were used to address outstanding questions of soil microbial community spatial heterogeneity and the methodologies best suited to the unique assumptions of these datasets. Depending on the intended scope of inference, much detail can be gained by investigation of microbial communities at the aggregate or soil particle scale, rather than through composite sampling. Additionally, beta-diversity patterns are apparent with relatively few sequences per sample. Advisors/Committee Members: Chairperson, Graduate Committee: Catherine A. Zabinski. (advisor), Catherine A. Zabinski was a co-author of the article, 'Linking symbiont community structures in a model Arbuscular mycorrhizal system' in the journal 'New phytologist' which is contained within this thesis. (other), Catherine A. Zabinski was a co-author of the article, 'Prokaryotic communities differ along a geothermal soil photic gradient' in the journal 'Microbial ecology' which is contained within this thesis. (other).

Subjects/Keywords: Soils.; Microbial ecology.; Mycorrhizas.

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APA (6^th Edition):

Meadow, J. F. (2012). Geothermal soil ecology in Yellowstone National Park. (Doctoral Dissertation). Montana State University. Retrieved from https://scholarworks.montana.edu/xmlui/handle/1/1849

Chicago Manual of Style (16^th Edition):

Meadow, James Francis. “Geothermal soil ecology in Yellowstone National Park.” 2012. Doctoral Dissertation, Montana State University. Accessed January 27, 2021. https://scholarworks.montana.edu/xmlui/handle/1/1849.

MLA Handbook (7^th Edition):

Meadow, James Francis. “Geothermal soil ecology in Yellowstone National Park.” 2012. Web. 27 Jan 2021.

Vancouver:

Meadow JF. Geothermal soil ecology in Yellowstone National Park. [Internet] [Doctoral dissertation]. Montana State University; 2012. [cited 2021 Jan 27]. Available from: https://scholarworks.montana.edu/xmlui/handle/1/1849.

Council of Science Editors:

Meadow JF. Geothermal soil ecology in Yellowstone National Park. [Doctoral Dissertation]. Montana State University; 2012. Available from: https://scholarworks.montana.edu/xmlui/handle/1/1849

Montana State University

22. Davis, Katherine Jean. Organic amendments for enhancing microbial coalbed methane production.

Degree: PhD, College of Engineering, 2017, Montana State University

URL: https://scholarworks.montana.edu/xmlui/handle/1/13718

► Coalbed methane (CBM) is natural gas found in subsurface coal beds and supplies approximately 4-6% of the annual U.S. natural gas requirements. Many unmineable coal… (more)

Subjects/Keywords: Coalbed methane.; Microalgae.; Microbial ecology.

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APA (6^th Edition):

Davis, K. J. (2017). Organic amendments for enhancing microbial coalbed methane production. (Doctoral Dissertation). Montana State University. Retrieved from https://scholarworks.montana.edu/xmlui/handle/1/13718

Chicago Manual of Style (16^th Edition):

Davis, Katherine Jean. “Organic amendments for enhancing microbial coalbed methane production.” 2017. Doctoral Dissertation, Montana State University. Accessed January 27, 2021. https://scholarworks.montana.edu/xmlui/handle/1/13718.

MLA Handbook (7^th Edition):

Davis, Katherine Jean. “Organic amendments for enhancing microbial coalbed methane production.” 2017. Web. 27 Jan 2021.

Vancouver:

Davis KJ. Organic amendments for enhancing microbial coalbed methane production. [Internet] [Doctoral dissertation]. Montana State University; 2017. [cited 2021 Jan 27]. Available from: https://scholarworks.montana.edu/xmlui/handle/1/13718.

Council of Science Editors:

Davis KJ. Organic amendments for enhancing microbial coalbed methane production. [Doctoral Dissertation]. Montana State University; 2017. Available from: https://scholarworks.montana.edu/xmlui/handle/1/13718

Montana State University

23. Field, Erin Kirby. Factors influencing the fate of chromium in soils : microbial ecology, physiology and metal transformation studies.

Degree: PhD, College of Letters & Science, 2011, Montana State University

URL: https://scholarworks.montana.edu/xmlui/handle/1/1251

► Chromium is a common contaminant in soil environments, especially at Department of Energy sites. The fate of chromium in the environment is influenced by a… (more)

Subjects/Keywords: Microbial ecology.; Chromium.; Soils.

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APA (6^th Edition):

Field, E. K. (2011). Factors influencing the fate of chromium in soils : microbial ecology, physiology and metal transformation studies. (Doctoral Dissertation). Montana State University. Retrieved from https://scholarworks.montana.edu/xmlui/handle/1/1251

Chicago Manual of Style (16^th Edition):

Field, Erin Kirby. “Factors influencing the fate of chromium in soils : microbial ecology, physiology and metal transformation studies.” 2011. Doctoral Dissertation, Montana State University. Accessed January 27, 2021. https://scholarworks.montana.edu/xmlui/handle/1/1251.

MLA Handbook (7^th Edition):

Field, Erin Kirby. “Factors influencing the fate of chromium in soils : microbial ecology, physiology and metal transformation studies.” 2011. Web. 27 Jan 2021.

Vancouver:

Field EK. Factors influencing the fate of chromium in soils : microbial ecology, physiology and metal transformation studies. [Internet] [Doctoral dissertation]. Montana State University; 2011. [cited 2021 Jan 27]. Available from: https://scholarworks.montana.edu/xmlui/handle/1/1251.

Council of Science Editors:

Field EK. Factors influencing the fate of chromium in soils : microbial ecology, physiology and metal transformation studies. [Doctoral Dissertation]. Montana State University; 2011. Available from: https://scholarworks.montana.edu/xmlui/handle/1/1251

Montana State University

24. Klatt, Christian Gerald. Ecological genomics of filamentous anoxygenic phototrophic bacteria inhabiting geothermal springs in Yellowstone National Park.

Degree: PhD, College of Agriculture, 2012, Montana State University

URL: https://scholarworks.montana.edu/xmlui/handle/1/1650

► The filamentous anoxygenic phototrophic bacteria (FAPs) are dominant members of many phototrophic microbial mat communities in geothermal springs. In non-sulfidic springs, FAPs are known to… (more)

Subjects/Keywords: Microbial ecology.; Cyanobacteria.; Geothermal resources.

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APA (6^th Edition):

Klatt, C. G. (2012). Ecological genomics of filamentous anoxygenic phototrophic bacteria inhabiting geothermal springs in Yellowstone National Park. (Doctoral Dissertation). Montana State University. Retrieved from https://scholarworks.montana.edu/xmlui/handle/1/1650

Chicago Manual of Style (16^th Edition):

Klatt, Christian Gerald. “Ecological genomics of filamentous anoxygenic phototrophic bacteria inhabiting geothermal springs in Yellowstone National Park.” 2012. Doctoral Dissertation, Montana State University. Accessed January 27, 2021. https://scholarworks.montana.edu/xmlui/handle/1/1650.

MLA Handbook (7^th Edition):

Klatt, Christian Gerald. “Ecological genomics of filamentous anoxygenic phototrophic bacteria inhabiting geothermal springs in Yellowstone National Park.” 2012. Web. 27 Jan 2021.

Vancouver:

Klatt CG. Ecological genomics of filamentous anoxygenic phototrophic bacteria inhabiting geothermal springs in Yellowstone National Park. [Internet] [Doctoral dissertation]. Montana State University; 2012. [cited 2021 Jan 27]. Available from: https://scholarworks.montana.edu/xmlui/handle/1/1650.

Council of Science Editors:

Klatt CG. Ecological genomics of filamentous anoxygenic phototrophic bacteria inhabiting geothermal springs in Yellowstone National Park. [Doctoral Dissertation]. Montana State University; 2012. Available from: https://scholarworks.montana.edu/xmlui/handle/1/1650

University of New Mexico

25. Winter, Ara. Patterns in richness and community structure: From bacteria to apex predators.

Degree: UNM Biology Department, 2016, University of New Mexico

URL: https://digitalrepository.unm.edu/biol_etds/128

► Patterns of community structure and richness provide context for studies from microbial ecology, global macroecology, languages, to Bayesian statistics. Diversity patterns for animals on land… (more)

Subjects/Keywords: macroecology; microbial ecology; bioinformatics; bacteria

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APA (6^th Edition):

Winter, A. (2016). Patterns in richness and community structure: From bacteria to apex predators. (Doctoral Dissertation). University of New Mexico. Retrieved from https://digitalrepository.unm.edu/biol_etds/128

Chicago Manual of Style (16^th Edition):

Winter, Ara. “Patterns in richness and community structure: From bacteria to apex predators.” 2016. Doctoral Dissertation, University of New Mexico. Accessed January 27, 2021. https://digitalrepository.unm.edu/biol_etds/128.

MLA Handbook (7^th Edition):

Winter, Ara. “Patterns in richness and community structure: From bacteria to apex predators.” 2016. Web. 27 Jan 2021.

Vancouver:

Winter A. Patterns in richness and community structure: From bacteria to apex predators. [Internet] [Doctoral dissertation]. University of New Mexico; 2016. [cited 2021 Jan 27]. Available from: https://digitalrepository.unm.edu/biol_etds/128.

Council of Science Editors:

Winter A. Patterns in richness and community structure: From bacteria to apex predators. [Doctoral Dissertation]. University of New Mexico; 2016. Available from: https://digitalrepository.unm.edu/biol_etds/128

Georgia Tech

26. Rodriguez Rojas, Luis Miguel. Bioinformatic tools for testing microbial ecology theory in natural environments through metagenomics.

Degree: PhD, Biology, 2016, Georgia Tech

URL: http://hdl.handle.net/1853/59154

► Metagenomics offers unique opportunities to close the gaps that exist between theory and empirical testing in microbial ecology given the windows it can provide into… (more)

▼ Metagenomics offers unique opportunities to close the gaps that exist between theory and empirical testing in microbial ecology given the windows it can provide into the large fraction of yet-unculturable organisms and species-level resolution. However, realizing the full potential of metagenomics requires the advancement of computational and statistical techniques for data analyses. In the first part of this dissertation I will present a general overview of the current state of quantitative methods for comparative metagenomics and introduce novel algorithms developed for these purposes. Particular emphasis will be placed on the issue of metagenomic coverage, i.e., what fraction of the microbial community was characterized by the sequencing effort, discussing its practical impact on metagenomic analyses and study design, and proposing a novel method for its accurate estimation, Nonpareil (Rodriguez-R and Konstantinidis, Bioinformatics 2014; –, ISME J 2014). Further, the Nonpareil approach can be leveraged for the estimation of extant diversity using a novel metric of sequence diversity, Nd, independent of databases, and with little impact of sequencing effort. In the second part of this dissertation, I will apply the computational and statistical toolbox described above to the characterization of community assembly processes in natural environments. First, I will describe the post-disturbance successional patterns following the deposition of large amounts of hydrocarbons in the shoreline of Florida following the 2010 Macondo Oil Spill in the Gulf of Mexico. We demonstrated that this secondary succession had only minor lasting effects in community composition post-recovery, and was mainly driven by hydrocarbon degradation and nutrient scavenging metabolic potentials in concert with the degree of specialization of community members (Rodriguez-R et al., ISME 2015). I will discuss these results as evidence in support of the specialization-disturbance ecologic hypothesis. Finally, I’ll describe variations within the meta-community of a freshwater interconnected system without recent major documented disturbances composed of five lakes and two estuarine locations along the Chattahoochee River (Southeast USA) monitored for a span of six years. Our results revealed strong seasonal patterns together with significant distance decay and minor landscape effects, indicating that both historic and contemporary factors shape the community assembly within this system in similar proportions. I will discuss these results in the framework of classic (macro-organismal) biogeographic theory, and illustrate in which ways they contradict the contemporary view of the now classic Baas-Becking dictum: “everything is everywhere, and the environment selects”. Advisors/Committee Members: Konstantinidis, Konstantinos T (advisor), Borodovsky, Mark (committee member), Jordan, King (committee member), Kostka, Joel (committee member), Tiedje, James M (committee member).

Subjects/Keywords: Microbial Ecology; Metagenomics; Bioinformatics

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APA (6^th Edition):

Rodriguez Rojas, L. M. (2016). Bioinformatic tools for testing microbial ecology theory in natural environments through metagenomics. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/59154

Chicago Manual of Style (16^th Edition):

Rodriguez Rojas, Luis Miguel. “Bioinformatic tools for testing microbial ecology theory in natural environments through metagenomics.” 2016. Doctoral Dissertation, Georgia Tech. Accessed January 27, 2021. http://hdl.handle.net/1853/59154.

MLA Handbook (7^th Edition):

Rodriguez Rojas, Luis Miguel. “Bioinformatic tools for testing microbial ecology theory in natural environments through metagenomics.” 2016. Web. 27 Jan 2021.

Vancouver:

Rodriguez Rojas LM. Bioinformatic tools for testing microbial ecology theory in natural environments through metagenomics. [Internet] [Doctoral dissertation]. Georgia Tech; 2016. [cited 2021 Jan 27]. Available from: http://hdl.handle.net/1853/59154.

Council of Science Editors:

Rodriguez Rojas LM. Bioinformatic tools for testing microbial ecology theory in natural environments through metagenomics. [Doctoral Dissertation]. Georgia Tech; 2016. Available from: http://hdl.handle.net/1853/59154

University of Nottingham

27. Khan, Intisar Chowdhury. Spreads microbiology in association with product matrix, structure and chemistry.

Degree: PhD, 2015, University of Nottingham

URL: http://eprints.nottingham.ac.uk/28996/ ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.666940

► The overall aim of this study was to eliminate the root cause of the ‘cheese flavour’ in spread caused by four key microbes Bacillus spp,… (more)

▼ The overall aim of this study was to eliminate the root cause of the ‘cheese flavour’ in spread caused by four key microbes Bacillus spp, Staphylococcus spp, yeasts and moulds. The major sources of these bacteria were in the product ingredients mainly sweet cream buttermilk and skimmed milk along with environmental aerosols. The causative organisms were present in about 63% of the products and mainly ‘feed’ on the oil element of the recipe, containing high level C12 that generates the distinctive cheese flavour when broken down by bacteria. The key hurdle factor in spread preventing microbial growth is water droplet size. The spread showing cheese off flavour had a droplet size distribution of 95% <10 micron. To achieve finer droplet size distribution, trial products were made in the Scrape Surface Heat Exchanger (SSHE) over the current churning method with a distribution of droplet size 98% <5 micron. The trial product showed a 50% reduction in the generation of the ‘cheese flavour’ methyl ketones. The Staphylococcus spp cross contamination source where from personnel with direct food contact processing area. Further education on personal hygiene helped to reduce the level of Staphylococcus spp contamination in the product. The trial product from the SSHE was further challenge tested with Listeria monocytogenes over a 10 week shelf life period to evaluate product robustness against microbial growth and spoilage. The organism did not show any growth over the period of time. The liquid phase of the emulsion was further modified with various salts at different concentrations and challenged with L. monocytogenes isolated from various parts of the dairy environment. It was observed that a pH range of 5.5 or lower with added 0.063% potassium sorbate showed significant antibacterial affect compared to the nutrient enriched MPC-broth and the unsalted liquid phase of the emulsion with no added potassium sorbate. To understand L. monocytogenes survival within a dairy process, the organism was further challenged by exposure to pasteurisation heat treatments and the standard CIP cycle of acid and caustic treatment. No recovery rate of the organism was observed. Therefore it could be concluded that the contamination within the industry is more likely to be post process or environmental contamination rather than survival through the plant itself as per RASFF alert of Listeria spp outbreak in dairy. Therefore, reducing the available water in the liquid phase of the spread and achieving a <5 μm droplet size and a finer distribution within the product will be limiting factors to microbial growth. An air purifier system BAXX has reduced the level of environmental contaminants, especially yeast and mould.

Subjects/Keywords: 579; QR100 Microbial ecology

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APA (6^th Edition):

Khan, I. C. (2015). Spreads microbiology in association with product matrix, structure and chemistry. (Doctoral Dissertation). University of Nottingham. Retrieved from http://eprints.nottingham.ac.uk/28996/ ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.666940

Chicago Manual of Style (16^th Edition):

Khan, Intisar Chowdhury. “Spreads microbiology in association with product matrix, structure and chemistry.” 2015. Doctoral Dissertation, University of Nottingham. Accessed January 27, 2021. http://eprints.nottingham.ac.uk/28996/ ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.666940.

MLA Handbook (7^th Edition):

Khan, Intisar Chowdhury. “Spreads microbiology in association with product matrix, structure and chemistry.” 2015. Web. 27 Jan 2021.

Vancouver:

Khan IC. Spreads microbiology in association with product matrix, structure and chemistry. [Internet] [Doctoral dissertation]. University of Nottingham; 2015. [cited 2021 Jan 27]. Available from: http://eprints.nottingham.ac.uk/28996/ ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.666940.

Council of Science Editors:

Khan IC. Spreads microbiology in association with product matrix, structure and chemistry. [Doctoral Dissertation]. University of Nottingham; 2015. Available from: http://eprints.nottingham.ac.uk/28996/ ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.666940

University of Nottingham

28. Janyakhantikul, Somwang. Evolution of CCL3L1/CCL4L1 haplotypes.

Degree: PhD, 2011, University of Nottingham

URL: http://eprints.nottingham.ac.uk/13404/ ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.555400

► CCL3LI and CCL4LI are chemokine genes, located on chromosome 17q12. They are copy number variable genes which share 95% sequence identity with their non-copy number… (more)

Subjects/Keywords: 616.079; QR100 Microbial ecology

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Janyakhantikul, S. (2011). Evolution of CCL3L1/CCL4L1 haplotypes. (Doctoral Dissertation). University of Nottingham. Retrieved from http://eprints.nottingham.ac.uk/13404/ ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.555400

Chicago Manual of Style (16^th Edition):

Janyakhantikul, Somwang. “Evolution of CCL3L1/CCL4L1 haplotypes.” 2011. Doctoral Dissertation, University of Nottingham. Accessed January 27, 2021. http://eprints.nottingham.ac.uk/13404/ ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.555400.

MLA Handbook (7^th Edition):

Janyakhantikul, Somwang. “Evolution of CCL3L1/CCL4L1 haplotypes.” 2011. Web. 27 Jan 2021.

Vancouver:

Janyakhantikul S. Evolution of CCL3L1/CCL4L1 haplotypes. [Internet] [Doctoral dissertation]. University of Nottingham; 2011. [cited 2021 Jan 27]. Available from: http://eprints.nottingham.ac.uk/13404/ ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.555400.

Council of Science Editors:

Janyakhantikul S. Evolution of CCL3L1/CCL4L1 haplotypes. [Doctoral Dissertation]. University of Nottingham; 2011. Available from: http://eprints.nottingham.ac.uk/13404/ ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.555400

University of Nottingham

29. Vanichpun, Apinya. Microbial populations and foodborne pathogens control of Mung bean sprouts.

Degree: PhD, 2011, University of Nottingham

URL: http://eprints.nottingham.ac.uk/28979/ ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.546506

► The two main objectives in this study were investigating the microbial quality and microbial communities of 'use-by date' Mung bean sprouts by using conventional culture… (more)

▼ The two main objectives in this study were investigating the microbial quality and microbial communities of 'use-by date' Mung bean sprouts by using conventional culture and 16S/18S rDNA PCR-DGGE methods, and evaluating the efficacy of natural antimicrobial substances, chemical disinfectants, and thermal treatments in reducing and inhibiting the growth of the pathogens on mung bean seeds. Retail samples of pre-packed mung bean sprouts were obtained from three retailers in the local area. The microbial quality and communities were evaluated on the 'use-by date'. The highest counts of total aerobic counts (7.86 log10 CFU/g), yeasts and moulds (7.0 log10 CFU/g), total lactic acid bacteria (6.24 log10 CFU/g) and total coliforms (6.63 log10 CFU/g) were found in samples from one shop and the DGGE band sequences also identified major populations of LAB from the same samples, These indicated poor quality and spoilage of the samples from this location and could be related to improper storage at temperatures above 5°C. The combination of conventional culture methods with the PCR-DGGE technique revealed a larger diversity of bacterial communities than eukaryotic ones based on the relative number of amplimers present on most of the OGGE gels. Identification based on band analysis revealed that the Enterobacteriaceae (29.6%), soil bacteria (20.4%), lactic acid bacteria (18.5%). yeast (14.8%). Pseudomonas spp. (13%), and Flavobacterium (3.7%) constituted the major populations in bean sprout samples. Cluster analysis of the OGGE patterns of both 16S and 18S rDNA amplimers found no strong relationship between sample sources and batches indicating the variability of natural populations. The use of natural antimicrobial products, such as a mixture of lime juice and vinegar (1: 1, pH 2.83) and bacteriocin-like substances produced by Pediococcus acidilactici, failed to reduce and inhibit the growth of Listeria monocytogenes on mung bean seeds. The former solution had higher antimicrobial efficiency in reducing the pathogen on seeds (1.93 log10 CFU/g) compared to the Pediococcus broth culture (1.22 log10 CFU/g), but both solutions failed to inhibit the re-growth of the pathogen during the sprouting process and also reduced seed germination percentage by 13-18%. The evaluation of efficacy of sequential washing using a combination of chemical treatments (two-step dipping) against the pathogens on seeds showed that a two-step dipping treatment in a solution containing 2% sodium hypochlorite for to min followed by 5% lactic acid solution for 5 min was the most effective treatment. This treatment achieved the highest reductions of L. monocytogenes (2.91 log10 CFU/g) and Salmonella Typhimurium (3.20 l0g10 CFU/g) after treatment and continued to reduce the pathogen during the sprouting process. This may be due to the chemical residues on treated seeds which lowered both pathogens on sprouted seeds to below the limit of detection <50 CFU/g) by direct plating without significantly affecting seed viability. The use of thermal treatments based on a…

Subjects/Keywords: 664; QR100 Microbial ecology

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Vanichpun, A. (2011). Microbial populations and foodborne pathogens control of Mung bean sprouts. (Doctoral Dissertation). University of Nottingham. Retrieved from http://eprints.nottingham.ac.uk/28979/ ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.546506

Chicago Manual of Style (16^th Edition):

Vanichpun, Apinya. “Microbial populations and foodborne pathogens control of Mung bean sprouts.” 2011. Doctoral Dissertation, University of Nottingham. Accessed January 27, 2021. http://eprints.nottingham.ac.uk/28979/ ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.546506.

MLA Handbook (7^th Edition):

Vanichpun, Apinya. “Microbial populations and foodborne pathogens control of Mung bean sprouts.” 2011. Web. 27 Jan 2021.

Vancouver:

Vanichpun A. Microbial populations and foodborne pathogens control of Mung bean sprouts. [Internet] [Doctoral dissertation]. University of Nottingham; 2011. [cited 2021 Jan 27]. Available from: http://eprints.nottingham.ac.uk/28979/ ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.546506.

Council of Science Editors:

Vanichpun A. Microbial populations and foodborne pathogens control of Mung bean sprouts. [Doctoral Dissertation]. University of Nottingham; 2011. Available from: http://eprints.nottingham.ac.uk/28979/ ; http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.546506

Louisiana State University

30. Achberger, Amanda Marie. Structure and Functional Potential of Microbial Communities in Subglacial Lake Whillans and at the Ross Ice Shelf Grounding Zone, West Antarctica.

Degree: PhD, Life Sciences, 2016, Louisiana State University

URL: etd-08152016-121651 ; https://digitalcommons.lsu.edu/gradschool_dissertations/4453

► The abundance of liquid water found beneath the Antarctic Ice Sheet (AIS) is thought to provide a suitable habitat for microbial life. However, the thick… (more)

▼ The abundance of liquid water found beneath the Antarctic Ice Sheet (AIS) is thought to provide a suitable habitat for microbial life. However, the thick ice sheet has posed a significant obstacle to accessing this isolated system and as a consequence, little data exists to infer ecosystem processes occurring beneath ice sheets. To address this deficit, data generated through 16S rRNA (genes and molecules) and metagenomic sequencing was used to evaluate the diversity and potential metabolic function of communities inhabiting Subglacial Lake Whillans (SLW) and the ocean basin into which it discharges (Whillans Ice Stream grounding zone; WIS-GZ). The analysis of SLW was found to be dominated by bacterial and archaeal species with little evidence for active eukaryotic organisms. The abundance of taxa related to chemolithoautrophic species (e.g., Thiobacillus, Sideroxydans, Nitrosospira, and Candidatus Nitrosoarcheaum) suggested that reduced sulfur, iron, and nitrogen compounds were important in fueling primary production in the permanently dark lake. Consistent with this, genes involved in inorganic carbon fixation, sulfide oxidation, and ammonia oxidation were also identified and taxonomically affiliated with species of Thiobacillus and Nitrosospira. Furthermore, the abundance of sequences related to Methylobacter¬ combined with the detection of methanogenic taxa provided evidence for methane cycling beneath the AIS. Although organic carbon and nutrients generated in SLW are transported to the WIS-GZ and may help support the diverse community found there, the prevalence of chemolithoautotrophic taxa (e.g., Thioprofundum and Thiohalophilus) suggests primary production coupled to the oxidation of reduced sulfur compounds may also provide a source of new fixed carbon to the system. The WIS-GZ community was distinct from those of SLW and the Ross Ice Shelf edge, signifying that it is structured based on the combined influences of input from the subglacial and marine systems. Collectively, these studies show that diverse microbial assemblages exist beneath ice sheets that are largely sustained through chemosynthesis and the weathering of bedrock minerals.

Subjects/Keywords: Antarctica; Subglacial Lake; Microbial Ecology

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Achberger, A. M. (2016). Structure and Functional Potential of Microbial Communities in Subglacial Lake Whillans and at the Ross Ice Shelf Grounding Zone, West Antarctica. (Doctoral Dissertation). Louisiana State University. Retrieved from etd-08152016-121651 ; https://digitalcommons.lsu.edu/gradschool_dissertations/4453

Chicago Manual of Style (16^th Edition):

Achberger, Amanda Marie. “Structure and Functional Potential of Microbial Communities in Subglacial Lake Whillans and at the Ross Ice Shelf Grounding Zone, West Antarctica.” 2016. Doctoral Dissertation, Louisiana State University. Accessed January 27, 2021. etd-08152016-121651 ; https://digitalcommons.lsu.edu/gradschool_dissertations/4453.

MLA Handbook (7^th Edition):

Achberger, Amanda Marie. “Structure and Functional Potential of Microbial Communities in Subglacial Lake Whillans and at the Ross Ice Shelf Grounding Zone, West Antarctica.” 2016. Web. 27 Jan 2021.

Vancouver:

Achberger AM. Structure and Functional Potential of Microbial Communities in Subglacial Lake Whillans and at the Ross Ice Shelf Grounding Zone, West Antarctica. [Internet] [Doctoral dissertation]. Louisiana State University; 2016. [cited 2021 Jan 27]. Available from: etd-08152016-121651 ; https://digitalcommons.lsu.edu/gradschool_dissertations/4453.

Council of Science Editors:

Achberger AM. Structure and Functional Potential of Microbial Communities in Subglacial Lake Whillans and at the Ross Ice Shelf Grounding Zone, West Antarctica. [Doctoral Dissertation]. Louisiana State University; 2016. Available from: etd-08152016-121651 ; https://digitalcommons.lsu.edu/gradschool_dissertations/4453

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