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Friedman, Jonathan Ph D. Massachusetts Institute of Technology. "Microbial adaptation, differentiation, and community structure." Thesis, Massachusetts Institute of Technology, 2013. http://hdl.handle.net/1721.1/81751.
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Thesis (Ph. D.)--Massachusetts Institute of Technology, Computational and Systems Biology Program, 2013.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student-submitted PDF version of thesis.
Includes bibliographical references (p. 112-119).
Microbes play a central role in diverse processes ranging from global elemental cycles to human digestion. Understanding these complex processes requires a rm under- standing of the interplay between microbes and their environment. In this thesis, we utilize sequencing data to study how individual species adapt to different niches, and how species assemble to form communities. First, we study the potential temperature and salinity range of 16 marine Vibrio strains. We nd that salinity tolerance is at odds with the strains' natural habitats, and provide evidence that this incongruence may be explained by a molecular coupling between salinity and temperature tolerance. Next, we investigate the genetic basis of bacterial ecological differentiation by analyzing the genomes of two closely related, yet ecologically distinct populations of Vibrio splendidus. We nd that most loci recombine freely across habitats, and that ecological differentiation is likely driven by a small number of habitat-specic alle-les. We further present a model for bacterial sympatric speciation. Our simulations demonstrate that a small number of adaptive loci facilitates speciation, due to the op- posing roles horizontal gene transfer (HGT) plays throughout the speciation process: HGT initially promotes speciation by bringing together multiple adaptive alleles, but later hinders it by mixing alleles across habitats. Finally, we introduce two tools for analyzing genomic survey data: SparCC, which infers correlations between taxa from relative abundance data; and StrainFinder, which extracts strain-level information from metagenomic data. Employing these tools, we infer a rich ecological network connecting hundreds of interacting species across 18 sites on the human body, and show that 16S-defined groups are rarely composed of a single dominant strain.
by Jonathan Friedman.
Ph.D.
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Hagley, Karen Jane. "Microbial community structure in sports turf soils." Thesis, Royal Holloway, University of London, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.402548.
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Datta, Manoshi Sen. "Microbial community structure and dynamics on patchy landscapes." Thesis, Massachusetts Institute of Technology, 2016. http://hdl.handle.net/1721.1/104464.
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Thesis: Ph. D., Massachusetts Institute of Technology, Computational and Systems Biology Program, 2016.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student-submitted PDF version of thesis.
Includes bibliographical references (pages 139-156).
Microbes are tiny metabolic engines with large-scale effects on industry, the environment, and human health. Understanding how the micron-scale actions (and interactions) of individual microbes give rise to macro-scale consequences remains a major challenge in microbial ecology. However, for the most part, studies employ coarsegrained sampling schemes, which average over the heterogeneous microscopic structure of microbial communities. This has limited our ability to establish mechanistic links between dynamics occurring across these disparate spatial scales. However, such links are critical for (a) making sense of the tremendous extant microbial diversity on Earth, and (b) predicting how perturbations (e.g., global climate change) may influence microbial diversity and function. In this thesis, I characterize the structure and dynamics of wild bacterial populations in the ocean at spatial scales of tens of microns. I then employ a simple, two-strain laboratory model system to link (cooperative) inter-species interactions at local scales to emergent properties at larger scales, focusing on spatially connected meta-communities undergoing range expansions into new territory. This work encompasses diverse environments (ranging from well-mixed communities in the laboratory to individual crustaceans) and approaches (including mathematical modeling, highthroughput sequencing, and traditional microbiological experiments). Altogether, we find that the microscale environment inhabited by a microbe - that is, "what the neighborhood is like" and "who lives next to whom" - shapes the structure and dynamics of wild microbial populations at local scales. Moreover, these local interactions can drive patterns of biodiversity and function, even at spatial scales much larger than the length of an individual cell. Thus, our work represents a small step toward developing mechanistic theories for how microbes shape our planet's ecosystems.
by Manoshi Sen Datta.
Ph. D.
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Ries, Mackenzie Lynn. "The Effect of Salinity on Soil Microbial Community Structure." Thesis, North Dakota State University, 2020. https://hdl.handle.net/10365/31807.
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Soil salinity is a widespread problem that affects crop productivity. We expect that saline soils also have altered microbial community structure, soil food webs and related soil properties. To test this, we sampled field soils across four farms in eastern North Dakota that host salinity gradients. We evaluated microbial biomass carbon, phospholipid fatty acid analysis and nematode counts in moderately saline and low saline soils. Additionally, we measured soil properties that represent potential food sources and habitat characteristics that influence microbial communities. We found higher microbial group abundance in moderately saline soils than in the lower saline soils. In contrast, we found lower nematode abundances in the moderately saline soils. We also observed increased labile carbon, nitrogen, phosphorus, and water content in the moderately saline soils. Based on our results, saline soils appear to have unique soil biological characteristics, which have implications for overall soil function along salinity gradients.
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Sudini, Hari Kishan Huettel Robin Norton. "Soil microbial community structure and aflatoxin contamination of peanuts." Auburn, Ala., 2009. http://hdl.handle.net/10415/1875.
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Van, Blerk Gerhardus Nicolas. "Microbial community structure and dynamics within sulphate- removing bioreactors." Diss., Pretoria : [s.n.], 2009. http://upetd.up.ac.za/thesis/available/etd-08122009-132505.
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Higgins, Logan Massie. "Insights into microbial community structure from pairwise interaction networks." Thesis, Massachusetts Institute of Technology, 2017. http://hdl.handle.net/1721.1/113465.
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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2017Cataloged from PDF version of thesis.
Includes bibliographical references.
Microbial communities are typically incredibly diverse, with many species contributing to the overall function of the community. The structure of these communities is the result of many complex biotic and abiotic factors. In this thesis, my colleagues and I employ a bottom-up approach to investigate the role of interspecies interactions in determining the structure of multispecies communities. First, we investigate the network of pairwise competitive interactions in a model community consisting of 20 strains of naturally co-occurring soil bacteria. The resulting interaction network is strongly hierarchical and lacks significant non-transitive motifs, a result that is robust across multiple environments. Multispecies competitions resulted in extinction of all but the most highly competitive strains, indicating that higher order interactions do not play a major role in structuring this community.
Given the lack of non-transitivity and higher order interactions in vitro, we conclude that other factors such as temporal or spatial heterogeneity must be at play in determining the ability of these strains to coexist in nature. Next, we propose a simple, qualitative assembly rule that predicts community structure from the outcomes of competitions between small sets of species, and experimentally assess its predictive power using synthetic microbial communities composed of up to eight soil bacterial species. Nearly all competitions resulted in a unique, stable community, whose composition was independent of the initial species fractions. Survival in three-species competitions was predicted by the pairwise outcomes with an accuracy of ~90%. Obtaining a similar level of accuracy in competitions between sets of seven or all eight species required incorporating additional information regarding the outcomes of the three-species competitions.
These results demonstrate experimentally the ability of a simple bottom-up approach to predict the structure of communities and illuminate the factors that determine their composition.
by Logan Massie Higgins.
Ph. D.
Ph.D. Massachusetts Institute of Technology, Department of Biology
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Moynihan, Emma Louise. "Interactions between microbial community structure and pathogen survival in soil." Thesis, Cranfield University, 2012. http://dspace.lib.cranfield.ac.uk/handle/1826/7297.
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Manure and slurry are valuable resources that may enhance many soil properties. However, organic amendments can pose a significant health risk to both humans and livestock if not managed correctly due to pathogenic loads that may be carried within them. Therefore it is crucial to identify the factors that affect pathogen survival in soil, in order to gain maximum benefit from such resources, whilst minimising the threat to public and animal welfare. This research aimed to elucidate the impact of microbial community structure on pathogen decline following entry of such organisms into the soil. It was hypothesised that pathogen survival would be significantly influenced by both diversity and phenotypic configuration of the microbial community. This was experimentally investigated within three distinctly different biological contexts. Firstly, it was shown that the survival of Escherichia coli 0157 was significantly affected by the presence of an intact microbial community. Microcosms consisting of sterile and non-sterile sand and clay soils were inoculated with E. coli and destructively sampled over time. The pathogen remained stable at 4°C, irrespective of biological status. However at 18°C, the pathogen grew in sterile soil and declined in non-sterile soil. This result was attributed to microbial antagonism in non-sterile soil, which only became apparent at 18°C, due to increased metabolic activity of the native community. The next experiment was designed to investigate the impact of microbial diversity and community configuration on the survival of a suite of model pathogens. A gradient of community complexity was created by inoculation of gamma-irradiated soil mesocosms with a serial-dilution of a suspension of a field soil. Soils were incubated to allow biomass equilibration and the establishment of distinct community phenotypes. Sub-samples were then inoculated with Listeria, Salmonella and E. coli strains and survival was monitored over 160 days. Death rates were calculated and plotted as a function of dilution, which represented diversity, and of principal component (PC) scores from PLFA profiles, which represented the phenotypic community context. There was some evidence of a diversity effect as weak negative linear correlations were observed between death rate and dilution for S. Dublin and environmentally-persistent E. coli. However, a much stronger correlation was observed between death rate and certain PC scores for these organisms. No effect of diversity or phenotype was detected on either L. monocytogenes or E. coli 0157. These results suggest that pathogen survival was affected by diversity, but the phenotypic community context was apparently much more influential. Additionally, such community effects were specific to pathogen type. Pathogen survival was also investigated in the context of highly-contrasting communities within a range of naturally-derived field soils. PLFA analysis was used to determine phenotypic community structure and soils were also characterized for a range of physico-chemical properties. They were inoculated with Listeria, Salmonella and E. coli strains as above. Pathogen survival was monitored over 110 days and death rates were calculated. Physicochemical and biotic data, including PC scores derived from PLFA profiles, were used in stepwise regression analysis to determine the predominant factor influencing pathogen-specific death rates. PC scores were identified as the most significant factor in pathogen decay for all organisms tested, with the exception of an environmentally-persistent E. coli isolate. Overall, these results demonstrate the importance of soil biological quality, specifically the configuration of the microbial community, in pathogen suppression, and provide a possible means to assess the inherent potential of soils to regulate pathogen survival. This may lead to the identification of management strategies which will ultimately accelerate pathogen decay, and therefore improve the safety of agricultural practice.
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Durno, W. Evan. "Precise correlation and metagenomic binning uncovers fine microbial community structure." Thesis, University of British Columbia, 2017. http://hdl.handle.net/2429/62360.
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Bacteria and Archaea represent the invisible majority of living things on Earth with an estimated numerical abundance exceeding 10^30 cells. This estimate surpasses the number of grains of sand on Earth and stars in the known universe. Interdependent microbial communities drive fluxes of matter and energy underlying biogeochemical processes, and provide essential ecosystem functions and services that help create the operating conditions for life. Despite their abundance and functional imperative, the vast majority of microorganisms remain uncultivated in laboratory settings, and therefore remain extremely difficult to study. Recent advances in high-throughput sequencing are opening a multi-omic (DNA and RNA) window to the structure and function of microbial communities providing new insights into coupled biogeochemical cycling and the metabolic problem solving power of otherwise uncultivated microbial dark matter (MDM). These technological advances have created bottlenecks with respect to information processing, and innovative bioinformatics solutions are required to analyze immense biological data sets. This is particularly apparent when dealing with metagenome assembly, population genome binning, and network analysis.
This work investigates combined use of single-cell amplifed genomes (SAGs) and metagenomes to more precisely construct population genome bins and evaluates the use of covariance matrix regularization methods to identify putative metabolic interdependencies at the population and community levels of organization. Applying dimensional reduction with principal components and a Gaussian mixture model to k-mer statistics from SAGs and metagenomes is shown to bin more precisely, and has been implemented as a novel pipeline, SAG Extrapolator (SAGEX). Also, correlation networks derived from small subunit ribosomal RNA gene sequences are shown to be more precisely inferred through regularization with factor analysis models applied via Gaussian copula. SAGEX and regularized correlation are applied toward 368 SAGs and 91 metagenomes, postulating populations’ metabolic capabilities via binning, and constraining interpretations via correlation. The application describes coupled biogeochemical cycling in low-oxygen waters. Use of SAGEX leverages SAGs’ deep taxonomic descriptions and metagenomes’ breadth, produces precise population genome bins, and enables metabolic reconstruction and analysis of population dynamics over time. Regularizing correlation networks overcomes a known analytic bottleneck based in precision limitations.Science, Faculty of
Graduate
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Perez, Sarah Isa Esther. "Exploring microbial community structure and resilience through visualization and analysis of microbial co-occurrence networks." Thesis, University of British Columbia, 2015. http://hdl.handle.net/2429/53928.
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Cultivation independent microbial ecology research relies on high throughput sequencing technologies and analytical methods to resolve the infinite diversity of microbial life on Earth. Microorganisms live in communities driven by genetic and metabolic processes as well as symbiotic relationships. Interconnected communities of microorganisms provide essential functions in natural and human engineered ecosystems. Modelling the community as an inter-connected system can give insight into the community's functional characteristics related to the biogeochemical processes it performs. Network science resolves associations between elements of structure to notions of function in a system and has been successfully applied to the study of microbial communities and other complex biological systems. Microbial co-occurrence networks are inferred from community composition data to resolve structural patterns related to ecological properties such as community resilience to disturbance and keystone species. However, the interpretation of global and local network properties from an ecological standpoint remains difficult due to the complexity of these systems creating a need for quantitative analytical methods and visualization techniques for co-occurrence networks. This thesis tackles the visualization and analytical challenges of modelling microbial community structure from a network science approach. First, Hive Panel Explorer, an interactive visualization tool, is developed to permit data driven exploration of topological and data association patterns in complex systems. The effectiveness of Hive Panel Explorer is validated by resolving known and novel patterns in a model biological network, the C. elegans connectome. Second, network structural robustness analysis methods are applied to study microbial communities from timber harvested forest soils from a North American longterm soil productivity study. Analyzing these geographically dispersed soils reveals biogeographic patterns of diversity and enables the discovery of conserved organizing principles shaping microbial community structure. The capacity of robustness analysis to identify key microbial community members as well as model shifts in community structure due to environmental change is demonstrated. Finally, this work provides insight into the relationship between microbes and their ecosystem, and characterizing this relationship can help us understand the organization of microbial communities, survey microbial diversity and harness its potential.Science, Faculty of
Graduate
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Das, Mitali. "Microbial Community Structure and Interactions in Leaf Litter in a Stream." Kent State University / OhioLINK, 2006. http://rave.ohiolink.edu/etdc/view?acc_num=kent1144953748.
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Nye, Mark Edward. "Microbial Community Structure in Soils Amended With Glyphosate Tolerant Soybean Residue." The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1396272020.
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Dedrick, Sandra. "Microbial Community Structure and Function: Implications for Current and Future Respiratory Therapies." Thesis, Boston College, 2021. http://hdl.handle.net/2345/bc-ir:109223.
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Thesis advisor: Babak MomeniDiseases of the upper respiratory tract encompass a plethora of complex multifaceted etiologies ranging from acute viral and bacterial infections to chronic diseases of the lung and nasal cavity. Due to this inherent complexity, typical treatments often fail in the face of recalcitrant infections and/or severe forms of chronic disease, including asthma. Thus, in order to provide improved standard of care, the mechanisms at play in hard-to-treat etiologies must be better understood. More recently, research has demonstrated a significant association between microbiota and many URT diseases. Previous work has also identified species capable of directly inhibiting standard treatments used to control asthma exacerbations. Despite an exhaustive collection of data characterizing microbiota composition in states of both health and disease, our knowledge of what microbiota profiles are observed in what specific disease etiologies is severely lacking. Yet, gaining these insights is crucial for the translation of such data into application. In this thesis I sought to: 1) identify gut microbiota profiles associated with severe and treatment resistant forms of childhood asthma, and 2) formulate a predictive model to facilitate the restructuring of microbiota for desired therapeutic outcomes. To identify gut microbiota and metabolites enriched in severe and treatment resistant childhood asthma, I looked to an ongoing longitudinal human study on vitamin D and childhood asthma. In this study, I find several fecal bacterial taxa and metabolites associated with more severe (i.e., higher wheeze proportion) and treatment resistant asthma in children at age 3 years. Specifically, several Veillonella species were enriched in children with higher wheeze proportion and in children that responded poorly to inhaled corticosteroid treatment (ICS) (i.e., non-responders). Haemophilus parainfluenzae, a species previously identified as enriched in the airway of adults with ICS-resistant asthma, was also uniquely enriched in children considered ICS non-responders in this study. Several metabolic pathways were also distinctly enriched: histidine metabolism was enriched in children with higher wheeze proportion while sphingolipid metabolism was enriched in ICS non-responders. Both metabolic pathways have been previously identified in association with asthma, further corroborating their role in this disease. Yet, this study is the first to identify these taxa and metabolites in children with preexisting and treatment resistant asthma. In the pursuit of improved treatment outcomes for recalcitrant URT diseases, recent efforts have turned towards microbiota-based therapies. While such treatments have proven successful in the treatment of gastrointestinal infections, these methods have not yet been extended to other conditions. Considering this, I ask whether a predictive model describing microbial interactions can facilitate the restructuring of microbiota for desired therapeutic outcomes. For this, I use a community of nasal microbiota to determine when a simply Lotka-Volterra-like (LV) model is a suitable representation for microbial interactions. I then utilize our LV-like model to examine whether environmental fluctuations have a major influence on community assembly and composition. For this, I looked specifically at pH fluctuations. In this study, I found that LV-like models are most suitable for describing community dynamics in complex low nutrient conditions. I also identified simple in vitro experiments that can reliably predict the suitability of a LV-like model for describing outcomes of a two-species community. When our LV-like model was applied to an in silico community of nasal species to determine the impact of environmental fluctuations, I find that nasal communities are generally robust against pH fluctuations and that, in this condition, facilitative interactions are a stabilizing force, and thus, selected for in in silico enrichment experiments. Overall, this thesis further corroborates the association of microbiota with URT diseases and treatment outcomes while also providing unique insight into their association with specific etiologies in childhood asthma. This thesis also provides a framework for developing models able to facilitate the development of future microbiota-based therapies while also determining how, and when, environmental factors impact community assembly and composition
Thesis (PhD) — Boston College, 2021
Submitted to: Boston College. Graduate School of Arts and Sciences
Discipline: Biology
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Crump, Byron C. "Bacterial activity and community structure in the Columbia River estuarine turbidity maxima /." Thesis, Connect to this title online; UW restricted, 1999. http://hdl.handle.net/1773/10989.
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Martin, Teri L. "Groundwater nitrate removal and soil microbial community structure in a riparian zone." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/tape17/PQDD_0011/MQ33250.pdf.
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Caleb, Oluwafemi James. "Microbial community structure as an indicator of soil health in apple orchards." Thesis, Stellenbosch : University of Stellenbosch, 2010. http://hdl.handle.net/10019.1/4133.
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Thesis (MSc (Microbiology))--University of Stellenbosch, 2010.ENGLISH ABSTRACT: The relationship between various land management practices, soil properties and the soil microbial communities are complex and little is known about the effect of these interactions on plant productivity in agricultural systems. Although it would be advantageous to have a single organism or property that can be used as a measure of soil health, it may not be possible. Soil organisms which include both the microorganisms as well as soil fauna are subjected to the effect of their immediate environment. This microenvironment in turn is determined by the soil properties as well as above ground flora and their interactions. Most soil indicators interact with each other, and these interactions can modify or influence the soil properties. The complexities of the interactions between critical soil indicator values often preclude its practical use by land managers and policy makers. However, soil microbial communities (e.g. diversity and structural stability) may serve as a relative indicator of soil quality. These communities are sensitive to land management practices and changes in the microenvironment. The objective of this study was to gain an understanding of the complex relationships by investigating the effect of conventional, integrated and organic apple production systems on the physical, chemical and biological (particularly soil microbial diversity) properties of the soil. Automated Ribosomal Intergenic spacer analysis (ARISA) was used to characterise fungal (F-ARISA) and bacterial (B-ARISA) communities from soil samples obtained from an experimental apple orchard in Elgin, Grabouw. The intergenic spacer (ITS) region from the fungal rRNA operon was amplified using ITS4 and fluorescently FAM (6- carboxylfluorescein) labelled ITS5 primers. Similarly, the 16S-23S intergenic spacer region from the bacterial rRNA operon was amplified using ITSR and FAM-labelled ITSF primers. The sensitivity of the technique allowed us to discriminate between the soil microbial communities of the different treatments. From our results we observed significant increase (p < 0.05) in the fungal community diversity between the February and April samples, while the bacterial community diversity was consistent (p > 0.05). Also, treatments with mulch showed a significantly higher microbial diversity than the other treatments at a 5 % significance level. Fungal communities showed significant correlation with the potassium concentration in the soil, while bacterial communities depicted a significant correlation with the soil phosphorous concentration. Based on the results we concluded that different management practices have a significant effect on the soil microbial communities and that these communities are particularly sensitive to small changes in the environment. However, there is still a need to determine what the composition of the soil microbial communities are to be able to correlate our observations with soil health.
AFRIKAANSE OPSOMMING: Die verhouding tussen verskillende landboubestuurspraktyke, grondeienskappe en die mikrobiese gemeenskappe in grond is kompleks en weinig is bekend oor die uitwerking van hierdie interaksies op die produktiwiteit van landboustelsels. Alhoewel dit voordelig sou wees om ‘n enkele organisme of eienskap te kan hê wat die gesondheid van grond kan meet, sal dit dalk nie moontlik wees nie. Grondorganismes wat die mikroörganismes sowel as die grondfauna insluit, is onderworpe aan die invloed van hulle onmiddelike omgewings. Hierdie mikro-omgewings op hulle beurt word weer beïnvloed deur die grondeienskappe sowel as die die oppervlak flora en hulle wisselwerkinge. Meeste van die grondaanwysers toon ook wisselwerkinge met mekaar, en hierdie wisselwerkinge kan die grondeienskappe beïnvloed or selfs verander. Die kompleksiteit van die wisselwerkinge tussen kritiese grond aanwysers is meestal die rede waarom dit nie deur grondbestuurders en beleidsmakers gebruik word nie. Dit is ongeag die feit dat grond mikrobiese gemeenskappe (bv. diversiteit en stukturele stabiliteit) mag dien as ‘n relatiewe aanwyser van grondkwaliteit. Hierdie gemeenskappe is sensitief vir bestuurspraktyke en veranderinge in die mikro-omgewing. Die doel van die studie was om die ingewikkelde verhoudings in die grondgemeenskappe te bestudeer en die uitwerking van konventionele, geïntegreerde en organiese appel produksie sisteme op die fisiese, chemiese en biologiese eienskappe (veral die grond mikrobiologiese diversiteit) te bepaal. Geoutomatiseerde Ribosomale Intergeniese Spasie Analise (ARISA) is gebruik om die fungus (F-ARISA) en bakteriese (B-ARISA) gemeenskappe van grondmonsters wat vanaf ‘n proef appelboord in Elgin (Grabouw) verkry is, te bepaal. Die intergeenspasie (ITS) area van die fungus rDNA operon is vermeerder deur die ITS4 en fluoresserende FAM (6-karboxylfluorescein) gemerkte ITS5 inleiers te gebruik. Soortgelyk is die 16S-23S intergeenspasie area van die bakteriese rDNA operon vermeerder deur ITSR en FAM-gemerkte ITSF inleiers te gebruik. Die sensitiwiteit van die tegniek laat ons toe om te onderskei tussen die grond mikrobiese gemeenskappe vanaf verskillende grondbehandelings. Vanuit die resultate kon ons aflei dat daar ‘n toename (p < 0.05) in die fungus gemeenskap diversiteit vanaf Februarie to April was terwyl die bakteriese gemeenskap ‘n konstante diversteit getoon het (p > 0.05). Behandelings met grondbedekking het ook ‘n beduidend hoër mikrobiese diversiteit getoon as ander behandelings. Fungus gemeenskappe het beduidende korrelasies getoon met kalium konsentrasies in die grond, terwyl bakteriese gemeenskappe ‘n beduidende korrelasie getoon het met grond fosfor konsentrasies. Gebaseer op die resultate kon ons aflei dat verskillende bestuurspraktyke ‘n uitwerking kan hê op die grond mikrobiese gemeenskappe en dat hierdie gemeenskappe sensitief is vir klein veranderinge in die omgewing. Dit sal egter nog nodig wees om die spesifieke samestelling van die grond mikrobiese gemeenskappe te bepaal voor ons hierdie waarnemings kan korreleer met grondgesondheid.
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Mombrikotb, Shorok Bashir. "The contribution of environmental selection on microbial community structure, function and biogeography." Thesis, Imperial College London, 2016. http://hdl.handle.net/10044/1/62903.
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Agriculture, which accounts for approximately 75% of land use in the UK, relies on microbial communities for many key processes. Despite their importance to the sustainability of agriculture, our understanding of the long-term effects of agricultural practices on soil microbial communities is limited. Agricultural practices not only alter many edaphic variables such as nutrient content and pH, they also introduce chemical stressors such as pesticides to the soil environment. In the UK, approximately 2x105 kg of insecticides and molluscicides are applied each year, with only 0.1% reaching target organisms. Using a long-term (>20 years), fully-factorial grassland field experiment (Nash’s Field), along with a series of microcosm experiment, this thesis assessed the impact of anthropogenic activity, particularly liming and pesticide application, on soil microbial community structure, functioning, and biogeography. Microcosm experiments indicated a direct impact of pesticides on soil bacterial community structure and metabolic activity. Findings highlighted an asymmetric interaction between pH and pesticide, and indicated that shifts in bacterial community structure were pesticide specific. These results were mirrored in long-term exposure to pesticide, which also significantly altered both community structure and functioning. These commonly used agricultural practices significantly reduced the gradient of the distance-decay relationship, creating increasingly similar communities by way of environmental selection. Given the link between community structure and functioning, anthropogenic induced disturbances pose a serious threat to agricultural sustainability as well as potentially altering landscape heterogeneity.
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Altrichter, Adam E. "Landscape history and contemporary environmental drivers of microbial community structure and function." Thesis, Virginia Tech, 2010. http://hdl.handle.net/10919/31883.
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Recent work in microbial ecology has focused on elucidating controls over biogeographic patterns and connecting microbial community composition to ecosystem function. My objective was to investigate the relative influences of landscape legacies and contemporary environmental factors on the distribution of soil microbial communities and their contribution to ecosystem processes across a glacial till sequence in Taylor Valley, Antarctica. Within each till unit, I sampled from dry areas and areas with visible evidence of recent surface water movement generated by seasonal melting of ephemeral snow packs and hillslope ground ice. Using T-RFLP 16S rRNA gene profiles of microbial communities, I analyzed the contribution of till and environmental factors to community similarity, and assessed the functional potential of the microbial community using extracellular enzyme activity assays. Microbial communities were influenced by geochemical differences among both tills and local environments, but especially organized by variables associated with water availability as the first axis of an NMDS ordination was strongly related to shifts in soil moisture content. CCA revealed that tills explained only 3.4% of the variability in community similarity among sites, while geochemical variables explained 18.5%. Extracellular enzyme activity was correlated with relevant geochemical variables reflecting the influence of nutrient limitation on microbial activity. In addition, enzyme activity was related to changes in community similarity, particularly in wet environments with a partial Mantel correlation of 0.32. These results demonstrate how landscape history and environmental conditions can shape the functional potential of a microbial community mediated through shifts in microbial community composition.Master of Science
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Veach, Allison Michelle. "Dynamics of microbial community structure and function in a tallgrass prairie ecosystem." Diss., Kansas State University, 2015. http://hdl.handle.net/2097/19145.
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Doctor of PhilosophyBiology
Walter K. Dodds
Ari M. Jumpponen
Due to agricultural practices and urbanization, tallgrass prairie ecosystems have become threatened as < 5% of its historical coverage exists today. The small remainder of praire that does exist is further threatened by the encroachment of woody plant species. Woody plant encroachment may not only alter prairie ecosystem function, but also prairie microbial communities responsible for these functional processes. Further, prairies are high disturbance ecosystems, especially prairie streams which are hydrologically harsh. They support communities that frequently undergo succession due to recurring flood and drought conditions, yet little is known about the response of microbial communities to these disturbances. In my dissertation, I first address the degree of woody vegetation expansion in riparian corridors (parallel to streams) in watersheds with variable fire frequency and grazing. I found that the rate of riparian woody expansion declines with higher fire intervals and is not affected by grazing, but even annual burns may not prevent woody plant expansion in riparian zones from occurring. Second, I quantified the effect of using restorations of riparian corridors, through removal of woody plants, on physical, chemical, and microbial community (bacteria and fungi) dynamics across stream to upslope soils. Removal restoration causes a decrease in NH₄⁺ and soil water content, and causes streams and upslope soils to become similar in fungal community richness unlike forested landscapes. Bacterial communities were minimally impacted by removals, but were highly structured among stream to upslope soils due to multiple environmental gradients (i.e., pH, NO₃⁻, soil moisture). Lastly, I examined the successional development of biofilm-associated microbial communities in a prairie stream from both a functional and structural perspective. I found that biofilm microbes exhibited strong successional trajectories, with communities developing towards net autotrophy and therefore becoming reliant upon in-stream derived carbon. Further, bacterial communities displayed spatial differences, but much stronger temporal patterns in community composition were detected. These studies highlight how woody plant encroachment may influence stream ecosystems in addition to spatiotemporal trends in microbial community assembly.
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Lopez-Velasco, Gabriela. "Molecular Characterization of Spinach (Spinacia Oleracea) Microbial Community Structure and its Interaction With Escherichia coli O157:H7 in Modified Atmosphere Conditions." Diss., Virginia Tech, 2010. http://hdl.handle.net/10919/37601.
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Leafy greens like lettuce and spinach are a common vehicle for foodborne illness in United States. It is unknown if native plant epiphytic bacteria may play a role in the establishment of enteric pathogens on leaf surfaces. The objective of this study was to characterize the bacterial communities of fresh and packaged spinach leaves and to explore interactions with E. coli O157:H7. We assessed the bacterial diversity present on the spinach leaf surfaces and how parameters such as spinach cultivar, field conditions, post-harvest operations and the presence of E. coli O157:H7 affected its diversity.
Differences in bacterial population size and species richness were associated with differences in plant topography; flat leaves had smaller bacterial populations than savoy leaves, which correlated with larger number of stomata and trichomes in savoy leaves. During spinach growing season shifts in environmental conditions affected richness and population size of the spinach bacterial community. Decreases in the overall soil and ambient temperature and increased rainfall decreased richness and bacterial population size.
Fresh spinach richness and composition assessed by parallel pyrosequencing of 16S rRNA elucidated 600 operational taxonomic units, with 11 different bacterial phyla. During postharvest operations diversity indexes and evenness tended to decrease, likely attributed to storage at low temperature and time of storage (4°C and 10°C), that promoted the dominance of g-Proteobacteria.
Bacteria isolated from fresh spinach elicited growth inhibition of E. coli O157:H7 in vitro, which was associated with nutrient competition. In contrast growth enhancement produced by epiphytes was associated to low correlations in carbon source utilization and the ability of E. coli O157:H7 to rapidly utilize carbon resources. In packaged spinach, E. coli O157:H7 altered the composition of the bacterial community and its growth was promoted on packaged spinach when a disinfection and temperature abuse occurred, removal of the epiphytic bacteria resulted in significant increases in numbers of E. coli O157:H7 at 10°C and was associated with increased expression of E. coli O157:H7 virulence and stress response genes. The large diversity present on the surface of spinach leaves significantly impacted the ecology of enteric pathogens like E. coli O157:H7 on the phyllosphere.Ph. D.
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Tun, Hein Min. "Microbial community structure and function in the gut of giant panda (Ailuropoda melanoleuca)." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2014. http://hdl.handle.net/10722/197106.
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Giant pandas are unique animals because of their digestive system is similar to carnivores but they have in fact adapted to a plant diet with bamboo as their main food source. According to fossils records, giant pandas were omnivorous approximately 7 million years ago, becoming almost vegetarian after 4.6 to 5 million years of evolution. However, their genome and anatomical structure do not favor bamboo digestion. For more than a decade, researchers have been questioning the underlying mechanism of their ability to digest bamboo. In 2010, the genome of giant panda was completed, which confirmed that their genome had no gene encoding for cellulolytic enzymes. Thus, the gut microbiota of giant panda, which has been hypothesized to play a key role in bamboo digestion, has garnered unprecedented attention. Researchers are also interested in the giant panda’s gut microbes due to their potential application in biomass conversion.
In Chapters 2 and 3 of this thesis, the microbial catalog of the giant panda’s gut microbiota was characterized, showing possible age-related microbial dysbiosis. Moreover, the microbiota, both bacterial and fungal was highly individualized because very few operational taxonomic units were shared among the four pandas in this study. Novel homoacetogens were also identified in the giant panda using functional gene clone-library sequencing. Using metagenomic sequencing, I uncovered the first evidence of human and animal related viruses in the giant panda’s gut. In addition to the community structure, I also determined the metabolic pathways of the microbiome. From KEGG annotation, a metabolic pathway for both cellulose and hemicellulose metabolism was identified. Comparative metagenomic analysis indicated that the giant panda’s gut microbiome was taxonomically and functionally distinct from those in mammals.
In Chapters 4 and 5, a total of 97 species of bacteria were isolated and identified using biochemical assays. Four of these bacteria showed powerful cellulolytic and hemicellulolytic activities on solid media. The gram-positive bacteria (HKUOP_BS) and the gram-negative bacteria (HKUOP_A14) were found to be rod shaped, facultative anaerobes that had the ability to powerfully hydrolyze both cellulose and hemicellulose using intracellular and extracellular enzymes respectively.
In Chapter 6, I determined the complete genome of a cellulolytic bacterium, Klebsiella oxytoca HKUOPL1, from giant panda and further described the annotated virulence, drug resistant, functional and potential horizontal transferring genes. The phylogenomic tree indicated that K. oxytoca HKUOPL1 closely resembled the K. oxytoca KCTC 1686 strain commonly used in 2,3-butanediol production.
In captive giant pandas, a mucous excretion episode usually occurs with mild to severe colic. To understand the host-microbial interactions during this episode, bacterial communities were compared between mucous excreta and normal feces. The shifts in community abundance (especially flooding of Clostridia) may be associated with the mucous excretion episode.
This study provides a better understanding of the microbial community structure and function in the giant panda’s gut.published_or_final_version
Biological Sciences
Doctoral
Doctor of Philosophy
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Smaill, Simeon John. "The Effects Of Forestry Management Practices on Microbial Community Properties." Thesis, University of Canterbury. Biology, 2006. http://hdl.handle.net/10092/1382.
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The structure and function of microbial communities are critical to the maintenance and sustainability of terrestrial ecosystem processes. Consequently, there is substantial interest in assessing how microbial communities respond to various land management practices, and if alterations to the characteristics of microbial communities has the potential to disrupt ecosystem processes. This thesis was conducted to identify the long term effects of fertilisation and different levels of post-harvest organic matter removal on the characteristics of the FH litter and soil microbial communities in six, second rotation Pinus radiata plantation forests located around New Zealand. The six sites, established between 1986 and 1994, were sampled in 2002 and 2003. Various physical and chemical properties of the sites were measured, and litterfall production was determined. The microbial biomass in the FH litter layer and soil was determined by chloroform fumigation-extraction, and Biolog plates were used to assess the relative differences in microbial community diversity, based on patterns of substrate utilisation. Fertilisation substantially altered the physical and chemical properties of the forest floor, including FH litter moisture content, mass, carbon content, nitrogen content and carbon: nitrogen ratio and soil pH, nitrogen content and carbon: nitrogen ratio. The same range of FH litter and soil properties were also significantly changed by different levels of organic matter removal. The biomass and diversity of the FH litter and soil microbial communities were significantly altered by fertilisation and organic matter removal, and the differences in the microbial community characteristics were significantly correlated to the effects of the fertilisation and organic matter removal treatments on the physical and chemical environment in the majority of cases. The physical and chemical properties of the sites were significantly correlated to estimates of wood production, and it was also found that the characteristics of the microbial community were strongly related to productivity at several sites. The results demonstrated that fertilisation and organic matter removal regimes have had long term effects on the microbial communities at the sites. The persistence of the effects of the organic matter removal treatments were particularly noteworthy, as these treatments were applied at site establishment, and despite no subsequent reinforcement over the life of the trials, were still substantially influencing the physical, chemical and microbiological properties of the FH litter and soil up to 17 years later. The results of this thesis also emphasised the value of long-term experiments in assessing the effects of disturbance on the physical, chemical and microbiological characteristics of forest ecosystems. Further research into the specific nature of the relationship between site productivity and microbial community characteristics was suggested as an important focus for future studies.
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Crossen, Kelsey B. "Investigation of Microbial Community Structure and Functional Groups from Thawing Permafrost Peat Incubations." The Ohio State University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=osu1512033177099274.
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Barren, Gregory John. "Epiphytic Diatom Community Structure in a Karst Riverine System." TopSCHOLAR®, 2015. http://digitalcommons.wku.edu/theses/1474.
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The goal of this study was to assess the epiphytic diatom community structure of two host species along a karst gradient in the upper Green River, Kentucky to a gain a better understanding of the role of diatoms in the food web. The host species studied were Podostemum ceratophyllum and Cladophora. Percent cover of P. ceratophyllum and Cladophora were quantified in the four study reaches. The host species were sampled near-shore and mid-channel in each reach in September and October of 2013. After diatoms were extracted from the host and enumerated the density and diversity were quantified. Twelve genera were identified with > 91% of the community in each reach being Cocconeis. The second most abundant genus was Achnanthes or Navicula depending on the reach. The density and diversity of diatoms increased longitudinally going downstream. Exceptions to this trend occurred when high flow events disturbed the community. Within reaches there were no differences in diatom diversity in near-shore and mid-channel habitats. Diatom density in near-shore and mid-channel habitats was only different in the most downstream reach. Cladophora had a community twice as dense as P. ceratophyllum, but less diverse. The results of this study indicate that there are longitudinal differences in diatom communities in the upper Green River and host species are an important factor in determining the community composition. The importance of epiphytic diatoms in the food web, however, remains unclear.
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Wagley, Pravin Kumar. "Molecular analysis of microbial community structure in open ponds for algal biodiesel production." Thesis, Wichita State University, 2012. http://hdl.handle.net/10057/5980.
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Algal farming in open ponds can be done with simple technology and low capital expenditures. However, in relatively uncontrolled ponds the likelihood that microbial contamination that could affect algal yield is high. We are interested in understanding natural contamination as an ecological process to better control the trajectory of microbial community assembly. Nannochloropsis salina was grown in small outdoor open ponds (100 L; 10 cm deep) through three cycles of batch culture using a simplified brackish growth medium. Time-course samples were monitored via pigment analyses, and direct microscopic counts. Extracted metagenomic DNA was subjected to touchdown PCR for amplification of 16S rRNA genes with universal bacterial primers and 18S rRNA genes with algae-specific primers, both using GC-clamps. PCR products of similar lengths were separated by melting characteristics using denaturing gradient gel electrophoresis (DGGE). Contamination of the open ponds by algae was not observed over three two-week batch culture cycles, however, contamination by bacteria was observed. Salinity and pH were likely major factors behind limited algal contamination. DGGE bands from bacterial 16S rRNA gene amplifications were excised, eluted, reamplified, and sequenced, revealing a diverse consortium of bacteria including Aeromonas, Loktanella, Marinobacter, and Pseudomonas. Most of the bands were seen on third and fourth day of the batch culture. As the culture progressed, the number of bands seen with DGGE decreased. Band migration was measured and relative front values were calculated. A 2% overall window was used to analyze how closely one band is associated with another. Overall there were 22 individual bands designated as novel based on relative front values. A dendrogram of relatedness was created to compare time-course samples from triplicate ponds, supporting the conclusion that community assembly was more of stochastic than deterministic in nature.Thesis (M.S.)--Wichita State University, College of Liberal Arts and Sciences, Dept. of Biological Sciences
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Cameron, Karen A. "Microbial community structure, diversity and biogeochemical cycling in Arctic and Antarctic cryoconite holes." Thesis, University of Sheffield, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.522500.
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Nunez, Andres Enrique. "MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS." UKnowledge, 2008. http://uknowledge.uky.edu/gradschool_diss/679.
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The entire stretch of the Ohio River is under fish consumption advisories due to contamination with polychlorinated biphenyls (PCBs). In this study, natural attenuation and biostimulation of PCBs and microbial communities responsible for PCB transformations were investigated in Ohio River sediments.
Natural attenuation of PCBs was negligible in sediments, which was likely attributed to low temperature conditions during most of the year, as well as low amounts of available nitrogen, phosphorus, and organic carbon. Moreover, surface sediments were relatively oxidized, as indicated by the prevalence of aerobic bacteria such as beta- Proteobacteria, alpha-Proteobacteria, Sphingobacteria, and Nitrospira in 16S rRNA sediment clone libraries. On the other hand, several reductive dechlorinators were detected in sediments, including Dehalococcoides, Desulfitobacterium spp. which suggested that reductive dechlorination might be possible in sediments under certain biogeochemical conditions.
Considerable amounts of PCBs were transformed by reductive dechlorination (80% in 177 days by pattern N) when sediments were maintained under anaerobic conditions, amended with nutrients and organic carbon, and incubated at 25 ºC in lab microcosms. Analysis of 16S rRNA clone libraries from these treatments revealed that Bacteroidetes, Chloroflexi and Firmicutes were enriched and Proteobacteria were depleted compared to clone libraries from treatment without organic amendments. Reductive dechlorination was decreased in sediments incubated at 10 and 40 ºC, and was not affected by FeSO4 amendments compared to unamended sediments incubated at 25 ºC.
Transformations of PCB-153 were investigated in sediments under anaerobic, aerobic and sequential anaerobic and aerobic conditions. Transformations were only observed in treatments with an anaerobic phase, which occurred by reductive dechlorination by pattern N. Neither PCB-153 nor dechlorination products PCB-99 or PCB-47 were transformed under aerobic conditions. Analysis of 16S rRNA clone libraries revealed that Bacteoridetes, Chloroflexi, and Firmicutes were enriched under anaerobic conditions and Proteobacteria were enriched under aerobic conditions.
Results from this study revealed that natural attenuation and biostimulation were not effective at removing PCBs from Ohio River sediments. Hence, other remediation methods will need to be employed to decrease PCB levels in this ecosystem.
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El, Semary Nermin Adel Hussein. "Anabaena and associated bacteria : molecular approaches to studying microbial community structure and taxonomy." Thesis, University of Bristol, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.420889.
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Gunina, Anna. "Biotic and abiotic control of microbial community structure and activity in forest soils." Doctoral thesis, Bangor University, 2017. http://hdl.handle.net/11858/00-1735-0000-002E-E453-7.
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LU, TING. "A NOVEL ECOLOGICAL APPROACH TO STUDY MICROBIAL COMMUNITY STRUCTURE IN AGGREGATED BIOMASS REACTOR." University of Cincinnati / OhioLINK, 2007. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1173065994.
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Wang, Ying. "Characterizing the structure and diversity of the eptc-degrading microbial community in soils /." The Ohio State University, 2002. http://rave.ohiolink.edu/etdc/view?acc_num=osu1486546889380622.
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Schulte, Nicholas O. "Controls on Benthic Microbial Community Structure and Assembly in a Karstic Coastal Wetland." FIU Digital Commons, 2016. http://digitalcommons.fiu.edu/etd/2447.
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The assembly mechanisms underlying microbial community abundance, biotic interactions, and diversity over space and time are unresolved, particularly in benthic microbial mats distributed along environmental gradients. Experimental enrichment of nutrient-limited microbial mats from the Florida Everglades along a nutrient subsidy-salinity stress gradient stimulated autotrophic and heterotrophic metabolism, growth, and diversity independent of autotroph-heterotroph interactions across treatments and space. These results suggest spatial segregation of autotrophic and heterotrophic components within mats. Considering only the diatom component of Everglades mats over space and time, the subsidy-stress gradient controlled diatom compositional turnover at broad spatial scales while environmental and dispersal-based processes structured diatom communities at the regional scale and environmental processes independent of the environmental gradient at the temporal scale. These results indicate environmental gradients may not necessarily increase connectivity and dispersal across space, and temporal microbial diversity is driven at the local and regional scales by environmental heterogeneity in benthic microbial communities.
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Carrino-Kyker, Sarah Rose. "MICROBIAL COMMUNITY RESPONSES TO ENVIRONMENTAL CHANGE: AN INVESTIGATION IN VERNAL POOLS." Case Western Reserve University School of Graduate Studies / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=case1275499406.
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Kim, Gwang Tae. "An investigation into the bacterial community structure of an electricity-generating microbial fuel cell." Thesis, Cardiff University, 2004. http://orca.cf.ac.uk/55526/.
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It was observed that Proteobacteria sequences were present at higher numbers within clone libraries from the bacterial clump and electrode biofilm compared to other parts of the fuel cell. It was also observed that results of the 16S rRNA gene libraries were in excellent agreement with those of the in situ probing and denaturing gradient gel electrophoresis (DGGE) analysis. DGGE analysis also showed that the enriched bacterial populations were different from those fond in the original activated sludge used to inoculate the microbial fuel cell at the start of the experiment. Conventional microbiological methods revealed that members of the family Enterobacteriaceae, such as Klebsiella sp. and Enterobacter sp. and of the Proteobacteria with Fe(III)-reduction and electrochemical activity had a significant potential for energy generation in this system.
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Abaye, Daniel. "Lipid derivatives and the relationships between microbial biomass, community structure and activity in soils." Thesis, University of Nottingham, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.324119.
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Malosso, Elaine. "Effects of plant amendment on microbial community structure and fungal biomass in Antarctic soils." Thesis, University of Newcastle Upon Tyne, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.289240.
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Fansler, Sarah J. "Using enzymes to link soil structure and microbial community function in a prairie chronosequence." Online access for everyone, 2004. http://www.dissertations.wsu.edu/Thesis/Summer2004/S%5FFansler%5F041404.pdf.
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Roberto, Alescia. "METAL EFFECTS ON FRESHWATER MICROBIAL COMMUNITY COMPOSITION, STRUCTURE, AND FUNCTION IN AN URBAN STREAM." Kent State University / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=kent1543839535987157.
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Hjorth, Ingrid. "Molecular genetic analysis of the microbial community structure in nitrifying biofilms adapted to different salinities." Thesis, Norges teknisk-naturvitenskapelige universitet, Institutt for bioteknologi, 2010. http://urn.kb.se/resolve?urn=urn:nbn:no:ntnu:diva-14053.
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Nitrification, the microbial oxidation of ammonia to nitrate, is a key step inthe biological cycling of nitrogen, and is often used in wastewater treatmentfor removal of ammonium. Fish-farming in flow-through systems such asopen net pens is the largest contributor to human discharge of inorganicnutrients along the Norwegian coast. It is important to limit these emissionsby converting to recirculating systems for nitrogen removal. However, thenitrification process is known to be sensitive to high concentrations of salts,a factor of importance when establishing technology for treatment of salinewastewaters.The aim of this thesis was to investigate and compare the microbialcommunities of nitrifying biofilms adapted to different salinities. Two con-tinuous biofilm reactor systems were operated, one supplied with seawater-based cultivation medium, while the other was supplied with tapwater-basedcultivation medium. The microbial communities in the two reactors wereinvestigated by denaturing gradient gel electrophoresis (DGGE) and fluo-rescence in situ hybridization (FISH). A batch culture salinity response testwas carried out to investigate the acute effect of different salinities on thenitrification activity in the seawater-adapted culture.DGGE analysis based on 16S rRNA and amoA sequences showed thatthe seawater-based reactor had lower microbial diversity than the tapwater-based reactor, and that different nitrifiers seemed to dominate in the tworeactors. Ammonia- and nitrite-oxidizers affiliated with the nitrosomonadsand with Nitrospira were identified in both reactors. Ammonia-oxidizersrelated to Nitrosomonas oligotropha seemed to dominate in the tapwater-based reactor, while Nitrosomonas halophila seemed to dominate in theseawater-based reactor. The batch culture salinity respons test, comparedto a similar experiment by (Kristoffersen 2004), indicated that the nitrify-ing culture adapted to high salinity was more halotolerant than a cultureadapted to low salinity.Nitrifikasjon er en mikrobiell prosess der ammonium oksideres til nitrat.Nitrifikasjon er en viktig prosess i den biologiske nitrogensyklus, og er oftebrukt innen vannrensing for ̊ fjerne ammonium. Fiskeoppdrett i ̊aapnemerder er den største bidragsyteren til menneskaskapte utslipp av uorgan-iske næringssalter langs norskekysten, og det er viktig begrense disse ut-slippene ved ̊ g ̊ over til resirkulerte systemer for nitrogenfjerning. Nitri-a afikasjonsprosessen er kjent for ̊ være følsom for høye saltkonsentrasjoner,aog det er viktig ̊ ta hensyn til dette n ̊ teknologi for rensing av avløpsvannaarmed høyt saltinnhold etableres.M ̊ med denne oppgaven var ̊ undersøke og sammenlikne mikro-aletabielle samfunn i nitrifiserende biofilmer adaptert til ulike saliniteter. Tokontinuerlige reaktorsystemer ble drevet, ́n ble forsynt med sjøvannsbasertekultiveringsmedium, den andre ble forsynt med springvannsbasert kultiver-ingsmedium. De mikrobielle samfunnene i de to reaktorene ble undersøktved hjelp av denaturerende gradient gelelektroforese (DGGE) og fluorescensin situ hybridisering (FISH). En salinitetsresponstest ble utført for ̊ un-adersøke den akutte effekten av ulike saliniteter p ̊ nitrifikasjonsaktiviteten iaden sjøvanns-adapterte kulturen.DGGE-analyse basert p ̊ sekvenser av 16S rRNA og amoA indikerteaat den sjøvannsbaserte reaktoren hadde lavere mikrobiell diversitet enn denspringvannsbaserte reaktoren, og at ulike nitrifiserende bakterier dominerte ide to reaktorene. Ammonium- og nitrittoksiderende bakterier beslektet medNitrosomonas og Nitrospira ble funnet i begge reaktorene. Ammonium-oksiderende bakterier beslektet med Nitrosomonas oligotropha s ̊ ut til ̊aadominere i den springvannsbaserte reaktoren, mens Nitrosomonas halophilavar mer dominerende i den sjøvannsbaserte reaktoren. Salinitetsrespons-testen, sammenliknet med et liknende eksperiment utført av Kristoffersen(2004), indikerte at den nitrifiserende kulturen adaptert til høy salinitet varmer halotolerant enn en kultur adaptert til lav salinitet.
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Reeve, Jennifer Rose. "Soil quality, microbial community structure, and organic nitrogen uptake in organic and conventional farming systems." Online access for everyone, 2007. http://www.dissertations.wsu.edu/Dissertations/Summer2007/j_reeve_071207.pdf.
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Buckley, Elan. "Change in the Structure of Soil Microbial Communities in Response to Waste Amendments." Thesis, Virginia Tech, 2020. http://hdl.handle.net/10919/101499.
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Soil microbial communities are affected extensively by addition of amendments to their environment. Of particular concern is the addition of poultry litter, which contains a substantial C, energy, and nutrient supply, but also antibiotic resistance genes (ARG), antimicrobials, and a multitude of microbial species. This project seeks to primarily assess if there is a change in bacterial community structure in response to poultry litter amendments to pasture land across geographically independent land across northern Georgia. It may be that changes in the relative abundance of bacterial communities also result in alteration in ARGs, and the community resistance to antibiotics (“resistome”) which in turn increases the potential threat of antibiotic resistance genes. While another part of this study will determine changes in integrons and specific ARGs, this project will focus on changes in bacterial communities and the potential functional changes in the community, which in turn have consequences for ARG levels and its horizontal transfer to various members of the soil community. Addition of waste from livestock is a historical method for increasing nutrients needed in the soil for the cultivation of crops, and in turn causes pronounced shifts in soil microbial communities due to the addition of large amounts of carbon, nutrients, foreign microbes, and other material. This study is unique because it utilizes a novel and relatively large landscape-scale to determine if there are discernable and repeatable patterns of bacterial community structure change in response to amendment regardless of exact soil type or source of chicken litter amendment. In the future, these data can also provide insight into the changes in the relative abundance antibiotic related genes associated with community change.M.S.
Soil is complicated, both in terms of its physical makeup and the organisms that live inside of it. Predicting changes in soil based on the addition of foreign material such as chemicals or biological waste is not an easy process, and whether or not it is even possible to reliably predict those changes is a matter of some dispute. This study is designed to illustrate that such changes can in fact be reliably and consistently predicted even with regard to the addition of complicated materials to the soil. In this study, specifically, the material in question is chicken litter. A mix of the bedding and waste produced by chickens, litter is commonly handled by composting and is added to soil in farms as a fertilizer rich in organic matter. It is possible to point at specific elements of the soil such as the chemistry and bacteria and see how it is changed with the addition of chicken litter, which allows us to determine the nature and extent of the change that chicken litter has on soil. This study is conducted on a larger scale than similar experiments conducted in the past, making it apparent that these relationships exist on a repeated basis. It is the object of this study to pave the way and make it easier for scientists in the future to determine these relationships in other unique contexts.
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Dietrich, Carsten [Verfasser], and Andreas [Akademischer Betreuer] Brune. "Ecological and evolutionary drivers of microbial community structure in termite guts / Carsten Dietrich. Betreuer: Andreas Brune." Marburg : Philipps-Universität Marburg, 2016. http://d-nb.info/1106381238/34.
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Veresoglou, Stravros D. "The impact of arbuscular mycorrhizal fungi on N-Cyclin related rhizosphere microbial community structure and function." Thesis, Manchester Metropolitan University, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.517616.
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Penton, Christopher Ryan. "Distribution, abundance, and activity of anaerobic ammonium oxidizing bacteria and microbial community structure in marine sediments." Diss., Connect to online resource - MSU authorized users, 2008.
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Hammer, Erin L. "Effects of garlic mustard (Alliaria petiolata) on soil nutrient dynamics and microbial community function and structure." Connect to full text in OhioLINK ETD Center, 2009. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=toledo1241126072.
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Thesis (M.S.)--University of Toledo, 2009.Typescript. "Submitted as partial fulfillment of the requirements for The Master of Science Degree in Biology (Ecology-track)." "A thesis entitled"--at head of title. Bibliography: leaves 44-55.
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Saha, Ria. "A Study of the Effects of Diet on Human Gut Microbial Community Structure and Mercury Metabolism." Thesis, Université d'Ottawa / University of Ottawa, 2017. http://hdl.handle.net/10393/36488.
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Background: Recent research showing how dietary interventions substantially influence the potential presence of widespread and stable bacterial core phyla in the human colon has garnered a considerable amount of attention. Because the human gut can play a major role in host health, there is currently some interest in observing how diet influences human gut microbial composition and how changes in diet affect the potential for gut microbiota to transform mercury.
This study aims to discover how different kinds of diet affect the nature and magnitude of microbial Hg transformations in the human gut environment.
Methods: Fecal samples have been collected from 5 human male individuals at University of Ottawa and stored at -80ºC for further investigation. Using high throughput DNA amplicon sequencing targeting the 16s rRNA V4 region, we investigated the microbial community structure of the gut in 5 healthy male. Mercury biotransformations in the pooled fecal sample have been carried out using stable isotopes of mercury (198HgCl2 and Me199HgCl) and analysis was conducted by using inductively coupled plasma mass spectrometry (ICP-MS).
Results and conclusions: We were not able to detect any significant Hg methylation or MeHg demethylation. We suspect this is due to Enterobacteria dominating the microbial community structure after 96h; Although Enterobacteria are part of the typical microbiota of a healthy individual, they do not possess genes required for Hg methylation. As such, our microbial data support our chemical analyses. We were not able to identify whether a change in diet affected Hg transformations in the human gut environment.
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Roussos, Jessica M. "Spatial and Temporal Variation in White Point, Palos Verdes Hydrothermal Sulfur Vent Microbial Mat Community Structure." Thesis, California State University, Long Beach, 2018. http://pqdtopen.proquest.com/#viewpdf?dispub=10689039.
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Sulfur-cycling microbial mats found around near-shore hydrothermal vents at White-Point, Palos Verdes are highly diverse communities that show variation in community structure over small spatial scales. This study investigated the within-site variability of the mats by comparing community structure, using 16S rRNA gene sequences, between mat samples collected in the intertidal and subtidal habitats at two different time points; March and June of 2015. The mats were dominated by two sulfur-oxidizers Sulfurovum and Arcobacter. Analysis showed that many of the same microbes were found across sample types; however, mat community structure was significantly different between the intertidal and subtidal habitats and between the two intertidal time points. Changes in community structure correlated to different environmental conditions across the four sample types, suggesting that community structure is driven by environmental selection over dispersal capabilities within this vent site.
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Shelton, Jenna L., Denise M. Akob, Jennifer C. McIntosh, Noah Fierer, John R. Spear, Peter D. Warwick, and John E. McCray. "Environmental Drivers of Differences in Microbial Community Structure in Crude Oil Reservoirs across a Methanogenic Gradient." FRONTIERS MEDIA SA, 2016. http://hdl.handle.net/10150/621561.
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Stimulating in situ microbial communities in oil reservoirs to produce natural gas is a potentially viable strategy for recovering additional fossil fuel resources following traditional recovery operations. Little is known about what geochemical parameters drive microbial population dynamics in biodegraded, methanogenic oil reservoirs. We investigated if microbial community structure was significantly impacted by the extent of crude oil biodegradation, extent of biogenic methane production, and formation water chemistry. Twenty-two oil production wells from north central Louisiana, USA, were sampled for analysis of microbial community structure and fluid geochemistry. Archaea were the dominant microbial community in the majority of the wells sampled. Methanogens, including hydrogenotrophic and methylotrophic organisms, were numerically dominant in every well, accounting for, on average, over 98% of the total Archaea present. The dominant Bacteria groups were Pseudomonas, Acinetobacter, Enterobacteriaceae, and Clostridiales, which have also been identified in other microbially-altered oil reservoirs. Comparing microbial community structure to fluid (gas, water, and oil) geochemistry revealed that the relative extent of biodegradation, salinity, and spatial location were the major drivers of microbial diversity. Archaeal relative abundance was independent of the extent of methanogenesis, but closely correlated to the extent of crude oil biodegradation; therefore, microbial community structure is likely not a good sole predictor of methanogenic activity, but may predict the extent of crude oil biodegradation. However, when the shallow, highly biodegraded, low salinity wells were excluded from the statistical analysis, no environmental parameters could explain the differences in microbial community structure. This suggests that the microbial community structure of the 5 shallow, up-dip wells was different than the 17 deeper, down-dip wells. Also, the 17 down-dip wells had statistically similar microbial communities despite significant changes in environmental parameters between oil fields. Together, this implies that no single microbial population is a reliable indicator of a reservoir's ability to degrade crude oil to methane, and that geochemistry may be a more important indicator for selecting a reservoir suitable for microbial enhancement of natural gas generation.
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Kostrytsia, Anastasiia. "Bioengineering optimization and microbial characterization of elemental sulfur-fueled denitrifying biofilms Nitrate removal effectiveness of fluidized sulfur-based autotrophic denitrification biofilters for recirculating aquaculture systems (2015) Aquacultural Engineering, 68, pp. 10-18." Thesis, Paris Est, 2018. http://www.theses.fr/2018PESC2188.
Full textAbstract:
De nos jours, la croissante population humaine et les ressources en eau limitées créent une demande pour des technologies durables de traitement des eaux usées. La dénitrification autotrophe à base de soufre élémentaire (S0) synthétisée chimiquement est une biotechnologie efficace et rentable pour l'élimination des nitrates (NO3-) des eaux usées carencées en substances organiques. Cependant, les propriétés hydrophobes du S0 synthétisé chimiquement limitent son utilisation pour la dénitrification. Par conséquent, l’objectif général de ce projet est d’optimiser les performances et d’explorer les mécanismes de traitement de la dénitrification au S0 dans les systèmes de biofilms, enquêtant l'élimination de NO3- et de nitrites (NO2-), ainsi que la compréhension des communautés microbiennes associées. Pour remédier aux limites des applications de dénitrification par S0 synthétisées chimiquement, la solubilisation de S0 avant la dénitrification et la dénitritation par S0 a été étudiée dans des essais biologiques en discontinu par une approche interdisciplinaire. Plus précisément, les expériences de biocinétique ont démontré que les taux de dénitrification et de dénitritation obtenus étaient respectivement de 20,9 et 10,7 mgN/L∙d. Une analyse microbiologique a mis en évidence la présence de la famille Helicobacteraceae sur des particules S0, probablement responsables de la solubilisation S0. En outre, le modèle d'hydrolyse du S0 catalysé par des organismes microbiens et de la dénitrification en deux étapes a été développé. L'analyse de sensibilité a identifié la dominance des paramètres liés à l'hydrolyse, et a suggéré que l'hydrolyse du S0 à base de surface à catalyse microbienne est l'étape limitante pendant la dénitrification par S0 synthétisée chimiquement. La dénitrification autotrophe avec biosulfure (ADBIOS), un sous-produit de la désulfuration biologique des gaz, a été étudiée dans des essais biologiques par lots comme solution technologique alternative pour le traitement de la pollution par le NO3- dans les eaux usées. Des biocinétiques de dénitrification et de dénitritation significativement plus élevées ont été obtenues avec le biosulfure par rapport au S0 synthétisé chimiquement, avec des activités spécifiques de 223,0 mg NO3--N/g VSS·d et 339,5 mg NO2--N /g VSS·d. Les genres Thiobacillus, Moheibacter et Thermomonas dominaient la communauté microbienne ADBIOS. Enfin, ADBIOS a été étendu au niveau du bioréacteur, et deux réacteurs de biofilm à lit mobile (MBBR) en double remplis de AnoxK1 (K1) et de nouveaux supports de biofilm AnoxK Z-200 (Z-200) ont été utilisés en continu pendant 309 jours. L'effet du taux de charge en nitrates (NLR) sur les performances d'ADBIOS a été évalué en diminuant le temps de rétention hydraulique (THS) de 72 à 21 h. Les taux de dénitrification de 236 et 234 mg NO3--N/L·d ont été atteints à un THS de 24 h pour K1 et à un THS de 21 h pour le support Z-200, respectivement. D'après l'analyse de l'ARN, les mêmes microorganismes actifs, appartenant aux genres Thiobacillus, Truepera, Flavobacterium, Hyphomonas et Sphingopyxiz, dominaient les MBBR avec des porteurs K1 et Z-200, mais leur occurrence était différenteNowadays, the increasing human population and limited water resources create a demand for sustainable wastewater treatment technologies. Chemically synthesized elemental sulfur (S0)-based denitrification is an effective and cost-efficient biotechnology for nitrate (NO3-) removal from organic-deficient wastewaters. However, the hydrophobic properties of S0 constrain its utilization for denitrification. Therefore, the goal of this project is to optimize the performance and explore the treatment mechanisms of S0-fueled denitrification in biofilm systems, through the investigation of NO3- removal, and the understanding of the associated microbial communities. To address the limitation of the chemically synthesized S0-driven denitrification applications, S0 solubilization prior to S0-driven denitrification was investigated in batch bioassays. The biokinetic experiments demonstrated that the achieved denitrification and denitritation rates were 20.9 and 10.7 mg N/L∙d, respectively. Microbiological analysis detected the presence of the Helicobacteraceae family onto S0 particles, that was likely responsible for the S0 solubilization. In addition, the model of microbially-catalyzed S0 hydrolysis and subsequent two-step denitrification was developed. The sensitivity analysis identified the dominance of the hydrolysis-related parameters, and suggested that microbially-catalyzed surface-based S0 hydrolysis is the rate-limiting step during chemically synthesized S0-driven denitrification.Autotrophic denitrification with biosulfur (ADBIOS), a by-product of biological gas desulfurization, was investigated in batch bioassays as an alternative technological solution for treating NO3- pollution in wastewaters. Significantly higher denitrification and denitritation biokinetics were obtained with biosulfur compared to chemically synthesized S0, with specific activities of 223.0 mg NO3--N/g VSS·d and 339.5 mg NO2--N/g VSS·d. The Thiobacillus, Moheibacter and Thermomonas genera were dominating the ADBIOS microbial community.Two duplicate moving-bed biofilm reactors (MBBRs) with AnoxK1 (K1) and AnoxK Z-200 (Z-200) biofilm carriers were operated for 309 days. The effect of the nitrate loading rate (NLR) on the ADBIOS performance was studied by decreasing hydraulic retention time (HRT) from 72 to 21 h. The denitrification rates of 236 and 234 mg NO3--N/L·d were achieved at an HRT of 24 h for K1 and an HRT of 21 h for Z-200 carrier, respectively. Based on RNA analysis, the same active bacteria, belonging to Thiobacillus, Truepera, Flavobacterium and Hyphomonas genera, were dominating MBBRs with K1 and Z-200 carriers, but they varied in occurrence
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Ditterich, Franziska [Verfasser], and Ellen [Akademischer Betreuer] Kandeler. "Microbial community structure and function is shaped by microhabitat characteristics in soil / Franziska Ditterich ; Betreuer: Ellen Kandeler." Hohenheim : Kommunikations-, Informations- und Medienzentrum der Universität Hohenheim, 2016. http://d-nb.info/1118571665/34.
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