Tesi: "Impact on microbial community"

1

Cartwright, Colin. "Biodegradation and impact of phthalate plasticisers on a soil microbial community". Thesis, University of Kent, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.264768.

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2

Lekkas, Panagiotis. "The Microbial Ecology Of Listeria Monocytogenes As Impacted By Three Environments: A Cheese Microbial Community; A Farm Environment; And A Soil Microbial Community". ScholarWorks @ UVM, 2016. http://scholarworks.uvm.edu/graddis/463.

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This dissertation examined the microbial ecology of Listeria monocytogenes in three distinctly different environments: a cheese microbial community; a farm environment; and a soil microbial community. The aim of the first study was to investigate the effects of L. monocytogenes on the composition of the surface microflora on washed rind soft cheese. Two trials with washed rind cheeses that were inoculated with 100cfu cm⁻² of a L. monocytogenes six strain cocktail were conducted. The first trial had to be terminated early (day 28) as contamination of Pseudomonas spp. from the initial brine did not produce the expected characteristics of the cheese during the aging period. For the second trial, cheese samples were aged in the lab for 60 days according to the cheesemakers specifications. Surface cheese rind samples were collected from both control and inoculated cheeses every 7 days. Cheese rind samples were analyzed through the standard BAM method for enumeration of L. monocytogenes and through amplification of the V4 region of 16S rRNA and ITS regions for identification of the surface rind bacterial and fungal communities, respectively. Our data showed that Pseudomonas spp. significantly changed the composition of the microorganisms found on the surface of the rind while L. monocytogenes had little effect. In addition, although the concentration of L. monocytogenes increased to levels of 10⁶ cfu cm⁻² based on the enumeration data, the genetic data was not able to identify it in the flora due to the fact that other genera were found at much higher concentrations, which is a limitation of molecular methods used for identification of pathogens in foods. For the second study the presence and incidence of L. monocytogenes on farms that either produce raw milk cheese or supply the milk for raw milk cheese production was investigated. Five farms were visited and in total 266 samples were collected from barn, environmental, and milk sites. L. monocytogenes prevalence was found to be at 6% from all the farms tested with 10 isolates found in the barn samples, 5 from environmental sites and 1 from milking equipment. Samples were identified to the genus level through a modified BAM method and speciated though multiplex PCR. Included in the pathogenic isolates was a DUP-1042B L. monocytogenes strain that has been implicated in major outbreaks, which emphasizes the adaptability and persistence of highly pathogenic stains in food manufacturing environments. Results from this study continue to support the fact that contaminated silage can be an important reservoir of the pathogen in a dairy farm setting. From our data and field observations we identified that drinking water sources for the animals is also an important reservoir of L. monocytogenes in farm environments. More importantly this study has shown the importance of continuous monitoring of environmental sites for the presence of the pathogen, particularly in silage. Lastly manure amended soils in the northeastern U.S. were tested for the presence and survival of rifampicin resistant Escherichia coli (rE. coli), generic E. coli (gE. coli) and Listeria spp.. Both gE.coli and rE.coli samples were processed using either direct enumeration, MPN or bag enrichment methods. Samples were taken from both tilled and surface dairy solid manure-amended plots. Listeria samples were processed using a modified BAM method. Listeria presence was constant throughout the study. In contrast, rE. coli and gE. coli levels declined with time. The main conclusions of this study were that soil type, location and physical characteristics have a significant role in the survival of bacterial populations of rE. coli, gE. coli and Listeria spp. in soil. Dairy solids application does not seem to have a long term effect on the natural microbial population of soils. Tilling of soils results in increased survival of the bacterial population due to the fact that it increases soil pore size and facilitates moisture entry, which in turn has been shown to increase bacterial survival rates. Data from this research will assist in the creation of preventative measures that lead to the elimination of pathogen reservoirs. It will be further used to verify that a 120 day interval following manure application should be sufficient to ensure food safety of edible crops subsequently planted on these soils.

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3

Elfstrand, Sara. "Impact of green manure on soil organisms : with emphasis on microbial community composition and function /". Uppsala : Department of Soil Sciences, Swedish University of Agricultural Sciences, 2007. http://epsilon.slu.se/200723.pdf.

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4

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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5

Phommasack, Kinnalone. "The impact of pH on microbial community structures in a long-term fertiliser experiment Palace Leas plot". Thesis, University of Newcastle upon Tyne, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.500930.

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6

Yu, Xiaolong. "FTOH Biodegradation Properties and PFOA Impact on Microorganisms in Activated Sludge". Kyoto University, 2018. http://hdl.handle.net/2433/231017.

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7

Suleman, Muhammad. "Fate of pesticides and assessment of their impact on the soil microbial community using liquid chromatography tandem-mass spectrometry". Thesis, University of York, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.547341.

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8

Tsigarida, Alexandra. "Investigations on the microbial community associated with peri-implantitis in smokers and non-smokers". The Ohio State University, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=osu1371071124.

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9

Papin, Marine. "Efficiency and impact of recurrent microbial inoculation in soil, a lab to field assessment". Electronic Thesis or Diss., Bourgogne Franche-Comté, 2024. http://www.theses.fr/2024UBFCK051.

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Face à l'urgence de mettre en place des pratiques plus durables pour protéger l'environnement tout en maintenant la production agricole, les inoculants microbiens suscitent un intérêt croissant en raison de leur potentiel pour réduire la dépendance aux intrants synthétiques. Cependant, malgré des décennies de recherche sur les inoculants microbiens du sol, leurs bénéfices sur les rendements agricoles restent très variables en fonction des sols, des climats, des génotypes végétaux et des souches inoculées, rendant les résultats difficiles à prédire et fragilisant in fine la confiance des agriculteurs. Ce travail explore la pertinence des inoculations récurrentes comme levier pour atténuer la résistance biotique de la communauté microbienne résidente du sol et favoriser l’établissement de l’inoculant. Ce travail étudie également les impacts de ces inoculations sur la communauté microbienne résidente. Dans une première expérience en microcosme, nous avons montré que l'inoculation récurrente pouvait améliorer, de manière transitoire l'abondance de l'inoculant (Pseudomonas fluorescens) avec un impact mineur sur la communauté bactérienne résidente. Une deuxième expérience en serre a mis en évidence le potentiel inattendu de l'inoculation récurrente, réalisée jusqu’au semis, pour favoriser la croissance du maïs avec un moindre impact sur la communauté bactérienne résidente par rapport à l'inoculation récurrente à partir du semis. La troisième expérience, réalisée au champ, a reflété les défis de transférer les bénéfices observés sur la croissance des plantes des conditions contrôlées vers des conditions non contrôlées. Finalement, ce travail suggère que le moment et la fréquence de l'inoculation doivent être ajustés de manière complémentaire. C’est-à-dire que l'inoculation récurrente peut augmenter temporairement l’abondance de l’inoculant lors des stades précoces critiques de la croissance des plantes. Cela peut soit favoriser la colonisation de l’hôte lorsqu’une dose adéquate est appliquée, soit influencer indirectement la communauté microbienne du sol au moment du semis
With the urgent need to adopt more sustainable practices that sustain agricultural production while protecting the environment, microbial inoculants are gaining increasing attention for their potential to reduce reliance on agrochemicals. However, despite decades of research, the benefits of soil microbial inoculants for crop yields remain highly variable across different soils, climates, plant genotypes, and inoculant strains. This variability makes outcomes difficult to predict and may ultimately reduce farmers’ confidence. This work explores the potential of recurrent inoculations as a strategy to overcome the biotic resistance of the resident soil microbial community and promote inoculant establishment. It also examines the effects of these inoculations on the resident microbial community. In a first microcosm experiment, we showed that recurrent inoculation could transiently improve the abundance of the inoculant (Pseudomonas fluorescens) with minimal impact on the resident bacterial community. A second experiment in greenhouse evidenced the unexpected potential of recurrent inoculation carried out until sowing to enhance maize growth while exerting a weaker impact on the bacterial resident community compared to recurrent inoculation starting at sowing. The third experiment conducted under field conditions reflected the challenges of translating the growth benefits observed in controlled environments to uncontrolled field conditions. Overall, this work suggests that both the timing and frequency of inoculation should be adjusted in a complementary way. Specifically, recurrent inoculation may transiently enhance the abundance of the inoculant during the critical early stages of plant growth. This may either promote successful host colonization when an adequate dose is applied, or indirectly influence the soil microbial community at sowing

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Cáliz, Gelador Joan. "Impact of chlorophenols and heavy metals on soil microbiota: their effects on activity and community composition, and resistant strains with potential for bioremediation". Doctoral thesis, Universitat de Girona, 2011. http://hdl.handle.net/10803/80914.

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Pollution by toxic compounds is one of the most relevant environmental damages to ecosystems produced by human activity and, therefore, it must be considered in environmental protection and restoration of contaminated sites. According to this purposes, the main goal of this doctoral thesis has been to analyse the impact of several chlorophenols and heavy metals on the microbial communities of two typical Mediterranean soils. The ecological risk concentrations of each pollutant, which have been determined according to respirometric activity and changes in the microbial community composition, and the factors that influence on their effective toxic concentrations (bioavailable pollutants) have been analysed in order to predict their potential impact on different soil ecosystems and provide scientific data for the regulation of the soil protection policies. Moreover, resistant microorganisms with pollutant removal capacities have been isolated from artificially contaminated soil microcosms and tested in axenic cultures, to infer their potential usefulness for bioremediation.
La contaminació amb compostos tòxics antropogènics és un dels perjudicis ambientals més rellevants per als ecosistemes i, per tant, cal tenir-ho en compte en la protecció ambiental i la restauració de llocs contaminats. Amb aquests propòsits, l’objectiu principal d’aquesta tesi doctoral ha estat analitzar l’impacte de clorofenols i metalls pesants sobre la microbiota de dos sòls típicament mediterranis. S’han analitzat les concentracions de risc ecològic de cada contaminant, determinades segons activitat respiromètrica i canvis en la composició de la comunitat microbiana, i els factors que influeixen en les seves concentracions tòxiques efectives (contaminants biodisponibles), per predir l’impacte potencial sobre diferents ecosistemes edàfics i proporcionar evidències científiques per a les polítiques de protecció del sòl. D’altra banda, a partir de microcosmos edàfics contaminats artificialment, es van aïllar també microorganismes resistents amb capacitat per eliminar els contaminants, que van ser analitzats en cultius purs per avaluar-ne la utilitat potencial en bioremediació.

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11

Nakagawa, Satoshi. "Microbial community in a backarc hydrothermal system in the Mid-Okinawa Trough : impacts of geophysicochemical heterogeneity". Kyoto University, 2005. http://hdl.handle.net/2433/145006.

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Kyoto University (京都大学)
0048
新制・課程博士
博士(農学)
甲第11604号
農博第1460号
新制||農||904(附属図書館)
学位論文||H17||N3997(農学部図書室)
23247
UT51-2005-D353
京都大学大学院農学研究科応用生物科学専攻
(主査)教授左子芳彦, 教授中原紘之, 教授平田孝
学位規則第4条第1項該当

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12

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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13

Black, Ellen Marie. "Assessing the impacts of native freshwater mussels on nitrogen cycling microbial communities using metagenomics". Diss., University of Iowa, 2018. https://ir.uiowa.edu/etd/6059.

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The Upper Mississippi River (UMR) basin contributes over 50,000 metric tons of nitrogen (N) to the Gulf of Mexico each year, resulting in a “dead zone” inhospitable to aquatic life. Land-applied N (fertilizer) in the corn-belt is attributed with a majority of the N-load reaching the Gulf and is difficult to treat as run-off is considered a non-point source of pollution (i.e. not from a pipe). One solution to this “grand challenge” of intercepting N pollution is utilizing filter-feeding organisms native to the UMR. Freshwater mussel (order Unionidae) assemblages collectively filter over 14 billion gallons of water, remove tons of biomass from overlying water, and sequester tons of N each day. Our previous research showed mussel excretions increased the sediment porewater concentrations of ammonium by 160%, and indirectly increased nitrate and nitrite by 40%, presumably from microbial degradation of ammonium. In response, the goal of this research was to characterize how mussels influenced microbial communities (microbiome) to determine the fate of N in UMR sediment. First, we used qPCR and non-targeted amplicon sequencing within sediment layers to identify the N-cycling microbiome and characterized microbial community changes attributable to freshwater mussels. qPCR identified that anaerobic ammonium oxidizing (anammox) bacteria were increased by a factor of 2.2 at 3 cm below the water-sediment interface when mussels were present. Amplicon sequencing of sediment at depths relevant to mussel burrowing (3 and 5 cm) showed that mussel presence reduced microbial species richness and diversity and indicated that sediment below mussels harbored distinct microbial communities. Furthermore, mussels increased the abundance of ammonia oxidizing bacteria (family Nitrosomonadaceae), nitrite oxidizing bacteria (genus Nitrospira), but decreased the abundance of ammonia oxidizing archaea (genus Candidatus Nitrososphaera), and microorganisms which couple denitrification with methane oxidation. These findings suggested that mussels may enhance microbial niches at the interface of oxic and anoxic conditions, presumably through excretion of N and burrowing activity. In response, we performed metagenomic shotgun sequencing to identify which genes of the microbiome were most impacted by mussels. We hypothesized that genes responsible for ammonia and nitrite oxidation would be greater in the sediment with mussel assemblages. We found the largest abundance of N-cycling genes were responsible for nitrate reduction and nitrite oxidation, which is corroborated by the high concentration of nitrates in UMR water. Linear discriminant analysis statistical analyses showed nitrification genes were most impacted by mussels, and this presented an opposing effect on genes responsible for producing nitrous oxide, a potent greenhouse gas. Further investigation showed an increased abundance of a novel organism capable of completely oxidizing ammonia to nitrate (Candidatus Nitrospira inopinata) and coexisted with metabolically flexible Nitrospira (sp. moscoviensis), likely enhancing both carbon and N-cycling. We demonstrated that native mussels harbor a unique niche for N-cycling microorganisms with large metabolic potentials to degrade mussel excretion products. Our findings suggest the ecosystem services of mussels extend beyond water filtration, and includes enhanced biogeochemical cycling of carbon, N, and reduces the potential for a potent microbially-produced greenhouse gas. Ultimately, this research could be used to advocate for mussel habitat restoration in the UMR to lessen the impacts of non-point pollution.

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Adhikari, Pratima. "IMPACT OF ENGINEERED TITANIUM DIOXIDE AND ZERO-VALENT IRON NANOPARTICLES ON CARBON DIOXIDE FIXATION BY AN AQUATIC MICROBIAL COMMUNITY: EFFECT AT ENVIRONMENTALLY RELEVANT CONCENTRATIONS". OpenSIUC, 2021. https://opensiuc.lib.siu.edu/theses/2856.

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AN ABSTRACT OF THE THESIS OFPratima Adhikari, for the Master of Science degree in Civil Engineering, presented on June 30, 2021, at Southern Illinois University Carbondale.TITLE: IMPACT OF ENGINEERED TITANIUM DIOXIDE AND ZERO-VALENT IRON NANOPARTICLES ON CARBON DIOXIDE FIXATION BY AN AQUATIC MICROBIAL COMMUNITY: EFFECT AT ENVIRONMENTALLY RELEVANT CONCENTRATIONSMAJOR PROFESSOR: Dr. Jia LiuThe purpose of this study is to investigate the effect of engineered nanoparticles (ENPs) on carbon dioxide reduction by aquatic microbial communities. Titanium dioxide (TiO2) nanoparticles and nanoscale zero-valent iron (nZVI) of different concentrations (10, 1, 0.1, 0.01, 0.001 mg/L and control), both environment-relevant and higher than the environmental concentrations as prediction for future concentrations, were selected. An anaerobic microbial community from the campus lake of Southern Illinois University Carbondale was studied. Different humic acid concentrations (100, 10, and 1 mg/L) were considered under pH 6.0 - 9.0. The research was conducted in two phases: 1) Transformation of TiO2 and nZVI nanomaterials in simulated environmental conditions, and 2) Inoculation of microbial community to the pristine nZVI nanoparticles as well as environmentally transformed nanoparticles, i.e. TiO2 and nZVI, to study their impacts on carbon dioxide reduction. The nanoparticles were suspended in a medium that simulates the aqueous environment for the growth of anaerobic bacteria. The nanoparticle suspension was kept in the simulated medium for 12 h light and 12 h dark for a period of one month and the transformed nanoparticles were then used for the study in its interaction with the microbial community. When the microbial community was inoculated, carbon dioxide gas was purged inside the vials to ensure no oxygen present in the vials. These samples were then monitored for a period of 2-3 weeks to see the carbon dioxide reduction. The results showed that the transformed nZVI had significant impact on the reduction of carbon dioxide concentration, whereas pristine nZVI and transformed TiO2 nanoparticles did not have significant impact on the reduction of carbon dioxide concentrations in the vials. The spearman correlation coefficient value showed that there is a somewhat monotonic relation between the reduction of carbon-dioxide and organic carbon formation for transformed TiO2 nanoparticles, however, for the transformed nZVI no such correlation was found. From this study, we can state that certain microbial communities can increase the rate of carbon dioxide fixation when exposed to the transformed zerovalent iron nanoparticles. This study can provide guidance on the industrial usage and environmental release of ENPs that are related to carbon fixation.

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Manis, Erin Evelyn. "Effect of Hydrological Regimes on Denitrification and Microbial Community Composition in Agriculturally Impacted Streams and Riparian Zones in Indiana, USA". Kent State University / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=kent1343006692.

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16

Zhou, Yanmin, e 周延敏. "Impacts of temperature and salinity on nitrification rate and microbial community in laboratory scale sequencing batch reactors(SBRs)". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2011. http://hub.hku.hk/bib/B47050718.

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17

Thiet, Rachel Kay. "Soil microbial community pattern and process : impacts on vascular plant communities in three ecosystems of high conservation value /". The Ohio State University, 2002. http://rave.ohiolink.edu/etdc/view?acc_num=osu1486459267521939.

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18

Gallego, Jefferson Cerquera [UNESP]. "Impacto do uso de antibióticos na microbiota do solo". Universidade Estadual Paulista (UNESP), 2016. http://hdl.handle.net/11449/148013.

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Devido ao grande número de antibióticos de uso veterinário que estão sendo liberados no solo através da urina e dejetos fecais dos animais de produção, algumas pesquisas têm verificado o impacto desses antibióticos na microbiota do solo. O presente estudo teve como objetivo avaliar o impacto dos antibióticos sobre a microbiota do solo em condições de microcosmos, de um solo de pastagem de bovinos e um solo de floresta, submetidos à presença de três antibióticos utilizados na produção animal, sendo estes, ampicilina, enrofloxacina e estreptomicina, nas concentrações de 0, 30 e 100 mg/kg de solo seco. A concentração de 0 mg/kg foi usada como controle. Os solos foram incubados em frascos de vidro de tampa rosca e mantidos a temperatura ambiente no escuro para reproduzir as condições reais encontradas na natureza. Foram avaliadas atividade respiratória microbiana, atividade da enzima desidrogenase e contagem de unidades formadoras de colônias (UFC) para estabelecer se existia ou não inibição do crescimento bacteriano nos dias 0, 1, 20 e 35. Os resultados mostram um aumento considerável nas UFC nos solos que receberam a ampicilina em ambas às concentrações durante o primeiro dia com relação ao controle. No dia 35 estas contagens se tornaram semelhantes ao controle ou menores. Os solos que receberam enrofloxacina e estreptomicina tiveram uma contagem menor que o controle inicialmente e com o tempo essas UFC aumentaram. A atividade respiratória microbiana e a atividade da enzima desidrogenase também confirmam esse achado. Esses resultados sugerem que os micro-organismos estão utilizando algum composto da ampicilina para o aumento das colônias e que os outros antibióticos diminuem a população microbiana do solo, especialmente a estreptomicina. Provavelmente alguns micro-organismos estejam sendo selecionados.
Due to the large number of veterinary antibiotics that are being released into the soil through urine and fecal waste of livestock, some research has linked the impact of those antibiotics in soil microflora. In the current study was evaluated the impact of antibiotics in the soil microbial community under microcosms conditions, cattle pasture soil and a forest soil under the presence of three antibiotics used in animal husbadry; ampicilin, enrofloxacyn and streptomycin, using a concentration of 0, 30 e 100 mg/kg dry soil. The concentration of 0mg/kg was used as control. The soils were incubated in screw cap glass jars and kept at room temperature in the dark to reproduce actual conditions found in nature. It was evaluated the microbial respiratory activity as well as the activity of dehydrogenase enzyme and colony forming units (CFU) to establish whether there was inhibition of bacterial growth or not at day 0, 1, 20 and 35. The results show a considerable increase in CFU in soils that received both concentrations of ampicillin during the first day compared with control. At day 35 these counting became similar to control or lower. The soils that received enrofloxacin and streptomycin, initially had lower countings than the control and over time these CFU increased. The microbial respiratory activity and the activity of dehydrogenase also confirmed these findings. These results suggest that some microorganisms are using a compound of ampicillin to grow. The other antibiotics decrease the soil microbial population, especially streptomycin. Probably some microorganisms are being selected.

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Zaghmouri, Imen. "Impact des fluctuations de salinité sur le cycle de l'azote dans les sédiments de l'étang de berre". Thesis, Aix-Marseille, 2013. http://www.theses.fr/2013AIXM4007/document.

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Dans l'étang de Berre, les apports excessifs en eau douce entraînent souvent des variations brusques de la salinité et des apports en azote parfois abondants. Les processus de régénération sédimentaire et d'élimination d'azote constituent des phénomènes majeurs pouvant expliquer le développement phytoplanctoniques et contrôler l'eutrophisation. L'étude de ces processus a été réalisée dans 2 stations ayant subi des historiques de variations de salinité différents. RDNA et anammox étaient négligeables. La dénitrification (couplée à la nitrification) serait le principal processus de sortie de N2 de l'étang. La forte production primaire pélagique utilisant l'ammonium a pu être expliquée par les processus de régénération, contrairement au nitrate dont la demande pélagique serait soutenue par des apports externes. Comme la salinité est susceptible d'influencer les processus d'azote, des microcosmes ont été utilisés afin d'évaluer la sensibilité de ces processus (résistance, résilience, shift) face aux variations à court terme de la salinité. Les 2 stations ont présenté des réponses différentes (dénitrification et nitrate réduction plus résilientes que la nitrification), suggérant que les stress halins à long terme influencent les réponses à court terme. Une hypothèse serait que la diversité et la structure des communautés joueraient un rôle crucial dans le maintien des taux d'activité. Dans cette étude, seule la communauté nitrifiante (AO) a été étudiée. Les AO et leurs transcrits étaient spécifiques aux sites et leurs abondances changeaient faiblement entre les microcosmes (résistance plus forte dans le site fréquemment soumis à des fluctuations de salinité)
The Berre lagoon receives excess freshwater leading to strong changes in the ecosystem salinity and in the nutrient inputs. Regeneration processes and the N2 removal of nitrogen are of a particular interest as they can explain the planktonic development and control the eutrophication state. These processes were studied in 2 stations with different patterns of long term stresses. DNRA and anammox were negligible. Denitrification (particularly the one coupled to nitrification) would be the main N2 removal in the lagoon. The high primary production based on N-NH4+ can be explained by the regeneration processes, while the primary production based on N-NO3- might be sustained by external inputs. As salinity susceptible to influence directly or indirectly the nitrogen processes, a microcosm approach was used in order to assess their sensitivity (resistance, resilience, shifts) to short term salinity fluctuations. Overall, towards the same kind of perturbations, the two stations responded differently (denitrification and nitrate reduction exhibited showed higher resilience than nitrification.), suggesting that long-term saline stresses would influence short-term responses. We suggest that the diversity and the structure of the communities would be crucial in their functional redundancy and thereby in the maintenance of the rates. In this study, we focused on the total structure of the nitrifying community (AO). AO and their transcripts were site-specific and their abundances changed slightly between microcosms (higher resistance in the site subject to frequent salinity fluctuations compared to the other site which is not affected by changes in the in situ salinity)

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Benomar, Saida. "Etude d'un écosystème bactérien synthétique anaérobie producteur d'hydrogène : Impact des interactions bactérie-bactérie sur le métabolisme". Thesis, Aix-Marseille, 2012. http://www.theses.fr/2012AIXM4718.

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Un grand nombre d'espèces microbiennes, issues d'environnements divers et présentant une large gamme de métabolismes différents, peuvent produire de l'hydrogène par voie fermentaire. Jusqu'à présent, les études ont principalement porté sur l'utilisation de cultures microbiennes pures, voire génétiquement modifiées, en vue d'optimiser la production de biohydrogène à partir de sucres simples ou peu complexes. Les efforts de recherche portent désormais sur l'utilisation de cultures microbiennes mixtes pour produire du biohydrogène à partir de sources organiques plus complexes issus par exemple du traitement de la biomasse. Toutefois, la présence de voies métaboliques alternatives tout comme l'instabilité du processus biologique constitue des verrous scientifiques et techniques qu'il conviendra de lever pour une application potentielle. Ceci nécessite entre autre une meilleur connaissance des interactions bactériennes et donc métaboliques présentent au sein du consortium.Pour cela, nous avons développé une approche innovante et pluridisciplinaire d'ingénierie écologique qui consiste en la conception, la construction et l'étude d'un consortium microbien synthétique afin d'établir les paramètres régissant les réseaux d'interactions métaboliques avec pour objectif d'optimiser la production d'hydrogène. Dans un premier temps nous avons choisit d'étudier les réseaux d'interactions métaboliques entre deux souches modèles connues comme partie prenante d'un consortium bactérien naturel, une bactérie du genre Clostridie et une du genre Desulfovibrio, la première étant productrice d'hydrogène par fermentation
Numerous microorganisms can produce hydrogen by “dark fermentation”. Isolated from various environments, they present a broad range of different metabolisms. Until now, literature reports have mainly dealt with the use of pure microbial cultures producing biohydrogen from simple sugars, such as glucose and sucrose. More recently, studies on biohydrogen production by mixed cultures from complex organic sources have been developed. Even though biohydrogen productivities and conversion yields can be interesting for industrial purposes, several scientific and technical constraints remain to be addressed. In particular, the presence of alternative metabolic ways of hydrogen consumption generally results in chronic instability of the biological processes. To increase the stability and the efficiency of dark fermentative processes, it is now necessary to acquire a better understanding of the metabolic interaction networks existing between producing and consuming microorganisms.We have developed an innovative and multidisciplinary approach to ecological engineering, which consists of the construction and study of synthetic microbial consortia to establish the metabolic networks existing between microorganisms for further optimization of biohydrogen production. First we have studied the networks of metabolic interactions between two bacterial models known as involved in a natural bacterial consortium: a bacterium from Clostridium genus; Clostridium acetobutylicum and one from Desulfovibrio genus, Desulfovibrio vulgaris Hildenborough. The first one being producing of hydrogen by fermentation of complex sugars and the second

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21

Haesler, Felix. "Microbial biocontrol of the pathogen Phytophthora citricola in the rhizosphere of European beech (Fagus sylvatica L.) : impact of elevated O 3 and CO 2 on the antagonistic community structure and function". kostenfrei, 2008. http://mediatum2.ub.tum.de/doc/645803/645803.pdf.

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22

Thorstenson, Candice [Verfasser], Matthias [Akademischer Betreuer] Ullrich, Matthias [Gutachter] Ullrich, Frank Oliver [Gutachter] Gloeckner e Mathias [Gutachter] Wegner. "The Impact of Environmental Changes on the Microbial Community Dynamics and Abundance of Pathogenic Vibrio species in Coastal Ecosystems / Candice Thorstenson ; Gutachter: Matthias Ullrich, Frank Oliver Gloeckner, Mathias Wegner ; Betreuer: Matthias Ullrich". Bremen : IRC-Library, Information Resource Center der Jacobs University Bremen, 2021. http://d-nb.info/1232075205/34.

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23

Maarastawi, Sarah Athea [Verfasser]. "Introduction of crop rotation and rice straw application in a former flooded rice system and their impact on the microbial community in bulk soil and the rhizosphere of Zea mays / Sarah Athea Maarastawi". Bonn : Universitäts- und Landesbibliothek Bonn, 2018. http://d-nb.info/1173789758/34.

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24

Macdonald, Karunia F. "Impacts of artisanal and large scale gold mining on tropical rivers in West Africa: A case study from the Brong Ahafo Region of Ghana". Thesis, Edith Cowan University, Research Online, Perth, Western Australia, 2016. https://ro.ecu.edu.au/theses/1932.

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Mining communities in more than 70 developing countries, mostly in the tropical regions, still practise artisanal and small scale gold mining (ASGM). ASGM commonly operates along rivers and streams for easy access to process water and as receptacles for mine water discharges. A largely unregulated industry, ASGM employs rudimentary mining and processing methods including the use of mercury amalgamation, and is often found near to larger scale and modern mining (LSM) operations. The substantial use of mercury by ASGM has drawn the attention of agencies and researchers but so has its persistent economic role in providing much needed rural employment. Mercury toxicity to human and environmental health has attracted much of researches, however ASGM impacts on riverine ecology, particularly at biota community levels, remains understudied. This study investigated the impacts of ASGM on the ecology of the Surow River and that of an LSM (the Ahafo mine) on the Subri River between February 2013 and April 2014. Both the Surow and Subri rivers are ephemeral tributaries of the Tano River, in Brong Ahafo, Ghana. The Ahafo mine, currently operated by Newmont Ghana Gold Limited (NGGL), has been operating on the Subri River catchment since December 2006, whilst ASGM started operations along the Surow River in 2007. Major ASGM operations ceased in May 2013 although smaller operators and processors remained. Specifically, the study aimed to determine whether and how ASGM and LSM impacted the respective river’s water and sediment quality, macroinvertebrate and microbial (Archaea and Bacteria) community structures and resulted in mercury biomagnification in fish. ASGM impact on river water and sediment quality was determined using a reversed BACI (Before/After and Control/Impact pairing) experimental design, whilst that of LSM used a conventional BACI design. Impacts on macroinvertebrate community structure were determined by comparing multiple control and impact sites sampled multiple times. The sequencing of 16S rRNA of Archaea and Bacteria was based on a one-off sampling and comparison between multiple control and impact sites on both rivers. The biomagnification of mercury in fish was tested via analysis of correlations between mercury concentrations in fish tissue and fish trophic level, fish length (proxy for age) and fish weight. The study demonstrated that gold mining, regardless of size and methods, significantly impacts the river ecosystems studied. Sediment particulates and minerals naturally available in the rock formation but exposed to the environment by mining activities were the most significant pollutants in the affected riverine ecosystems. The study area is in the tropic and experiences intensive rainfall. This, results in excess water which may come into contact with exposed rocks and wastes in the mining areas that eventually runs into or is discharged into the Surow and Subri rivers. Changes in the sediment and water quality due to mining were reflected in the macroinvertebrate communities of both rivers, while the sediment microbial communities tended to respond to differences in water quality. The study, however, strongly indicated that the types, magnitudes and effects of the environmental impacts of ASGM were different from that of LSM. The use, or the lack of, environmental management systems to mitigate impacts appeared to be the most important differentiating factor. The study also witnessed significant improvements in both water and sediment quality in the Surow River with the cessation of major ASGM in the area. Mercury, which was used in the ASGM (in relatively small quantities in Ghana compared to other countries) was detected in the Surow River sediment (despite naturally low concentrations of Hg in the local soils), but was largely undetectable in the waters. However, it posed health risks to humans and biota. This study found mercury biomagnified in fish from both the Surow and Subri rivers as well as the Tano River, indicating the presence of mercury in the rivers. The source of Hg, however, could not be clearly established but may have been from artisanal amalgamation processes and from smelting. Although mercury remains a concern in ASGM impacted rivers, it is not the only contaminant of concern. Sedimentation and particulate bound elements such as Al, As, Cu, Fe, Hg, and Pb were the main river pollutants resulting from ASGM operations. Elevated concentrations of metals in the turbid water due to the lack of sediment controls exceeded the Ghanaian and US EPA standards for the protection of aquatic life as well as that of Ghanaian raw water to be processed as drinking water. ASGM also significantly elevated the concentrations of salt ions and sulfate in river water particularly due to discharges of water from mine dewatering. During the active ASGM period, concentrations of Cu, Cr, Hg and Ni in the Surow River’s sediment exceeded the threshold effect level / TEL, lowest effect level / LEL, Australian effect low range /ERL and threshold effect level for Hylella azteca 28-day test or TEL HA28. Increased sediment load and decreased sediment quality in the Surow River were reflected in the macroinvertebrate community structure that was dominated by sediment-tolerant taxa but with only a few pollutant-sensitive taxa including Ephemeroptera and Trichoptera families. In the Subri River affected by the Ahafo gold mine, the impacts of mining were ameliorated by sediment control measures applied by the mine. The sediment control measures on the Subri River included the use of environmental control dams (ECD), one on a major tributary stream to the river, the other on a minor tributary. The ECDs reduced not only turbidity and total suspended solids, but also electrical conductivity, concentrations of most salt ions, nitrates and sulfate, and most metals both as total and dissolved forms from in the mine water being discharged into the environment. The improved water quality in downstream Subri River compared to that of the mine site and upstream was also reflected in the sediment quality, which had lower concentrations of most pollutants than that of the Surow River. The mine affected area in downstream Subri River also had more sensitive taxa including Ephemeroptera families than the Surow River. Nevertheless, mine discharge in downstream Subri appeared to alter the ecosystem compared to upstream control sections. Cessation of mine discharges at closure could see downstream sections of the river return to conditions more consistent with upstream. The exploratory microbial community study, a relatively novel study in the region, showed that the composition and diversity of the Archaea and Bacteria communities found in the Surow and Subri Rivers were comparable to those found in other studies including in the temperate regions. We also observed that microbial composition spatial variability within was greater than between rivers and that the variability was unrelated to riverine sediment chemistry but significantly related to water chemistry, particularly turbidity and concentrations of sulfate, Fe and FRP. The study also demonstrated a shift in sediment microbial community composition due to mine dewatering, particularly in the Surow River reaches affected by ASGM dewatering discharges. Given the one-off sampling nature of the sediment microbiology study, however, further study with repeated sampling regime is recommended. Sedimentation at ASGM sites dramatically altered the river morphology and biota. Further, metals carried by the sediments were deposited along the river downstream during the dry season and remobilised during the rainy seasons. The use of simple small scale ECD equivalents would substantially sediment based pollution. Discharges from mine dewatering from ASGM activities increased conductivity of the river and under full scale operations would have been problematic for biota and water quality. Although discharges from the LSM were of higher quality, they were also in high quantity and substantially altered downstream water quality and biota. Although these changes resulted in increased sensitive taxa, the long-term sustainability of these discharges is unknown. This study demonstrated that impact assessment of ASGM or LSM on rivers should not be limited to the physical and chemical properties of water and sediment, but also include its riverine biota. This study supports the use of macroinvertebrate and potentially microbes as indicators of impact of ASGM and mining in tropical rivers. Moreover, an understanding of the ecological impacts of mining large and small can assist in the

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25

Foulon, Julie. "Impact du phytomanagement de sites pollués par les éléments traces métalliques sur les micro-organismes du sol". Thesis, Besançon, 2016. http://www.theses.fr/2016BESA2090.

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Les activités anthropiques et la pollution qu’elles engendrent peuvent entraîner des changements drastiques dans les structures des écosystèmes et de leurs services écologiques. Le phytomanagement basé sur l’utilisation d’espèces ligneuses peut contribuer à la restauration des sols et de la diversité microbienne, tout en permettant la production de biomasses d’intérêt. Dans le cadre des projets PROLIPHYT (2013-2018, ADEME), BIOFILTREE (2010-2014, ANR) et PHYTOPOP (2007-2011, ANR) gérés par le laboratoire Chrono-environnement, des parcelles de phytomanagement ont été installées sur sites pollués par les éléments traces métalliques (ETMs), pour déterminer le potentiel de croissance d’espèces ligneuses, ainsi que les voies de valorisation des biomasses produites. Dans le cadre de mon projet de thèse, différentes approches ont été mises en œuvre afin d’identifier et de caractériser les microorganismes inféodés aux végétaux ligneux implantés, avec pour finalité la production de ressources microbiennes permettant d’améliorer la reprise et la croissance des arbres sur sols pollués. La première approche a consisté à étudier les communautés microbiennes en association avec les espèces ligneuses par une approche innovante de séquençage à haut débit associée à l’analyse physico-chimique des sols. Cette méthode a été mise au point et testée sur trois sites expérimentaux contaminés par des ETMs. Elle a permis de révéler les changements dans la structure et la composition des communautés microbiennes dus à la nature du couvert végétal et aux caractéristiques du sol (Zappelini et al., 2015; Foulon et al., 2016a; b). La deuxième approche a consisté à isoler et caractériser les champignons mycorhiziens et endophytes associés à des peupliers (Berthelot et al., 2016; Lacercat-Didier et al., 2016). Ces champignons sont connus pour favoriser la croissance des végétaux qu’ils colonisent mais également pour conférer une meilleure tolérance face à un stress métallique. Plusieurs campagnes de prélèvements de racines et de champignons sur différents sites pollués ont permis l’isolement de souches fongiques tolérantes aux ETMs (comme Serendipita vermifera) et améliorant la croissance (Phialophora sp. et Leptodontidium sp.). Dans une troisième approche, les mécanismes impliqués dans la résistance aux ETMs ont été étudiés i) chez Paxillus involutus pour le Hg (Foulon et al. manuscrit en préparation) ii) par métatranscriptomique fonctionnelle pour le Zn et Cd (Lehembre et al., 2013). L’ensemble de ces travaux a permis i) d’améliorer nos connaissances sur l’impact du couvert ligneux sur la structure et la composition des communautés microbiennes, et sur la compréhension des mécanismes physiologiques mis en jeu ii) de constituer une collection de souches fongiques d’intérêt pour le phytomanagement de sols contaminés par les ETMs
Anthropogenic activities can cause dramatic changes in ecosystem structures and their ecological services. Phytomanagement based on the use of woody species can contribute to soil and microbial diversity restoration, while allowing the production of biomass of interest. As part of PROLIPHYT (2013-2018, ADEME), BIOFILTREE (2010-2014, ANR) and PHYTOPOP (2007-2011, ANR) projects, managed by the Chrono-environment laboratory, phytomanagement plots were installed on trace elements (TE) polluted sites to determine the growth potential of woody species and the recovery methods of biomass produced. In my PhD project, different approaches have been implemented to identify and characterize microorganisms subservient to implanted woody plants, with the aim of producing microbial resources to improve the recovery and growth of trees on polluted soil. The first approach was to study microbial communities in association with woody species by innovative high throughput sequencing approach associated with the physical and chemical analysis of soils. This method was developed and tested on three experimental sites contaminated by TE. It revealed changes in the structure and composition of microbial communities due to the nature of the vegetation cover and the soil characteristics (Zappelini et al., 2015; Foulon et al., 2016a; b). The second approach was to isolate and characterize mycorrhizal fungi and endophytes associated with poplars (Berthelot et al., 2016; Lacercat-Didier et al., 2016). These fungi are known to promote the growth of the plants they colonize but also to increase their TE tolerance. Several sampling campaigns of roots and sporocarps on different polluted sites have allowed the isolation of fungal strains tolerant to TE (like Serendipita vermifera) and enhancing growth (Phialophora sp. and Leptodontidium sp.). In a third approach, the mechanisms involved in TE resistance were studied i) in Paxillus involutus for Hg (Foulon et al. In prep) ii) by functional metatranscriptomics for Zn and Cd (Lehembre et al., 2013). In conclusion, this work allowed to i) improve our understanding of the impact of a woody cover on the structure and composition of microbial communities, and on the understanding of the physiological mechanisms involved ii) to constitute a collection of fungal strains that will be of great interest for future phytomanagement projects

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26

Moreau, Sébastien D. V. "Effets combinés du réchauffement climatique et du rayonnement UVB sur la composition et le métabolisme de la communauté microbienne marine dans l'ouest de la Péninsule Antarctique : impact potentiel sur le cycle du carbone". Thesis, Montpellier 2, 2011. http://www.theses.fr/2011MON20028.

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Le réchauffement régional de l'ouest de la Péninsule Antarctique (WAP) combiné à la diminution attendue de glace de mer et à l'apparition printanière du trou d'ozone pourrait modifier la composition et la structure de la communauté microbienne. De plus, ces variations environnementales pourraient modifier le potentiel de la WAP en tant que puits de CO2. Dans ce contexte, cette thèse visait à évaluer les effets combinés du changement climatique sur la production primaire et sur la composition et la structure de la communauté microbienne de la WAP. Cette thèse visait également à évaluer le rôle de la structure, de la composition, de la production primaire et de la respiration de la communauté microbienne sur les échanges de CO2 entre l'atmosphère et l'océan. Cette étude a premièrement permis de décrire les variations de l'étendue de glace de mer, de l'épaisseur de la couche d'ozone et de la température de surface de l'eau dans la WAP au cours des 30 dernières années (1972-2007) et notamment d'observer le retrait de plus en plus précoce de la glace de mer en relation avec le réchauffement des eaux de la WAP. L'évolution de ces paramètres environnementaux offre une nouvelle fenêtre temporelle de production primaire. Ainsi, cette étude a permis de montrer que la production primaire annuelle a augmenté de 1997 à 2007, et ceci, en relation avec l'anomalie de glace de l'hiver précédent. En effet, la production primaire journalière était négativement et positivement corrélée avec, respectivement, l'étendue de glace de mer et la température de l'eau de septembre à novembre et de février à mars, suggérant que le réchauffement régional de la WAP favorise plus de production primaire durant le printemps et l'automne. En revanche, le retrait précoce de la glace de mer en coïncidence avec l'apparition printanière du trou d'ozone a provoqué l'augmentation de la photoinhibition au printemps (avec 11,6 ± 2,8 % de la production primaire journalière en moyenne). En conséquence, le changement climatique régional de la WAP a, à la fois, un effet positif et un effet négatif sur la production primaire. Cette étude a également permis de décrire la dynamique de la communauté microbienne marine dans l'archipel de Melchior (dans la WAP) de l'automne au printemps 2006. En raison des conditions environnementales extrêmes, l'abondance et la biomasse de la communauté microbienne étaient faibles durant l'automne et l'hiver et dominées par les petites cellules (< 2 µm) et donc par un réseau trophique microbien. En effet, la biomasse phytoplanctonique était faible durant l'automne et l'hiver (avec une concentration moyenne en chlorophylle a, Chl-a, de 0,3 et 0,13 µg l-1, respectivement). La biomasse phytoplanctonique a augmenté au printemps (avec un maximum de Chl-a de 1,13 µg l-1), mais, en dépit des conditions de croissance favorables, est restée faible et le phytoplancton était toujours dominé par de petites cellules (2-20 µm) et donc par le réseau trophique microbien ou multivore. De plus, la disparition précoce de glace de mer durant le printemps 2006 a exposé les eaux de la WAP à de fortes radiations ultraviolettes B (RUVB, 280-320 nm), qui ont eu un effet négatif sur la communauté microbienne des eaux de surface. Cette étude a également mis en évidence la relation existante entre les échanges CO2 et d'O2 entre l'atmosphère et l'océan dans la WAP et la biomasse, la composition, la production primaire et la respiration de la communauté microbienne. Il existait tout d'abord une relation positive entre la concentration en Chl-a et la proportion de diatomées dans la communauté phytoplanctonique. De plus, il existait une corrélation négative significative entre la Chl-a et le ΔpCO2. La production primaire nette de la communauté (NCP) était principalement contrôlée par la production primaire et était négativement et positivement reliée avec le ΔpCO2 et le pourcentage de saturation de l'O2, respectivement, suggérant que la production primaire joue un rôle majeur dans les échanges de CO2 et d'O2 entre l'atmosphère et l'océan dans la WAP. Par ailleurs, le ΔpCO2 moyen au cours des trois années étudiées était de -20,04 ± 44,3 µatm, menant à un puits de CO2 potentiel durant l'été et l'automne dans la région. Le sud de la WAP était un puits potentiel de CO2 (-43,60 ± 39,06 µatm) durant l'automne alors que le nord de la WAP était principalement une source potentielle de CO2 durant l'été ou l'automne (-4,96 ± 37,6 et 21,71 ± 22,39 µatm, respectivement). Les plus fortes concentrations en Chl-a mesurées dans le sud de la WAP pourraient expliquer cette distribution spatiale
Regional warming in the western Antarctic Peninsula (WAP), along with the expected decrease in sea-ice cover and the seasonal ozone layer breakdown could modify the composition and the structure of the microbial community. In addition, these environmental changes could modify the potential of the WAP as a CO2 sink. In this context, this thesis aimed at evaluating the combined effects of regional climatic changes on the primary production and the composition and structure of the microbial community in the WAP. In a second time, this thesis aimed at evaluating the role of the microbial community structure, composition, primary production and respiration on air-sea CO2 gas exchanges.First, the variations in sea-ice cover, stratospheric ozone layer thickness and sea surface temperature over the last 30 years (1972-2007) were described. Related to the warming of WAP waters, the retreat of sea-ice was happening earlier each decade in the WAP. The observed changes in these environmental parameters offer a new temporal window for primary production. Indeed, the annual primary production increased from 1997 to 2007, in relation with the sea-ice cover anomaly for the previous winter. In addition, daily primary production was negatively and positively correlated to, respectively, sea-ice cover and sea-water temperature from September to November and from February to March, suggesting that regional warming favoured more primary production during spring and fall. On the contrary, the early retreat of sea-ice in spring, in coincidence with the spring ozone layer breakdown, led to an increase in photoinhibition (with an average of 11.6 ± 2.8 % of the daily primary production being photoinhibited). Therefore, regional climatic changes in the WAP had both a positive and a negative impact on primary production.The microbial community variability was also described in the Melchior Archipelago (in the WAP) from fall to spring 2006. Because of the extreme environmental conditions, the microbial community abundance and biomass were low in fall and winter and the community was dominated by small cells (< 2 µm), hence by a microbial food-web. Indeed, phytoplanktonic biomass was low during fall and winter (with respective chlorophyll a concentration, Chl-a, of 0.3 and 0.13 µg l-1). Phytoplankton biomass increased in spring (with a maximum Chl-a of 1.13 µg l-1) but, despite favourable growth conditions, phytoplankton was still dominated by small cells (2-20 µm), hence by a microbial or multivorous food-web. In addition, the early retreat of sea-ice in the spring 2006 exposed the WAP waters to strong ultraviolet B radiations (UVBR, 280-320 nm) that had a negative impact on the microbial community in surface waters.Finally, the relationship between air-sea CO2 and O2 exchanges in the WAP with the phytoplankton community biomass and composition and with the microbial community primary production and respiration was described. A positive relationship existed between Chl-a and the proportion of diatoms in the phytoplankton community. In addition, a negative relationship existed between Chl-a and ΔpCO2. The net community production (NCP) was mainly controlled by primary production and was negatively and positively related to ΔpCO2 and the %O2 saturation, respectively, suggesting that primary production was the main driver of air-sea CO2 and O2 gas exchanges in the WAP. In addition, the average ΔpCO2 for the summers and falls 2002 to 2004 was -20.04 ± 44.3 µatm, leading to a potential CO2 sink during this period in the WAP. The southern WAP was a potential CO2 sink (-43.60 ± 39.06 µatm) during fall while the northern part of the Peninsula was mainly a potential CO2 source during summer and fall (-4.96 ± 37.6 and 21.71 ± 22.39 µatm, respectively). The higher Chl-a concentrations measured in the southern WAP may explain this spatial distribution

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Chew, Yi Vee. "Host and microbial factors influencing the gut microbial community structure". Thesis, The University of Sydney, 2013. http://hdl.handle.net/2123/10031.

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Gut microbial colonization begins at birth and dynamic ecological succession occurs before establishment of a stable, resilient adult community structure. Colonization outcomes in early life have long-term effects on host health. Understanding factors governing neonatal gut community structure development and adult structure modulation will allow therapeutic manipulation of the gut community for disease prevention/treatment. Submetagenomic analysis was done to identify microbial factors potentially triggering community stability in neonate piglets. Piglet faecal microbiota was fractionated before and after key points in community development using suppression subtractive hybridization. Analysis of immunoglobulin A bound to gut microbes showed that distinct groups are bound, potentially influencing colonization outcomes. Comparisons using pyrosequencing showed that colon and cecum microbiota of mice on a standard diet were similar at higher taxonomic levels, with minor differences at finer scale reflecting spatial location. Changes in host nutrient intake were found to generically drive community shift in 2 independent mouse genotypes - low energy density (LED) diet samples showed significantly higher relative abundances of mucin-degrading Verrucomicrobiae and Bacteroidia. Ability to use host secretions as an alternative energy source is predicted to confer selective advantage under reduced host nutrient intake. To track host secretion uptake, mice were intravenously injected with 13C and 15N-labeled threonine. Isotope incorporation by bacteria was tracked with nanoscale secondary ion mass spectrometry. Greater uptake was seen in LED diet mice, indicating increased importance of host secretions to bacterial nutrition relative to host-ingested nutrients. Different populations showed differential uptake, suggesting varied ability to utilise host secretions. This is expected to influence population fitness and drive community shift under host nutrient intake limitation.

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28

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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29

Gilliam, Lucy. "Impact of anti-microbial GM plants on soil microbial populations". Thesis, University of Reading, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.485401.

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The environmental risk assessment of GM plants is a fast moving area of science. Much research has focused on developing methods to evaluate potential effects on a range of organisms. Microorganisms play an essential role in many soil processes, with the rhizosphere as the prominent site of microbial activity. There is a general need for protocols to assess the effect of anthropogenic influences, the use of different crops and crop rotation an.d as well as GM plants, on the microbial community within the soil. The rhizosp~eres of three crop plants Brassica napus (Oilseed rape), Triticum aestivum (Wheat) and Solanum tuberosum (Potato) were compared using both genetic and functional diversity methods. The rhizospheres of four cultivars of potato were compared; GM potato (variety Kardal) modified with an anti-fungal transgene, GM potato (variety Kardal) with no transgene inserted (empty vector), parental .- line of potato (variety Kardal) and a different cultivar (variety Russet-Burbank). Genetic diversity of bacterial populations isolated from the rhizosphere were compared using PCR amplified DNA of 168 rRNA with denaturing gradient gel electrophoresis (DGGE) to obtain community fingerprints. Activity of the microbial populations was assessed using Biolog G.N MicroPlateÃ‚Â™ community substrate utilisation and enzyme activity using a microplate method based on substrates linked to the fluorescent compounds methylumbelliferone (MUB) and 7-amino-4-methyl coumarin (AMC). By comparing the ~M plants to non-GM plants and other crops, observed differences are placed in context. This work shows that the GM line examined.appears to have little effect on soil microbial populations. Detected effects of1he GM potato line were minor compared with other sources of variation observed between plants cultivar or crop species, management practices and sampling time. To date, there has been little evidence that cultivation of GM plants leads to significant changes in microbial popUlations.

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30

Barberán, Torrents Albert. "Microbial Macroecology understanding microbial community pattems using phylogenetic and multivariate statistical tools". Doctoral thesis, Universitat de Barcelona, 2012. http://hdl.handle.net/10803/101511.

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El estudio de los microorganismos en cultivo puro ha propiciado el desarrollo de la genética, la bioquímica y la biotecnología. Sin embargo, la ecología ha permanecido reticente a incorporar a los microorganismos en su acervo teórico y experimental, principalmente debido a las dificultades metodológicas para observar a los microbios en la naturaleza, y como resultado de los caminos divergentes que han trazado las disciplinas de la microbiología y la ecología general. Esta tesis trata de demostrar que los patrones ecológicos de comunidades microbianas son susceptibles de ser analizados mediante la combinación de técnicas filogenéticas y herramientas de estadística multivariante. El uso de técnicas filogenéticas permite solventar, o al menos paliar, el hecho de la no independencia de los organismos vivos debido a la ascendencia común. Con la información ambiental adicional (como reflejo del determinismo abiótico) y la información espacial (como amalgama de eventos históricos y de dispersión), es posible explorar los posibles mecanismos que subyacen a la estructura y a la diversidad de las comunidades microbianas.
The study of microorganisms in pure laboratory culture has delivered fruitful insights into genetics, biochemistry and biotechnology. However, ecology has remained reluctant to incorporate microorganisms in its experimental and theoretical underpinnings mainly due to methodological difficulties in observing microorganisms in nature, and as a result of the different paths followed by the disciplines of microbiology and general ecology. In this dissertation, I argue that novel insights into microbial community patterns arise when phylogenetic relatedness are used in conjunction with multivariate statistical techniques in the context of broad scales of description.

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31

Thomas, Andrew Maltez. "Microbial community profiling of human gastrointestinal cancers". Universidade de São Paulo, 2018. http://www.teses.usp.br/teses/disponiveis/95/95131/tde-07022019-134344/.

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The human microbiome - defined as the microbial communities that live in and on our bodies - is emerging as a key factor in human diseases. The expanding research field that investigates the role of the microbiome on human cancer development, termed oncobiome, has led to important discoveries such as the role of Fusobacterium nucleatum in colorectal cancer carcinogenesis and tumor progression. Motivated by these discoveries, this thesis studied the oncobiome from different perspectives, investigating whether alterations to microbial profiles were associated with disease status or an adverse response to treatment. We used both biopsy tissue samples and 16S rRNA amplicon sequencing (N = 36), as well as privately and publicly available fecal whole metagenomes (N = 764) to investigate microbiome-colorectal cancer (CRC) associations. We observed significant increases in species richness in CRC, regardless of sample type or methodology, which was partially due to expansions of species typically from the oral cavity, as well as an overabundance of specific taxa such as Bacteroides fragilis, Fusobacterium, Desulfovibrio and Bilophila in CRC. Functional potential analysis of CRC metagenomes revealed that the choline trimethylamine-lyase (cutC) gene was over-abundant in CRC, with the strength of association dependent on four identified sequence variants, pointing at a novel potential mechanism of CRC carcinogenesis. Predictive microbiome signatures trained on the combination of multiple datasets showed very high and consistent performances on distinct cohorts (average AUC 0.83, minimum 0.81). To investigate the microbiomes role in response to treatment, we profiled microbial communities of gastric wash samples in gastric cancer patients (N = 36) before and after neoadjuvant chemotherapy through 16S rRNA amplicon sequencing. Gastric wash microbial communities presented remarkably high inter-individual variation, with significant decreases in richness and phylogenetic diversity after treatment and associations with pH, pathological response and sample collection. The most abundant genera found in patients before or after chemotherapy treatment included Streptococcus, Prevotella, Rothia and Veillonella. Despite limitations inherent to differing experimental choices, this thesis provides microbiome signatures that can be the basis for clinical prognostic tests and hypothesis-driven mechanistic studies, as well as supporting the role of the human oral microbiome in whole-body diseases.
O microbioma humano - definido como as comunidades microbianas que vivem sobre e dentro do corpo humano - está se tornando um fator cada vez mais importante em doenças humanas. O campo de estudo que investiga o papel do microbioma no desenvolvimento do câncer humano, denominado oncobioma, está crescendo e já levou a importantes descobertas como o papel da espécie Fusobacterium nucleatum na carcinogênese e progressão tumoral de tumores colorretais. Motivado por estas descobertas, esta tese de doutorado analisou o oncobioma por diferentes perspectivas, investigando se alterações nos perfis microbianos estavam associados à presença da doença ou a uma resposta adversa ao tratamento. Usamos tanto amostras de tecidos de biópsias e o sequenciamento do gene 16S rRNA (N = 36), quanto metagenomas fecais públicos e privados (N = 764), para investigar associações entre o microbioma e o câncer colorretal (CCR). Observamos um aumento significativo da riqueza microbiana no CCR, independentemente do tipo da amostra ou metodologia, que era em parte, devido ao aumento de espécies tipicamente presentes na cavidade oral. Observamos também um aumento da abundância de táxons específicos no CCR, que incluíam Bacteroides fragilis, Fusobacterium, Desulfovibrio e Bilophila. Analisando o potencial funcional dos metagenomas, encontramos um aumento significativo da enzima liase colina trimetilamina (cutC) no CCR, cuja associação era dependente de 4 variantes de sequência, demonstrando ser um possível novo mecanismo de carcinogênese no CCR. Assinaturas preditivas do microbioma treinadas na combinação dos estudos demonstraram ser altamente preditivas e consistentes nos diferentes estudos (média de AUC 0.83, mínimo de 0.81). Para investigar o possível papel do microbioma na resposta ao tratamento, analisamos os perfis microbianos do suco gástrico de pacientes com câncer gástrico (N = 36) antes e depois do tratamento quimioterápico neoadjuvante. As comunidades microbianas apresentaram uma variabilidade inter-individual notavelmente grande, com diminuições significativas na riqueza e diversidade filogenética pós tratamento, além de estarem associadas principalmente ao pH, mas também à resposta patológica e ao tempo da coleta. Os gêneros mais abundantes encontrados nos pacientes antes ou depois da quimioterapia incluíam Streptococcus, Prevotella, Rothia e Veillonella. Apesar das limitações inerentes às escolhas experimentais, esta tese proporciona assinaturas do microbioma que podem servir de base para testes clínicos prognósticos e estudos mecanísticos, além de dar mais suporte ao papel do microbioma oral em doenças humanas.

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32

Roach, Ty Noble Frederick. "Nonequilibrium Thermodynamics, Microbial Bioenergetics, and Community Ecology". Thesis, University of California, San Diego, 2019. http://pqdtopen.proquest.com/#viewpdf?dispub=10827422.

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While it is clear that thermodynamics plays a nontrivial role in biological processes, exactly how this affects the macroscopic structuring of living systems is not fully understood. Thus, the objective of this dissertation was to investigate how thermodynamic variables such as exergy, entropy, and information are involved in biological processes such as cellular metabolism, ecological succession, and evolution. To this end, I have used a combination of mathematical modelling, in silico simulation, and both laboratory- and field-based experimentation.

To begin the dissertation, I review the basic tenets of biological thermodynamics and synthesize them with modern fluctuation theory, information theory, and finite time thermodynamics. In this review, I develop hypotheses concerning how entropy production rate changes across various time scales and exergy inputs. To begin testing these hypotheses I utilized a stochastic, agent-based, mathematical model of ecological evolution, The Tangled Nature Model. This model allows one to observe the dynamics of entropy production over time scales that would not be possible in real biological systems (i.e., 10⁶ generations). The results of the model’s simulations demonstrate that the ecological communities generated by the model’s dynamics have increasing entropies, and that this leads to emergent order, organization, and complexity over time. To continue to examine the role of thermodynamics in biological processes I investigated the bioenergetics of marine microbes associated with benthic substrates on coral reefs. By utilizing both mesocosm and in situ experiments I have shown that these microbes change their power output, oxygen uptake, and community structure depending upon their available exergy.

Overall, the data presented herein demonstrates that ecological structuring and evolutionary change are, at least in part, determined by underlying thermodynamic mechanisms. Recognizing how physical processes affect biological dynamics allows for a more holistic understanding of biology at all scales from biochemistry, to ecological succession, and even long-term evolutionary change.

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33

Brown, Shawn Paul. "Rules and patterns of microbial community assembly". Diss., Kansas State University, 2014. http://hdl.handle.net/2097/18324.

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Doctor of Philosophy
Division of Biology
Ari M. Jumpponen
Microorganisms are critically important for establishing and maintaining ecosystem properties and processes that fuel and sustain higher-trophic levels. Despite the universal importance of microbes, we know relatively little about the rules and processes that dictate how microbial communities establish and assemble. Largely, we rely on assumptions that microbial community establishment follow similar trajectories as plants, but on a smaller scale. However, these assumptions have been rarely validated and when validation has been attempted, the plant-based theoretical models apply poorly to microbial communities. Here, I utilized genomics-inspired tools to interrogate microbial communities at levels near community saturation to elucidate the rules and patterns of microbial community assembly. I relied on a community filtering model as a framework: potential members of the microbial community are filtered through environmental and/or biotic filters that control which taxa can establish, persist, and coexist. Additionally, I addressed whether two different microbial groups (fungi and bacteria) share similar assembly patterns. Similar dispersal capabilities and mechanisms are thought to result in similar community assembly rules for fungi and bacteria. I queried fungal and bacterial communities along a deglaciated primary successional chronosequence to determine microbial successional dynamics and to determine if fungal and bacterial assemblies are similar or follow trajectories similar to plants. These experiments demonstrate that not only do microbial community assembly dynamics not follow plant-based models of succession, but also that fungal and bacterial community assembly dynamics are distinct. We can no longer assume that because fungi and bacteria share small propagule sizes they follow similar trends. Further, additional studies targeting biotic filters (here, snow algae) suggest strong controls during community assembly, possibly because of fungal predation of the algae or because of fungal utilization of algal exudates. Finally, I examined various technical aspects of sequence-based ecological investigations. These studies aimed to improve microbial community data reliability and analyses.

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34

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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35

Mueller, Sabrina R. "Chromium, DNA, and Soil Microbial Communities". Cincinnati, Ohio : University of Cincinnati, 2006. http://rave.ohiolink.edu/etdc/view.cgi?acc_num=ucin1141334651.

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Thesis (Ph. D.)--University of Cincinnati, 2008.
Advisor: Brian K. Kinkle. Title from electronic thesis title page (viewed Apr. 23, 2009). Keywords: SEC-ICP-MS; Fungal community; bacterial community; DGGE. Includes abstract. Includes bibliographical references.

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36

Beecroft, Nelli. "Development of a microbial fuel cell (MFC) and analysis of microbial community dynamics". Thesis, University of Surrey, 2010. http://epubs.surrey.ac.uk/770152/.

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The basis of this work was to understand how the performance of Microbial Fuel Cells (MFCs) can be understood and improved by analysing the behaviour of the microbial communities in the anodic chamber. It was hypothesized that specific types of species generally become more abundant in MFCs over time leading to enhanced power production. An acclimatised microbial consortium obtained from a tubular MFC was used as the inoculum for the MFC described in this study: It was found to lead to a different bacterial composition, but similar power density, to those observed in an MFC inoculated with the unacclimatised community (anaerobic sludge). Using anaerobic sludge as inoculum in four replicate MFCs, both the anodic biofilm and the suspended communities evolved differently. The spatial and temporal dynamics of microbial communities were studied in the tubular MFCs. Although the removal of organic compounds was spatially different, the dynamics of the dominant bacteria showed spatial similarity, probably attributed to the versatile metabolic capabilities of species. No specific species were found the relative abundance of which would have clearly enhanced and correlated with the power production. Using similar substrate feeds and inocula, the communities consisted of metabolically different species in the two reactor types studied. Functional redundancy was observed in the anodic communities of both reactor designs. These findings suggest that the exoelectrogenic ability could be present among a range of bacteria wider than generally thought. 2 The results of this study suggest that the development of the microbial communities in MFCs with a given inoculum and substrate are determined by the reactor design and the operational conditions. Secondly, the adaptation of bacterial communities to produce electricity may not require specific changes in community composition but instead be based on the ability of bacteria to adapt generating electricity and enhance their exoelectrogenic capacity over time.

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37

Albarracín, María. "SOIL MICROBIAL COMMUNITY DYNAMICS IN FLORIDA SCRUB ECOSYSTEM". Master's thesis, University of Central Florida, 2005. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/3498.

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Pyrogenic ecosystems are maintained by fires which vary in frequency, seasonality, and intensity. Florida oak-saw palmetto scrub ecosystem is characterized by fires occurring at intervals of 10-20 years. Diverse factors as private land acquisition and development has created a patchy distribution of scrub ecosystems and also interrupted the natural fire cycle. The effects of fire over plant regeneration and fauna habitat utilization of the scrub have been well characterized in previous research. In the present paper the objective is to characterize the short- and long-term fire effects on the soil microbial community. Fire effects were studied in a chronosequence, comprising a recently burned scrub during a winter-prescribed fire to scrub where fire did not occur for 40 years. The number of culturable cells was reduced by two orders of magnitude by indirect fire effects and environmental factors, principally hydric stress. However, the duration of fire effects was very short since the microbial community returned to pre-fire numbers and activity by day 47 after fire. Microbial community activity was distinctively related to inoculum density in the soil and litter samples. Soil and litter microbial communities showed differences in metabolic activity. There was no difference in substrate utilization pattern, but there was significant seasonal variation related to the decrease in water content during the month of May. Substrate utilization by litter microbial communities was higher during the month of January compared to soil microbial communities and this relationship was inversed during the month of May probably associated to the more stringent conditions, low water availability, on the litter layer. Seasonal effects outweighed fire effects in this study as this environmental constraint determined the microbial community structure and activity.
M.A.
Department of Biology
Arts and Sciences
Biology

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38

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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39

Smart, Trevor Blake. "Microbial Community Response to Fumigation in Potato Soils". BYU ScholarsArchive, 2018. https://scholarsarchive.byu.edu/etd/7355.

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Soil microorganisms have a variety of beneficial and deleterious effects on plants, impacting such processes as plant growth, soil nutrient cycling, crop yield, disease resistance and tolerance to an array of biotic and abiotic stressors. The disruption of soil microbial community structures, particularly when beneficial soil biota are altered, has been shown to reduce crop yield and leave plants susceptible to disease. Long-term disruption of microbial communities may occur with repeated fumigation, being the application of gaseous pesticides, in agricultural soils. For this reason, we characterized bacterial, fungal, oomycete and nematode populations in paired fumigated and nonfumigated potato fields located in Idaho, Oregon, Washington and Minnesota. Samples were taken at three distinct timepoints: one before a fall fumigation event and two others at important stages in potato production, row closure and vine death. Soil biota populations were assessed by targeting the 16S, 18S and ITS1 gene regions. FunGuild, a database capable of guild and trophic assignment of fungal lineages, was used to sort fungal OTUs in different trophic modes. Fungal analyses indicated an increase in relative abundances of saprotrophic fungal populations and a decrease in pathotrophic fungal populations, both during row closure. Principally, the fungal genera of Humicola and Mortierella were responsible for the increase of saprotrophs while Alternaria decreased the most for pathotrophs. Other fungi occupying multiple trophic modes, such as Fusarium, also decreased during row closure. We found that fumigation treatments, in combination with various pesticide and fertilizer applications, alter both alpha- and beta- bacterial soil diversity although certain treatments, i.e. chloropicrin, may alter bacterial populations more than other treatment types such as metam-sodium. Nematode populations were likewise distinct at each location with soils from Boardman, OR, Minidoka, ID and Pine Point, MN with these having higher levels of nematodes associated with better soil health, i.e. Dorylaimidae. Conversely, nematodes associated with plant pathogenesis were found in higher relative abundances at Minidoka, ID and Quincy, WA. In this study, we characterize the populations of bacteria, fungi, oomycetes and nematodes with an emphasis on fungal taxa. We found that relative abundances of fungal trophic modes vary temporally. Additionally, we catalogue several other high abundance taxa with seasonal differential abundances whose functional capacity in potatoes remain uncharacterized.

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40

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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41

Saup, Casey Morrisroe. "Biogeochemical Cycling in Pristine and Mining-Impacted Upland Fluvial Sediments". The Ohio State University, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=osu1593664378874682.

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42

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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43

Faulwetter, Jennifer Lynn. "Analysis of microbial biofilm community composition within constructed wetlands". Diss., Montana State University, 2010. http://etd.lib.montana.edu/etd/2010/faulwetter/FaulwetterJ1210.pdf.

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Constructed wetlands (CWs) are ecologically-based water treatment systems that provide cost-effective amelioration of waterborne pollutants. Fundamental understanding of removal mechanisms, especially microbial processes, limits greater usage of constructed wetlands as a wastewater treatment system. The influence of plant species selection, season, and organic load rate on pollutant removal was previously linked to the redox condition of the sub-surface wetland environment. The goal of this research was to determine which of these environmental variables (including spatial location within the CW) influenced the dominant microbial populations and/or the activity of various sub-populations. Once identified, a constructed wetland might be optimized for growth of microorganisms involved in removal of a specific pollutant. To assess environmental factors, microbial population samples were taken in six locations (effluent, 3 root and 2 gravel areas) within replicate unplanted microcosms and wetland microcosms planted with Deschampsia cespitosa or Leymus cinereus during the summer (24Â°C) and winter (4Â°C) seasons. Microcosms were fed a synthetic domestic wastewater in 20-day batches for at least 12 months prior to sampling. The most recent techniques in molecular biology including denaturing gradient gel electrophoresis (DGGE) and quantitative PCR were utilized and included treatment with and without propidium monoazide (PMA) to distinguish between "live" and "dead" microbial communities. Primer sets targeted the entire bacterial community (16S rDNA) and two functional groups, nitrifying bacteria (amoA gene) and sulfate reducing bacteria (dsrB gene). Results indicated that overall microbial community structure (16S rDNA) was affected by general location within the microcosm (effluent, root, gravel) as well the plant species present. Specific microbial groups appeared to be affected differently with relative gene quantities of sulfate reducing bacteria and nitrifying bacteria being influenced by a combined effect of plant species and season. For dsrB, D. cespitosa had the lowest relative gene quantities overall. Both genes were more abundant in the summer season, indicating seasonal importance. Location within the microcosms was also important, with anoxic environments (column bottom) being more important for dsrB presence and a diverse population of cultivated sulfate reducers. The roots were an important location for both microbial diversity and activity for all genes investigated. 'Co-authored by Vincent Gagnon, Carina Sundberg, Florent Chazarenc, Mark D. Burr, Jacques Brisson, Anne K. Camper, Otto R. Stein, Albert E. Parker, Alfred B. Cunningham, and Frank M. Stewart.'

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44

Wigfull, Sharon Denise. "Recovery of the indigenous soil microbial community after landfilling". Thesis, University of East London, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.279148.

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45

Newbold, Lindsay Kate. "Microbial community organisation and functioning under ocean acidification conditions". Thesis, University of Newcastle upon Tyne, 2014. http://hdl.handle.net/10443/2576.

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Since industrialisation global CO2 emissions have increased, and as a consequence oceanic pH is predicted to drop by 0.3-0.4 units before the end of the century - a process coined ‘ocean acidification’ (OA). There is significant interest therefore in how pH changes will affect the oceans’ biota and integral processes. This thesis investigates microbial community organisation and functioning in response to predicted end of century CO2 concentrations using an elevated CO2 (~750ppm), large volume (11,000 L) contained seawater mesocosm. This thesis utilises RNA stable isotope probing (SIP) technologies, in conjunction with quantitative reverse transcriptase PCR (RT-qPCR), to investigate the response of microbial communities to elevated CO2. This thesis finds little evidence of changes occurring in bacterial abundance or community composition with elevated CO2, under both phytoplankton pre-bloom/bloom and post-bloom conditions. It is proposed that they represent a community resistant to the changes imposed. In contrast, significant differences were observed between treatments for a number of key eukaryote community members. These findings were investigated in the context of functional change, using the uptake of two key substrates (bicarbonate and glucose) as analogues for photosynthesis and respiration respectively. Unlike community abundance, distinct changes in carbon assimilation were detected in dominant members of the picoplankton. In conclusion the data presented suggest that although current microbial communities hold the capacity to respond to elevated CO2, future responses will likely be taxa specific and controlled by wider community dynamics.

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46

Trexler, Ryan Vincent. "Lipid Analysis and Microbial Community Characterization of Subsurface Shale". The Ohio State University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=osu1480679153855158.

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47

McCormick, Paul V. "Patterns of microbial community development in isolated aquatic systems". Thesis, Virginia Polytechnic Institute and State University, 1986. http://hdl.handle.net/10919/101124.

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The purpose of this research was to compare the process of microbial community development in isolated aquatic systems to the MacArthur-Wilson equilibrium theory of island biogeography and suggest alternative models for the observed patterns. Water-filled plastic containers were used as aquatic islands to investigate the colonization dynamics of protozoan, algal and microinvertebrate taxa. Polyurethane foam (PF) artificial substrates were used as sampling devices in these systems. Distance from another aquatic system was found to have a significant effect colonization in these systems. Exclusion of macroscopic organisms, however, did not strongly affect the process of microbial community development in these systems. The results of short-term (36 day) and long-term (170 day) experiments suggest that no protracted species equilibrium is achieved in these systems; an initial asymptotic increase in species richness was followed by large oscillations in the number of species. There was no correlation between rates of species colonization and the number of species present. Rates of species extinction, however, increased with increasing species number. The estimated rate of species colonization was a non-monotonic function of time, increasing during the early stages of colonization and decreasing thereafter. These results, coupled with an analysis of temporal changes in species composition suggest that microbial community development in isolated systems is a deterministic process which may be best explained by an interactive model of species succession.
M.S.

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48

Friedline, Christopher J. "Phylometagenomics: a new framework for uncovering microbial community diversity". VCU Scholars Compass, 2013. http://scholarscompass.vcu.edu/etd/499.

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Microbial communities are recognized as major drivers of global biogeochemical processes. However, the genetic diversity and composition, as well as processes leading to the origin and diversification of these communities in space and time, are poorly understood. Character- ization of microbial communities using high-throughput sequencing of 16S tags shows that Operational Taxonomic Unit (OTU) abundances can be approximated by a gamma distribu- tion, which suggests structuring around small numbers of highly abundant OTUs and a large proportion of rare OTUs. The current methods used to characterize how communities are structured rely on multivariate statistics, which operate on pair-wise distance matrices. My analyses demonstrate that use of these methods, by reducing a highly-dimensional data set (tens of samples, thousands of OTUs), results in a significant loss of information. I demon- strate that, in some cases, up to 80% of the least abundant OTUs may be removed while still recovering the same community relationships; this indicates these metrics are biased toward the highly abundant OTUs. I also demonstrate that the observed patterns of OTU abundance detected from microbial communities can be robustly modeled using techniques similar to those used to model the presence and absence of genes in genome evolution. Using simulation studies, I show that general Markov models in a Bayesian inference framework out- perform traditional, multivariate ecological methods in recovering true community structure. Applying this new methodology to Atlantic Ocean communities uncovered a distance-decay effect which was not revealed by the traditional methods; applying to communities discov- ered on Hog Island point toward mechanisms of thicket establishment. Although the ocean data set operated on a much larger, continental scale, characterization of the sequence data generated from the nutrient-poor soil on Hog Island, a barrier island off the Virginia coast, allows for a better characterization of the processes affecting these communities on a much smaller scale. Finally, using 16S data from the Human Vaginal Microbiome Project, gener- ated here at VCU under the umbrella of the overall NIH HMP initiative, I give examples of the quality control, analysis and visualization pipeline that I developed to support the efforts of this project. In conclusion, my analyses of the metagenomic sequence data from bacterial communities sampled from different environments demonstrate that the proper identification of the biological processes influencing these communities requires the development and im- plementation of new statistical and computational methodologies that take advantage of the extensive amount of information generated in next-generation, high-throughput sequencing projects.

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Cuthbertson, Leah Forbes. "The microbial community ecology of the cystic fibrosis lung". Thesis, King's College London (University of London), 2015. https://kclpure.kcl.ac.uk/portal/en/theses/the-microbial-community-ecology-of-the-cystic-fibrosis-lung(7ae2ec94-0325-4d0c-93a3-449da53f6b1f).html.

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Respiratory failure, due to infection and concomitant inflammation is the major cause of morbidity and mortality in people suffering from the genetic disorder, cystic fibrosis (CF). Consequently, the CF Foundation currently estimates that patients with CF have a median predicted life expectancy of only 41.1 years. Understanding the relationship between the complex and diverse bacterial community present within the lower respiratory tract and patient outcomes has therefore become a top priority. Through the use of next generation sequencing technologies (Roche 454 and Illumina MiSeq) and ecological statistics and modelling, the complex relationships between the bacterial community within the CF lung and host related clinical factors were investigated. By first establishing guideline methodologies for the reduction of bias in the collection, storage and treatment of respiratory samples, this thesis aimed to use large scale spatial and longitudinal studies to investigate key relationships between the bacterial community and clinical factors. It has been well established that a complex and diverse bacterial community exists within the CF lung. Spatial sampling revealed key relationships between the bacterial community and other diagnostic parameters including, FEV1, gender, and clinic location. Longitudinal sampling aimed principally to investigate CF pulmonary exacerbations (CFPE), implicated in the progressive loss of lung function associated with CF lung disease. Over the course of a CFPE the common bacterial taxa show resistance to perturbations while the rare taxa show resilience. Through this investigation, Veillonella parvula was identified as a potential bioindicator of CFPE, introducing the potential for a rapidly testable parameter for clinicians to identify a CFPE. This finding could provide one of the most important recent developments in CF therapy.

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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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Tesi sul tema "Impact on microbial community"

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