Дисертації: "Microbial ecology"

1

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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2

Yates, Philippa Dawn. "Microbial ecology of windrow composting." Thesis, University of Hull, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.418762.

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3

夏江瀛 and Kong-ying Ha. "Microbial ecology of arid environments." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2013. http://hdl.handle.net/10722/193421.

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Deserts comprise the largest terrestrial biome, making up approximately one third of the Earth’s land mass. They are defined in terms of moisture deficit using the Aridity Index with values <1. A further delineation based on mean annual temperatures into hot (>18°C), cold (<18°C) and polar (<0°C) deserts is employed. In the absence of significant macrobiota, microorganisms are key to desert ecosystems. They are located in near-surface soils, and include a widespread hypolithic mode of colonization, where microbial biomass develops on the ventral surfaces of quartz and other translucent stones. A literature review was conducted to appreciate the status of existing knowledge on these systems. Amongst unresolved questions that arose were the following, which form the basis of this inquiry: What are the taxonomic and functional differences between hypolithic and near-soil communities? Do hypolithic communities assemble differently in deserts of different xeric and thermal stresses? Can the keystone cyanobacterial taxa be cultivated under laboratory conditions to allow manipulative studies? The Mojave Desert in the USA was used as a model to test the extent to which hypolithic and near-surface soil communities vary in both taxonomic and putative functional composition. A common phylogenetic marker (16S rRNA gene ITS region) was used to conclude that soil and hypolithic communities are significantly different, although both were dominated by cyanobacteria. The ubiquitous hypolithic cyanobacterial taxon Chroococcidiopsis was encountered, although communities appeared to be dominated functionally by the diazotrophic genus Nostoc. The data strongly suggest that carbon and nitrogen fixation pathways in desert soils are mediated by the same taxa, although heterotrophic pathways may differ and support distinct assemblages of heterotrophic bacteria. An opportunistic sampling of three sites along a latitudinal gradient in China allowed some inference about adaptations in hypoliths. Communities recovered from the cold Tibetan Desert, Taklamakan Basin Desert, and exposed hillsides in tropical Hong Kong, did not display significant differences at the level of community assembly. This suggests that hypolithic taxa undergo strong selection for xeric and extreme thermal stresses. A cultivation strategy for the keystone taxon Chroococcidiopsis has been lacking and is an obvious impediment to manipulative physiological studies. Here various methods for laboratory cultivation were attempted. This bacterium proved extremely fastidious and displayed slow growth rates. After extensive trials a novel cultivation method was developed. This involved using plastic petri dishes containing liquid growth medium, into which glass coverslips were introduced along with cell suspensions. The surface energy of glass served as a nucleation site for Chroococcidiopsis biofilms (which do not develop on plastic surfaces) and this method was evaluated in growth studies as a means of quantifying growth. This research includes key advances to demonstrate that hypoliths and soil, whilst supporting different communities, likely perform similar functional roles in the desert soil. Selection due to the severe environmental stresses results in similar communities across large latitudinal and environmental gradients. The development of a cultivation strategy paves the way for manipulative physiological studies on these important organisms. published_or_final_version Biological Sciences Doctoral Doctor of Philosophy

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4

Fraraccio, Serena <1986&gt. "Microbial ecology of biotechnological processes." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2015. http://amsdottorato.unibo.it/6913/1/Fraraccio_Serena_tesi.pdf.

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The investigation of phylogenetic diversity and functionality of complex microbial communities in relation to changes in the environmental conditions represents a major challenge of microbial ecology research. Nowadays, particular attention is paid to microbial communities occurring at environmental sites contaminated by recalcitrant and toxic organic compounds. Extended research has evidenced that such communities evolve some metabolic abilities leading to the partial degradation or complete mineralization of the contaminants. Determination of such biodegradation potential can be the starting point for the development of cost effective biotechnological processes for the bioremediation of contaminated matrices. This work showed how metagenomics-based microbial ecology investigations supported the choice or the development of three different bioremediation strategies. First, PCR-DGGE and PCR-cloning approaches served the molecular characterization of microbial communities enriched through sequential development stages of an aerobic cometabolic process for the treatment of groundwater contaminated by chlorinated aliphatic hydrocarbons inside an immobilized-biomass packed bed bioreactor (PBR). In this case the analyses revealed homogeneous growth and structure of immobilized communities throughout the PBR and the occurrence of dominant microbial phylotypes of the genera Rhodococcus, Comamonas and Acidovorax, which probably drive the biodegradation process. The same molecular approaches were employed to characterize sludge microbial communities selected and enriched during the treatment of municipal wastewater coupled with the production of polyhydroxyalkanoates (PHA). Known PHA-accumulating microorganisms identified were affiliated with the genera Zooglea, Acidovorax and Hydrogenophaga. Finally, the molecular investigation concerned communities of polycyclic aromatic hydrocarbon (PAH) contaminated soil subjected to rhizoremediation with willow roots or fertilization-based treatments. The metabolic ability to biodegrade naphthalene, as a representative model for PAH, was assessed by means of stable isotope probing in combination with high-throughput sequencing analysis. The phylogenetic diversity of microbial populations able to derive carbon from naphthalene was evaluated as a function of the type of treatment.

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5

Fraraccio, Serena <1986&gt. "Microbial ecology of biotechnological processes." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2015. http://amsdottorato.unibo.it/6913/.

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The investigation of phylogenetic diversity and functionality of complex microbial communities in relation to changes in the environmental conditions represents a major challenge of microbial ecology research. Nowadays, particular attention is paid to microbial communities occurring at environmental sites contaminated by recalcitrant and toxic organic compounds. Extended research has evidenced that such communities evolve some metabolic abilities leading to the partial degradation or complete mineralization of the contaminants. Determination of such biodegradation potential can be the starting point for the development of cost effective biotechnological processes for the bioremediation of contaminated matrices. This work showed how metagenomics-based microbial ecology investigations supported the choice or the development of three different bioremediation strategies. First, PCR-DGGE and PCR-cloning approaches served the molecular characterization of microbial communities enriched through sequential development stages of an aerobic cometabolic process for the treatment of groundwater contaminated by chlorinated aliphatic hydrocarbons inside an immobilized-biomass packed bed bioreactor (PBR). In this case the analyses revealed homogeneous growth and structure of immobilized communities throughout the PBR and the occurrence of dominant microbial phylotypes of the genera Rhodococcus, Comamonas and Acidovorax, which probably drive the biodegradation process. The same molecular approaches were employed to characterize sludge microbial communities selected and enriched during the treatment of municipal wastewater coupled with the production of polyhydroxyalkanoates (PHA). Known PHA-accumulating microorganisms identified were affiliated with the genera Zooglea, Acidovorax and Hydrogenophaga. Finally, the molecular investigation concerned communities of polycyclic aromatic hydrocarbon (PAH) contaminated soil subjected to rhizoremediation with willow roots or fertilization-based treatments. The metabolic ability to biodegrade naphthalene, as a representative model for PAH, was assessed by means of stable isotope probing in combination with high-throughput sequencing analysis. The phylogenetic diversity of microbial populations able to derive carbon from naphthalene was evaluated as a function of the type of treatment.

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6

Santos, Anderson Secco dos [UNESP]. "Condicionamento de um subsolo exposto no cerrado por meio de resíduos e da revegetação." Universidade Estadual Paulista (UNESP), 2015. http://hdl.handle.net/11449/138448.

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Made available in DSpace on 2016-05-17T16:51:22Z (GMT). No. of bitstreams: 0 Previous issue date: 2015-08-14. Added 1 bitstream(s) on 2016-05-17T16:54:58Z : No. of bitstreams: 1 000864109.pdf: 2175142 bytes, checksum: fff8a8ccb57c55f7ae5759469cbc46dd (MD5) Para que um subsolo exposto tenha restabelecido, mesmo que parcialmente, a dinâmica de seus atributos na camada superficial e, com isto, apresente condições para receber e dar suporte à vegetação de cerrado é necessário a utilização de técnicas específicas. Para acelerem esta etapa uma alternativa seria a introdução de resíduos, como as macrófitas aquáticas removidas das águas de represas de usinas hidrelétricas, como resíduo orgânico e cinza de bagaço de cana-de-açúcar produzida em usinas sucroalcooleiras, como resíduo agroindustrial. Desta forma, o objetivo do trabalho foi o condicionamento de um subsolo exposto no Cerrado por meio de resíduos e da revegetação. A área foco tem extensão de 10,66 km 2, em área contínua, localizada à margem direita do Rio Paraná e degradada na década de 60 durante construção da Usina Hidrelétrica de Ilha Solteira-SP. Realizou-se a caracterização inicial da área e as demais avaliações foram feitas após 12 e 24 meses da implantação do experimento. A área foi gradeada (grade pesada), para rompimento do encrostamento superficial e escarificada, à profundidade média de 0,37 m. A área foi novamente gradeada para desmanchar os torrões produzidos durante a subsolagem e para a incorporação dos resíduos (macrófitas aquáticas e cinza de cana-de-açúcar) distribuídos a lanço. Após seis meses, mudas de dez espécies arbóreas de Cerrado foram introduzidas aleatoriamente, no espaçamento de plantio 4,0 x 5,0 m, totalizando 1.080 mudas. O delineamento experimental foi o de blocos ao acaso, em esquema fatorial 3 x 4, sendo os tratamentos composto de 3 doses de macrófitas (0, 16 e 32 t ha -1 ) e 4 doses de cinza (0, 15, 30 e 45 t ha -1 ), totalizando 12 tratamentos, com 03 repetições, estabelecidos em parcelas de 20 x 30 m (600 m 2 ), separadas por faixas de 5 m de largura. Após 24 meses da instalação do experimento... To restore in an exposed subsoil, even partially, the dynamics of their attributes in the surface layer and, thus, presents conditions to receive and support the Cerrado vegetation, the use of specific techniques is required. To accelerate this step, an alternative could be the introduction of waste, such as aquatic weeds removed from water reservoirs of hydro power plants, as an organic waste, and ash sugarcane bagasse produced in sugarcane mills, as an agroindustrial waste. Thus, the objective was the conditioning of exposed subsoil in the Cerrado, through organic and inorganic waste addition and revegetation. The focus area has an extension of 10.66 km 2, in continuous area, located on the right bank of the Paraná River and degraded in the 60s during construction of the Ilha Solteira hydroelectric power. It conducted the initial characterization of the area and other evaluations were done after 12 and 24 months of implementation of the experiment. The area was fenced (heavy grade), to break the surface crusting, and scarified, at the average depth of 0.37 m. The area was again barred to break up the clods produced during the subsoil and the incorporation of waste (aquatic weeds and sugarcane ash) happened after them being spread on the subsoil surface. After six months, seedlings of ten Cerrado tree species were introduced randomly, in planting spacing of 4.0 x 5.0 m, totaling 1,080 seedlings. The experimental was a randomized block in a 3 x 4 factorial design, consisting of 3 doses of macrophytes (0, 16 and 32 t ha -1 ) and 4 ash levels (0, 15, 30 and 45 t ha -1 ), a total of 12 treatments, with 03 repetitions, established in plots 20 x 30 m (600 m 2 ), separated by 5 m wide ranges. After 24 months of experiment installation were evaluated: density, macro and microporosity, fertility, height and diameter of the plants, released CO 2 -carbon (CO 2 -C) and number of spores of arbuscular ...

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7

Santos, Anderson Secco dos. "Condicionamento de um subsolo exposto no cerrado por meio de resíduos e da revegetação /." Ilha Solteira, 2015. http://hdl.handle.net/11449/138448.

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Orientador: Ana Maria Rodrigues Cassiolato Co-orientador: Kátia Luciene Maltoni Banca: Renato Alberto Momesso Franco Banca: Carolina dos Santos Batista Bonini Resumo: Para que um subsolo exposto tenha restabelecido, mesmo que parcialmente, a dinâmica de seus atributos na camada superficial e, com isto, apresente condições para receber e dar suporte à vegetação de cerrado é necessário a utilização de técnicas específicas. Para acelerem esta etapa uma alternativa seria a introdução de resíduos, como as macrófitas aquáticas removidas das águas de represas de usinas hidrelétricas, como resíduo orgânico e cinza de bagaço de cana-de-açúcar produzida em usinas sucroalcooleiras, como resíduo agroindustrial. Desta forma, o objetivo do trabalho foi o condicionamento de um subsolo exposto no Cerrado por meio de resíduos e da revegetação. A área foco tem extensão de 10,66 km 2, em área contínua, localizada à margem direita do Rio Paraná e degradada na década de 60 durante construção da Usina Hidrelétrica de Ilha Solteira-SP. Realizou-se a caracterização inicial da área e as demais avaliações foram feitas após 12 e 24 meses da implantação do experimento. A área foi gradeada (grade pesada), para rompimento do encrostamento superficial e escarificada, à profundidade média de 0,37 m. A área foi novamente gradeada para desmanchar os torrões produzidos durante a subsolagem e para a incorporação dos resíduos (macrófitas aquáticas e cinza de cana-de-açúcar) distribuídos a lanço. Após seis meses, mudas de dez espécies arbóreas de Cerrado foram introduzidas aleatoriamente, no espaçamento de plantio 4,0 x 5,0 m, totalizando 1.080 mudas. O delineamento experimental foi o de blocos ao acaso, em esquema fatorial 3 x 4, sendo os tratamentos composto de 3 doses de macrófitas (0, 16 e 32 t ha -1 ) e 4 doses de cinza (0, 15, 30 e 45 t ha -1 ), totalizando 12 tratamentos, com 03 repetições, estabelecidos em parcelas de 20 x 30 m (600 m 2 ), separadas por faixas de 5 m de largura. Após 24 meses da instalação do experimento... Abstract: To restore in an exposed subsoil, even partially, the dynamics of their attributes in the surface layer and, thus, presents conditions to receive and support the Cerrado vegetation, the use of specific techniques is required. To accelerate this step, an alternative could be the introduction of waste, such as aquatic weeds removed from water reservoirs of hydro power plants, as an organic waste, and ash sugarcane bagasse produced in sugarcane mills, as an agroindustrial waste. Thus, the objective was the conditioning of exposed subsoil in the Cerrado, through organic and inorganic waste addition and revegetation. The focus area has an extension of 10.66 km 2, in continuous area, located on the right bank of the Paraná River and degraded in the 60s during construction of the Ilha Solteira hydroelectric power. It conducted the initial characterization of the area and other evaluations were done after 12 and 24 months of implementation of the experiment. The area was fenced (heavy grade), to break the surface crusting, and scarified, at the average depth of 0.37 m. The area was again barred to break up the clods produced during the subsoil and the incorporation of waste (aquatic weeds and sugarcane ash) happened after them being spread on the subsoil surface. After six months, seedlings of ten Cerrado tree species were introduced randomly, in planting spacing of 4.0 x 5.0 m, totaling 1,080 seedlings. The experimental was a randomized block in a 3 x 4 factorial design, consisting of 3 doses of macrophytes (0, 16 and 32 t ha -1 ) and 4 ash levels (0, 15, 30 and 45 t ha -1 ), a total of 12 treatments, with 03 repetitions, established in plots 20 x 30 m (600 m 2 ), separated by 5 m wide ranges. After 24 months of experiment installation were evaluated: density, macro and microporosity, fertility, height and diameter of the plants, released CO 2 -carbon (CO 2 -C) and number of spores of arbuscular ... Mestre

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Louca, Stilianos. "The ecology of microbial metabolic pathways." Thesis, University of British Columbia, 2016. http://hdl.handle.net/2429/59313.

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Microbial metabolic activity drives biogeochemical cycling in virtually every ecosystem. Yet, microbial ecology and its role in ecosystem biochemistry remain poorly understood, partly because the enormous diversity found in microbial communities hinders their modeling. Despite this diversity, the bulk of global biogeochemical fluxes is driven by a few metabolic pathways encoded by a small set of genes, which through time have spread across microbial clades that can replace each other within metabolic niches. Hence, the question arises whether the dynamics of these pathways can be modeled regardless of the hosting organisms, for example based on environmental conditions. Such a pathway-centric paradigm would greatly simplify the modeling of microbial processes at ecosystem scales. Here I investigate the applicability of a pathway-centric paradigm for microbial ecology. By examining microbial communities in replicate "miniature" aquatic environments, I show that similar ecosystems can exhibit similar metabolic functional community structure, despite highly variable taxonomic composition within individual functional groups. Further, using data from a recent ocean survey I show that environmental conditions strongly explain the distribution of microbial metabolic functional groups across the world's oceans, but only poorly explain the taxonomic composition within individual functional groups. Using statistical tools and mathematical models I conclude that biotic interactions, such as competition and predation, likely underlie much of the taxonomic variation within functional groups observed in the aforementioned studies. The above findings strongly support a pathway-centric paradigm, in which the distribution and activity of microbial metabolic pathways is strongly determined by energetic and stoichiometric constraints, whereas additional mechanisms shape the taxonomic composition within metabolic guilds. These findings motivated me to explore concrete pathway-centric mathematical models for specific ecosystems. Notably, I constructed a biogeochemical model for Saanich Inlet, a seasonally anoxic fjord with biogeochemistry analogous to oxygen minimum zones. The model describes the dynamics of individual microbial metabolic pathways involved in carbon, nitrogen and sulfur cycling, and largely explains geochemical depth profiles as well as DNA, mRNA and protein sequence data. This work yields insight into ocean biogeochemistry and demonstrates the potential of pathway-centric models for microbial ecology. Science, Faculty of Graduate

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Wong, Ka-yu, and 黃家愉. "Molecular ecology of lithic microbial communities." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2010. http://hub.hku.hk/bib/B43703951.

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10

Simmons, Susan. "The microbial ecology of acidic environments." Thesis, University of Warwick, 2001. http://wrap.warwick.ac.uk/58964/.

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The microflora of two acidic environments was investigated using analysis of 16S rDNA amplified by the polymerase chain reaction (PCR) from environmental DNA. These environments had different chemical characteristics from most of the acidic environments studied by others. The first sample site, a coal spoil (Birch Coppice, Warwickshire), might have been expected to produce niches enriched in humic matter. The second, comprising geothermal vents on the Island of Vulcano, was unusual for natural acidic environments since it was saline. Three vent regions of different temperatures (30°C, 45°C and 80°C) were examined. Prior to the 16S rDNA analysis of the sites, a brief investigation into selection of a suitable method of DNA extraction was carried out. A bead-beating method and a chemical lysis/freeze-thaw method were compared. With regard to clone types found via each method, there was little qualitative difference. DNA was extracted from the two sites and 16S rRNA genes were amplified by PCR. PCR products were ligated and competent E. coli cells were transformed to produce clone libraries. Restriction fragment length polymorphisms (RFLPs) were examined and representatives of each RFLP type were sequenced and analysed with reference to RNA gene sequence data bases. The coal spoil clone library was dominated by sequences related to those from uncultured actinobacteria, particularly those found previously in peat bogs and various soils. Representatives of some well-known acidophiles were also found (e.g. Leptospirillum species). The clone bank from the saline, geothermal site DNA comprised sequences from acidophiles capable of growth at the respective temperatures of different samples. The lowest temperature samples produced sequences from a novel Acidithiobacillus species and also indicated a novel species probably related to Thiobacillus prosperus (which was isolated previously from Vulcano). A high temperature sample gave sequences from archaeal acidophiles, Acidianus brierleyi and, previously isolated from Vulcano, Acidianus infernus and Thermoplasma volcanium. Where the clone banks revealed the presence of novel organisms, attempts were made to isolate and characterise them. The novel actinobacteria did not appear to grow in laboratory enrichment cultures. The novel Acidithiobacillus species and two novel Thiobacillus prosperus-like species were characterised.

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Hoy, Christine Muriel. "The microbial ecology of necrotising enterocolitis." Thesis, University of Aberdeen, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.400663.

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Abnormal gastrointestinal colonisation has been implicated in the development of necrotising enterocolitis (NEC). Organisms capable of rapid fermentation of excess carbohydrate in the small bowel were postulated to produce adverse intraluminal conditions leading to intestinal injury. Quantitative culture of duodenal aspirates from 122 very low birth weight newborns revealed a high prevalence of Gram-negative colonisation, with counts up to 108 cfu/g. Gram-negative colonisation occurred in infants who had been fed, increased with postnatal age and was associated with a longer stay on the neonatal unit. Molecular typing of E. coli, Klebsiella spp. and Enterobacter spp. demonstrated marked temporal clustering of indistinguishable strains. Colonisation with particular strains of Enterobacteriaceae was not associated with subsequent development of NEC. Faecal flora, from NEC cases and control infants, comprised predominantly aerobic Gram-negative organisms and enterococci, with anaerobes isolated infrequently. Prior to clinical onset of confirmed NEC, Enterobacteriaceae isolates remained at high levels or increased, while there was a significant fall in enterococci. This fall in enterococci was not apparent in infants with suspected NEC. Asymptomatic infants were colonised with Enterobacteriaceae isolates indistinguishable from NEC cases, but enterococci were also present in high numbers, often being the predominant strain. One E. coli from a post-mortem peritoneal sample, was fully induced for b-galactosidase expression. Isolates identical by PFGE, from the same infant and controls were not induced. Other strains, from NEC cases and control infants, showed no difference in b-galactosidase activity. NEC appears not to be associated with colonisation with particular strains of Enterobacteriaceae, but the decline in enterococci preceding NEC should be investigated.

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Panas, Panayiotis. "Molecular microbial ecology of organophosphonate degradation." Thesis, University of Ulster, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.414100.

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Oates, Angela. "The microbial ecology of chronic wounds." Thesis, University of Manchester, 2011. https://www.research.manchester.ac.uk/portal/en/theses/the-microbial-ecology-of-chronic-wounds(54e6dce0-cffa-4f03-9701-7bc1ea907af9).html.

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Within the five experimental chapters of this doctoral thesis (i) the eubacterial diversity of the microbiota of chronic wounds and healthy skin was investigated, (ii) biofilm formation and associated coaggregation interactions of wound and skin-associated bacterial isolates was examined, (iii) formulation of media which reproduced some aspects of the nutritional conditions of wounds and healthy skin were developed, (iv) novel wound biofilm models were developed and validated and (v) microbial population interactions associated with healthy skin and chronic wounds were investigated using a novel model system. (i) The microbial diversity of chronic wounds and contralateral skin swabs was investigated using culture, denaturing gradient gel electrophoresis (DGGE) and microscopy. Intrapersonal analysis identified that non-infected wounds had a proportionally higher incidence of bacteria which were identified on contralateral healthy skin according to DGGE analysis when compared to infected wounds indicating that taxonomically distinct consortia are associated with infection. Microcolonies and putative biofilms structures were identified in both culture-defined infected and non-infected wounds indicating that the presence of biofilms may not be linked to infection. (ii) By assessing pair-wise combinations of skin and wound-associated bacteria, the role of coaggregation in the formation of wound polymicrobial communities was assessed using a quantitative spectrophotometric assay. Aggregation interactions were weak or not detectable, apart from those associated with Corynebacterium xerosis. This bacterium produced a high autoaggregation score (c. 50%). The limited coaggregation interactions suggest that coaggregation may be comparatively unimportant in the development of wound biofilms. (iii) In order to facilitate the development of biofilm models specific to chronic wounds, the formulation of representative growth media is important in order to reproduce the in situ nutrient environment. Therefore complex, artificial sweat and serum media broadly reflective of the nutrient availability in wounds and healthy skin were developed and validated based upon their ability to support realistic phenotypes (assessed by proteomics) and the growth of a range bacterial isolates. Developed media maintained the sessile growth the test bacteria and produced broadly similar proteomic profiles to foetal calf serum. (iv) Two novel model systems were developed to study cross-sectional population interactions and to investigate longitudinal population development of wound consortia and biofilm formation. A fine celled foam (FCF) multi-well wound model and a multiple membrane FCF model maintained dynamic steady state of axenic and mixed populations of bacteria associated with chronic wounds and supported the development of biofilms. (v) The FCF multi-well wound model was used to investigate population interactions in environments broadly reflective of healthy skin and wounds. When grown in artificial sweat prior colonisation with Staphylococcus saprophyticus resulted in a significant reductions in methicillin resistant Staphylococcus aureus (99%) and P. aeruginosa (75%) whilst prior colonisation by C. xerosis resulted in a significant reduction in P. aeruginosa (91%) only. However no significant reductions in pathogenic bacteria were noted in artificial serum indicating colonisation resistance could be simulated in the model and the outcome of immigration was markedly influenced by the species of established bacterium and nutrient availability.

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Mwatha, Wanjiru Elizabeth. "Microbial ecology of Kenyan soda lakes." Thesis, University of Leicester, 1991. http://hdl.handle.net/2381/35400.

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A combination of geological, geographical and climatic conditions; favour the evolution of stable alkaline environments, such as the soda lakes of East African Rift Valley. These lakes are often saline as well as alkaline. Soda lakes are potentially the best sources of alkaliphilic microoganisms, but they are virtually unexplored. The few studies done indicate that soda lakes have very high primary productivity, due to the dense population of phototrophic microorganisms, either cyanobacteria or phototrophic eubacteria or both. Soda lakes are therefore, likely to support a large population of organotrophic bacteria. A quantative study of major nutrients, cyanobacteria and organotrophic bacteria was undertaken from Oct. 1988 to Sept 1989 on Lakes Bogorla, Elmenteita, Nakuru and to a lesser extent Lake Magadi. The cyanobacteria, especially Spirulina platensis were the major primary producers in the less saline lakes (Bogorla, Nakuru and Elmenteita), while the photosynthetic bacteria probably Ectothiorhodospira are the major primary producers in the more saline Lake Magadi. The algal population was significantly limited by phosphate, nitrogen and conductivity levels. The population of alkaliphilic organotrophic bacteria in the Kenyan soda lakes was 10s CFU/ml (viable count) and total bacterial count of l0'.;-l0'.;bacteria/ml. The organotrophic bacterial populationwas also limited by total phosphate, total nitrogen and conductivity levels, and was determined more by the water chemistry than by organic carbon availability. Majority of the aerobic organotrophic bacteria were Gram-negative comprising of six distinct clusters when analysed using the procedures of numerical taxonomy. These Gram-negative alkaliphilic bacteria formed clusters distinct from any of the known gram-negative bacteria tested and are likely to be totally new organisms. Chemotaxonomic studies showed that these organisms possesed ubiquinones with 7 or 8 isoprene units, and the polar lipids lacked glycolipids but had large amounts of phosphclipids. The % mol G+C of the gram-negative alkaliphiles ranged from 53.1 to 65.0 (Tm). Organisms in the same cluster group were related at 60% homology by DNA-DNA hybridization; indicating that the majority of the Gram-negatives may belong to a large supraspecific grouping. The few Gram-positive isolates formed less distinct clusters, and two Gram-positive isolates N12 and N16 formed spores and closely resembled isolates WN11 and WN13 (Weisser & Truper, 1985) from Wadi Natrun which have been positively identified as Bacillus spp. Arcbaeobacteria were not isolated Lakes Bogoria, Elmenteita and Nakuru. In the more saline Lake Magadi, eubacterial haloalkaliphlies dominated at low conductivity and archaeobacterial haloalkaliphiles dominated at high conductivity. A new haloalkaliphilic archaeobacterium which has rod-shaped, gas-vacuolated cells and different polar lipid patterns from the 3 Natronobacterium species already described (Ross, et al, 1985) was isolated from Lake Magadi. A new species, 'Natronobacterium vacuolata' is proposed. A coccoid Gram-positive organism, MU5 was also isolated from Lake Magadi, and resembled the type species in the genus Natronococcus. However, polar lipid patterns and SDS-PAGE gels show that MU5 is not identical to SP4.

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15

Wong, Ka-yu. "Molecular ecology of lithic microbial communities." Click to view the E-thesis via HKUTO, 2010. http://sunzi.lib.hku.hk/hkuto/record/B43703951.

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16

Korin, Tetyana Olegivna. "Microbial ecology of anaerobic biodegradation of benzoate : microbial communities and processes." Thesis, University of Newcastle upon Tyne, 2018. http://hdl.handle.net/10443/4138.

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Microbial conversion of hydrocarbons and other aromatic compounds has been studied extensively under various electron accepting conditions, by investigating cultured microorganisms and by using samples collected directly from diverse environments. However, the functions of the principal microbial organisms taking part in the biodegradation process are not fully understood, especially when the organisms comprise complex microbial communities. The focus of the research reported here is the identification of a microbial community enriched during methanogenic benzoate degradation using inocula from two contrasting environments, river sediment and oil sands. Benzoate is a monoaromatic compound used extensively as a model compound in studies of hydrocarbons and other aromatics. The microorganisms which were most abundant and which had been shown by earlier work to take part in syntrophic benzoate degradation were investigated. Their functional potential was also investigated using metagenomic approaches. It was found that enrichments from different environments contained different microbial communities, different members of which were thought to take part in the syntrophic degradation of benzoate. In benzoate enrichments with Tyne sediment, two types of methanogen were enriched: hydrogenotrophic Methanofollis and acetoclastic Methanosaeta. In contrast, in oil sands enrichments with benzoate, the most abundant methanogens were metabolically versatile Methanosarcina spp. The primary benzoate degrader in enrichments with Tyne sediment was Syntrophus, most likely Syntrophus aciditrophicus as was suggested by 99% sequence identity. In oil sands enrichments the supposed primary benzoate degrader was an unknown species of Desulfotomaculum. Syntrophic acetate oxidisers (e.g. Syntrophomonas) were not found in abundance in Tyne sediment cocultures with benzoate. Instead, the conversion of acetate into hydrogen and carbon dioxide appeared to be mediated by acetoclastic methanogenesis, which utilised acetate directly as has been evidenced by the enrichment of acetoclastic methanogens Methanosaeta and Methanosarcina. In the oil sands, syntrophic acetate oxidation was likely to have been carried out by the known acetoclastic methanogen Methanosarcina. However, it was conjectured that unclassified Sphingobacteriales clone WCHB1.69 could have taken part in the acetate utilisation. Regardless of the observed differences between the microbial communities, investigation of the metabolic potential showed the presence of the same pathways, key genes and enzymes that are known to take part in the degradation of benzoate iv and the production of methane. The same four pathways were found in both sets of methanogenic enrichments, namely the benzoate degradation pathway and hydrogenotrophic, acetoclastic and methylotrophic methanogenesis pathways. The same key genes that take part in benzoate degradation, namely dienoyl-CoA hydratase (dch), β-hydroxyacyl-CoA dehydrogenase (had) and β-oxoacyl-CoA hydrolase (oah) were found in high abundance in both enrichment cultures. The same key genes coding for essential proteins involved in methanogenesis were also found in high abundance in all the methanogenic archaea tested in both Tyne sediment and oil sands methanogenic enrichment cultures with benzoate, namely tetrahydromethanopterin S-methyltransferase (mtrA), methyl-coenzyme M reductase A (mcrA) and heterodisulfide reductase subunit A (hdrA). Other genes found in high abundance were methanogenic pathway specific genes, namely formylmethanofuran dehydrogenase, subunit A (fmdA) involved in hydrogenotrophic methanogenesis, phosphate acetyltransferase (pta), acetate kinase (ackA) and acetyl-CoA synthetase (ACSS) involved in acetoclastic methanogenesis and coenzyme M methyltransferase (mtaA) involved in methylotrophic methanogenesis. These results suggest that the functional capabilities of the microorganisms in different environments remain constant but the communities might vary from one environment to another. In addition, a comparison was made between two sequencing platforms, Illumina MiSeq and Ion Torrent PGM. The result suggested that, overall, the two sequencers concurred. The sequencers found the same most abundant taxa, but there were instances where both sequencers detected some microorganisms which were not detected by the other sequencer. Syntrophic degradation of many different types of compound such as alcohols, saturated and unsaturated fatty acids, hydrocarbons and aromatic compounds has been identified in methanogenic environments, suggesting the global importance of this process and of the microorganisms involved. Further work on the syntrophic processes, including methanogenesis, would clarify which microorganisms take part in syntrophy, in which environments syntrophy occurs, what substrates can be utilised, which members of the microbial community participate and how. Such knowledge would be useful in understanding the processes that attenuate the contamination of industrial land and the development of strategies for bioremediation. A quantitative model of syntrophic biodegradation could also assist in understanding the processes that release greenhouse gases. There is also a likelihood that microbial degradation could find a use in the development of sustainable and environmentally innocuous sources of energy.

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17

Mikucki, Jill Ann. "Microbial Ecology of an Antarctic Subglacial Environment." Thesis, Montana State University, 2005. http://etd.lib.montana.edu/etd/2005/mikucki/MikuckiJ1205.pdf.

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The research presented in this dissertation focused on the microbial ecology of the subglacial discharge from the Taylor Glacier in the McMurdo Dry Valleys, Antarctica. The major objectives of my research were to 1) define the biogeochemistry of the subglacial outflow 2) describe the microbial diversity of the subglacial outflow and 3) examine the impact of subglacial outflow on the geochemistry and biology of the west lobe of Lake Bonney, a lake that abuts the glacier. The subglacial outflow from the Taylor Glacier is known as Blood Falls owing to a visible accumulation of iron-oxides at the point where it flows from the snout of the glacier. The subglacial reservoir is thought to originate from the Pliocene Epoch (~5 Mya) when the dry valleys were fjordlands. The episodic release of subglacial water at Blood Falls provides a sample of what is believed to be ancient seawater trapped in the upper Taylor Valley and eventually covered by the Taylor Glacier as it advanced. Biogeochemical measurements, culture-based techniques, and molecular analysis (based on 16S rDNA sequences), were used to characterize microbes and chemistry associated with the subglacial outflow. Culture and molecular-based techniques, along with geochemical data, indicate the presence of a diverse chemoautotrophic and heterotrophic bacterial assemblage that utilizes iron and sulfur minerals for growth. 16S rDNA clone library phylotypes and cultured isolates were related to organisms that inhabit permanently cold environments. The biological and geochemical component of the ancient outflow changes as it travels from the subglacial environment to the moat of the west lobe of Lake Bonney and eventually into the saline deep water in the lake proper. The bottom water of the west lobe of Lake Bonney is geochemically similar to ancient subglacial outflow, but the microbial diversity in the two systems is distinct, and ancient subglacial brine does not appear to provide the microbial seed for the deep water of Lake Bonney. Collectively, my data indicate that the habitat beneath the Taylor Glacier harbors a functional microbial ecosystem that utilizes chemosynthetic and heterotrophicactivity to obtain carbon and energy in the absence of light.

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18

Encarnacion, Gem Deangkinay. "Microbial ecology of nitrifying simulated premises plumbing." Diss., Montana State University, 2012. http://etd.lib.montana.edu/etd/2012/encarnacion/EncarnacionG0512.pdf.

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

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19

Marshall, Joanna. "The microbial ecology of the human foot." Thesis, University of Leeds, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.328884.

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20

Bradshaw, Claire Elizabeth. "Molecular microbial ecology of hospital ward environments." Thesis, Sheffield Hallam University, 2013. http://shura.shu.ac.uk/19390/.

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Evidence indicates that the hospital environment plays a role in hospital acquired infections (HAI). Previous studies have focused on outbreaks and the role of specific culturable pathogens. There is still considerable debate about the role of the environment and the importance of cleaning, therefore more comprehensive culture-independent microbial ecology studies are required. This study aimed to utilise culture-independent methods to characterise the microbial communities in an orthopaedic ward and theatre environment under normal operating conditions, to determine the distribution of different microorganisms, their viability and persistence following routine cleaning. Culture was used to quantify culturable bacteria present and select bacterial populations of interest. Antibiotic-resistance gene specific PCRs were used to investigate the presence of resistance determinants. PCR-DGGE was used to resolve fragments of the 16S rRNA gene from total DNA extractions and the resulting sequence data was used to identify microorganisms present. Cell viability was assessed using RNA as the template for reverse transcriptase PCR-DGGE. Quantification of bacteria on environmental surfaces using culture indicated that near patient surfaces rarely exceeded the recommended 2.5 CFU/cm2 limit, providing evidence that current cleaning regimes employed on these wards are sufficient to keep microbial contamination low. PCR-DGGE showed that sequences similar to Staphylococci dominated the environment, particularly S. hominis, and S. haemolyticus, which were retrieved from the floor before and immediately after cleaning. Antibiotic gene specific PCRs were used to demonstrate the presence of the mecA gene, aminoglycoside modifying enzyme genes and qac genes in isolated environmental non-aureus Staphylococci. This data has highlighted the potential role of this environment as a reservoir of pathogenic Staphylococci. Using PCR-DGGE the orthopaedic wards yielded sequences from DNA and RNA templates similar to species associated with human skin and large intestine. While Staphylococci were shown to dominate most environmental sites, Kocuria and Corynebacterium species were found to be specifically associated with the bed rails. Few Gram negative species were detected by molecular methods or selective culture in the ward environment. Sequences similar to Cupriavidus and Chryseobacterium species were detected in the operating theatre environment using PCR-DGGE, in contrast using culture; Staphylococci were readily isolated from the theatre environment. PCR-DGGE was also used to investigate the presence of fungi in sink drains on an orthopaedic and intensive care ward. While Fusarium species were widely distributed on both wards, sequences similar to Candida were only detected in samples from the ICU wards using PCR-DGGE. When culture was used Candida species were readily grown from both environments. The differences between the species detected using culture and PCR-DGGE suggest that the two techniques should be used together to provide complementary data. Overall PCR-DGGE has been used for direct identification of the dominant viable bacteria and fungi in the hospital environment, to provide an estimate the relative abundance of species, and give an overview of the effect of routine ward cleaning on the bacterial community.

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21

McGenity, Terence John. "Halobacterial phylogeny and salt mine microbial ecology." Thesis, University of Leicester, 1994. http://hdl.handle.net/2381/35396.

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Salt deposits are the remains of ancient hypersaline waters, which presumably supported dense populations of halophilic archaebacteria (halobacteria). Winsford salt mine in Cheshire exploits salt from the Triassic period (195-225 Ma), and Boulby potash mine in Cleveland, which is Permian (225-270 Ma) has been mined since 1973. Halobacteria were isolated in large numbers from brine pools, crusts of recrystallised salt and solution-mining brine, and were even occasionally isolated from rock salt, in both salt mines. Eubacteria from Winsford brine pools are the first described aerobic, non-phototrophic, obligately halophilic eubacteria. Chemotaxonomy showed that most halobacte rial strains were similar to Halobacterium saccharovorum and representatives of the genus Haloarcula. This is a common feature of salt-saturated environments throughout the world. However, definite differences between most strains were revealed by 16S rRNA sequencing. Several salt mine strains were phylogenetically close to Hb. salinarium, despite having previously undescribed polar lipids. Strain Br3, isolated from a solution-mining brine, was most closely related to Halococcus morrhuae, but was subsequently found to be much more similar to a halococcus, isolated from Permian rock salt in Austria. A colourless strain (2Bbr13.2), isolated from a potash core in Boulby salt mine, had unusual polar lipids and morphology, and was also phylogenetically unrelated to any other halobacteria. Analysis of partial sequences demonstrated the diversity of the halobacteria, and served to develop signature sequences, to help in halobacterial identification. Discussion centres on whether salt deposit microorganisms are the descendants of populations entrapped when the salts were deposited, or whether they entered the mine in recent times.

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22

Barton, Andrew David. "Trait-based approaches to marine microbial ecology." Thesis, Massachusetts Institute of Technology, 2011. http://hdl.handle.net/1721.1/69465.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences, 2011. Cataloged from PDF version of thesis. Includes bibliographical references. The goal of this thesis is to understand how the functional traits of species, biotic interactions, and the environment jointly regulate the community ecology of phytoplankton. In Chapter 2, I examined Continuous Plankton Recorder observations of diatom and dinoflagellate abundance in the North Atlantic Ocean and interpreted their community ecology in terms of functional traits, as inferred from laboratory- and field-based data. A spring-to-summer ecological succession from larger to smaller cell sizes and from photoautotrophic to mixotrophic and ieterotrophic phytoplankton was apparent. No relationship between maximum net growth rate and cell size or taxonomy was found, suggesting that growth and loss processes nearly balance across a range of cell sizes and between diatoms and dinoflagellates. In Chapter 3, I examined a global ocean circulation, biogeochemistry, and ecosystem model that indicated a decrease in) phytoplankton diversity with increasing latitude, consistent with observations of many marine and terrestrial taxa. Ii the modeled subpolar oceans, seasonal variability of the environment led to the competitive exclusion of phytoplankton with slower growth rates and to lower diversity. The relatively weak seasonality of the stable subtropical and tropical oceans in the global model enabled long exclusion timescales and prolonged coexistence of multiple phytoplankton with comparable fitness. Superimposed on this meridional diversity decrease were "hot spots" of enhanced diversity in soc regions of energetic ocean circulation which reflected a strong influence of lateral dispersal. In Chapter 4, I investigated how small-scale fluid turbulence affects phytoplankton nutrient uptake rates and community structure in an idealized resource competition model. The flux of nutrients to the cell and nutrient uptake are enhanced by turbulence, particularly for big cells in turbulent conditions. Yet with a linear loss form of grazing, turbulence played little role in regulating model community structure and the smallest cell size outcompeted all others because of its significantly lower R* (the minimum nutrient requirement at equilibrium). With a quadratic loss form of grazing, however, the coexistence of many phytoplankton sizes was possible and turbulence played a role in selecting the number of coexisting size classes and the dominant size class. The impact of turbulence on community structure in the ocean may be greatest in relatively nutrient-deplete regions that experience episodic inputs of turbulence kinetic energy. by Andrew David Barton. Ph.D.

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23

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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24

Travis, Emma Rachel. "Microbial ecology of soil contaminated with trinitrotoluene." Thesis, University of Cambridge, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.613973.

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25

Post, Richard D. "Decomposition and microbial ecology in roadside soils." Thesis, London South Bank University, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.334601.

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26

Monaghan, Emma M. "Microbial ecology of the sheep mammary gland." Thesis, University of Warwick, 2015. http://wrap.warwick.ac.uk/69096/.

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Intramammary infections (IMI) in sheep have a major economic impact through reduced milk production, premature culling and even death of ewes. This study hypothesizes that the sheep mammary gland could host a microbiome with certain members affecting SCC. Previous studies have been cross-sectional, using only one sample per subject and not conducted in sheep. This limits understanding causality; that is, how infection develops and what triggers development of disease. A longitudinal study of 30 sheep, each with two mammary gland halves, collected over 8 weeks, provided 379 milk samples and data on ewe parity and milk SCC. DNA was extracted from milk samples and processed using a bacterial 16S rRNA gene targeted PCR. Bacterial community diversity was visualised using denaturing gradient gel electrophoresis (DGGE). DGGE fingerprints were analysed in a mixed effects regression model to identify associations between individual DGGE bands and changes in SCC. Those bands associated with SCC were sequenced. Corynebacterium efficiens, Psychrobacter maritimus, Streptococcus uberis, Burkholderia cepacia, Fusobacterium necrophorum, Trueperella pyogenes, Pseudomonas chlororaphis and Psychrobacter faecalis were significantly associated with a higher SCC. Achromobacter xylosoxidans, Nocardia globerula or Rhodococcus qingshengii, Atopostipes suicloacalis, Mannheimia haemolytica, Jeotgalicoccus psychrophilus and Sharpea azabuensis were significantly associated with a lower SCC. A protocol to analyse all study samples using Illumina MiSeq sequencing was developed to elucidate the complex interactions between the sheep mammary gland microbiome and SCC. The DGGE and MiSeq results show a persistent community has been detected over time, with similarities and differences by mammary gland half, lactation and age. Associations between individual bacterial species and SCC were identified through mixed effect modelling. The DGGE results were comparable to the MiSeq results from 5 sheep. Analysis of all 379 samples by MiSeq sequencing and mixed effects models will be used to directly test the study hypotheses.

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27

Clarke, Anna Maria. "The microbial ecology of sulphidogenic lignocellulose degradation." Thesis, Rhodes University, 2007. http://hdl.handle.net/10962/d1008181.

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Acid mine drainage is a well known environmental pollutant, not only in South Africa, but throughout the world, and the use of microbial processes in the treatment of these wastes has been the subject of investigation over past decades. Lignocellulose packed-bed reactors have been used in passive treatment systems, and, although effective initially, they show early decline in performance while the packing material remains largely un-utilized. Little is known about this phenomenon which remains a severe constraint in the development of efficient passive mine water treatment systems. It has been proposed that the degradation pathways of the complex lignocellulose substrate may be limited in some way in these systems during the manifestation of this effect. This study has addressed the problem using a molecular microbial ecology methodology in an attempt to relate trophic functions of the microbial population to the physico-chemical data of the system. A field-scale lignocellulose packed-bed reactor located at Vryheid Coronation Colliery (Northern Kwa-Zulu Natal province, South Africa) was monitored for six years and the results showed the classic profile of performance decline related to a slowdown in sulphate reduction and alkalinity production. The reactor was decommissioned , comprehensive samples were collected along the depth profile and the microbial populations investigated by means of 16S rRNA gene methodology. The population was found to include cellulolytic Clostridia spp., CytophagaIFlavobacterlBacteroidetes, Sphingomonadaceae and as yet uncultured microorganisms related to microbiota identified in the rumen and termite gut. These are all known to be involved as primary fermenters of cellulose. Oesulphosporosinus was present as sulphate reducer. A comparison of substrata sampling and population distribution suggested that spatial and temporal gradients within the system may become established over the course of its operation. Based on these findings, a laboratory-scale reactor was constructed to simulate the performance of the packed-bed reactor under controlled experimental conditions. The laboratory-scale reactor was operated for 273 days and showed comparable performance to that in the field in both biomolecular and physicochemical data. Clearly defined trophic niches were observed. These results suggested that a sequence of events does occur in lignocellulose degradation over time. Based on the spatial and temporal column studies, a descriptive model was proposed to account for these events. It was found that fermentative organisms predominate in the inlet zone of the system using easily extractable compounds from the wood, thus providing feedstock for sulphate reduction occurring in the succeeding compartments. Production of sulphide and alkalinity appears to be involved in the enhancement of lignin degradation and this, in turn, appears to enhance access to the cellulose fraction. However, once the readily extractables are exhausted, the decline in sulphide and alkalinity production leads inexorably to a decline in the overall performance of the system as a sulphate reducing unit operation. These observations led to the proposal that with the addition of a limited amount of a readily available carbon source, such as molasses, in the initial zone of the the reactor, the ongoing generation of sulphide would be sustained and this in turn would sustain the microbial attack on the lignocellulose complex. This proposal was tested in scale-up studies and positive results indicate that the descriptive model may, to some extent, provide an account of events occurring in these systems. The work on sustaining lignocellulose degradation through the maintenance of sulphate reduction in the initial stages of the reactor flow path has led to the development of the Degrading Packed-bed Reactor concept and that, has subsequently been successfully evaluated in the field.

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28

Hart, Murray. "Effects of pesticides on the soil microbial biomass and microbial activity." Thesis, University of Nottingham, 1995. http://eprints.nottingham.ac.uk/11542/.

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This thesis describes research investigating the side-effects of pesticides on soil microbial biomass and microbial activity, with particular reference to two recently developed pesticides, a fungicide, epoxiconazole, and a herbicide, quinmerac. In a dose-responsee xperiment,a pplication of thesep esticidest o a sandy loam soil, at up to 10 and 20 times field rate, had no significant effect on soil microbial biomass C or ninhydrin-reactive N, over 84 days incubation. There was also no effect on soil respiration, except for the higher rate quinmerac-treated soil, which evolved 13% lessC02-Cthan the control. The rate of mineralisation of epoxiconazole and quinmerac, and their long-term effect on soil respiration, were measured in three contrasting soils: a sandy loam, a silty clay loam, and a clay soil, using 14C -labelled active ingredients. The kinetics of the pesticides' mineralisation were quite different, epoxiconazole being hyperbolic, while quinmerac was sigmoidal. The maximum amount of mineralisation of both pesticides occurred in the silty clay loam soil, which had the lowest microbial biomass content. The mineralisation of the pesticides was increased by the addition of ryegrass, with the greatest effect in the silty clay loam soil, probably because of the large ryegrass C: biomass C ratio. The mineralisation of epoxiconazole was affected by the ryegrass amendment much more than quinmerac. Further additions of the pesticides had no significant effect on soil respiration or pesticide mineralisation. The mineralisation of epoxiconazole and quimnerac was further investigated in the silty clay loam soil, using samples with different crop management histories, and the effects of ryegrass and glucose amendment. Pesticide mineralisation was shown to be related to the amount of soil microbial biomass, indicating that the difference in mineralisation rate between the three soil types above was not due to differences in their crop management, but innate differences in soil chemistry and microbiology. Ryegrass addition stimulated the mineralisation of epoxiconazole more than quinmerac, while the reverse was true for glucose, indicating that the pesticides were being degraded by two distinct fractions of the microbial biomass. The effects of long-term cumulative field application of the pesticides benomyl, chlorfenvinphos, aldicarb, triadimefon and glyphosate, on soil microbial biomass and mineralisation of soil organic matter were investigated. The addition of aldicarb consistently increased the microbial biomass, due to its beneficial effect on crop growth, but this effect was not reflected in the rate of organic matter mineralisation. However, in general, the continued application of these pesticides for up to 19 years, at slightly higher than the recommended rates, had very little effect on the soil microbial population. The effects of epoxiconazole and triadimefon on soil ergosterol content and microbial biomass C were compared in a sandy loam soil. Both pesticides temporarily reduced soil ergosterol by about 30%, while biomass C remained largely unaffected. However, when straw was added to the soils, the inhibition of ergosterol was still evident, as was an inhibitory effect on biomass C. The measurement of soil ergosterol was more sensitive to the pesticide effects than biomass C, and could be a useful test in determining changes in fungal populations.

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29

O'Flaherty, S. M. "Microbial diversity in contaminated soil." Thesis, Cranfield University, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.274042.

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30

Rao, Subramanya. "Microbial ecology of hot and cold desert soils." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2012. http://hub.hku.hk/bib/B49617667.

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Deserts are the most abundant terrestrial biome on Earth, and microbial processes assume a major role since environmental stress severely limits higher plant and animal life. A major hurdle to developing an understanding of microbial ecology in deserts has been the lack of knowledge at the fundamental biodiversity level. This is due to lack of research focus and also the inherent bias in ‘traditional’ microbial diversity estimates based upon cultivation. In this thesis an evaluation of culture-independent approaches employing both DNA and RNA from environmental samples was made with comparison to more traditional cultivation techniques. These were then applied to soils from hot and cold deserts, and along stress gradients from semi-arid to hyper-arid. A literature review was first conducted to assess the extent of current knowledge and identify critical knowledge gaps. The scientific study was then carried out as follows. The second chapter presents an evaluation of fungal taxa using cultivation, DNA and RNA based techniques. The findings indicated major taxa are revealed in all approaches, yet differences in less abundant taxa occur. The third chapter describes fungal assemblages in the soils of the McMurdo Dry Valleys, a cold polar desert. In this study, RNA based approaches tracked active fungal assemblages, whilst DNA and cultivation revealed additional taxa. Chapter four analyzed microbial communities in the Thar Desert, a hot monsoon desert in India. This study revealed a diverse community that comprised known desiccation-tolerant taxa but also a phylogenetically broad range of bacteria, archaea and eukarya. Chapter 5 focuses on the delineation of total versus active microorganisms in environmental samples from the hot deserts. As with the initial experiments, this revealed that total and active assemblages track each other broadly in desert soils. A synthesis of the study revealed that certain common microbial phyla are likely well-adapted to xeric stress, although distinct hot and cold desert assemblages also develop. For such low-diversity systems it is likely that DNA-based approaches are reasonable tools for diversity analysis, and will be especially useful in arid systems when long periods of inactivity may confound attempts to estimate active populations. Broader significance of the study includes an increased appreciation of eukaryotic microbial presence in arid soils, and how latent soil microbiota may act as a reservoir for development of future microbial macro-structures (e.g. soil crust) that function in soil stabilization, and should therefore be included in conservation planning for deserts. published_or_final_version Biological Sciences Doctoral Doctor of Philosophy

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31

Sacristán, Soriano Oriol. "Chemical and microbial ecology of thc demosponge Aplysina aerophoba = Ecología química y microbiana de la demosponja Aplysina aerophoba." Doctoral thesis, Universitat de Barcelona, 2013. http://hdl.handle.net/10803/128858.

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Phylum Porifera (Grant, 1836) are sessile metazoans with a differentiated inhalant and exhalant aquiferous system with external pores. Lacking a tissue grade of construction, sponges can reach two well-differentiated regions, the ectosome (external layer free of choanocytes) and the choanosome (internal region with choanocytes). As the most likely primitive metazoans, their challenging structural organization, physiology for biocalcification and trophic requirements allowed sponges to rapidly colonize distinct environments and built important sponge reefs during the Paleozoic and Mesozoic eras, making them an ecologically relevant group principally in marine benthic communities. To date, sponges are still ecologically important among benthic fauna although the role as reef builders in modern coral reefs has changed in favor of scleractinian corals. Nonetheless, sponges have demonstrated a huge capacity to adapt and spread in many habitats contributing to organization and functioning at both community and ecosystem levels. One of the keys of the evolutionary success of this group lies in the close association between sponges and microbes that dates back to the Precambrian era. The need to be defended may have arisen from the lack of motility of sponges and several mechanisms emerged to fulfill their demand including a chemical protection. Many sponges would have taken advantage of associated microbes to use their metabolites as a defense barrier against predators, competitors or foulers. This particular symbiosis has consequently become a key factor in biotic interactions within the sponge research. To date, chemical ecology and microbial ecology are two independent areas of the sponge research with ecological implications that occasionally converge at the same point. We want to analyze the evolution of the sponge chemical and microbial ecology from the very beginning, to quantify their impact on the scientific community, and to compare both research areas. This PhD dissertation has been conceived to study the chemical and microbial ecology of sponges using the demosponge Aplysina aerophoba (Nardo, 1833) as a model species because its secondary chemistry and its associated microbial community are well studied and it is quite abundant in our study area (Northwestern Mediterranean and Canary Islands). Beyond the knowledge achieved about the major chemistry and bacterial assemblages in A. aerophoba, we have been able to explore the variation sources of the natural products and the sponge microbial consortium. Additionally, we have assessed the putative relationships between the host bacterial community and the production of secondary metabolites in this species. We explored changes in the abundance of secondary metabolites and the relative composition of bacterial assemblages in A. aerophoba at multiple spatial (from few centimeters to thousand kilometers) and temporal (months and years) scales. The approach used allowed us to investigate which is the magnitude of the variance attributable to the distinct spatial and temporal scales and the most relevant scale at which the abundance of secondary metabolites and bacterial symbionts varied. We also investigated the relationship between natural products and microbial community structure by assessing whether both parameters covary at multiple scales. Finally, we experimentally addressed whether different light exposures can modify chemical and microbial profiles in the external and internal regions of A. aerophoba. In summary, the production of natural products in sponges and the abundance and phylogenetic composition of the host-associated microbial community mainly depend to a large extent on the sponge-species and the ecological factors with spatial and temporal variations (e.g., light, predation, competition, fouling). The host state (i.e., stress) is also a key factor that may be the main driver of symbiotic shifts causing a breakdown in the sponge health and making the symbiont communities unstable and likely the sponge chemical defense. The combination between abiotic and biotic factors may finally determine the concentration of bioactive compounds and associated microbial diversity as the abiotic environmental context can control the outcomes of biotic interactions, and biotic interactions often moderate the effect of abiotic factors. For that reason, it is not an easy task to actually figure out the factors that limit or enhance chemical and microbial variability. Further experiments and time-series observations are needed to reveal the underlying processes hidden. El filo Porifera (Grant, 1836) está compuesto por metazoos sésiles con un sistema acuífero diferenciado del que forman parte los coanocitos que generan un flujo de agua unidireccional. A pesar de no presentar auténticos tejidos, las esponjas pueden llegar a desarrollar dos regiones bien definidas, el ectosoma (capa externa) y el coanosoma (región interna). Estos organismos representan un grupo ecológicamente importante del bentos marino con gran capacidad de adaptación y dispersión en muchos hábitats, contribuyendo así en la organización y funcionamiento a nivel de comunidad y ecosistema. Una de las claves del éxito evolutivo de las esponjas yace en la relación estrecha que presentan desde el Precámbrico con microorganismos a través de la cual desarrollaron una protección química. Muchas esponjas habrían utilizado los metabolitos secundarios de origen microbiano como defensa química. A día de hoy se han desarrollado dos áreas de investigación, la ecología química y la microbiana de esponjas, de las que realmente desconocemos su origen o su impacto. Dado el vacío existente de estudios que evalúen la comunidad bacteriana de esponjas como fuente de compuestos bioactivos, teníamos la oportunidad de integrar estos dos campos de la ecología de esponjas investigando la relación entre productos naturales y microorganismos simbiontes, con el fin de entender la funcionalidad de la comunidad bacteriana en el huésped. Esta tesis fue concebida para estudiar la ecología química y microbiana de la esponja Aplysina aerophoba (Nardo, 1833), cuya química y comunidad bacteriana asociada han sido objeto de muchos estudios previos. El principal objetivo fue explorar las fuentes de variación tanto de los productos naturales adscritos a Aplysina como de su estructura microbiana e inferir una posible relación entre comunidad de microorganismos y la producción de metabolitos secundarios. La aproximación que utilizamos consistía en explorar la variabilidad natural de los compuestos bioactivos y de la estructura microbiana de la esponja Aplysina aerophoba a distintas escalas espaciales (desde pocos centímetros hasta miles de kilómetros) y temporales (meses, años), y evaluar el efecto de factores ambientales, como la luz, en los perfiles químicos y microbianos. Posteriormente, correlacionar ambos patrones de variación e inferir alguna asociación potencial entre productos naturales y simbiontes microbianos. Resumiendo, la producción de metabolitos secundarios en esponjas y la composición filogenética de la microbiota asociada depende esencialmente de la especie de esponja, de los factores ecológicos con variación espacial y temporal, como también del estado del huésped (si presenta o no estrés). La combinación entre factores abióticos y bióticos determinará en última instancia la abundancia de defensas químicas y la diversidad microbiana debido a una autorregulación entre ambos tipos de factores.

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32

Wepking, Carl. "Soil microbial function in a time of global change: effect of dairy antibiotics on soil microbial communities and ecosystem function." Diss., Virginia Tech, 2018. http://hdl.handle.net/10919/85125.

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Antibiotic resistance is ubiquitous due to high usage of antibiotics and the capability of bacteria to transfer genes both horizontally and vertically. While this has dire implications for human health, the potential to disturb microbial communities and ecosystem functions they regulate is under appreciated. Antibiotics are commonly used in the livestock sector, accounting for 80% of antibiotic use domestically. This dissertation addresses three facets of this problem. Chapter 2 is a nation-wide survey of antibiotic resistance at dairy operations, aimed at understanding how ecosystem function is affected in situ. Chapter 3 describes a field-experiment, seeking to determine whether antibiotics have effects beyond soil through impacts on plant-microbe-soil feedbacks, thus potentially altering terrestrial ecosystem function. Chapter 4 investigates how rising global temperature interacts with antibiotic exposure through a microcosm-incubation experiment. These multiple stressors (i.e. temperature and antibiotics) could alter microbial community composition or physiology with repercussions on function. Additionally, chapter 4 seeks to determine whether microbes acclimate to continued antibiotic exposure. In chapter 2 I present evidence that increased antibiotic resistant gene (ARG) abundance with exposure to antibiotics and manure, and a correlation between ARGs and microbial stress. This increase in microbial stress results in elevated soil carbon loss. Chapter 3 shows that antibiotic exposure can change plant function – presumably through impacts on rhizospheric microbial community composition. Plants assimilate more nitrogen, but more carbon is lost from the system overall seemingly due to plant-soil-microbe tradeoffs. Chapter 4 shows a temporally dependent temperature–antibiotic interactive effect. Initially, pirlimycin increased microbial respiration at high temperatures, however this diminishes with time. Additional studies of microbial respiration at a range of temperatures show that microbial acclimation to antibiotic exposure may be taking place. However, interactive effects of high temperature and antibiotics appear to inhibit active microbial biomass production. Possible explanations to both of these patterns are the underlying differences in microbial community composition, specifically the fungal:bacterial. My results show that antibiotics not only lead to increased ARG abundance, but also have wide ranging effects on communities and ecosystem processes that are likely to be compounded in the face of global change. Ph. D.

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33

Fear, Lesley Anne. "Microbial ecology of the gut of Gammarus pulex." Thesis, Lancaster University, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.250026.

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34

Coupe, Stephen John. "Oil biodegradation and microbial ecology within permeable pavements." Thesis, Coventry University, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.404727.

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35

Lenaerts, Jeremy. "Molecular beacons as hybridisation probes in microbial ecology." Thesis, University of Exeter, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.493638.

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Microorganisms are of fundamental importance to global biogeochemical cycling, yet aspects of their ecology are poorly understood. Within the present methods used to study microbial ecology are limitations with regards to sensitivity, applicability and automation. This study aimed to investigate the potential application of novel nucleic acid probes (molecular beacons and locked nucleic acid probes) in microbial ecology.

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36

Enticknap, Julie Jane. "The microbial ecology of methanotrophs in agricultural soils." Thesis, University of Warwick, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.340087.

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37

Olesen, Scott Wilder. "Quantitative modeling for microbial ecology and clinical trials." Thesis, Massachusetts Institute of Technology, 2016. http://hdl.handle.net/1721.1/107277.

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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biological Engineering, 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. Microbial ecology has benefited from the decreased cost and increased quality of next-generation DNA sequencing. In general, studies that use DNA sequencing are no longer limited by the sequencing itself but instead by the acquisition of the samples and by methods for analyzing and interpreting the resulting sequence data. In this thesis, I describe the results of three projects that address challenges to interpreting or acquiring sequence data. In the first project, I developed a method for analyzing the dynamics of the relative abundance of operational taxonomic units measured by next-generation amplicon sequencing in microbial ecology experiments without replication. In the second project, I and my co-author combined a taxonomic survey of a dimictic lake, an ecosystem-level biogeochemical model of microbial metabolisms in the lake, and the results of a single-cell genetic assay to infer the identity of taxonomically-diverse, putatively-syntrophic microbial consortia. In the third project, I and my co-author developed a model of differences in the efficacy that stool from different donors has when treating patients via fecal microbiota transplant. We use that model to compute statistical powers and to optimize clinical trial designs. Aside from contributing scientific conclusions about each system, these methods will also serve as a conceptual framework for future efforts to address challenges to the interpretation or acquisition of microbial ecology data. by Scott Wilder Olesen. Ph. D.

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38

Sarma-Rupavtarm, Ramahi Bhushan 1977. "A mouse model for studying gastrointestinal microbial ecology." Thesis, Massachusetts Institute of Technology, 2005. http://hdl.handle.net/1721.1/31133.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 2005. Includes bibliographical references (p. 131-133). The mammalian gastrointestinal (GI) tract harbors a complex microbial ecosystem with hundreds of bacterial species at total levels as high as 10¹¹⁻¹² cells/g tissue. These bacteria play an important role in the health of the host as well as in causing disease, but studies on the roles of the GI microflora are hindered by the lack of a suitable model system. This thesis characterizes and uses a defined flora mouse model to study interactions between exogenous bacteria and the GI microflora. The first part of the thesis characterizes a defined flora mouse model consisting of immunodeficient C.B-17 SCID mice colonized with the eight bacterial strains of the altered Schaedler flora (ASF). Specific and sensitive molecular methods were developed to accurately estimate the levels of different ASF strains. Distribution of specific ASF strains along the GI tract was dependent on the oxygen tolerance of the strains. Fecal levels of different strains, which are typically used as a model for colonic bacteria, were different from colonic levels, although all colonic strains were present in feces. ASF strains were persistent in the mouse GI tract even in the face of long-term exposure to other bacteria. The second part of the thesis evaluates the presence of different ASF strains in inbred and outbred mouse models from different vendors to establish the potential for widespread use of these strains as representatives of the mouse GI microflora. Seven of the eight strains were persistent in both inbred and outbred mice from all vendors studied. This indicates the potential for the ASF strains to be used as a model system even in mouse models that do not harbor a defined flora. (cont.) The third part of the thesis explores ecological interactions following infection by an intestinal pathogen, Citrobacter rodentium, in defined flora C.B-17 SCID mice. Bulk levels of the pathogen and the ASF strains in different regions of the large intestine and their spatial localization across the luminal-mucosal cross-section were assessed. C. rodentium exhibited accelerated dynamics, and infection was followed by increases in levels of specific ASF strains and in total bacterial levels in infected mice as compared to control mice. Different ASF strains were observed to have specific spatial niches that did not vary between infected and control mice. These results suggest that the role of the microflora in preventing colonization of pathogens is a complex process that potentially involves more than one bacterial species. by Ramahi Bhushan Sarma-Rupavtarm. Ph.D.

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39

Coyte, Katharine. "The ecology and evolution of complex microbial communities." Thesis, University of Oxford, 2016. https://ora.ox.ac.uk/objects/uuid:61ef24cb-93b5-4c5a-8a49-f2aea4eff3db.

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Microbial communities colonise virtually every habitable environment on earth. They live on us, inside us, and all around us, and are key components of the earth's ecosystem. However, due to the complexity of microbial communities we still understand relatively little about the mechanisms that drive their ecology and evolution. The aim of this thesis is to develop novel experimental and mathematical approaches, in order to investigate complex microbial communities. Specifically, this thesis is split into two parts, focussing in turn on how environmental complexity, and interspecies interactions shape microbial ecology and evolution. In the first part I have studied microbial evolution in porous environments such as one might find in soil or aquifers. Here I have combined microfluidic experiments, mechanistic models, and game theory to study how hydrodynamics mediate competition between bacterial genotypes. With these I have demonstrated how even subtle environmental complexity can fundamentally affect microbial competition, enabling slow growing genotypes to outcompete their faster counterparts. In the second part of this thesis I have investigated how interspecies interactions influence the stability and initial assembly of microbial communities. Here I have developed new tools - from theoretical ecology - in order to study the microbial communities within the mammalian gastro-intestinal tract. With these I have demonstrated how strong, cooperative interactions between species can undermine both the stability, and the assembly of communities. Moreover, I have illustrated how these tools can be applied to real microbiome data, in order to better understand these important communities. In sum, this thesis explores two key drivers of microbial ecology and evolution, and presents a new set of tools for the future investigation of complex microbial communities.

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40

Shaw, L. P. "The microbial ecology of human-associated bacterial communities." Thesis, University College London (University of London), 2018. http://discovery.ucl.ac.uk/10046977/.

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The bacterial communities within the human body have important associations with health and disease. Understanding their complexity requires ecological approaches. In this thesis, I apply ecological techniques and models to explore the microbial ecology of human-associated bacterial communities at multiple scales. In the first half of this thesis, I explore the oral microbiome using 16S rRNA gene sequencing data to characterise the effect of various factors on its diversity. Multiple factors apart from disease can also affect the oral microbiome, but their relative importance remains a matter of debate. In Chapter 2, I use a dataset of saliva samples from a family of related Ashkenazi Jewish individuals to show that host genetics plays much less of a role than shared household in explaining bacterial community composition. In Chapter 3, I use a large dataset of plaque samples from women in Malawi to investigate associations between bacterial taxa and periodontal disease. I show that the signals from gingivitis and periodontitis can be distinguished, and use correlation networks to identify important taxa for the development of disease. The second half of this thesis deals with the effect of antibiotics on the human microbiome. I demonstrate new approaches at two extremes of scale: abstracting the gut microbiome to a single metric, and also investigating the worldwide distribution and diversity of a single resistance gene. In Chapter 4, I develop a new and simple mathematical model of the gut microbiome's response to antibiotic perturbation and fit it to empirical data, showing that in some individuals the gut microbiome appears to return to an alternative stable state, raising questions about the long-term impact of antibiotics on previously healthy bacterial communities. Antibiotic use also selects for resistance, which is a growing concern, particularly as resistance can be transmitted horizontally on mobile genetic elements. In Chapter 5, I describe a global dataset of isolates containing the mobilized colistin resistance gene mcr-1 and use the diversity present within a composite transposon alignment to explore its distribution and spread across multiple bacterial communities.

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41

Axelrod, Kevin Connor. "Bistable dynamics in microbial ecology and systems biology." Thesis, Harvard University, 2016. http://nrs.harvard.edu/urn-3:HUL.InstRepos:33493470.

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Bistability, in which a system has two stable states, is a common property of many dynamic systems. This thesis explores the properties of such systems across a range of length scales, from gene circuits to ecosystems. Cells often store memories of environmental stimuli using bistable gene circuits. High fidelity memory storage requires that a state has a long lifetime. However, an underappreciated aspect of stable memory is that the distance from a bifurcation could determine how sensitive a state is to perturbations in the extracellular environment. We predict that cell memory should become increasingly sensitive to perturbations near a bifurcation and test this idea in three different gene circuits: a toggle switch, the yeast galactose utilization network, and the E. coli lactose utilization network. In a second study, we explore how the environmental context in which two species interact can influence their mode of interaction. Two species in nature often form reciprocally beneficial partnerships termed mutualisms, but in certain environmental regimes the species might shift to competing with one another for resources. This mutualism-competition transition has been understudied in experimental ecosystems. Using a synthetic yeast cross-feeding mutualism, we modulate the degree to which two partners rely on each other by supplementing the cells with variable amounts of nutrients. Surprisingly, we find that as the amount of supplemented nutrients is increased, the system passes through eight qualitatively distinct dynamic regimes: extinction, obligatory mutualism, obligatory/facultative mutualism, facultative mutualism, parasitism, amensalism, competition, and competitive exclusion. In a third study, we probe how population growth dynamics can influence the probability of evolutionary rescue. Natural populations frequently face harsh environments in which their death rate exceeds their birth rate and population size tends toward zero. In such scenarios, populations can either go extinct, migrate to a better habitat, or adapt to the harsh environment. Natural populations often exhibit an “Allee effect,” in which populations grow slowly at low density due to struggles with such behaviors as finding a mate or collective hunting. We hypothesize that the presence of an Allee effect could impede evolutionary rescue and confirm this hypothesis in a model laboratory yeast ecosystem. Biophysics

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42

Vazquez, Baeza Yoshiki. "Statistical Representations Of Microbial Systems." Thesis, University of California, San Diego, 2018. http://pqdtopen.proquest.com/#viewpdf?dispub=10684635.

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Technological developments in the past thirty years have transformed sequencing-based microbiology into a data-intensive field. Here, computing and efficient representations are catalyzers of insight into omnipresent and complex microbial interactions. Notably, classical ecologists have set the foundations for the way we analyze these systems, with some techniques dating back to the beginning of the twentieth century. In this thesis, we expand and where possible reuse these techniques to unravel the hidden patterns comprising the human gut microbiome. To set an appropriate motivation and context for the rest of this work, Chapter 1 reviews recent discoveries on the human microbiome and how the communities within can influence the effectiveness of therapeutic agents. Next, in Chapter 2, we introduce EMPeror, an interactive analysis and visualization tool that is crucial to the findings presented in later chapters. The following three chapters study concrete examples where the microbiome has been implicated as a driver or marker for dysbiosis. Chapter 3 describes how the microbial signature associated with Crohn's disease (CD) in humans, described in our previous work, is overlapping but distinct to that of dogs affected with inflammatory bowel disease (IBD). Surprisingly, unlike with humans, dog fecal samples alone are strong indicators of the disease. In Chapter 4, we study IBD from a longitudinal perspective, revealing increased volatility in the gut microbiomes of subjects with IBD, a property that does not appear to be present in unaffected controls. Furthermore, we use this as a predicting feature of the disease, and improve on the classification accuracy possible through a single fecal sample. In Chapter 5, we study the effect of fecal microbiota transplants (FMTs) to treat Clostridium difficile infection (CDI) and, using the techniques described in Chapter 2, we show the first animated visualization of this process, a dramatic microbial transformation as the subjects recover from all CDI symptoms. In addition, for CDI patients who also suffer from a subtype of IBD, a treatment with a FMT results in an increased number of relapses and decreased microbial diversity. The closing chapter discusses these results and their possible applications, as well as future directions for computationally-centric microbiome research.

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43

Boyd, Philip W. "Carbon fluxes in marine microbial ecosystems." Thesis, Queen's University Belfast, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.334553.

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44

Fernández, Guerra Antonio. "Ecology and evolution of microbial nitrifiers / Ecología y evolución de los microorganismos nitrificantes." Doctoral thesis, Universitat de Barcelona, 2013. http://hdl.handle.net/10803/108001.

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Ammonia oxidation, the first and the rate-limiting step in nitrification, is one of the cornerstones of the cycle. Members from the bacterial and archaeal domains are key players in ammonia oxidation in many different environ- ments. Usually these organisms are found coexisting but the most recent studies suggests that archaeal ammonia oxidizers show an incredible ability to adapt and oxidize ammonia under different environmental conditions and have displaced their bacterial counterparts in terms of importance in the global biogeochemical cycle, providing an avalanche of AOA molecular data (16S rDNA and amoA gene sequences) from very diverse environments worldwide. As far as we don’t have enough genomic data to perform an holistic approach using population genomics and reverse ecology to unveil the ecological and evolutionary mechanisms driving the adaptation; we focused our experiments on the amoA gene sequence. Because ammonia monooxygenase is supposed to be the key enzyme in the ammonia oxidation, we applied a combination of community ecology and molecular evolution methods to understand the mechanisms of the diversification patterns observed in the amoA gene. Another unsolved question in the archaeal ammonia oxidation is the unusual biochemistry found in the genome sequences from cultured archaeal ammonia oxidizers. In archaea, all the elements of the bacterial ammonia oxidizing pathway are missing but the genes coding for the presumptive AMO. To unveil missing pathways in this process, we have developed a powerful approach based on graphical models to capture all the functional associations present in metagenomes based in their ecological co-ocurrence. The results of the analyses revealed for the first time a global picture of the phylogenetic community structure of ammonia- oxidizing assemblages. Our study unveiled larger phylogenetic richness in AOA with more dissimilar communities and clear monophyletic groups for the different habitats. The rates of diversification in AOA were higher than in AOB and the archaeal diversification dynamics showed an unusual feature, with an initial diversification process followed by a long period of stasis and a final burst of diversification. The variations observed between AOB and AOA in terms of community structure, phylogenetic diversity, diversification patterns, and habitat dispersion were unexpected just a very few years ago, and the community phylogenetics approach has nicely captured these differences. Understand the diversification processes observed in AOA and their successful performance under a myriad of different environmental conditions such as low pH, different ammonia concentrations, high hydrostatic pressures, high light exposure, low oxygen availability among others, needs however of a deeper insight adding the evolutionary processes. Individual changes at the level of nucleotides were translated to the global diversification patterns of archaeal ammonia oxidizers. Thus, this resulted in a step further from the results obtained after applying community phylogenetics methods providing precise evolutionary information behind the phylogenetic patterns observed within an ecological context. We will gain the full picture once the results can be integrated in a comparative genomics framework. After applying methods of reverse engineering of regulatory the associations between the known and the unknown fraction were reconstructed offering a pioneering fresh view for microbial ecology. One especially relevant result obtained from this approach on AOA was the reconstruction of the association network of the different AMO subunits to the other proteins previously reported in the marine AOA Nitrosopumilus. The information recovered from metagenomics combined with available genomes fuels hypothesis for the particular and yet unknown biochemistry of ammonia oxidation in Archaea. La oxidación del amonio es una de las piezas clave del ciclo del Nitrógeno. Tanto las bacterias como las arqueas oxidadoras del amonio se pueden encontrar coexistiendo a lo largo de diferentes ambientes. Pero cuando la primera arquea oxidadora del amonio fue aislada, se puso en relevancia la importancia de estas en comparación con las bacterias en los ciclos biogeoquímicos globales. Desde entonces hemos sido inundados por una avalancha de secuencias génicas de estas arqueas, mostrando una gran capacidad de diversificación y adaptación a ambientes diferentes. Al no disponer de suficientes datos para realizar una aproximación holistica utilizando genómica de poblaciones y de ecología inversa para poder discernir los mecanismos ecológicos y evolutivos relacionados con la adaptación; nos hemos centrado en estudiar la secuencia del amoA. La amonio monooxigenasa es la enzima responsable de la oxidación del amonio, para su estudio hemos aplicado una combinación de técnicas de ecología de comunidades y de evolución molecular con el objetivo de entender los mecanismos de los patrones de diversificación observados. Por otra banda, otro de los misterios asociados a la oxidación del amonio por parte de las arqueas, es su inusual bioquímica para realizar la oxidación del amonio. En arqueas faltan todos los elementos necesarios para llevar a cabo la oxidación del amonio a excepción del AMO. Para poder aportar algo de luz a este misterio hemos desarrollado un potente método basado en modelos gráficos para capturar todas las asociaciones funcionales presentes en los metagenomas basado en sus co-ocurrencias ecológicas.

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45

Flores, Gilberto Eugene. "Microbial Ecology of Active Marine Hydrothermal Vent Deposits: The Influence of Geologic Setting on Microbial Communities." PDXScholar, 2011. https://pdxscholar.library.pdx.edu/open_access_etds/250.

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The discovery of deep-sea hydrothermal vents in 1977 revealed an ecosystem supported by chemosynthesis with a rich diversity of invertebrates, Archaea and Bacteria. While the invertebrate vent communities are largely composed of endemic species and exist in different biogeographical provinces, the possible factors influencing the distribution patterns of free-living Archaea and Bacteria are still being explored. In particular, how differences in the geologic setting of vent fields influence microbial communities and populations associated with active vent deposits remains largely unknown. The overall goal of the studies presented in this dissertation was to examine the links between the geologic setting of hydrothermal vent fields and microorganisms associated with actively venting mineral deposits at two levels of biological organization. At the community level, bar-coded pyrosequencing of a segment of the archaeal and bacterial 16S rRNA gene was employed to characterize and compare the microbial communities associated with numerous deposits from several geochemically different vent fields. Results from these studies suggest that factors influencing end-member fluid chemistry, such as host-rock composition and degassing of magmatic volatiles, help to structure the microbial communities at the vent field scale. At the population level, targeted cultivation-dependent and -independent studies were conducted in order to expand our understanding of thermoacidophily in diverse hydrothermal environments. Results of these studies expanded the phylogenetic and physiological diversity of thermoacidophiles in deep-sea vent environments and provided clues to factors that are influencing the biogeography of an important thermoacidophilic archaeal lineage. Overall, these studies have increased our understanding of the interplay between geologic processes and microorganisms in deep-sea hydrothermal environments.

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46

Zactiti, Erica Marostica. "Desenvolvimento e caracterização de filmes biodegradaveis de alginato de calcio sem e com sorbato de potassio." [s.n.], 2004. http://repositorio.unicamp.br/jspui/handle/REPOSIP/267668.

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Orientador: Theo Guenter Kieckbusch Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Engenharia Quimica Made available in DSpace on 2018-08-04T01:55:31Z (GMT). No. of bitstreams: 1 Zactiti_EricaMarostica_D.pdf: 5513893 bytes, checksum: 1d3ab4df0091663092f98ac6015a9abe (MD5) Previous issue date: 2004 Resumo: Questões relacionadas à preservação ambiental têm sido intensamente discutidas, não somente devido à escassez de recursos naturais, mas também, em função da legislação que está cada vez mais rigorosa. Visando o desenvolvimento sustentável, a procura por novos materiais e tecnologias capazes de minimizar os danos ao meio ambiente tem aumentado consideravelmente. Filmes biodegradáveis estão inseridos nesse contexto. Eles são produzidos a partir de polímeros naturais, principalmente polissacarídeos e proteínas, com potencial aplicação nas indústrias farmacêutica e alimentícia. Filmes confeccionados a partir de biopolímeros podem ser utilizados como embalagens antimicrobianas para produtos alimentícios se os agentes ativos são incorporados. Alginato de sódio foi utilizado como substância formadora de filme, cloreto de cálcio como agente reticulante e glicerol como plastificante. Um processo de confecção de filmes reticulados realizado em dois estágios foi desenvolvido, sendo possível obter filmes com baixa solubilidade em água. Filmes com diferentes graus de reticulação foram caracterizados em relação a suas propriedades, tais como: solubilidade em água, permeabilidade ao vapor de água, resistência mecânica, grau de intumescimento e temperatura de transição vítrea. Para o desenvolvimento de embalagens ativas, sorbato de potássio foi incorporado ao filme. Medidas de permeabilidade utilizando uma célula de diafragma indicaram que o processo de migração do sorbato foi afetado pela concentração de sorbato na solução e que o aumento do grau de crosslinking da matriz polimérica diminui a taxa de transferência de massa. Experimentos de liberação de sorbato realizados com água (22 °C) como sorvedouro mostraram rápida liberação do material ativo por difusão (95 % da massa total liberada em aproximadamente 4 minutos). Dados de massa de sorbato liberada apresentaram bom ajuste ao modelo difusional derivado da segunda lei de Fick, com os valores de difusividade variando entre 2,32 x10-7 a 3,32 x10-7cm2/s. Estes valores são inferiores aos dados de difusão de sorbato em filmes de proteína, indicando um uso potencial como sistemas de liberação de substâncias antimicóticas Abstract: The concern and consciousness relative to the environmental preservation is raising global issues, not only due to the shortage of natural resources, but also because of the legislation that is becoming more and more stringent. Seeking the sustainable development, the number of researches on new materials and technologies that are able to minimize the environmental damages have grown considerably. Biodegradable films are inserted in this context. They are produced from natural polymers, mainly polysaccharides and proteins, with potential applications in the pharmaceutical and food industries. Films manufactured with biopolymers can be used as antimicotic packaging for food products if active agents are incorporated. Sodium alginate was used as film matrix, calcium chloride as reticulating (crosslinking) agent and glycerol as plasticizer. A two-stage reticulation film manufacture process was developed and rendered films with low solubility in water. Films with different degree of reticulation were characterized according to properties such as water solubility, water vapor permeability, mechanical resistance, degree of swelling and glass transition temperature. For the development of active packaging, potassium sorbate was incorporated into the film. Permeability measurements using a diaphragm 0011 indicated that the sorbate migration process was affected by the sorbate concentration and that higher crosslinking degree of the polymeric matrix decreases the mass transfer rates. Sorbate release experiments conducted with water at 22°C as a sink showed rapid exhaustion of the active material by diffusion (95 % of total mass delivered in about 4 minutes). The mass of sorbate release data were well fitted to Fick's second law diffusional model, with O values ranging from 2,32 x10-7 to 3,32 x10-7 cm2/s. These values are lower than published data of sorbate diffusion in protein film, foreseeing a potential use of calcium alginate as an antimicotic packaging Doutorado Engenharia de Processos Doutor em Engenharia Química

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47

Park, Tae Jin, and 朴台鎮. "Microbial community ecology in bioelectrochemical systems (BESs) using 16S ribosomal RNA (rRNA) pyrosequencing." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2014. http://hdl.handle.net/10722/212634.

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48

Fritz, Alyce T. "Trophodynamics of estuarine (salt marsh) heterotrophic nanoplankton (microbial ecology, salt marsh ecology, choanoflagellates, Virginia)." W&M ScholarWorks, 1986. https://scholarworks.wm.edu/etd/1539616651.

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Seasonal occurrence and activity of heterotrophic nanoflagellates (HNANO or heteroflagellates) and bacteria were studied in a sheltered brackish water embayment of Chesapeake Bay wetlands (Virginia, USA) over a three year period (1981 - 1984). Epifluorescence direct counts and Scanning and Transmission Electron Microscopy (SEM and TEM) techniques were used for the description of organisms, enumeration, and biomass determinations. Seasonal bacterial growth rates and growth and grazing rates of bactivorous HNANO were estimated using diffusion chambers equipped with Nuclepore polycarbonate membrane filters in natural salt marsh tidal pools. Environmental monitoring of nanoplankton populations revealed a seasonal pattern of bacterial abundances with temperature while heteroflagellate abundances and growth rates showed no seasonal pattern nor correlation with fluctuations in bacterial densities. Heteroflagellate populations were dominated by 34 to 50 (mu)m('3) sized monads, choanoflagellates, bodonids, and Paraphysomonas sp., all found in varying abundances throughout the year. Blooms were concurrent with extended low tide or specific bacterial populations (i.e., cyanobacteria) typical of spring and autumn periods. Heteroflagellate growth in diffusion chambers reflected the environmental blooms and increased diversity of low water assemblages. Growth and grazing rates of heteroflagellates at ambient densities thus could account for 20 to 80% of daily bacterial carbon production. Although heteroflagellate ingestion rates did not regulate seasonal bacteria densities or vice versa, maximum growth of bacteria and heteroflagellates in chambers was closely coupled. Heteroflagellate grazing activity may regulate the rate of bacterial production by preventing substrate limitation and maintaining the population in an active growth phase. The seasonal study demonstrated the dynamic nature of nanoplankton populations during autumn and spring transitional periods. SEM photomicroscopy revealed that the dominant component of spring blooms may be composed of several members of the loricate choanoflagellate family, Acanthoecidae. Using modified EM techniques, eleven Acanthoecidae choanoflagellates species, identified from spring in situ chamber experiments, were described. In situ growth and grazing rates for the spring chamber populations ranged from 0.023 h('-1) to 0.196 h('-1) and 40 to 210 bacteria h('-1) respectively. These high rates represent an opportunistic response to optimum conditions and an expression of maximum grazing potential. (Abstract shortened with permission of author.).

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Fabrizzi, Karina Paola. "Microbial ecology and C and N dynamics in Agroecosystems." Diss., Manhattan, Kan. : Kansas State University, 2006. http://hdl.handle.net/2097/241.

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Walker, Jeffrey James. "Endolithic microbial ecosystems: Molecular phylogenetic composition, ecology and geobiology." Diss., Connect to online resource, 2005. http://wwwlib.umi.com/dissertations/fullcit/3165820.

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Дисертації з теми "Microbial ecology"

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