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Handley, Kim Marie. "Microbial diversity and respiratory processes in hydrothermal sediment." Thesis, University of Manchester, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.492237.
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In marine hydrothermal sediments metal-rich, reduced fluids and oxidised seawater form steep geochemical gradients supporting abundant, but as yet poorly defined, chemosynthetic life and biogeochemical cycling. This project elucidates the functional diversity of chemosynthetic micro-organisms, and metabolic processes on the geochemistry of ferruginous (-50% Fe), arsenic-rich (-400 ppm As) hydrothermal sediment at Santorini, Greece (20-40°C, pH 6.0-6.3, Eh 0 to 155 mV). Culture and molecular-phylogenetic techniques revealed abundant chemosynthetic prokaryotes capable of transforming a range of chemical species common to marine and hydrothermal sediments via: anaerobic Fe(III), sulfate, nitrate and As(V) reduction, and nitrate-dependant Fe(lI) oxidation; micro-aerobic Fe(lI) monosulfide (FeS) oxidation; and aerobic As(lII) and free-sulfide oxidation. Geochemical analyses showed that oxidised species [Fe(III), As(V), sulfate and presumably Mn(IV)] dominated in the suboxic surface sediment layer (0-5 cm deep), but that reduced species [namely Fe(II), As(III), Mn(II)] increased in the lower suboxic-anoxic transition zone (5-20 em depth). From a biological perspective sulfate is the energetically least favourable of the oxidised species to be reduced, and sulfate concentrations were consistent throughout the portion of the sediment column analysed (0-30 em depth). The presence of a black precipitate (probably FeS) at the lower limit of the transition zone, however, did suggest at least a small amount of sulfate reduction was occurring. In contrast, no nitrate was detected indicating rapid reduction of this . energetically favourable compound at· the water-sediment interface. Microbiological and geochemical data, in combination, indicated that redox cycling of Fe, Mn and As were most likely key biogenic processes in biogeochemically stratifying the sediment, whereas S-cycling bacteria were comparatively minor contributors. Other principal findings included the cultivation of a novel neutrophilic Fe(II)-oxidiser related to marine microaerophilic Fe(II)oxidising bacterium Mariprofundus ferroxydans. This bacterium dominated the Fe(lIl) (oxy-)hydroxide-rich surface sediment, and most probably plays a significant role in catalysing suboxic Fe(lI) oxidation. Fe(II)-oxidising prokaryotes comprise a functional group not well understood in marine settings. Additionally, bacteria belonging to a ubiquitous, heterotrophic marine genus, Marinobacter, were shown to oxidise Fe(II). Of these, Marinobacter santoriniensis, was isolated and characterised, and also shown to both oxidise As(llI) and respire As(V), providing a rare example of a marine prokaryote capable of these functions. Futher to this, incubation experiments, conducted to establish the effect of microbial respiration on arsenic mobilisation, demonstrated that microbial Fe(lll) reduction largely controlled shifts in arsenic partitioning in the sediment. Specifically, results support other studies (mainly concerned with the toxic effects of arsenic) showing arsenic sequestration by Fe(II)-bearing minerals. This is contrary to the more common supposition of arsenic release to porewaters upon reductive dissolution of Fe(lIl) minerals. Overall, these results highlight the importance of microbial enzymatic processes in sediment geochemistry.
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Weinmann, Birgit Ellen. "Microphytobenthic diversity and function in estuarine soft sediment." Thesis, University of St Andrews, 2012. http://hdl.handle.net/10023/3664.
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Corophium volutator (Pallas) fit the criteria of ‘ecosystem engineers' as defined by Jones and colleagues (1994, 1997): they are widely distributed within and across North Atlantic estuaries, are often present in intertidal soft sediment in vast numbers, and build semi-permanent burrows in the sediment matrix, which they irrigate continuously. Previous studies have demonstrated that C. volutator burrowing and feeding not only modifies the sediment biogeochemistry but can also modify the overlying water biogeochemistry (during immersion). C. volutator activities have also been shown to be detrimental to microphytobenthic (MPB) biofilms in the immediate vicinity of the burrows. As MPB are the stabilizing force in the estuary, the decimation of biofilm destabilizes the habitat for all the organisms colonising it. However, several aspects of C. volutator ecology remain unclear. First, previous studies on the effect of C. volutator on local (within burrow proximity) MPB diversity have not presented a clear signal as to whether they increase or decrease biodiversity or established whether there is preferential survival amongst MPB taxa with certain cell shapes and sizes or lifestyles. Second, as it has been established that C. volutator have the potential to change the water column, it is possible for them to effect MPB populations remotely (outwith burrow proximity). It is therefore of interest to determine the effects they have, whether such an effect can be achieved within a tidal period, and whether these effects can change MPB biomass, behaviour or diversity over time. A series of controlled mesocosm experiments were carried out to quantify those effects of C. volutator on the water column which were likely to impact MPB survival, to determine whether those effects were specific to C. volutator or common to deposit‐feeding bioturbators, to determine to what degree they could be achieved within a single immersion period, and to separate the effects of C. volutator on MPB bulk (chlorophyll-a in top 5 mm) and photosynthesizing (fluorescing) biomass and diversity both ‘locally' and ‘remotely'. The results of the first 3 experiments consistently showed that C. volutator substantially increased the resuspension of sediment to the overlying water column and that the resulting turbidity could reduce lightpenetration to the sediment by as much as 50% within one immersion period. Results of nutrient fluxes were less consistent and clear within and between experiments but there was some suggestion that increased bioirrigation increased inorganic nitrogen flux to the overlying water column in accordance with previous studies. The effects of C. volutator on local and remote MPB biomass (bulk and surface) and diversity varied between experiments but, broadly speaking: (1) bulk biomass was unaffected, reduced locally, or increased remotely; (2) surface biomass was reduced both locally and remotely; and (3) community diversity (Simpson's diversity index) was consistently unaffected, both locally and remotely. Because increased water column turbidity is the most distinctive calling card of C. volutator but is only likely to affect the photosynthetically active (surface) MPB biomass during immersion, a controlled laboratory experiment was designed to examine the extent to which turbidity could influence MPB migratory behaviour and photosynthetic activity. MPB bulk migration was shown to be driven by sitespecific, entrained rhythms of light availability and spatial variation in light availability only drove micro‐cycling in the photic zone during the immersion period. So, in the absence of C. volutator, or any other turbidity producing phenomenon (deep water columns, high flow rates, physical disturbance, etc.), MPB will remain at the surface to photosynthesize during immersion and the productivity during this period is determined by total light intensity and exposure hours (or ‘light dose'). Therefore, the proximity and size of C. volutator populations to a site is likely to be influential in determining local productivity patterns of MPB. In addition, differences in MPB assemblage composition were shown to influence the biofilm productivity but what drives changes in MPB assemblage composition is still unclear and requires further investigation.
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Edlund, Anna. "Microbial diversity in Baltic Sea sediments /." Uppsala : Dept. of Microbiology, Swedish University of Agricultural Sciences, 2007. http://epsilon.slu.se/200726.pdf.
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Vidal, Dura Andrea. "Controls on microbial diversity and sediment biogeochemistry along a dynamic estuary." Thesis, University of Leeds, 2017. http://etheses.whiterose.ac.uk/18218/.
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Estuaries are the transition between freshwater and marine environments, and regulate the delivery of riverine fluxes to the oceans. The Humber estuary (UK) is considered a major source of nutrients to the North Sea. It is a highly turbid and dynamic macrotidal estuary that receives contaminated fluxes from agriculture, urbanisation, industry and historical mining activities. The chemistry of the river water and the sediments is modified within the estuarine continuum due to mixing. Sediments are subjected to resuspension periodically (on a tidal cycle timescale) and occasionally or seasonally (due to extreme rainfall or flooding episodes), which triggers a series of redox processes that control nutrient and pollutant cycling. During simulated sediment resuspension in aerated conditions, the release of accumulated reduced substrates (ammonium, manganese, iron, sulphur) and trace metals were reversed within relatively short timescales, which is important when assessing the environmental consequences of different resuspension episodes. However, the position in the salinity gradient was the dominant control on sediment geochemistry since a transition from the inner estuary (Mn/Fe-dominated redox chemistry) to the outer estuary (Fe/S-dominated redox chemistry) was observed. To better understand the role of the benthic biogeochemical denitrification processes in the nitrogen cycling, nitrate-dependent oxidation was also investigated in microcosm experiments. The same transition was observed in the nitrate reduction coupled with the oxidation of different inorganic species from the inner to the outer estuary. In this oxidation scenario there was also evidence of trace metal mobilisation. Due to the greater availability of electron donors in the mudflats of the outer estuary, they showed the greatest potential for denitrification and therefore are considered a relevant nitrogen sink in the Humber estuary. Furthermore, in this context of highly spatiotemporal variability, benthic microbial diversity showed a decreasing trend with increasing salinity, but sediment mixing and transport and the presence of strong redox transitions were also environmental parameters shaping the microbial communities in the Humber sediments.
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Barua, Sutapa. "Microbial Diversity and Zinc Toxicity to Pseudomonas sp. from Coeur d' Alene River Sediment." Thesis, Montana State University, 2007. http://etd.lib.montana.edu/etd/2007/barua/BaruaS0807.pdf.
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Coeur d'Alene River (CDAR) in northern Idaho is one of the metal contaminated rivers in US. The sediments of the river are enriched with As, Cd, Cu, Pb, and Zn which are toxic metals to humans and animals. It is hypothesized that microorganisms living in this river sediment can remove the metals and thus detoxify their environment. The objective of this work is to investigate the microbial communities existing in CDAR sediment using 16S ribosomal RNA (rRNA) gene sequencing and 16S rRNA gene microarray (PhyloChip) analysis. According to our phylogenetic analysis, the CDAR clones fell into 13 distinct phylogenetic classes including 2 environmental samples, 1 uncultured bacterium, and an unclassified Chloroflexi. The major representative genera found were Thiobacillus (7 of 91), Azoarcus (7/91), Acidobacterium (6/91), Burkholderia (5/91), Flavobacterium (5/91) and Janthinobacterium (5/91). PhyloChip data showed the presence of 1551 operational taxonomic units (OTUs). 97% of the clone library sequences matched at various taxonomic levels with the microarray results. The results from the clone library and PhyloChip have provided the broad picture of the microorganisms found in the metal polluted CDAR sediment. To better understand the metal toxicity kinetics of specific isolates, Pseudomonas sp. strain JM001 from the CDAR sediment was selected for further study. Cell growth and aqueous Zn removal rate of strain JM001 was observed in batch kinetic experiments. It was found that cell growth rate depends on substrate and nutrient concentration and incubation temperature. The minimum inhibitory concentration (MIC) of Zn to the cells was 0.024 mM and the 50% inhibition in specific growth rate was found at 0.011 mM Zn when cells were grown in nutrient limited defined media at 22 °C. The MIC was 1 mM Zn and 50% inhibition occurred at 0.515 mM Zn in minimal salts medium with vitamin solutions at 35 °C. The results are significant to develop a dose-response model that will quantify the effects of toxic metals on microbial growth and inhibition in complex CDAR environment.
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Nguyen, Thi Tuyet Nga. "Analysing the effect of industrial and urban polluted zones on microbial diversity in the SaiGon -DongNai river system (Vietnam)." Thesis, Université Paris-Saclay (ComUE), 2017. http://www.theses.fr/2017SACLS582/document.
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Le système fluvial Saigon-Dong Nai (SG- DN) est la plus importante source d'eau pour les douze villes et provinces du sud du Vietnam. Il est aujourd'hui gravement pollué par les activités humaines, agricoles, industrielles et domestiques, constituant une menace pour la vie de millions de personnes. Le ministère vietnamien des Ressources naturelles et de l'environnement a rapporté que les rivières ont reçu environ 1,54 milliard de litres d'eaux usées provenant de 70 parcs industriels par jour, dont 35% de déchets médicaux non traités, et que des tests effectués depuis 2006 ont montré des niveaux élevés de pollution, en particulier de substances toxiques organiques. Jusqu'à présent, il n'y a pas de données sur la diversité microbienne dans le système fluvial SG-DN, en particulier dans les sédiments, où la plus grande partie de la biomasse microbienne est généralement localisée. Les échantillons de sédiments ont été recueillis, réseau hydrographique national SG-DN, à 13 endroits dans les rivières représentant des emplacements pollués. Afin de caractériser les populations microbiennes présentes sur nos sites choisis, l'ADN total des échantillons environnementaux a été extrait et amplifié dans les régions V3 à V1 de l'ADNr 16S. L'étude a révélé que la population microbienne changeait de l'amont vers l'aval au niveau du phylum, du genre et de l'OTU après avoir traversé la zone de population industrielle et dense. De plus, les canaux du bassin versant SG-DN sont fortement pollués par de fortes concentrations de composés organiques (PAH) et possèdent différentes communautés bactériennes par rapport aux échantillons des rivièresThe SaiGon-DongNai (SG-DN)river system is the most important major water source for all twelve Southern Vietnam cities and provinces and is now dramatically polluted by industrial and living activities, giving “a threat” to the lives of millions people sharing this water source. The Ministry of Natural Resources and Environment of Vietnam reported that the rivers received around 1.54 billion liters of waste water from 70 industrial parks per day, including 35 percent of untreated medical waste, and tests since 2006 have found pollution in this river has increased to “serious levels”, an especially high concentration of organic toxic substances. Until now, there is no data on the microbial diversity in SG-DN river system especially in the sediments, where most of the microbial biomass is generally located. The sediment samples were collected in 13 locations across the rivers representing warning polluted locations done by Mr. Nguyen Thanh Hung of the National Water Qualifying in SG-DN river system. In order to characterize the microbial populations present at our chosen sites, the total DNA from the environmental samples were extracted and amplified at the V3 to V1 regions of the 16S rDNA. The study revealed that microbial population changed from upstream to downstream at the phylum, genus and OTUs levels after running through the industrial and dense population zone. Moreover, the canals of the SG-DN river catchment are heavily polluted with high concentrations of organic compounds (PAHs) and possessed different bacterial communities compared to the samples from the rivers
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Radl, Viviane. "Influence of trenbolone on the structural and functional diversity of microbial communities from a lake sediment." [S.l.] : [s.n.], 2005. http://deposit.ddb.de/cgi-bin/dokserv?idn=978952626.
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Suárez, Suárez Ana Belén. "Sulphate‐reducing bacterial diversity in a calcareous sandy sediment of Mallorca and community response to hydrocarbon contamination." Doctoral thesis, Universitat de les Illes Balears, 2012. http://hdl.handle.net/10803/84117.
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Aquesta tesi tracta sobre l'efecte de la contaminació per cru de petroli sobre
l'ecosistema costaner mediterrani i sobre el paper fonamental dels sediments marins
en la regulació i el manteniment dels processos biogeoquímics. L'estudi presta especial
atenció a les comunitats bacterianes reductores de sulfat i la seva implicació en la
degradació de contaminants orgànics. La diversitat, abundància i fisiologia dels bacteris
reductors de sulfat que habiten el sediment arenós del nord de Mallorca (Illes Balears),
van ser analitzades mitjançant un enfocament polifàsic, basat en la combinació
d'experiments in situ i in vitro, biologia molecular clàssica i d’última generació, cultius i
determinació d'activitats metabòliques. Els resultats obtinguts durant aquesta tesi
demostren que el sediment mediterrani alberga una microbiota autòctona que podria
prosperar després d'un vessament de cru de petroli i el paper de la qual podria ser
crucial per a la transformació i l'eliminació de compostos orgànics xenobiòtics en
aquest ambient.Esta tesis trata sobre el efecto de la contaminación por crudo de petróleo en el ecosistema costero mediterráneo y sobre el papel fundamental de los sedimentos marinos en la regulación y el mantenimiento de los procesos biogeoquímicos. El estudio presta especial atención a las comunidades bacterianas reductoras de sulfato y a su implicación en la degradación de contaminantes orgánicos. La diversidad, abundancia y fisiología de las bacterias reductoras de sulfato que habitan el sedimento arenoso del norte de Mallorca (Islas Baleares), fueron analizadas mediante un enfoque polifásico, basado en la combinación de experimentos in situ e in vitro, biología molecular clásica y de última generación, cultivos y determinación de actividades metabólicas. Los resultados obtenidos durante esta tesis demuestran que el sedimento mediterráneo alberga una microbiota autóctona que podría prosperar después de un derrame de crudo de petróleo y cuyo papel podría ser crucial para la transformación y la eliminación de compuestos orgánicos xenobióticos en este ambiente.
This thesis discusses the fate and behave of crude oil contamination in the Mediterranean coastal ecosystem, and the essential role of the marine sediments in the regulation and maintenance of biogeochemical processes. The study pays particular attention to the role of sulphate reducing bacterial communities in the degradation of organic matter and pollutants entering the Mediterranean environment. A polyphasic approach based in the combination of in situ and in vitro experiments, next generation and classical molecular biology, cultivation, and the determination of metabolic activities, provided first insights into the diversity, abundance and physiology of sulphate reducing bacteria inhabiting the undisturbed sandy sediment at the north of Mallorca (Balearic Islands). The results obtained during the thesis demonstrate that the undisturbed Mediterranean sediment harbours an autochthonous microbiota that could prosper after a crude oil spill and which role might be crucial for the transformation and removal of hazardous organic compounds in this environment.
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Haynes, K. "Bacterial diversity in intertidal sediment : the effect of algal-derived carbohydrates : an in situ and microcosm approach." Thesis, University of Essex, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.437824.
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Mansoori, Amir Reza. "Study on Flow and Sediment Transport around Series of Spur Dikes with Different Head Shape." 京都大学 (Kyoto University), 2014. http://hdl.handle.net/2433/192160.
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Sanderson, Louis M. "Changes in Fish Diversity Due To Hydrologic and Suspended Sediment Variability in the Sandusky River, Ohio: A Genetic Programming Approach." Bowling Green State University / OhioLINK, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1245699638.
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Sanderson, Louis. "Changes in fish diversity due to hydrologic and suspended sediment variability in the Sandusky River, Ohio a genetic programming approach /." Bowling Green, Ohio : Bowling Green State University, 2009. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=bgsu1245699638.
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Kervroëdan, Léa. "Plant traits and functional diversity effects on runoff and sediment retention : application to soil erosion control in temperate agricultural catchments." Thesis, Amiens, 2018. http://www.theses.fr/2018AMIE0031/document.
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Au sein des communautés végétales, les traits fonctionnels dirigent et influencent les processus sol-plantes. Le ruissellement et l'érosion concentrés, causes principales de la dégradation des sols, peuvent être contrôlés par des végétations herbacées qui créent une rugosité hydraulique induisant la réduction de la vitesse des flux de ruissellement et la rétention des sédiments. L'approche des traits, plutôt que taxonomique, permet de comprendre et caractériser les effets directs de la végétation sur le ruissellement et la rétention des sédiments. Ce projet de recherche vise à approfondir les connaissances vis-à-vis des effets (i) des traits fonctionnels (Chapitre 1), (ii) de la complémentarité des traits (Chapitre 2), et (iii) de la diversité fonctionnelle (Chapitre 3) sur les écoulements concentrés et la rétention des sédiments afin d'évaluer l'efficacité et le design de haies herbacées pour réduire les impacts de l'érosion des sols dans les bassins versants limoneux d'Europe. Parmi les combinaisons de traits principaux identifiées comme augmentant la rugosité hydraulique (densité et diamètre des tiges, et densité et surface foliaire), certains traits sont négativement corrélés. Un meilleur effet pourrait donc être atteint au sein d'assemblage d'espèces par un effet complémentaire des traits. Cependant, des effets non-additifs des diversités en espèces et fonctionnelle ont été trouvés, chacun généré par un effet dominant des traits dans les communautés testées. Ces effets des traits et de la diversité fonctionnelle sur la rugosité hydraulique et la rétention des sédiments constituent une nouvelle avancée dans la compréhension des effets de l'assemblage des traits sur les processus d'écoulement et d'érosion des sols ainsi qu'une base pour le design et la modélisation des haies herbacées pour le contrôle du ruissellement et de l'érosionPlant-soil processes are driven and influenced by plant functional traits in vegetation communities. Concentrated runoff and erosion constitute the main cause of soil degradation and can be managed by herbaceous vegetation creating hydraulic roughness that induces flow velocity reduction and sediment retention. Using plant trait-based approach, unlike taxonomical approach, allows to understand and characterise the direct effects of the vegetation on runoff and sediment retention. This research project aims to deepen the knowledge regarding the effects of (i) plant functional traits (chapter 1), (ii) traits' complementarity (chapter 2) and (iii) functional diversity (chapter 3) on concentrated runoff and sediment retention processes, in order to evaluate the efficiency and design of herbaceous hedges to reduce the impacts of soil erosion in loamy European agricultural catchments. The identification of the main efficient traits and traits' combinations towards hydraulic roughness increase (stem density, diameter, leaf area and density) highlighted negatively correlated traits, suggesting that a trade-off could be reached within a plant species assemblage through a complementarity effect of the traits. However, non-additive effects of plant species diversity and functional diversity were found, both driven by dominant traits in the community. The effects of traits and functional diversity on the hydraulic roughness and sediment retention constitute a new advance in the understanding of plant trait assemblage on runoff and soil erosion processes and a baseline for the design and modelling of herbaceous hedges for runoff and erosion control
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Rowlands, Gwilym. "Remote Sensing the Diversity, Distribution and Resilience of Coral Reef Environments." NSUWorks, 2013. http://nsuworks.nova.edu/occ_stuetd/75.
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Chapter 2:
This chapter introduces the five study sites (Ras Al‐Qasabah; Al Wajh; Yanbu; Farasan Banks; and Western Farasan Islands) along with the fieldwork and detailed benthic mapping and bathymetry mapping conducted in the Saudi Arabian Red Sea. In the Western Farasan Islands two candidate mapping technologies were compared. Firstly, the QuickBird multispectral satellite sensor and secondly the CASI‐550 airborne hyperspectral sensor. In processing the CASI imagery, it was necessary to customize processing to correct for an unusual across‐track artifact caused by lens condensation. On the basis of cost, logistical constraints, spectral reliability, and project needs, multispectral imagery was found to be the most appropriate technology for regional‐scale mapping. Over 20,000 sq. km of high quality QuickBird imagery were amassed across the five study sites. This represents approximately half the shallow water (<20 m) environment of the Saudi Arabian Red Sea. The work presented in this chapter provides a blueprint for processing such large image data sets. Maps with a minimum mapping unit (MMU) of 7.5 sq. m, and a thematic resolution of fifteen habitat classes were produced at an overall accuracy (Tau statistic) of 70%. The five study sites were found to differ substantially in terms of the type, quantity and spatial arrangement of habitats present. The study illustrates the power of remote sensing for delivering regional‐scale audits of coral reef environments.
Chapter 3:
Coral reefs and their associated accumulations of carbonate sediment adopt particularly complex planform geometries atop the coastal shelf of the Saudi Arabian Red Sea. By assembling 95,000 sq. km of remote sensing data into a GIS, this study aims to relate the morphology of these shallow‐water depositional environments to processes that sculpt the coastal zone. A typology is developed that sorts carbonate systems into end‐members on the basis of their morphology and relationship to the coastline. The resulting GIS was interrogated for spatial patterns in the distribution and abundance of the end‐members. While several depositional morphologies are present throughout the length of the Saudi Arabian Red Sea, the occurrence of others is restricted to narrow regions of latitude. Such differences in distribution can be explained in process‐terms by the rift tectonics of the Red Sea basin, spatial variability in the presence of sub‐seafloor evaporites, and the input of siliciclastic detritus onto the coastal shelf via wadis. This chapter provides a foundation for understanding the morphological diversity of shallow‐water carbonate systems in both the modern ocean and rock record.
Chapter 4:
In this chapter a framework is proposed for spatially estimating a proxy for coral reef resilience using remote sensing. Data spanning over 20,000 sq. km of coral reef habitat were obtained using the commercial QuickBird satellite, and freely available imagery (NASA, Google Earth). Principles of coral reef ecology, field observation, and remote observations, were combined to devise mapped indices. These indices capture important and accessible components of coral reef resilience. Indices are divided between factors known to stress corals, and factors incorporating properties of the reef landscape that resist stress or promote coral growth. The first‐basis for a remote sensed resilience index (RSRI), an estimate of expected reef resilience, is proposed. Developed for the Red Sea, the framework of the analysis is flexible and with minimal adaptation, could be extended to other reef regions. The chapter illustrates how remote sensing can be used to deliver more than simply habitat maps of coral reefs.
Chapter 5:
In this chapter, a fundamental measure of coral reef health, coral cover, is assessed in relation to two physical parameters, water depth and wave height. Light availability declines rapidly with depth, which influences the photosynthetic productivity of coral. Where waves break, they produce a severe increase in marine turbulence, and generate currents that may extend beyond the surf zone. The study is focused on the Farasan Banks where some 4000 sq. km of reef habitat are spread across 12,000 sq. km of the Saudi Arabian coastal shelf. The size of the system creates logistical challenge for standard field‐based monitoring methodologies, such as SCUBA surveys. Here, rapid video assessments were employed to deliver measures of coral health across eight percentage cover classes at 472 locations. Whilst water depth can be reliably derived from satellite, assessing wave height is problematic since the parameter is both spatially and temporally variable. Using daily, satellite derived meteorology, a spatially explicit wave model was developed spanning the nine year period from 1999 to 2008. For the majority of the
video sites in the Farasan Banks, coral cover was found to be <11%. This statistic hides the counter trend, however that there are robust patterns in higher coral abundance that can be characterized by water depth and wave height. In the inshore, wave height had little bearing on coral cover, instead video sites with a high coral cover were found with a greater probability in shallow (<9m, reef environments. In the offshore, wave exposure exercises stronger control on coral cover than in the inshore, such that video sites with a coral cover greater than 50% were exclusively found in areas where significant wave height exceeds 2 m. The water depth at which the highest coral cover occurs is also deeper offshore than inshore. Once quantified, the conservative behavior of coral cover with respect to water depth and hydrodynamic exposure offers relevant insight to the management of coral reef environments at regional extent.
Chapter 6:
Carbonate sequence stratigraphy is founded on the principle that changes in relative sea level are recorded in the rock record by the accumulation of sediment with relative‐water‐depth dependent attributes. While at the scale of a shelf‐to‐basin transect, facies clearly stratify by water depth, the relationship blurs for depths <40 m, the most vigorous zone of carbonate production, where the intrinsic processes of storm and wave reworking influence the seabed through submarine erosion and sediment redistribution. Remote sensing imagery, field observations, and hydrodynamic models for two reef‐rimmed shore‐attached carbonate platforms in the Red Sea show neither water depth nor energy regime to be reliable indicators of facies type when considered in isolation. Considered simultaneously, however, the predictive power of the two variables rises significantly. The results demonstrate it to be an oversimplification to assume a direct link between palaeo‐water depth and depositional lithofacies diversity, while highlighting the importance of hydrodynamics in directing the accumulation of carbonate sediments in the shallow photic zone. While the size distributions of facies in the two focus areas, Al Wajh and Ras Al‐Qasabah, follow power laws, no direct relationship between the lateral continuity of the facies belts and water depth or wave height are reported. The work is relevant for the interpretation of meter‐scale subtidal carbonate cycles throughout the geologic record.
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Pandolfo, Alana. "Efetividade de um corredor ecológico à manutenção da diversidade bentônica em ecossistemas aquáticos lóticos." Universidade Estadual do Oeste do Parana, 2014. http://tede.unioeste.br:8080/tede/handle/tede/705.
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The presence of riparian vegetation is unquestionable for the water quality of streams and rivers, because it buffers impacts coming from the surroundings of these ecosystems, particularly in areas used for agricultural and livestock activities. In this sense, this study aimed to evaluate and compare the composition and structure of the benthic invertebrate community in two first order streams, one located in an ecological corridor and another in continuous vegetation, but not set up as a corridor. We assumed that the riparian vegetation is the main factor influencing the water quality of these environments, especially the one inside the ecological corridor. To test our hypothesis, bimonthly sediment samples were taken with kick sampling for community analysis in three regions (headwaters, middle and mouth) of each stream. Samples were subjected to subsampling technique and invertebrates were identified to genus levels. The distribution and composition of taxa were similar between the two streams, with the exception of the headwaters of Apepu. In this sampling site, the sediment type and the successional stage of the riparian vegetation were not conducive to the integrity of the benthic community. However, community reestablishment was observed along the longitudinal axis of the stream according to the characteristics of natural environments and the presence of sensitive organisms. Furthermore, the similarity in biotic and abiotic composition of both streams highlight the importance of creating one more ecological corridor in the riparian vegetation of the Gualberto Stream, covering its watershed. These actions seek to preserve and maintain the biological diversity of water resources and ensure that measures aimed at water resource management are implemented and enforced as provided for in environmental legislation.
Este trabalho teve o objetivo avaliar espacialmente a influência da vegetação ciliar para a formação de corredores ecológicos, através da comparação da fauna de zoobentos de dois riachos, localizados em áreas internas e externas a um Corredor de Biodiversidade. Foram realizadas coletas bimestrais do sedimento com o coletor kick sampling para análise da comunidade, em três regiões (nascente, meio e foz) de cada riacho. As amostras foram submetidas à técnica de subasmotragem e os invertebrados foram identificados à nível de gênero. A distribuição dos táxons foi semelhante entre os dois riachos, com excessão da nascente do Apepu. Nesse ponto amostral o tipo de sedimento e o estágio sucessional da vegetação ciliar influenciaram negativamente na composição da comunidade. No entanto, foi possível observar a capacidade de resiliência desse riacho, através do reestabelecimento da comunidade de acordo com as carcaterísticas de ambientais naturais e a presença de organismos sensíveis. Devido a similaridade na composição biótica e abiótica ressaltamos a importância da criação de um corredor ecológico na região de mata ciliar do riacho Gualberto, a fim de preservar e manter a diversidade da comunidade de macroinvertebrados bentônicos na da região.
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Domingues, Mercia Regina. "Investigação sobre a diversidade microbiana e a filogenia de arquéias e bactérias em consórcios anaeróbios metanogênicos, originados de sedimentos estuarinos enriquecidos com clorofenóis." Universidade de São Paulo, 2007. http://www.teses.usp.br/teses/disponiveis/18/18138/tde-01122008-165904/.
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Este trabalho investigou a diversidade microbiana e a filogenia de arquéias e bactérias em consórcios anaeróbios metanogênicos, originados de sedimentos estuarinos enriquecidos com pentaclorofenol (PCP) e 2,6-diclorofenol (2,6-DCP). Para tanto foram construídas bibliotecas genômicas e utilizados métodos moleculares independentes de cultivo como a Eletroforese em Gel de Gradiente Desnaturante (DGGE) e o seqüenciamento de segmentos específicos do DNAr 16S microbiano. Os resultados da DGGE permitiram verificar alterações na estrutura das comunidades microbianas, as quais provavelmente ocorreram devido às adversidades ocorridas nos sistemas durante o período de incubação como a entrada de oxigênio nos frascos e o acúmulo de compostos clorados no meio de cultivo, principalmente o 2,6-DCP. A estimativa da diversidade beta, realizada pela comparação dos padrões de bandas da DGGE, também permitiu inferir que as alterações nas composições das comunidades de arquéias e bactérias foram devidas às duas estratégias empregadas para o enriquecimento da microbiota autóctone do estuário estudado, ou seja, a pasteurização/não pasteurização das amostras de sedimentos estuarinos. Os resultados das análises filogenéticas revelaram que as seqüências analisadas dos clones bacterianos foram relacionadas ao grupo das bactérias Gram-positivas com baixo conteúdo de G+C pertencentes à Ordem Clostridiales (100%) do Filo Firmicutes e as das arquéias relacionadas ao grupo das metanogênicas pertencentes às Ordens Methanobacteriales (7,1%), Methanosarcinales (14,3%), Methanomicrobiales (57,1%) e arquéias não identificadas (21,4%) do Filo Euryarchaeota. Em relação às bactérias, alguns clones foram identificados como pertencentes aos gêneros Sedimentibacter, Clostridium e Alkalibacter, os quais são representados por microrganismos que apresentam metabolismo fermentativo e requerem a presença de extrato de levedura para o crescimento. Provavelmente as bactérias analisadas neste trabalho fermentaram a glicose e o piruvato, os quais foram utilizados como doadores de elétrons, com conseqüente produção de lactato, etanol, butirato, acetato, formiato e hidrogênio/gás carbônico, que podem ter sido utilizados por outros grupos de microrganismos no processo global da digestão anaeróbia. Tais bactérias foram importantes para o processo global de degradação dos clorofenóis, pois também utilizaram como doadores de elétrons os produtos parcialmente degradados por outras bactérias fazendo com que não houvesse acúmulo desses compostos no sistema. Enquanto que algumas arquéias foram relacionadas a organismos hidrogenotróficos pertencentes aos gêneros Methanoculleus e Methanocalculus, Methanobacterium, e acetotróficos do gênero Methanosaeta, as quais utilizaram como substratos para a metanogênese os subprodutos da fermentação bacteriana, ou seja, o \'H IND.2\'/\'CO IND.2\', o formiato e o acetato, contribuindo assim para a manutenção do equilíbrio das demais reações ocorridas no sistema. Desta forma, os dados obtidos neste trabalho poderão auxiliar na compreensão do funcionamento de ecossistemas contaminados por compostos clorados, bem como contribuir para o desenvolvimento de novos processos biotecnológicos aplicados aos problemas ambientais.This work aimed to investigate microbial diversity and phylogeny of archaea and bacteria microrganisms methanogenic in estuarine sediment samples enriched with organic sources under methanogenic and halophlic conditions. The samples were obtained from previous study on anaerobic degradation of pentachlorophenol (PCP) and 2,6-dichlorophenol (2,6-DCP). Microbial studies were done by the molecular methods without cultivation requirement, Denaturing Gradient Del Electrophoresis (DGGE) and specific segments of 16S rDNA sequencing. DGGE-profile showed structure changes in microbial community. Probably, as a consequence of \'O IND.2\' intake and accumulation of chlorinated compounds, mainly 2,6-DCP, in the culture medium. The beta diversity estimation showed that changes in arquaea and bacteria communities probably occurred as a consequence of the two enrichment strategies used for estuarine indigenous microorganisms, pasteurization and non-pasteurization of the estuarine sediments samples. Phylogenetic analysis indicated the presence of gram-positive bacterium with low G+C content related to Clostridiales Order (100%) belonging to Firmicutes Phylum, as well as related to methanogenic archaea from Methanobacteriales (7,1%), Methanosarcinales (14,3%) and Methanomicrobiales (57,1%) Order. Non-identified archaeas from Euryarchaeota Phylum were also found (21,4%). Concerning to bacterias, it was identified clones related to genera Sedimentibacter, Clostridium and Alkalibacter, which have fermentative metabolism and require yeast extract to grow. Probably, bacterial cells analised in this work fermented glucose and pyruvate producing lactate, ethanol, butirate, acetate, formiate and hydrogen/carbon dioxide. All these products could be used for other microbial groups in the global process of anaerobic digestion. The bacterial microorganisms were important to global process of chlorophenol degradation because contributed in the overall process utilizing the products partially degraded by other bacterias and preventing its accumulation in the system. Identified archaeal cells were related to hydrogenotrophs microorganisms of the genera Methanosaeta, Methanoculleus, Methanocalculus and Methanobacterium, which utilized the bacterial fermentation sub-products as acetate, \'H IND.2\'/\'CO IND.2\' and formiate as substrate for the methanogenesis, contributing for the maintenance of the balance of other reactions occurred in the system. The results of this work give advanced knowledge about understanding biotechnological process of contaminated ecosystems by chlorinated compounds. Therefore, it could contribute to development of new biotechnological processes applied to environmental problems.
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Queiroz, Luciano Lopes. "Padrões de diversidade microbiana em sedimentos marinhos profundos influenciados por uma exsudação de asfalto." Universidade de São Paulo, 2015. http://www.teses.usp.br/teses/disponiveis/42/42132/tde-26082015-171953/.
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Sedimentos de mar profundo são ambientes estáveis e homogêneos, apesar disso, eles apresentam uma grande variedade de habitats disponíveis, possibilitando uma alta diversidade microbiana. A distribuição espacial dos micro-organismos é influenciada por fatores locais e regionais. Os fatores locais são associados à estrutura do ambiente e os fatores regionais, a limitação na dispersão dos micro-organismos que compõem as comunidades e eventos históricos que eventualmente podem modificar o ambiente. Eventos como a liberação de hidrocarbonetos das camadas mais profundas do sedimento para superfície podem alterar os padrões de distribuição espacial das comunidades microbianas, devido o aumento na disponibilidade de carbono e consequentemente selecionando as espécies capazes de degradá-los. Esses eventos são denominados de exsudações de asfalto e foram encontradas na região de estudo. Considerando a falta de conhecimento e a importância dos micro-organismos em sedimentos de mar profundo do oceano Atlântico Sul, o objetivo desse estudo foi compreender os padrões de diversidade microbiana nessas regiões e também investigar como o óleo proveniente da exsudação de asfalto influência as comunidades de micro-organismos no seu entorno. Esse estudo foi realizado na região do Platô de São Paulo que foi dividido em duas regiões, norte e sul. A diversidade microbiana foi estudada em 14 amostras de sedimento de mar profundo, nove amostras na região norte e cinco na sul. A exsudação de asfalto foi encontrada na região norte, influenciando diretamente três das nove amostras. As comunidades foram estudadas através dos métodos de eletroforese em gel de gradiente desnaturante (DGGE), PCR quantitativa (qPCR) e sequenciamento de última geração (Ion Torrent). A distribuição espacial das comunidades foi analisada em diferentes escalas espaciais: verticalmente, variando com a profundidade do sedimento (≤ 4 cm), localmente, em cada uma das regiões amostradas (1-34 Km) e regionalmente, comparando as regiões norte e sul (> 250 Km). O perfil da comunidade obtido com a técnica de DGGE mostrou que as comunidades microbianas foram menos similares entre as regiões e apresentaram relação com a distância geográfica para arqueia e bactéria. Os valores de similaridade foi maior localmente do que regionalmente. A similaridade obtida nas camadas de profundidade analisadas foi alta e não houve relação com a distância geográfica. O número de células entre as camadas de profundidades foi diferente, com tendência de diminuição com o aumento da profundidade. As classes bacterianas mais abundantes foram Alphaproteobacteria (30%), Acidimicrobiia (18%), Gammaproteobacteria (16%), Deltaproteobacteria e Gemmatimonadetes (3%). A composição das comunidades influenciadas pela exsudação de asfalto não teve relação com a presença do óleo ou com as camadas de profundidade. A distância geográfica e a exsudação de asfalto foram importantes fatores para determinação da distribuição geográfica das comunidades microbianas em sedimento marinhos profundos do Platô de São Paulo. Apesar da ausência de relação entre o óleo proveniente da exsudação de asfalto e a composição das comunidades, a alta abundância de Alphaproteobacteria e a importância da distância dentro da região norte são indicativos do aumento da heterogeneidade causado pela exsudação de asfalto. Mais estudos procurando compreender a composição geoquímica dos sedimentos e do óleo são necessários para explicar como esses fatores influenciam a estruturação das comunidades microbianas estudadas.Deep-sea sediments are stable and homogeneous environments, however, they have a high variety of available habitats, allowing a high microbial diversity to occur. Microbial spatial distribution is determined by local and regional factors. Local factors are associated to environment structure and regional factors, to microbial dispersal limitation and historical events that may cause environmental changes. Historical events such as hydrocarbon emanation from sub-seafloor to seafloor may change the patterns of microbial spatial distribution, due to an increase of carbon, thus, selecting species capable to degrade them. These events are denominated as asphalt seep and they were found on the studied region. Considering the lack of knowledge and the importance of microorganisms on deep-sea sediments from South Atlantic ocean, this study aims to understand the patterns of microbial spatial distribution and how the oil from asphalt seep influence the microbial communities. This study was realized in São Paulo Plateau region. The plateau was divided in two regions, north and south. Microbial diversity was studied from 14 deep-sea sediment samples, nine samples from north region and five from south region. The asphalt seep was found in north region from São Paulo Plateau, directly affecting three of the nine samples. The communities were studied through denaturing gradient gel electrophoresis (DGGE), quantitative PCR (qPCR) and next generation sequencing (Ion Torrent). The spatial distribution of the communities was analyzed at different spatial scales: sediment depth (≤ 4 cm), local (1-34 Km) and regional (> 250 Km). Microbial communities were less similar between regions and showing relation with geographic distance to achaea and bacteria. Similarity values within regions were higher then between them, but the geographic distance was also important to both domains, despite samples being closer. Similarity values between sediment depths were high and have no relation with geographic distance. The cell number between sediment depths was different, with tendency to decrease with depth increase. The most abundant classes were Alphaproteobacteria (30%), Acidimicrobiia (18%), Gammaproteobacteria (16%), Deltaproteobacteria e Gemmatimonadetes (3%). The communities composition influenced by asphalt seep have no relation with oil presence and sediment depths. Geographic distance and asphalt seep were important factors to determine the spatial distribution of microbial communities in deep-sea sediments from São Paulo Plateau. Despite the absence of relation between oil from asphalt seep and communities composition, the high abundance of Alphaproteobacteria and the importance of distance within north region are indicative of heterogeneity increase caused by asphalt seep. More studies aiming to understand the geochemical composition from sediments and oil are necessary to explain how these factors influence the communities structure.
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Bleul, Catrin. "Molekularbiologische Analyse mikrobieller Gemeinschaften in Talsperrensedimenten." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2004. http://nbn-resolving.de/urn:nbn:de:swb:14-1097570982718-83940.
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Mikrobielle Prozesse spielen eine wichtige Rolle im Sediment von Talsperren und Seen. Demgegenüber stehen nur unzureichende Erkenntnisse über die Zusammensetzung mikrobieller Biozönosen in Sedimenten sowie deren Aktivität zur Verfügung. Das Ziel dieser Studie war die Untersuchung und der Vergleich der Zusammensetzung und der Struktur mikrobieller Gemeinschaften in Sedimenten um eine Abschätzung der mikrobiellen Diversität in Talsperrensedimenten unterschiedlicher Trophie zu erreichen. Durch die Kombination der in dieser Arbeit verwendeten Methoden (Vergleichende 16S rDNA Analyse, Fingerprinttechniken, klassische Methoden) konnte eine Charakterisierung der mikrobiellen Zusammensetzung der obersten 5 cm von den Talsperrensedimenten Neunzehnhain, Muldenberg, Quitzdorf und Saidenbach erzielt werden. Die vergleichende 16S rDNA Analyse offenbarte in 2541 analysierten rekombinanten Klonen 528 verschiedene Sequenztypen, welche zu 293 OTUs zusammengefaßt werden konnten. Obwohl die Gemeinschaften der verschiedenen Talsperren nur schwach auf der Ebene der phylogenetischen Gruppen differierten, konnte durch die Verwendung von Ähnlichkeitsindices gezeigt werden, dass jede Talsperre eine spezifische mikrobielle Sedimentgemeinschaft aufweist. Über 60% aller Klone zeigten Ähnlichkeiten von mehr als 97% zu 16S rDNA-Sequenzen kultivierter Organismen oder phylogenetisch eingeordneten Sequenzen (14 bekannte phylogenetische Gruppen). Alle anderen Klone zeigten hohe Sequenzhomologien zu unidentifizierten, phylogenetisch bisher nicht eingeordneten Bakterien. Diese Bakterien waren mit Anteilen zwischen 19,8% (Muldenberg) und 54,6% (Saidenbach) in den 16S rDNA Bibliotheken repräsentiert. Mittels Fingerprinttechniken (DGGE, T-RFLP, ARISA) konnten komplexe Muster der mikrobiellen Diversität erzeugt werden. Dabei konnten die Ergebnisse der 16S rDNA Analyse bestätigt werden. Durch die verwendeten Methoden konnte eine komplexe mikrobielle Diversität in den Sedimenten aufgedeckt werden und die Ergebnisse weisen darauf hin, dass die mikrobielle Diversität in Sedimenten wesentlich höher ist als bisher angenommen.
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Blythe, Demitra E. "Assessing the Ecological Implications of the Altered Flow and Sediment Regimes of the Rio Grande Along the West Texas-Mexico Border." DigitalCommons@USU, 2018. https://digitalcommons.usu.edu/etd/7358.
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Large, exotic (those whose headwaters are in distant places) rivers are some of the most unique and diverse ecosystems on earth. Because they often flow through a multitude of biomes and climates, their waters are a vital resource not only for the organisms that inhabit these rivers, but for human societies as well. Thus, large rivers, like the Rio Grande, that flow through arid and agricultural regions are highly regulated and diverted. Regulation and dewatering upset a river’s natural flow regime (e.g., magnitude, duration, timing of large flood events), subsequently impacting the river’s ability to transport its sediment supply, and eventually perturbing a river into either sediment surplus or deficit. The combination of altered flow and sediment regimes influence the availability of habitat essential for the survival and viability of aquatic organisms, such as fish and invertebrates. In addition, increased deposition of sediment creates areas suitable for invasive riparian vegetation to establish, likely affecting habitat complexity and increasing the abundance of leaf litter deposited into the river. The altered flow and sediment regimes, in combination with invasive riparian vegetation, culminate and eventually affect the food resources and aquatic communities present in a river ecosystem. Most often, the links between the physical perturbations to a system with the biological factors are poorly understood. In this study, we use distinct segments of the Rio Grande along the US-Mexico border to compare areas with greater and lower habitat heterogeneity, water quality, and invasive riparian species abundance to better understand what physical factors can influence aquatic species such as fish and invertebrate communities. We identify critical limiting factors for the native fish community present, and link the altered flow and sediment regimes with the aquatic ecological template of the Rio Grande.
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Gill, Hardeep. "The Effect of Aluminium Industry Effluents on Sediment Bacterial Communities." Thèse, Université d'Ottawa / University of Ottawa, 2012. http://hdl.handle.net/10393/23423.
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The goal of this project was to develop novel bacterial biomarkers for use in an industrial context. These biomarkers would be used to determine aluminium industry activity impact on a local ecosystem. Sediment bacterial communities of the Saguenay River are subjected to industrial effluent produced by industry in Jonquière, QC. In-situ responses of these communities to effluent exposure were measured and evaluated as potential biomarker candidates for exposure to past and present effluent discharge. Bacterial community structure and composition between control and affected sites were investigated. Differences observed between the communities were used as indicators of a response to industrial activity through exposure to effluent by-products. Diversity indices were not significantly different between sites with increased effluent exposure. However, differences were observed with the inclusion of algae and cyanobacteria. UniFrac analyses indicated that a control (NNB) and an affected site (Site 2) were more similar to one another with regard to community structure than either was to a medially affected site (Site 5) (Figure 2.4). We did not observe a signature of the microbial community structure that could be predicted with effluent exposure. Microbial community function in relation to bacterial mercury resistance (HgR) was also evaluated as a specific response to the mercury component present in sediments. Novel PCR primers and amplification conditions were developed to amplify merP, merT and merA genes belonging to the mer-operon which confers HgR (Table 5.6). To our knowledge, the roles of merP and merT have not been explored as possible tools to confirm the presence of the operon. HgR gene abundance in sediment microbial communities was significantly correlated (p < 0.05) to total mercury levels (Figure 3.4) but gene expression was not measurable. We could not solely attribute the release of Hg0 from sediments in bioreactor experiments to a biogenic origin. However, there was a 1000 fold difference in measured Hg0 release between control and affected sites suggesting that processes of natural remediation may be taking place at contaminated sites (Figure 3.7). Abundance measurements of HgR related genes represent a strong response target to the mercury immobilized in sediments. Biomarkers built on this response can be used by industry to measure long term effects of industrially derived mercury on local ecosystems. The abundance of mer-operon genes in affected sites indicates the presence of a thriving bacterial community harbouring HgR potential. These communities have the capacity to naturally remediate the sites they occupy. This remediation could be further investigated. Additional studies will be required to develop biomarkers that are more responsive to contemporary industrial activity such as those based on the integrative oxidative stress response.
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Seitz, Steffen [Verfasser], and Thomas [Akademischer Betreuer] Scholten. "Mechanisms of Soil Erosion in Subtropical Chinese Forests - Effects of Species Diversity, Species Identity, Functional Traits and Soil Fauna on Sediment Discharge / Steffen Seitz ; Betreuer: Thomas Scholten." Tübingen : Universitätsbibliothek Tübingen, 2015. http://d-nb.info/1197693580/34.
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Durbin, Alan Teske Andreas. "Microbial diversity of oligotrophic marine sediments." Chapel Hill, N.C. : University of North Carolina at Chapel Hill, 2009. http://dc.lib.unc.edu/u?/etd,2627.
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Thesis (M.S.)--University of North Carolina at Chapel Hill, 2009.Title from electronic title page (viewed Oct. 5, 2009). "... in partial fulfillment of the requirements for the degree of Master of Science in the Department of Marine Sciences." Discipline: Marine Sciences; Department/School: Marine Sciences.
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Brink, C. J. "Bend diversion to minimise sediment intake." Thesis, Stellenbosch : University of Stellenbosch, 2004. http://hdl.handle.net/10019.1/16262.
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Thesis (MScIng)--University of Stellenbosch, 2004.ENGLISH ABSTRACT: The primary aim of the research was to determine the optimum diversion location in a curved channel to minimise the abstraction of sediment. The secondary aim was to determine the optimum diversion angle for a diversion channel located on the outside of a bend at the optimum diversion location. The velocity distribution in the curved channel was investigated to try obtain a better understanding of curvilinear flow. The scour patterns in the channel were monitored in order to compare them with the measured velocity distributions. Simulations were carried out with the DELFT 3D (hydrodynamics) and Mike21C (sediment dynamics) modelling programmes and compared with the results obtained from laboratory experiments and with existing empirical formulas. The optimum diversion location was found to be located on the outside of the bend in the downstream section of the bend. Three main scour zones were identified with the third scour zone at the location of the maximum velocity. The location of the maximum velocity was found to be relatively constant with varying Froude numbers, but moving in the downstream direction with increasing radius of curvature-to-width ratio. The velocity distributions in the horizontal and vertical planes are well defined and correspond to descriptions in the literature. It is evident that the diverted discharge ratio increases with an increase in the diversion angle while it decreases with an increase in Froude number. Higher Froude numbers in the curved channel lead to more favourable conditions for the diversion of water. The diversion does not influence the secondary flow patterns (for the range of Diversion Discharge Ratio’s tested) and that the maximum velocity zone stayed in the same location as in the tests without a diversion. The hydrodynamics of the laboratory experiments were well simulated with the DELFT 3D hydrodynamic model, using three-dimensional and two-dimensional formulations. Mike21C was used to simulate the sediment dynamics of some of thelaboratory experiments that gave relatively good agreement with experimental data. A two-dimensional depth averaged model could therefore be used with reliability to simulate field conditions in relatively shallow rivers, and is preferred to empirical methods to predict maximum scour that were calibrated under very specific hydraulic conditions.
AFRIKAANSE OPSOMMING: Die primêre doel van navorsing was om die optimum uitkeer-posisie in ‘n draai te bepaal om sodoende sediment onttrekking te minimiseer. Die sekondêre doel was om die optimum uitkeringshoek vir ‘n uitkeerkanaal te bepaal wat geleë is aan die buitekant van ‘n draai by die voorgestelde optimum uitkeer-posisie. Die snelheidsverspreiding in die draai was ook ondersoek om te probeer om spiraalvloei beter te verstaan. Die uitskuurpatrone in die kanaal is ook gemonitor om dit te kon vergelyk met die gemete snelheidsverspreiding. Numeriese simulasies is gedoen met DELFT 3D (hidrodinamika) en Mike21C (sediment dinamika) modelleringsprogrammatuur en is vergelyk met die resultate van die laboratorium eksperimente asook met die van bestaande empiriese vergelykings. Daar is gevind dat die optimum uitkeer-posisie aan die buitekant van ‘n draai aan die stroomaf-kant van die draai geleë is. Drie hoof uitskurings-areas is gevind terwyl die derde area ooreenstem met die posisie van maksimum snelheid. Die posisie waar die maksimum snelheid voorkom is relatief konstant met ‘n verandering in Froude-getal, maar beweeg in die stroomaf-rigting met ‘n styging in die radius-tot-wydte verhouding. Die vertikale en horisontale snelheidsverspreiding is goed gedefinieer en stem ooreen met soortgelyke beskrywings in die literatuur. Die uitkeer-vloei verhouding styg met ‘n stygende uitkeerhoek terwyl dit daal met ‘n styging in Froude-getal. Daar is ook gevind dat groter Froude-getalle meer gunstige omstandighede skep vir die uitkeer van water. Die uitkeer-kanaal beïnvloed nie die sekondêre vloei-patrone nie (vir die reeks van uitkeer vloei-verhoudings wat getoetsis) en die sone van maksimum snelheid bly in dieselfde omgewing vir hierdie toetse as vir die toetse sonder ‘n uitkeer kanaal. Die hidrodinamika van die laboratorium eksperimente is goed gesimuleer m.b.v die DELFT 3D numeriese program, terwyl Mike21C gebruik is om die sedimentdinamika te simuleer. Die resultate van die Mike21C simulasies vergelyk relatief goed met die eksperimentele data en kan met ‘n redelike graad van vertroue aangewend word om veldkondisies te simuleer in relatiewe vlak riviere. Dit word aanbeveel bo die empiriese vergelykings om maksimum uitskuring te voorspel aangesien die empiriese vergelykings gekalibreer is vir baie spesifieke hidroulise kondisies.
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Luglia, Mathieu. "Caractérisation et facteurs structurants des fonctions microbiennes des sédiments de la zone intertidale en Guyane française : des vasières estuariennes aux mangroves matures." Thesis, Aix-Marseille, 2014. http://www.theses.fr/2014AIXM4340/document.
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En contexte équatorial, les sédiments intertidaux sont colonisés par un continuum écologique allant de vasières en cours de stabilisation à des sols colonisés par divers faciès de mangroves. Les fonctions microbiennes édaphiques de ces écosystèmes sont méconnues. Ces recherches ont donc eu pour objectif de définir les facteurs de contrôle et de variabilité spatio-temporelle des fonctions microbiennes des milieux estuariens et littoraux de Guyane française. Elles ont été conduites sur divers stades de colonisation biologique de ces habitats et à diverses échelles spatio-temporelles en tenant compte du rôle de l'instabilité hydro-sédimentaire et des variabilités induites par les saisons hydro-climatiques. Différents facteurs pouvant influencer les fonctions microbiennes ont été considérés : i) la qualité chimique (RMN solide du 13C) de la MOS en fonction de la composition des formations végétales et de leurs stades de développement ; ii) les caractéristiques physico-chimiques des sédiments et des eaux interstitielles en fonction de la localisation des divers faciès de mangroves. Les résultats ont mis en évidence l'importance des instabilités hydro-sédimentaires dans la mise en place et la structuration des fonctions microbiennes sédimentaires de Guyane. En outre, pour les différents modèles étudiés, les facteurs de structuration sont apparus variables. Néanmoins, la MO, en termes de quantité et de qualité, s'est révélée être un facteur prépondérant pour l'expression de ces fonctions des stades allant de la vasière nue à la jeune mangrove. En revanche, il est apparu plus difficile de discerner des facteurs structurants génériques pour les divers faciès de mangroves maturesUnder equatorial conditions, coastal sediments of intertidal mudflats form an ecological continuum, from bare mud being stabilized to soil settled by various mangrove facies. Edaphic microbial functions of terrestrial ecosystems are extensively documented; on the contrary, this is not the case with regards to sedimentary environment. This study had the main objective defining the drivers of the spatiotemporal variability of microbial functions (aerobic respiration, metabolic diversity, and enzyme activities) in coastal sediments of French Guiana. These researches were carried out according to biological colonization states (mudflats, pioneer and mature mangroves) and using various spatiotemporal scales considering the fundamental role of the hydro-sedimentary instability and potential variability due to hydro-climatic seasons. Different factors which can influence microbial functions were studied: i) the chemical quality (13C solid-state NMR) of OM with respect to vegetation presence and composition, and its development state; ii) the physicochemical characteristics of sediments and porewaters according to localization and topography of the different mangrove facies. Generally, results showed the importance of hydro-sedimentary instability for the establishment and structuring of microbial functions. Moreover, giving the different models, structuring factors were variables. However, OM, in terms of quantity and quality, was overriding for the expression of these functions and this was true for the evolution states from mudflat to young mangrove. By contrast, it appeared much more difficult discerning generalizable drivers for mature mangroves
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Franco, Diego Armando Castillo. "Estudo da diversidade molecular de bactérias e arquéias e enriquecimento de comunidades metanogênicas em sedimentos marinhos antárticos." Universidade de São Paulo, 2014. http://www.teses.usp.br/teses/disponiveis/87/87131/tde-06122014-091409/.
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O sedimento marinho da Península Antártica representa uma área sensível a mudanças ambientais. No entanto, pouco se conhece sobre as comunidades microbianas que habitam esse ecossistema, incluindo a sua diversidade, distribuição e variações temporais. O objetivo foi determinar a estrutura das comunidades microbianas nos sedimentos marinhos da Baía do Almirantado, Ilha Rei George, Península Antártica. Sedimentos da Baía apresentam uma predominância dos Filos Proteobacteria, Firmicutes e Actinobacteria. Análise temporal revelou que comunidades microbianas em sedimentos próximos à estação Ferraz são mais estáveis quando comparadas aos sedimentos em áreas de menor atividade antrópica. No gradiente de profundidade foi observado que a estrutura de comunidade não mudou, indicando tolerância a variações de pressão hidrostática. Organismos heterotróficos dos gêneros Psychrobacter, Psychromonas e Loktanella foram os mais abundantes, sugerindo uma alta concentração de matéria orgânica disponível. O enriquecimento de culturas metanogênicas produziu até 1,70 mmol de CH4 após 120 dias de incubação. Este estudo sugere que as condições dos sedimentos favorecem organismos psicrofílicos de metabolismo heterotrófico.Marine sediment of the Antarctic Peninsula is a susceptible area to environmental changes. However, little is known about the microbial communities inhabiting this ecosystem, including its diversity, distribution and variations over time. The aim of this study was to determine the structure of microbial communities present in marine sediments of Admiralty Bay, King George Island, on the Antarctic Peninsula. Sediments from Admiralty Bay shown a predominance of the Proteobacteria, Firmicutes, and Actinobacteria phyla. Temporal analysis revealed that microbial communities in sediment, near Ferraz station, are more stable compared to that in the sediments in areas of lower human activity. No variation on the community structure was observed in depth gradient, indicating tolerance to hydrostatic pressure variations. Heterotrophic organisms of the genera Psychrobacter, Psychromonas and Loktanella were the most abundant, suggesting a high concentration of organic matter in the sediment. Enrichment of methanogenic cultures enrichment yielded 1.70 mmol of CH4. This study suggests that conditions in sediments favoring metabolism of heterotrophic and psychrophilic organisms.
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Hamilton, Heather C. "A molecular method for assessing meiofauna diversity in marine sediments." [Tampa, Fla.] : University of South Florida, 2003. http://purl.fcla.edu/fcla/etd/SFE0000624.
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Hamilton, Heather C. "A Molecular Approach to Assessing Meiofauna Diversity in Marine Sediments." Scholar Commons, 2003. https://scholarcommons.usf.edu/etd/1382.
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A Molecular Approach to Assessing Meiofauna Diversity in Marine Sediments Heather C. Hamilton Abstract The purpose of this study was to determine if a molecular approach could be applied to calculating the diversity of meiofauna in marine sediments from two sites in Tampa Bay, FL, similar to the approach of McCaig et al, 1999 in calculating the diversity of microbes in pastureland soils. The approach includes extracting total DNA directly from the sediment and amplifying the 18S rRNA gene by PCR. Clone libraries from the 18S gene would be created for each site and 300 sequences from each clone library would be obtained. These sequences would then be phylogenetically analyzed and assigned to an OTU, from which diversity indices can be calculated.
The phylogenetic analysis of the sequences from the two sites revealed that of the 102 OTUs assigned from the sequences, only 7 OTUs included sequences from both sites, while 93 OTUs contained sequences from one site or from the other. Thus the sites were phylogenetically different from each other. Shannon diversity indices calculated for each site showed a difference between the two sites and paralleled diversity indices for macrofauna data for each site collected by the Hillsborough County Environmental Protection Commission. Sequences from 30 OTUs were completely sequenced and identified by phylogenetic comparison with a metazoan reference alignment. A discrepancy between the sequence data and data collected from preserved samples taken at each site was evident upon analysis: roughly 60% of each preserved sample consisted of nematodes and 10% consisted of copepods, while roughly 30% of the identified OTUs consisted of copepods and 10% consisted of nematodes. This discrepancy could be explained if the OTUs that were not identified consisted of nematode sequences or if a primer bias were present in the PCR amplification such that the regions flanking the primer site in the nematode sequences inhibited primer annealing.
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Compte, Port Sergi. "Factors affecting the distribution, abundance and diversity of uncultured archaeal groups in freshwater sediments." Doctoral thesis, Universitat de Girona, 2018. http://hdl.handle.net/10803/663927.
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Archaea are abundant in extreme environments but they are also a prevalent component of microbial communities in soils, marine or freshwater plankton and sediments. Many studies highlighted the prominent role of marine sedimentary Archaea in global nutrient cycles. Less information is available, however, on the diversity, abundance and ecological role of Archaea in freshwater sediments. A serious pitfall for the study of Archaea is their low cultivability under laboratory-controlled conditions thus constraining the progress towards the complete understanding of their metabolic capabilities and ecological functions. Most of the work is thus based on molecular techniques that allow the identification and quantification of target microorganisms without their cultivation. In this PhD project, we applied a combination of high-throughput sequencing and quantitative PCR to investigate the distribution, abundance and composition of archaeal communities in sediments from different freshwater systems (lakes, lagoons and reservoirs encompassing a wide range of conditions and typologies). The work has been focused in two archaeal groups consistently found, and especially abundant, in sediments: the phylum Bathyarchaeota and the class ThermoplasmataEls arqueus abunden en ambients extrems però també són un component rellevant dels sòls, del plàncton oceànic i lacustre i dels sediments. Molts estudis han destacat la importància dels arqueus en els cicles de nutrients dels sediments marins tant a escala local com global. En canvi, es disposa de menys informació sobre la diversitat, abundància i paper que juguen els arqueus en sediments d’aigua dolça a excepció dels metanògens. Com a dificultat afegida, la majoria d’arqueus sedimentaris no s’han pogut cultivar encara al laboratori, el que dificulta el seu estudi. La solució a aquests problemes passa per l’aplicació de tècniques moleculars que permeten la identificació i recompte dels microorganismes diana sense necessitat de cultivar-los. En aquesta tesi s’han combinat diferents tècniques moleculars (seqüenciació massiva i PCR quantitativa) per a conèixer la distribució, abundància i composició de les comunitats d’arqueus en sediments de sistemes aquàtics d’aigua dolça (llacs, llacunes i embassaments amb diferents condicions i tipologies). La tesi s’ha centrat en dos grups d’arqueus que són ubics i especialment abundants en sediments: el fílum Bathyarchaeota i la classe Thermoplasmata
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Thompson, Chris J. Physical Environmental & Mathematical Sciences Australian Defence Force Academy UNSW. "The geomorphology of Southeast Australian mountain streams." Awarded by:University of New South Wales - Australian Defence Force Academy. School of Physical, Environmental and Mathematical Sciences, 2006. http://handle.unsw.edu.au/1959.4/38681.
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This thesis is a study of the morphology and sediment transport dynamics of mountain streams in southeast Australia. Mountain streams represent important geomorphological and ecological systems in Australia which have hitherto been poorly studied. The variability of mountain stream reach morphology was investigated at the regional scale using topographical surveys and sediment sampling techniques. Study sites were stratified by slope and local lithology. Eight channel-morphologies including Bedrock, Cascade, Step-pool, Planebed, Pool-Riffle, Cascade-pool, Riffle-step and Infilled, were identified using an objective statistical approach. Overall, channel types were found to correspond to existing reach-scale mountain stream templates. Five morphologies were associated with a specific lithology type which controlled the size and shape of grains supplied to the channels. Differences in coarse sediment transport processes between morphologies were investigated using stream monitoring techniques and Optically Stimulated Luminescence (OSL) dating. Monitoring results from a 3 year period indicated that channel beds are resistant to entrainment with shear stress thresholds for bedload transport ranging between 64 to 74 N/m2. Transport of reach median grain sizes requires floods that exceed bankfull discharge. Existing competence equations were found to over-predict the hydraulic driving force and consequently, a modified entrainment model was used to account for the regional channel characteristics. OSL dating was investigated as a tool to provide data on long-term sediment transport processes. Minimum age model results from the OSL dates show overall agreement with a selected entrainment model, and indicate differences in sediment transport dynamics between some reach morphology types. A regime model was used to quantify the physical domains of different channel morphologies. Limitations of the model were overcome by modifying the sediment supply surrogate to better reflect the dominant transported bedload size. Morphology types were delineated according to different sediment transport capacity-sediment supply domains. The distribution of channel morphology types within a series of catchments in southeast Australia was modelled within a GIS platform using the diagnostics of reach morphology derived from this study. The model provides a conceptual framework to evaluate the potential link between channel form, potential habitat diversity and aquatic biodiversity within the channel network in mountain streams.
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Zhang, Wen. "Dynamics and diversity of prokaryotic communities in marine sediments of Hong Kong /." View abstract or full-text, 2007. http://library.ust.hk/cgi/db/thesis.pl?AMCE%202007%20ZHANG.
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Nigro, Lisa M. "Distribution and Diversity of Bacterial Chemolithotrophs in Marine and Freshwater Sediments." Fogler Library, University of Maine, 2006. http://www.library.umaine.edu/theses/pdf/NigroLM2006.pdf.
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Pfoller, Stacy Lynn. "DIVERSITY AND ACTIVITY OF SPHINGOMONAS IN PAH-IMPACTED SOILS AND SEDIMENTS." University of Cincinnati / OhioLINK, 2001. http://rave.ohiolink.edu/etdc/view?acc_num=ucin984589035.
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Van, Heerden Morne Jandre. "Control of sediment diversion in run-of-river hydropower schemes." Thesis, Stellenbosch : Stellenbosch University, 2012. http://hdl.handle.net/10019.1/71849.
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Thesis (MEng)--Stellenbosch University, 2012.ENGLISH ABSTRACT: Sedimentation and the effects it has on turbine blades was the primary problem identified in run-of-river (RoR) hydropower schemes. Sedimentation in RoR hydropower schemes also increases trash rack blockage and reduces energy output in the long-term. Damage occurs to all underwater parts that come into contact with sediment. The main concern is sediment passing through the hydropower intake and causing turbine damage. The reason for the abrasion and cavitation of turbine blades is increased sediment loads in river channels. This problem can be overcome in two ways. The first is the use of existing lakes or reservoir storage upstream as natural sand traps, and the second is by investigating the three features associated with river bend diversion, which are: the optimum diversion location in a river bend to minimise the abstraction of sediment, the optimum diversion structure angle to limit coarse sediment diversion, and the sediment load diverted through the intake. The first objective of the research was investigated by construction of a physical model of a curved river channel to determine the location of the deepest scour forming on the outside of the bend. The second objective was to test the diversion orientation to maximize the local scour and thereby limiting sediment diversion at the intake. A third objective was to compare mathematical 2D model simulated scour results with the findings of the laboratory tests to evaluate the reliability of the numerical model predictions. Finally different diverted discharge ratios were tested with different intake setups in the physical model, to evaluate the sediment load diverted. . The first experiment in the curved laboratory channel was to predict where the deepest scour takes place without a diversion structure. This was then followed by placing a diversion structure at the maximum scour position, retrieved from experiment one, and by angling the structure with reference to the flow direction. The flow direction vector was placed as a tangent to the bend and orientated at angles of 0⁰, 30⁰, 45⁰ and 60⁰ into the bend direction. The optimum diversion location was found to be positioned on the outside of the bend, approximately 60⁰ into the channel bend. The final position of maximum scour in a 90⁰ bend corresponds with the Sediment Committee and the Chinese Hydraulic Engineering Societies (1992) prediction of 60⁰ into the bend. The optimal diversion had a 30⁰ angle to the flow direction, as this presented the most efficient and effective scouring in front of the model intake. Numerical simulations were performed with the CCHE 2D (hydrodynamics and sediment dynamics) modelling program. The numerical results were compared to the physical results to validate CCHE as a beneficial simulation tool. It was found that the numerical model predicted the scour depths at the intakes tested with an accuracy of 43.8%, which is within the accuracy range of the sediment transport equation used by the numerical model. The final experiment was the diversion of sediment with different intake level heights and discharges. It was evident from the results that low sediment diversion ratios were achieved with a diverted discharge ratio of 50% or less. The intake elevation highest above the channel bed diverted the least sediment. The interrelationship between Diverted Discharge Ratio (DDR), Diverted Froude number Ratio (DFrR) and Diverted Sediment load Ratio (SDR) was established in the study. It is recommended that RoR schemes have sand traps downstream of the diversion structures and that turbines are coated with HVOF to overcome the power loss arising due to the excessive erosion of hydro turbines.
AFRIKAANSE OPSOMMING: Sedimentasie en die invloed wat dit het op turbines was die primêre probleem geïdentifiseer in “run-of-river” (RoR) hidrokrag-skemas. Die sediment wat saam met die water uit ‟n rivier uitgekeer word beskadig die inlaatrooster en verlaag kragopwekking in die langtermyn. Skade word aangerig aan alle onderwatertoerusting en masjinerie wat aan sediment blootgestel word. Die grootste probleem tydens die uitkering van water is die growwe sediment wat daarmee deur die onttrekking inlaat gaan en turbineskade veroorsaak. Soos wat die sedimentlading in die rivier drasties toeneem, sal afslyting en kavitasie van turbinelemme meer gereeld voorkom. Dié probleem kan op twee maniere beperk word. Die een is die gebruik van bestaande opgaardamme stroomop, en die tweede is deur die ondersoek van drie kenmerke van rivierdraaie en uitkeringstrukture, bv. die optimale uitskurings posisie in 'n rivierdraai (sonder ʼn struktuur) om die diepste uitskuringposisie op die buitekant van die draai te bepaal, die optimale uitkeringsstruktuuroriëntasie wat maksimum uitskuring verseker en die sediment uitkering beperk, en die lading van sedimentonttrekking deur die inlaat. Die eerste doelwit van die navorsing is ondersoek deur ʼn fisiese model te bou van ʼn kronkelkanaal en te bepaal waar die diepste uitskring plaasvind op die buitekant van die draai. Die tweede doelwit van die studie was om die optimale uitkeringshoek te bepaal vir 'n uitkeringstruktuur sodat die uitskuring by die inlaat ʼn maksimum is om die uitkering van sediment te beperk. ʼn Derde doelwit was om die akkuraatheid van ʼn wiskundige model se uitskuring voorspelling te toets teen die waargenome laboratorium resultate. Die finale doelwit was om vir verskillende inlaatontwerpe, rivier- en uitkeervloeie die sedimentladings wat uitgekeer word te ondersoek. Die eerste eksperiment in die kronkelende kanaal was voorberei om die optimale uitskuring in die draai te bepaal. Dit is gevolg deur toetse met uitkeerstrukture by die maksimum uitskurings posisie te plaas en die hoek van die struktuur dan te verander met verwysing na die vloeirigting. Die vloeirigting vektor was as 'n raaklyn geplaas op die kanaal draai en georiënteer met hoeke: 0⁰, 30⁰, 45⁰ en 60⁰, in die rigting van die draai. Die optimale uitskurings posisie was aan die buiterand van die kanaal draai gevind, ongeveer 60⁰ in die draai in. Die maksimum uitskuur posisie van 'n 90⁰ kanaal draai stem ooreen met SC en CHES (1992) se resultaat van 60⁰ in die draai in. Daar was ook genoegsame bewyse dat 'n optimale uitkeerwerke oriëntasie van 30⁰ die doeltreffendste en effektiefste uitskuring sal gee. Numeriese simulasies is deur middel van 'n twee dimensionele wiskundige model CCHE 2D (hidro- en sedimentdinamika) uitgevoer. Die numeriese resultate was vergelyk met die laboratoriumresultate om die CCHE program te verifieer as 'n voordelige simulasie program. Daar is gevind dat die wiskundige model die uitskuurdieptes by die inlate met ʼn akkuraatheid van 43.8 % voorspel, wat binne die akkuraatheid is van die sedimentvervoervergelyking wat deur die numeriese model gebruik word. Die finale eksperiment was die uitkering van sediment met verskillende inlaathoogtes en uitkerings sedimentladings. Uit die toetse was dit duidelik dat 'n lae sediment uitkeerverhouding behaal kan word met 'n uitkeerverhouding van 50% en minder. Verdere waarnemings het ook gewys dat die inlaathoogte van die uitkeerstruktuur met die optimale resultate die hoogste bokant die rivierbedding was. Die verwantskap tussen die uitgekeerde deurstromingverhouding, die uitgekeerde Froude getal verhouding en die uitgekeerde sedimentlading is bepaal in die navorsing. Dit word aanbeveel dat sandvangkanale stroomaf van uitkeerwerke geplaas word en dat turbines met HVOF as bedekkingsmateriaal beskerm word om kragverliese as gevolg van buitensporige erosie van die turbines te voorkom.
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Prieto-Davó, Alejandra. "Phylogenetic and chemical diversity of marine-derived actinomycetes from Southern California sediments." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2008. http://wwwlib.umi.com/cr/ucsd/fullcit?p3296893.
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Thesis (Ph. D.)--University of California, San Diego, 2008.Title from first page of PDF file (viewed April 7, 2008). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references (p. 113-127).
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Tang, Chao. "Microbial diversity studies in sediments of perennially ice-covered lakes, McMurdo Dry Valleys, Antarctica." Diss., [Riverside, Calif.] : University of California, Riverside, 2009. http://proquest.umi.com/pqdweb?index=0&did=1957340921&SrchMode=2&sid=1&Fmt=2&VInst=PROD&VType=PQD&RQT=309&VName=PQD&TS=1269022997&clientId=48051.
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Thesis (Ph. D.)--University of California, Riverside, 2009.Includes abstract. Available via ProQuest Digital Dissertations. Title from first page of PDF file (viewed March 20, 2010). Includes bibliographical references. Also issued in print.
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O'Neill, Andrew. "The microbial diversity of wetland sediments constructed to treat acid mine drainage as determined by molecular techniques /." St. Lucia, Qld, 2001. http://www.library.uq.edu.au/pdfserve.php?image=thesisabs/absthe16527.pdf.
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Du, Plessis Lodewicus Johannes. "Hydraulic model investigation of sediment control measures at low weir river diversion works." Thesis, Stellenbosch : Stellenbosch University, 2015. http://hdl.handle.net/10019.1/96954.
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Thesis (MSc)--Stellenbosch University, 2015.ENGLISH ABSTRACT: Rivers are one of the earth's major readily available sources of fresh water. Abstractions from rivers are however not without problems. Firstly, river ow is variable and to deliver a constant yield is difficult. Secondly, rivers transport sediment which will be included in the diverted ow. Sediment control at diversion works have been studied for many years and this study attempts to gain further knowledge on certain sediment control features of diversion works. Sediment control at diversion works and abstraction works is crucial to prolong the life of the mechanical components like pumps and turbines. A Commonly used diversion works design is one with a low weir and a graveltrap. The weir dams water for abstraction, which is of importance in South Africa with its variable rainfall and river ow. The study focused on the following design features of diversion works: (1) the intake angle, which is the angle at which the structure is pushed into the river, (2) the intake opening height above a datum, (3) the river ow range where sediment is sufficiently scoured from the graveltrap and (4) the efficiency and river ow range of sediment ushing through a sluice gate at the graveltrap. A Physical model study was conducted in the laboratory of the University of Stellenbosch, which consisted of designing the diversion works that were to be tested. The designs were based on guidelines from previous studies, case studies and hydraulic principles. The above mentioned features (1-4) were studied at three structures with prototype weir sizes of 2.5 m, 3.5 m and 4.5 m. The river was modelled as a straight rectangular channel with a loose bed surface, which was simulated with crushed peach pips. Sediment was also fed into the system with a conveyor belt feed system. Pumps were used to abstract water and sediment through the intake opening, during the diverted sediment tests. Flow was diverted at a specific ow rate for each structure. The diverted sediment was caught and weighed. Each structure was designed to divert sediment through one of three intake opening heights, to determine whether a higher intake opening sufficiently reduces the amount of diverted sediment. The self-scour efficiency at the graveltrap was determined with a sediment level survey in the graveltrap. From the survey a clearance ow was determined, which is the minimum river ow that clears the intake opening of sediment along its complete length. It was also determined what intake angle induces secondary ow which results in the lowest clearance ow. The sediment ushing through the sluice gate was evaluated by recording the time it takes a full graveltrap to be ushed clean at various river ow rates. The maximum river ow at which the graveltrap still ushes efficiently was determined for each structure. It was found that between the 300, 450 and 600 intake angle that were tested, the 60 0 angle yields the lowest diverted sediment ratio (DSR) over the range of structures as well as river ows tested. The tests yielded a river ow at each structure where the DSR is at minimum. During the self-scour tests of the graveltrap, it was determined that a 450 intake angle promotes better self-scour at the graveltrap. To promote both features, a 450 intake angle is suggested, as it reduces diverted sediment and has a lower risk of issues due to too large ow constriction. The intake opening height was evaluated with analysis of diverted load and concentration. The conclusions on the intake opening vary between structure sizes. In the case of the smallest structure, with a 2.5 m weir height, the improvement observed for intake openings higher than the first (lowest) were variable. In the case of the 3.5 m weir structure, the results showed three consecutive intake openings could be feasible. In the case of the 4.5 m weir structure, less improvement was observed between the highest two intakes. Flood frequency should determine whether an intake opening with top-of-inlet of 1.6 m or 3.3 m above the minimum operating level should be designed. It was observed during the sediment ushing tests that submergence of either the graveltrap wall and/or the downstream water level affects the ushing efficiency. y3/y2, which is the downstream ow depth over the contracted ow depth under the sluice gate of the graveltrap, was evaluated as an indicator of efficient ushing. The study found that a good guideline would be to ush during river ows where y3/y2 < 1, while also ensuring the ow over the graveltrap wall entrains the sediment in the graveltrap. A figure which plots the downstream ow depth over sluice gate opening size was developed to serve as an operational guideline to efficient sediment ushing. The figure shows zones of efficient and non-efficient ushing. Further, the observed sediment ushing and self-scour ranges at each structure are also represented graphically. The fact that there was designed for a specific river scenario and also the lack of varied model sediment size, limits the applicability of the findings and conclusions.
AFRIKAANSE OPSOMMING: Riviere is van die aarde se hoof, maklik beskikbare bronne van vars water. Onttrekking uit riviere is wel nie sonder probleme nie. Eerstens is rivier vloei wisselvallig en om 'n konstante lewering te handhaaf is moeilik. Tweedens, vervoer riviere sediment wat ingesluit sal wees in die uitgekeerde vloei. Sediment beheer by uitkeerwerke word al vir baie jare bestudeer en hierdie studie poog om verdere kennis te verkry oor sekere sediment beheer funksies van uitkeerwerke. Sediment beheer by uitkeerwerke en onttrekkingswerke is noodsaaklik om die lewensduur van meganiese komponente soos pompe en turbines te verleng. 'n Algemeen toegepaste uitkeerwerke ontwerp is een met n lae keerwal en gruisvangkanaal. Die keerwal dam water op, wat nodig kan wees om die lewering te handhaaf, veral met Suid-Afrika se wisselvallige reënval en rivier vloei. Die studie het gefokus op die volgende ontwerp funksies van uitkeerwerke: (1) die inlaathoek, wat die hoek is waarteen die struktuur in die rivier ingedruk is, (2) die inlaatopening hoogte bo 'n datum, (3) die rivier vloei reeks waar sediment voldoende uitgeskuur word uit die gruisvangkanaal uit en (4) die effektiwiteit en rivier vloei reeks van 'n sediment spoel aksie deur 'n sluishek in die gruisvangkanaal. 'n Fisiese model studie was onderneem in die laboratorium van die Universiteit van Stellenbosch, wat bestaan het uit die ontwerp van die uitkeerwerke wat getoets sou word. Die ontwerp is gebasseer op riglyne van vorige studies, gevallestudies en hirouliese beginsels. Die bogenoemde funksies (1-4) was bestudeer by drie strukture met prototipe keerwal hoogtes van 2.5 m, 3.5 m en 4.5 m. Die rivier was gemodelleer as 'n reguit, reghoekige kanaal met 'n los bed oppervlakte, wat gesimuleer is met fyngemaakte perske pitte. Sediment was ook in die sisteem ingevoer met 'n vervoerband voer sisteem. Pompe was gebruik om water en sediment te onttrek deur die inlaatopening tydens die uitgekeerde sediment toetse. Vloei was uitgekeer teen 'n spesifieke vloeitempo vir elke struktuur. Die uitgekeerde sediment was gevang en geweeg. Elke struktuur was ontwerp om sediment uit te keer deur een van drie inlaatopening hoogtes, om te bepaal of 'n hoër inlaatopening hoogte die hoeveelheid uitgekeerde sediment voldoende verminder. Die self-uitskuur effektiwiteit van die gruisvangkanaal was bepaal deur 'n sediment vlak opmeting in die gruisvangkanaal. Vanaf die opmeting was 'n skoonmaak vloei bepaal, wat die minimum rivier vloei is wat die inlaatopening skoon maak van sediment oor die totale lengte. Dit was ook bepaal watter inlaathoek veroorsaak sekondêre vloei wat die laagste skoonmaak vloei oplewer. Die sediment spoel aksie deur die sluishek was geëvalueer deur die tyd wat dit neem om 'n vol gruisvangkanaal skoon te spoel, teen verskeie rivier vloeitempos te bepaal. 'n Maksimum rivier vloei waarteen die guisvangkanaal steeds effektiewelik skoon spoel was bepaal vir elke struktuur. Dit was bevind dat tussen die 300, 450 en 600 inlaathoeke wat getoets is, lewer die 600 hoek die laagste uitgekeerde sediment verhouding (USV) oor die reeks van strukture, asook rivier vloeitempos wat getoets is. Die toetse het 'n rivier vloei opgelewer by elke struktuur, waar USV 'n minimum was. Gedurende die self-uitskuur toetse was dit bepaal dat 'n 450 inlaathoek beter uitskuur in die gruisvangkanaal bevorder. Om beide funksies te bevorder word 'n 450 inlaathoek voorgestel, omdat dit ook uitgekeerde sediment verminder en 'n laer risiko van probleme as gevolg van te groot vloei vernouing het. Die inlaatopening hoogte was geëvalueer met analise van die uitgekeerde sediment lading en konsentrasie. Die gevolgtrekkings oor die inlaatopening hoogte varieer tussen struktuur groottes. In die geval van die kleinste struktuur, met 'n 2.5 m keerwal hoogte, was die verbetering wat waargeneem was by inlaatopeninge hoër as die eerste (laagste) inlaat, wisselvallig. In die geval van 'n 3.5 m keerwal struktuur het die resultate getoon dat drie opeenvolgende inlaatopeninge kan uitvoerbaar wees. In die geval van 'n 4.5 m keerwal struktuur was minder verbetering waargeneem tussen die hoogste twee inlate. Vloed frekwensie moet bepaal of 'n inlaatopening hoogte met 'n bokant-van-inlaat vlak van 1.6 m of 3.3 m bo minimun bedryfvlak moet ontwerp word. Dit was waargeneem dat gedurende die sediment spoel toetse dat versuiping van die gruisvangkanaal muur en/of die stroomaf watervlak die spoel effektiwiteit beïnvloed. y3/y2, wat die stroomaf vloeidiepte oor die vernoude vloeidiepte onder die sluishek van die gruisvangkanaal is, was geëvalueer as 'n indikator van effektiewe spoel aksie. Die studie het bevind dat 'n goeie riglyn sal wees om te spoel tydens rivier vloeie waar y3/y2 < 1 is, terwyl dit ook verseker moet word dat vloei oor die gruisvang kanaal sediment meevoer in die gruisvangkanaal. 'n Figuur wat die stroomaf vloeidiepte teenoor die sluisopening grootte plot was ontwikkel om te dien as 'n bedryfsriglyn tot effektiewe spoel aksie. Die figuur toon zones van effektiewe en nie-effektiewe spoel aksie aan. Verder is die waargeneemde sediment spoel aksie en self-uitskuur reekse van elke struktuur ook grafies voorgestel. Die feit dat daar ontwerp is vir 'n spesifieke rivier scenario asook die gebrek aan variëerende model sediment grootte, beperk die toepasbaarheid van die bevindings en gevolgtrekkings.
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Hieke, Anne-Sophie Charlotte. "Diversity and distribution of bacterial communities in dioxin-contaminated sediments from the Houston ship channel." [College Station, Tex. : Texas A&M University, 2008. http://hdl.handle.net/1969.1/ETD-TAMU-2796.
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Oliveira, Cynthia. "Diversité des intégrons dans des sédiments estuariens anthropisés." Thesis, Normandie, 2017. http://www.theses.fr/2017NORMR093.
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Les intégrons sont des plateformes génétiques bactériennes de capture et d'expression de gènes. Les intégrons cliniques sont les principaux responsables de la forte augmentation récente des bactéries multirésistantes aux antibiotiques. Cependant, dans l’environnement, ils ne représentent qu’une part minime de l’importante diversité des intégrons. Ainsi, les objectifs de cette thèse étaient (i) d’évaluer l’étendue de la diversité des intégrons dans l’environnement, (ii) de comprendre les phénomènes responsables de la structuration du pool d’intégrons dans le compartiment sédimentaire d’un milieu estuarien anthropisé et (iii) de rechercher l’existence potentielle d’intégrons indicateurs du niveau de contamination chimique.Le suivi des intégrons de classes 1, 2 et 3 et des populations d’E. coli dans des sédiments du bassin versant de la Risle impactés par des sources de contamination fécale bien caractérisées ont montré qu’en étiage, les souches d’E. coli d’origine humaine se disséminaient sur de courtes distances. Les intégrons de classe 1 se disséminent sur des distances un peu plus importantes et se maintiennent dans les 12 premiers centimètres du compartiment sédimentaire au moins.Une méthode a été développée permettant, pour la première fois, l’analyse de la diversité des intégrons via séquençage haut-débit. L’application de cette méthode sur une carotte sédimentaire de 4,8 m de profondeur prélevée dans l’estuaire fluvial de la Seine a permis de mettre en évidence plusieurs milliers de classes d’intégrons dont de nombreuses intégrases encore jamais répertoriées. La diversité des intégrons chute fortement avec la profondeur. Les intégrons de classe 1, majoritaires dans les sédiments de surface, ont une abondance qui chute fortement avec la profondeur cependant ils répondent plutôt positivement à la contamination chimique renforçant l’idée de leur utilisation comme proxy de pollutions anthropiques récentes. Trois classes d’intégrons dominent dans la vase consolidée représentant 38% des séquences obtenues dans la carotte sédimentaire mais répondant plutôt négativement à la contamination chimique. Enfin, la structure du pool d’intégrons est fortement corrélée à celle de la communauté bactérienne mais semble en partie indépendante de la communauté bactérienne dans deux des fractions sédimentaires profondes avec la dominance d’une nouvelle classe d’intégrons qui semble sélectionnée par les HAPIntegrons are bacterial genetic platforms allowing acquisition and expression of genes. Clinical integrons play a major role in the strong increase of antibiotic multi-resistant bacteria recently observed. However, in the environment, they represent only a tiny fraction of the large integron diversity. Therefore, the aims of this thesis were (i) estimating the extent of the integron diversity in the environment, (ii) understanding phenomena responsible for integron pool structure in anthropized estuarine sediments and (iii) looking for integrons potentially proxy of chemical pollution level. The research of class 1, 2 and 3 integrons and the analysis of E. coli populations in sediments from the Risle drainage basin impacted by well-characterized fecal contamination sources show that E. coli strains with human origins were spread on short distances during low water level periods. However, class 1 integrons are spread on slightly longer distances and remain present in the 12 first centimeters of sediments at least. A methodology was developed allowing, for the first time, the analysis of integron diversity by high-throughput sequencing. In this way, the analysis of a 4.8 meter core sediment from the fluvial Seine estuary highlighted several thousands integron classes including many new integrases absent from data bases. Integron diversity decreases along with depth. Class 1 integrons are the majority integrons in surface sediments but their abundance strongly decreases in deep sediments. Class 1 integron abundance rather responds positively to chemical pollutions accentuating the idea that class 1 integrons could be used as proxy of recent anthropogenic pollutions. In the sediment core, three integron classes outshine the whole dataset: they represent 38% of all the sequences from the sediment core. However, abundances of these three majority integron classes rather respond negatively to chemical pollution levels. Integron pool structure is highly correlated to bacterial community diversity but seems to be partially independent to bacterial community diversity within two deep fractions from the sediment core: in these two sediment fractions, a new integron class outshines the rest of integron classes and seems to be specific to these two sediment fractions. Furthermore, this new integron class seems to be selected by PAH
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Allen, Jennifer. "Ammonia oxidation potential and microbial diversity in sediments from experimental bench-scale oxygen-activated nitrification wetlands." Pullman, Wash. : Washington State University, 2009. http://www.dissertations.wsu.edu/Thesis/Spring2009/J_Allen_061109.pdf.
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Thesis (M.S. in civil engineering)--Washington State University, May 2009.Title from PDF title page (viewed on July 15, 2009). "Department of Civil and Environmental Engineering." Includes bibliographical references (p. 21-31).
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Mills, Heath Jordan. "Microbial diversity in sediments and gas hydrates associated with cold seeps in the Gulf of Mexico." Diss., Available online, Georgia Institute of Technology, 2004:, 2004. http://etd.gatech.edu/theses/available/etd-07072004-215909/unrestricted/Mills%5FHeath%5FJ%5F200407%5Fphd.pdf.
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Thesis (Ph. D.)--School of Biology, Georgia Institute of Technology, 2005. Directed by Patricia Sobecky.Frank Loeffler, Committee Member ; Roger Wartell, Committee Member ; Joseph Montoya, Committee Member ; Thomas DiChristina, Committee Member ; Patricia Sobecky, Committee Chair. Vita. Includes bibliographical references.
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Li, Meng, and 李猛. "Diversity of anammox bacteria in coastal and ocean sediments and interactions among ammonia oxidizers and nitrite reducers." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2011. http://hub.hku.hk/bib/B46924681.
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Queiroz, Silva Silvana de. "Activity and diversity of sulphate-reducing bacteria and methanogenic archaea in contrasting sediments from the River Colne estuary." Thesis, University of Essex, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.409980.
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Scheer, Maria. "Charakterisierung der Diversität von Mikroorganismen im Nationalpark “Unteres Odertal”." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2011. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-63999.
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Gewässersedimente stellen für den Stoffkreislauf ein wichtiges Ökosystem dar. Durch die Stoffwechselleistungen einer komplexen mikrobiellen Lebensgemeinschaft wird sowohl das Sediment selbst, sein Interstitialwasser, das überstehende Freiwasser als auch die Atmosphäre und die darin lebenden Mikro- und Makroorganismen beeinflusst. Die grundlegenden chemischen Prozesse im Sediment sind bereits gut untersucht. Auch sind die mikrobiellen Großgruppen im Sediment bekannt. Im Hinblick auf die Diversität der Mikroorganismen, insbesondere in Süßwassersedimenten, gibt es noch Forschungsbedarf.
Das Auengebiet des Nationalparks „Unteres Odertal“ stellt durch seine jährlich kontrollierten Flutungen ein interessantes und wegen seiner Vielfalt verschiedenartiger Gewässertypen einen idealen Ort zur Untersuchung mikrobieller Biozönosen in Gewässersedimenten dar.
Ziel dieser Arbeit war es, eine erste Charakterisierung der mikrobiellen Biozönose in den Gewässersedimenten des Auennationalparks „Unteres Odertal“ durchzuführen und mit den Ergebnissen der Talsperre Saidenbach und der Elbaue bei Dornburg zu vergleichen. Hierfür kam ein breites Spektrum an Methoden zum Einsatz, das klassische mikrobiologische Methoden und molekularbiologische Techniken umfasste. Die Analysen sollten dabei über mehrere Jahre hinweg erfolgen, um die Variabilität der mikrobiellen Populationen in Abhängigkeit von sich ändernden Umweltparametern zu erfassen.
Die Charakterisierung der Umweltparameter erfolgte durch Messungen chemisch-physikalischer Parameter im Freiwasser, Sediment und seinem Interstitialwasser. Die untersuchten Probenahmestellen unterschieden sich in ihren chemischen Profilen. Damit waren Unterschiede in der mikrobiellen Zusammensetzung dieser Probenahmestellen zu erwarten.
Die Identifizierung und Quantifizierung der Prokaryoten mittels CARD FISH wies auf eine hohe Abundanz von Alpha- und Beta-Proteobakterien sowie Bacteroidetes, Planctomycetes, Verrucomicrobia und Chloroflexi in den Proben des Odertals hin. Die Proben Dornburgs wurden von Planctomyceten und die Proben des Haselbachs von Alpha-Proteobakterien oder Verrucomicrobien dominiert. Obwohl die Hybridisierbarkeit der Proben gut war, wurde mit den angewendeten Sonden in der Summe weniger als 50 % der Gesamtzellzahl erfasst.
Die Anwendung der ARISA Methode zeigte strukturelle Unterschiede zwischen den untersuchten Proben in Abhängigkeit von der Sedimenttiefe und dem Probenahmemonat. Die größte Ähnlichkeit besaßen die Biozönosen des Anglerteichs und des Bogengrabens. Ein Einfluss der Flutung auf die Zusammensetzung der mikrobiellen Biozönose konnte deutlich gezeigt werden.
Die Identifikation der Eubakterien in den Proben des Odertals durch die Erstellung von 16S rDNA Eubakterien Klonbanken ergab eine Dominanz der Beta-Proteobakterien und Bacteroidetes und wies auf die Bedeutung der Delta-Proteobakterien hin. Die eubakterielle Lebensgemeinschaft im Haselbach wurde von Alpha-Proteobakterien und Acidobakterien dominiert. Variabilitäten im Zusammenhang mit dem Probenahmedatum und der Flutung des Odertals konnten gezeigt werden. Die größte eubakterielle Biodiversität wurde im Sediment der Oder-Zollstation (April 2007) geschätzt.
Die Anwendung der Pyrosequenzierung ergab eine hohe Biodiversität in allen Proben und bestätigte die Dominanz der Beta-Proteobakterien im Anglerteich. Im Bogengraben dominierten die Delta-Proteobakterien knapp vor den Beta-Proteobakterien. In der Oder waren neben den Beta-Proteobakterien die Bacteroidetes abundanter. Die genannten Taxa dominierten auch die Bibliotheken der Talsperre Saidenbach. Die höchste Biodiversität wurde für die Bibliothek des Bogengrabens angegeben, dessen Lebensgemeinschaft die meisten Gemeinsamkeiten mit der Bibliothek des Anglerteichs aufwies.
Sulfatreduzierende Bakterien (SRB) wurden durch die Sequenzierung von Klonbanken und die Anwendung der Fingerprintmethoden T-RFLP und DGGE charakterisiert. Die hohe Biodiversität der SRB konnte je nach erstellter Klonbank unterschiedlich gut beschrieben werden. Neben zahlreichen nicht identifizierbaren Vertretern waren Desulfobacterales und Clostridiales abundant. Die größte Diversität wurde wiederum in der Bibliothek des Bogengrabens nachgewiesen. Die Zusammensetzung der SRB in den Klonbanken variierte in Abhängigkeit der Parameter gelöster reaktiver Phosphor (SRP), organische Substanz, DOC und Nitrat. Mit T-RFLP und DGGE konnte eine sedimenttiefenabhängige Variabilität der SRB festgestellt werden, die sich zwischen den Proben Anglerteich und Bogengraben am meisten glich. Mit der DGGE erfolgte eine erste zeitabhängige Untersuchung, die deutlich verschiedene Biozönosen zwischen der Talsperre Saidenbach und den Proben des Nationalparks „Unteres Odertal“ zeigte. Das enorm hohe Bandenspektrum erschwerte die Analyse der zeitlichen Variabilität.
Die Nitrat-Stickstoffkonzentrationen waren in den Sedimenten mit zunehmender Tiefe unverändert niedrig, was sich in einer mit T-RFLP untersuchten niedrigen Diversität der Denitrifikanten wiederspiegelte, die nur wenige vertikale oder zeitliche Varianzen zeigten.
Die Anwendung von Kultivierungsversuchen ermöglichte die Isolation und eine erste Charakterisierung von Cyano- und Eisenbakterien. Insbesondere fädige Cyanobakterien der Gattungen Leptolyngbya, Nostoc und Pseudanabaena wiesen ein interessantes Sekundärmetabolitspektrum auf. Die Untersuchung erster Extrakte (Firma Cyano Biotech) wies auf biologisch aktive Substanzen hin.
Die Untersuchung hygienisch relevanter Mikroorganismen zeigte ein höheres Vorkommen coliformer Bakterien im Sediment der Oder-Zollstation als im Anglerteich oder Bogengraben.
Neben den Eubakterien wurde die Lebensgemeinschaft der Archaea durch Sequenzierung generierter Klonbanken identifiziert sowie die vertikale und temporale Variabilität ihrer Struktur untersucht (T-RFLP, DGGE). Die für aquatische Sedimente vergleichsweise hohe archaeale Diversität unterschied sich enorm zwischen den Klonbibliotheken. Die höchste Diversität wurde in der Klonbank der Probe Dornburgs festgestellt, die neben Vertretern des „Rice Clusters V“ (RC-V) überwiegend aus Crenarchaea bestand. RC-V Archaea dominierten, bis auf die Oder-Zollstation, alle generierten Bibliotheken. Methanogene Archaea waren besonders abundant in der Bibliothek der Oder-Zollstation (Methanomicrobiaceae, Methanosaetaceae) und des Haselbachs (Methanospirillaceae). Einflussnehmende Umweltfaktoren waren Sulfat (Dornburg), Nitrat (Entnahmestelle), DIC (Anglerteich), Sauerstoff (Haselbach) und Ammonium (Oder-Zollstation). Die T-RFLP Analyse zeigte die methanogenen Archaea Methanosarcinales/Methanomicrobiales (Msm) als besonders abundant an. Eine erwartete tiefenabhängige Varianz konnte mit T-RFLP gezeigt werden. Die Unterschiede zwischen den Probenahmestellen waren jedoch deutlicher und zeigten anhand der DGGE Analyse ein breiteres Msm Bandenspektrum für den Anglerteich und Bogengraben im Vergleich zur Oder-Zollstation und zum Haselbach. Die zeitabhängige Variabilität der Archaea und Msm konnte mit T-RFLP und DGGE gezeigt werden. Der Einfluss der Flutung war im Vergleich zu allen anderen Probenahmedaten nicht so ausschlaggebend wie erwartet.
Insgesamt zeigen die Ergebnisse eine hohe Biodiversität der Mikroorganismen im Nationalpark Unteres Odertal. Die Flutung hatte insbesondere auf die Eubakterien einen großen Einfluss. Zeitliche Variabilität der Zusammensetzung der Lebensgemeinschaften der Prokaryoten lässt sich im Odertal nicht mit einer Jahreszeit in Zusammenhang bringen. Hingegen sind die mikrobiellen Biozönosen im Haselbach nachweislich von den wechselnden Zirkulationsphasen beeinflusst.
Die hier verwendeten Methoden sind zur Charakterisierung mikrobieller Biozönosen in der Umweltmikrobiologie weit verbreitet. Die Anwendung der neuen Pyrosequenzierungsmethode ermöglichte trotz enormer Anzahl analysierter Sequenzen keine vollständige Erfassung der hohen Biodiversität, aber durch das Fehlen des Klonierungsschrittes wurde eine Fehlerursache in der Darstellung der realen Biozönose ausgeschlossen. Unstimmigkeiten in den Ergebnissen der verschiedenen Experimente beruhen meist auf methodischen Limitationen. Die DNA Isolationsmethode, die Vorauswahl von Primern, die bevorzugte Amplifikation, die allen PCR-basierten Methoden zu Grunde liegen, verschieben die reale Darstellung der Struktur einer Biozönose. Die fehlende Aussagekraft über die Aktivität der Mikroorganismen durch DNA basierte Analysen kann durch die Beobachtung der zeitlichen Änderungen ihrer Abundanz reduziert werden. Erste einflussnehmende Umweltparameter konnten ermittelt werden. Zusätzliche Analysen weiterer Elektronenakzeptoren über einen längeren Zeitraum sind jedoch nötig, um eine hinreichend sichere Aussage treffen zu können.
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Vera, Mabel Patricia Ortiz. "Caracterização da comunidade fúngica do sedimento e da água do rio Tietê." Universidade de São Paulo, 2015. http://www.teses.usp.br/teses/disponiveis/42/42132/tde-10052016-103733/.
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Fungos aquáticos são o maior grupo microbiano decomponedor de sustâncias orgânicas, atuando na ciclagem de nutrientes, fluxo de energia e equilíbrio biológico. O Brasil é tido como um dos países com a maior biodiversidade, porém, existem poucos estudos sobre a diversidade microbiana em ambientes aquáticos e o prejuízo e consequências dos poluentes. O Rio Tietê foi estudado com o objetivo de caracterizar a diversidade de fungos da água e do sedimento por meio de técnicas dependentes e independentes de cultivo e correlacioná-las às variáveis ambientais. A diversidade fúngica foi avaliada em 30 pontos de água, entre Agosto e Novembro de 2013, e Fevereiro à Abril de 2014 e 10 pontos de sedimento, entre agosto a outubro de2013 e de julho a setembro de 2014. Foram obtidos 451 e 442 fragmentos terminais de restrição (TRFs) para a primeira e segunda coleta de água, 349 e 354 TRFs para o sedimeto. As análises de Redundância (RDA) agruparam as amostras de acordo com o índice de qualidade de agua, sendo os parâmetros de pH, temperatura, nitrato e D.O. os mais significativos para a estruturação na água; e cadmio, níquel e zínco para o sedimento, confirmando que a alteração destes pode modificar a estrutura da comunidade fúngica do Rio Tietê.Aquatic fungi are the most decomposer microbial group of organic substances, developing a key role in nutrient cycling, energy flow and biological equilibrium. Brazil is considered one of the countries with the highest biodiversity, hence, few studies exist about microbial diversity in aquatic environments and the damage of pollution. Tiete River was studied in order to characterize the diversity of water fungi and the sediment of the river basin through independent and dependent culture techniques and correlate them to environmental variables. Therefore, the fungal diversity was evaluated in 30 points of water between August - November of 2013, and February - April of 2014 and 10 sediment points, between August - October of 2013 and July - September of 2014. 451 and 442 Terminal Restriction Fragments - TRFs were obtained for the first and second collection of water, and 349 and 354 TRFs for the sediment collection. The redundancy analyses - RDA showed the grouping of samples according to water quality index, being the pH, temperature, nitrate and DO the most significant parameters for the structuring of water; and cadmium, nickel and zinc of sediment, confirming that the change of these parameters may modify the structure of the fungal community in Tiete River.
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Inforsato, Fábio José [UNESP]. "Fungos de sedimentos marinhos da Antártica: diversidade e prospecção de enzimas." Universidade Estadual Paulista (UNESP), 2017. http://hdl.handle.net/11449/149887.
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Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
Os micro-organismos que habitam o continente Antártico podem apresentar produção de compostos de interesse industrial e ambiental com propriedades específicas por estarem adaptados às condições adversas da Antártica. Dentre os compostos produzidos por micro-organismos da Antártica podemos destacar as enzimas adaptadas ao frio. O presente trabalho teve como objetivo principal estudar a diversidade dos fungos filamentosos e leveduriformes isolados de cinco amostras de sedimentos marinhos da Antártica, bem como prospectar as enzimas lipase e protease. Para o isolamento dos fungos duas estratégias foram aplicadas (com e sem enriquecimento das amostras). Para ambas as estratégias, os sedimentos marinhos foram diluídos em solução salina e após homogeneização inoculados em placas de Petri contendo quatro diferentes meios de cultura (PDA, BSA, PDA diluído 10x, MA), as quais foram incubadas a 5 e 15ºC. Um total de 226 isolados foi recuperado, sendo 60 fungos filamentosos e 166 leveduras. A maioria dos fungos foi isolada a 15ºC (68%) De acordo com os dados de sequenciamento e análise filogenética, representantes de oito gêneros e quatro espécies de fungos filamentosos foram isolados das amostras de sedimentos marinhos. Os gêneros Penicillium e Pseudogymnoascus foram os mais abundantes (40,00%), seguidos pelo gênero Cadophora (6,67%), Cladosporium (5,00%), Toxicocladosporium, Pseudocercosporella, Pestalotiopsis e Paraconiothyrium (1,67%). Para as leveduras, representantes de nove gêneros e 13 espécies foram recuperadas das amostras, sendo a espécie Metschnikowia australis (45,18%) a mais abundante, seguida por representantes do gênero Mrakia (21,68%), Cryptococcus e Glaciozyma (7,83%), Meyerozyma e Holtermanniella (5,42%), Rhodotorula (4,21%), Cystobasidium (1,80%) e Phenoliferia (0,60%). Alguns dos fungos filamentosos identificados no presente trabalho não haviam sido ainda reportados em ambientes Antárticos (Toxicocladosporium, Pseudocercosporella e Paraconiothyrium). As análises de diversidade revelaram que a amostra A5 coletada no Refúgio 2 (20 m, 0,1ºC) apresentou a maior riqueza de espécies, enquanto a amostra A2 coletada no Botany Point (24,7 m, 0,6ºC) se mostrou mais diversa. Com relação à diversidade β, as amostras A5 e A6 coletadas na mesma região geográfica (Refúgio 2) apresentaram o maior compartilhamento de espécies (42,3%). Os isolados foram avaliados quando à capacidade de produção de lipase e protease. Os resultados revelaram que a levedura 6A-1C2II (M. australis) apresentou a maior atividade lipolítica (0,88 U.mL-1) e o fungo filamentoso 4A-1C615III (Pseudogymnoascus sp.) a maior atividade proteolítica (6,21 U.mL-1). Ambos os isolados foram submetidos aos estudos de avaliação de diferentes fatores na produção das enzimas visando maximização da produção enzimática. Após a condução de planejamentos experimentais do tipo Plackett-Burman (PB), a produção de lipase por M. australis 6A-1C2II aumentou 1,36 vezes e a produção de protease por Pseudogymnoascus sp. 4A-1C615III 4,72 vezes. Nos experimentos de validação das condições otimizadas, as médias das triplicatas apresentaram valores inferiores aos alcançados nos planejamentos. A condução do presente trabalho permitiu a ampliação do conhecimento sobre a diversidade de fungos e leveduras que habitam os sedimentos marinhos da Antártica. Em adição, resultou na obtenção de isolados de fungos filamentosos e leveduras de ambiente extremo, os quais estão sendo mantidos na coleção de pesquisa associada à Central de Recursos Microbianos da UNESP (CRMUNESP) e poderão ser utilizados em estudos futuros de prospecção e aplicação biotecnológica.
Microorganisms that inhabit the Antarctic continent can produce compounds of industrial and environmental interest with specific characteristics, since they are adapted to the adverse conditions in Antarctica. Among the compounds that are produce by Antarctic microorganisms we can enhance the cold-adapted enzymes. The main objective of this research was to study the diversity of filamentous fungi and yeasts from five Antarctic marine sediments samples, as well as to prospect lipase and protease enzymes. Two strategies were applied for fungal isolation (with and without enrichment of the samples). For both strategies, the sediments were diluted with saline solution and after homogenization the dilutions were inoculated in Petri dishes containing four different culture media (PDA, BSA, PDA diluted 10x, and MA), which were incubated at 5 and 15 ºC. The total amount of isolates recovered was 226, being 60 fungi and 166 yeasts. Most of the fungi were isolated at 15ºC (68%). According to sequencing data and phylogenetic analyses, eight genera and four species of filamentous fungi were isolated from the marine sediment samples. The genera Penicillium and Pseudogymnoascus were the most abundant (40.00%); followed by genus Cadophora (6.67%), Cladosporium (5.00%), Toxicocladosporium, Pseudocercosporella, Pestalotiopsis, and Paraconiothyrium (1.67%). Representatives of nine genera and thirteen yeast species were recovered from the sediment samples, the specie Metschnikowia australis was the most abundant (45.18%), followed by isolates from genus Mrakia (21.68%), Cryptococcus and Glaciozyma (7.83%), Meyerozyma and Holtermanniella (5.42%), Rhodotorula (4.21%), Cystobasidium (1.80%), and Phenoliferia (0.60%). Some of the fungi identified in the present work were not reported in Antarctic environments before (Toxicocladosporium, Pseudocercosporella e Paraconiothyrium). The diversity analyses showed that the sample A5 collected from Refúgio 2 (20 m, 0.1ºC) presented higher species richness, while sample A2 that was collect from Botany Point (24,7 m, 0.6ºC) was the most diverse. According to β diversity data, the samples A5 and A6 that were collect in the same geographic region (Refúgio 2) showed the higher species sharing (42.3%). The capacity to produce lipase and protease were evaluated. The results revealed that the yeast 6A-1C2II (M. australis) presented the best lipolytic activity (0.88 U.mL-1) and the fungus 4A- 1C615III (Pseudogymnoascus sp.) the best proteolytic activity (6.21 U.mL-1). Both isolates were submitted to the evaluation of different factors in the enzyme production process aiming the enzymatic production maximization. After the conduction of Plackett-Bruman (PB) experimental designs, the lipase production by M. australis 6A- 1C2II increased 1.36 times and the protease production by Pseudogymnoascus sp. 4A- 1C615III increased 4.72 times. In the optimized conditions validation experiments, results from the triplicates averages were lower than that one reached during the experimental designs. This work allowed the improvement in the knowledge of fungal diversity in the Antarctic marine sediments ecosystem. In addition, resulted in the obtaining of fungi and yeasts from extreme environment, which are being maintained in the research culture collection associated to the Central of Microbial Resources (CRMUNESP) and can be used in future studies related to prospection and biotechnology application.
FAPESP: 2013/19486-0
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Mavraganis, Theodoros. "An investigation of environmental impacts on sediments by marine cage fish farms using long term metadata analysis." Thesis, University of Stirling, 2012. http://hdl.handle.net/1893/9797.
Full textAbstract:
Many studies have investigated the impacts of marine cage fish farming on seabed sediments. Most of these studies have focused on organic loading or toxic chemicals used for the treatment of disease, normally for a single or a small number of sites over short time periods. Only very rarely has there been the opportunity to use large data sets consisting of a large number of fish farm sites over a long time scale. In Scotland, localised nutrient impacts have been well documented for marine cage salmon farms, but mixed effects of nutrient and chemicals such as SLICE (the active ingredient of which is emamectin benzoate) have not been investigated in the long term. The aim of this project was to investigate the ecological impacts on sediments from farming activities using very large spatial and temporal data to investigate the long term effects of nutrient and chemical waste. This was achieved using a metadata set collected from 403 sampling stations at 31 fish farms on the west coast of Scotland over a 9 year period. Data consisted of sediment macrofauna, carbon and nitrogen levels, redox potential, particle size for sediment characterisation and sediment concentrations of SLICE. The data was analysed for trends using statistical and multivariate analysis to look for changes in sediment community and related conditions, and the relationships between these parameters were investigated. At sampling stations that were less than 50 metres from the sea cages, 72% of the macrofauna communities were correlated with regard to their species composition and abundance. A significant relationship between the concentration of SLICE and sediment characteristics was represented as: SLICE= 0.000644*(median size particle size) + 0.0311*(C %) – 0.00213*(redox potential) + 1.453. Annelids were the most sensitive to the presence of emamectin benzoate, with the sipunculid Phascolion strombi, the echinoderm Ophiura affinis, and the custaceans Iphinoe, Diastylis and Iphimedia also showing sensitivity. During the data period, there was a clear change in species composition associated with improved seabed conditions. This correlated with biomass changes at the relevant sites, where there was a consequent decrease in nutrient input and SLICE usage. The statistical comparison of the AMBI and ITI indices indicated a 68.9% correlation, but they differed in their ability to indicate levels of organic disturbance. AMBI was shown to correlate more closely with conditions and thus a more reliable index when working with large databases. Univariate and multivariate analysis indicated that a combination of abundance (N), Shannon Wiener (H’) and AMBI, as biological indices for describing the status of the ecological level associated with the carbon percentage and redox potential of sediments gave the most reliable representation of environmental change over a series of sampling stations. In conclusion, the overall results suggest that, in the long-term, sampling stations which contained significant levels of SLICE had a higher impact status than those affected only by nutrient inputs. The accuracy of multiple regression models were increased by adding biotic and abiotic parameters, though fish biomass at the sites were not considered be as important factor for the prediction of impacts. However, this model could be sensitive to natural environmental conditions and variations. In light of these results and conclusions, recommendations can be made both for updating the existed environmental regulation of marine fish farms and in the development of meaningful models to relate sediment conditions to accurate estimations of overall environmental impacts.
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Liu, Xiao-Lei [Verfasser], Kai-Uwe [Akademischer Betreuer] Hinrichs, and Roger [Akademischer Betreuer] Summons. "Glycerol ether lipids in sediments: sources, diversity and implications / Xiao-Lei Liu. Gutachter: Kai-Uwe Hinrichs ; Roger Summons. Betreuer: Kai-Uwe Hinrichs." Bremen : Staats- und Universitätsbibliothek Bremen, 2011. http://d-nb.info/1071897551/34.
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Rédou, Vanessa. "Communautés fongiques de sédiments marins de subsurface : diversité, origine et rôle écologique." Thesis, Brest, 2014. http://www.theses.fr/2014BRES0095/document.
Full textAbstract:
Au cours des vingt dernières années, les études sur les sédiments marins profonds ont révélé la présence et l'activité de communautés microbiennes inattendues. Il est maintenant formellement établi que la biosphère profonde héberge de nombreux représentants des domaines des Archaea et des Bacteria. Cependant,les micro-eucaryotes et plus particulièrement les champignons n’ont été que très peu étudiés dans ces écosystèmes singuliers. Dans ce contexte, des approches moléculaire et culturale ont été utilisées afin de caractériser la diversité des communautés fongiques des sédiments marins profonds en utilisant le bassin de Canterbury comme modèle d’étude. Les résultats principaux obtenus lors de ce travail de thèse sont les suivants : (i) L’approche moléculaire basée sur l’ADN a fourni la preuve directe que les communautés fongiques peuvent persister jusqu’à la profondeur record de 1740 mètres sous la surface du plancher océanique. (ii) Des approches complémentaires ciblant les ARNr et les ARNm ont permis de préciser leur activité métabolique et d’obtenir de premiers indices sur les fonctions de ces champignons à 350m sous la surface du plancher océanique, principalement liées à la croissance, à l’adaptation aux contraintes environnementales in situ et aux interactions entre communautés microbiennes. (iii) L’approche culturale a permis de constituer une collection de culture de 183 isolats fongiques avec des caractéristiques écophysiologiques témoignant leur capacité d’adaptation aux conditions in situ. (iv) Le potentiel biotechnologique des isolats obtenus a été estimé via la recherche de gènes impliqués dans la synthèse de métabolites secondaires et a permis de positionner cette collection d’organismes originaux comme une ressource d’intérêt biotechnologique potentiel. Ce travail qui témoigne de la persistance et de l’activité des communautés fongiques dans les sédiments marins profonds élargit notre vision de la diversité microbienne dans ces milieux et soulève des hypothèses sur le rôle écologique des champignons au sein de la biosphère profondeOver the past two decades, investigations on deep marine sediments have revealed the occurrenceand activity of unexpected microbial communities. Many representatives of Archaea and Bacteria were reportedbut micro-eukaryotes and especially fungal communities are still poorly studied in this ecosystem. In this underexplored context, molecular- and culture-based approaches were used to characterize the diversityof fungal communities in deep subsurface sediments using the Canterbury Basin as a model system. The main results of this work are: (i) The molecular DNA-based approach provided direct evidence that the fungal communities persist until the record depth of 1,740 meters below sea floor. (ii) Supplementary approaches targeting rRNA and mRNA revealed their metabolic activity and highlighted first hints into the fungal functions at350 meters below sea floor, mainly related to growth, adaptation to in situ environmental constraints andmicrobial interactions. (iii) The culture based approach allowed establishing a culture collection of 183 fungal isolates with ecophysiological characteristics indicating their ability to adapt to in situ conditions. (iv) This culture collection seems to represent a reservoir of secondary metabolites as many genes involved in secondary metabolites pathways were revealed. The fungal collection established may be considered as an untapped resource to explore for biotechnological applications. This work demonstrating the persistence and activity of fungal communities in deep subsurface sediments (i)broadens our view of microbial diversity in these environments and (ii) raises hypotheses about the ecologicalroles of fungi in the deep biosphere
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Bourque, Amanda. "Ecosystem structure in disturbed and restored subtropical seagrass meadows." FIU Digital Commons, 2012. http://digitalcommons.fiu.edu/etd/792.
Full textAbstract:
Shallow seagrass ecosystems frequently experience physical disturbance from vessel groundings. Specific restoration methods that modify physical, chemical, and biological aspects of disturbances are used to accelerate recovery. This study evaluated loss and recovery of ecosystem structure in disturbed seagrass meadows through plant and soil properties used as proxies for primary and secondary production, habitat quality, benthic metabolism, remineralization, and nutrient storage and exchange. The efficacy of common seagrass restoration techniques in accelerating recovery was also assessed.
Beyond removal of macrophyte biomass, disturbance to seagrass sediments resulted in loss of organic matter and stored nutrients, and altered microbial and infaunal communities. Evidence of the effectiveness of restoration actions was variable. Fill placement prevented additional erosion, but the resulting sediment matrix had different physical properties, low organic matter content and nutrient pools, reduced benthic metabolism, and less primary and secondary production relative to the undisturbed ecosystem. Fertilization was effective in increasing nitrogen and phosphorus availability in the sediments, but concurrent enhancement of seagrass production was not detected. Seagrass herbivores removed substantial seagrass biomass via direct grazing, suggesting that leaf loss to seagrass herbivores is a spatially variable but critically important determinant of seagrass transplanting success.
Convergence of plant and sediment response variables with levels in undisturbed seagrass meadows was not detected via natural recovery of disturbed sites, or through filling and fertilizing restoration sites. However, several indicators of ecosystem development related to primary production and nutrient accumulation suggest that early stages of ecosystem development have begun at these sites. This research suggests that vessel grounding disturbances in seagrass ecosystems create more complex and persistent resource losses than previously understood by resource managers. While the mechanics of implementing common seagrass restoration actions have been successfully developed by the restoration community, expectations of consistent or rapid recovery trajectories following restoration remain elusive.