Ph.D. Theses

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Building resilience to climate change impacts in the Ikel watershed in the Republic of Moldova : a system dynamics approach
(Thesis (Ph.D.) - Bogazici University. Institute of Environmental Sciences, 2022., 2022) Ciobanu, Natalia.; Saysel, Ali Kerem.
Climate change threatens social-ecological systems (SES) across the globe. Developing countries where agriculture is a major income source for both local communities and the national economy are especially affected. In conjunction with their reliance on climatic resources, these countries face the challenge of data scarcity. Assessing and building the resilience of these communities to climate change impacts is equally important and challenging. As the relationship between science, policy, and practice changes, the demand increases on research to engage productively with stakeholders and ensure positive outcomes for all parties. Efforts are increasingly focusing on building the resilience of SES to climate impacts. In this research, I design, build and implement a client-based process under data scarcity conditions in a network governance setting within Republic of Moldova. The process includes analyzing a complex socio-ecological problem to identify policies helpful in meeting development objectives: improving crop yields, preserving groundwater resources and securing habitats for biodiversity conservation. To this end, I first develop a computer simulation model – Ikel CliRes – using a participatory approach that combines several methods, techniques and tools from two related fields: system dynamics and resilience of socio ecological systems. I then use Ikel CliRes to design policy interventions that increase the desirable resilience of Ikel SES to some climate impacts. Ongoing implementation of several policies discussed with decision-makers is underway pointing to the effectiveness and usefulness of the process. Results should be regarded within the limitations of the model architecture and of the assumptions underlying both the model and the analysis.
Importance of integration of public participation into environmental management
(Thesis (Ph.D.)-Bogazici University. Institute of Environmental Sciences, 2009., 2009.) Celep, Ayşe Beyza.; İnce, Nilsun.; Üstün, Beyza
Technical approaches such as wastewater treatment technologies and other pollution prevention methods have generally been considered as the means of improving the environmental conditions in a basin. However, generation and prevention of environmental pollution in a water basin is principally based on socio-economic structures and environmental awareness of the basin population. This study was conducted to integrate a social approach based on basin population and environmental awareness with the classical environmental management approach. The region of study Küçükçekmece, is a precious natural system with the Küçükçekmece Lagoon, its basin and a variety of endemic species. In addition, it is a cosmopolitan social system which is a representative of Turkey’s population suffering heavy pollution due to mismanagement. The method of study was such that preliminary face-to-face interviews and open ended questionnaire were followed by development and evaluation of closed ended questionnaire. Analysis of results showed that the basin generally consisted of people who have low level of education and income. According to these people, environment is mostly defined as ‘people’ such as friends and neighbors. The perception of environmental pollution and problems by five senses was found to be an important factor for the identification of these problems. Within environmental qualifications, ‘environmental attitude’ was the main indicator in the level of environmental awareness of local community in Küçükçekmece. It is followed by ‘system knowledge’ and ‘indigenous knowledge’. Primary school graduation and middle age are the socio-economic characteristics of the people who have the highest score in system knowledge, indigenous knowledge and environmental attitude queations.
Evaluation advanced oxidation technologies and nanoscale particles for water and groundwater remediation
(Thesis (Ph.D)-Bogazici University. Institute of Environmental Sciences, 2008., 2008.) Aksoy, Dila.; İnce, Nilsun.; Copty, Nadim.
Advanced Oxidation Processes (AOP) that are based on the in-situ generation of hydroxyl radicals in solution are extremely powerful tools for the destruction of recalcitrant compounds in water and groundwater. Recent research has shown that subsurface injection of nanoparticles may also be a viable technology for the in-situ remediation of contaminated groundwater resources. The purpose of this study was to assess the degradability of typical groundwater contaminants, namely phenol and 2-chlorophenol by advanced oxidation processes, nanoparticles and combinations thereof. Advanced oxidation processes investigated were ozonation, UV irradiation, sonolysis, and sono-Fenton process. In the second part of the research, flow-through reactors were used to test the mobility of the selected nanoparticle solutions in porous media under different flow configurations. Continuous flow experiments mainly focused on the assessment of the mobility of nanoparticle solutions in porous media under different flow configurations. Comparison of the nanoparticle breakthrough curves to that of the conservative tracers showed that the transport of nanoparticles is influenced by their concentration, which strongly controls the particle size and hence, their mobility. Overall, this study has demonstrated that phenolic compounds in contaminated water and groundwaters may be effectively destroyed by use of optimized hybrid processes involving Advanced Oxidation Processes and nanoparticles.|Keywords: advanced oxidation, ultrasound, nanoparticle, groundwater remediation, phenolic compounds
Transcriptional responses to long-term salinity stress and acclimation in Mytilus galloprovincialis from Bosphorus
(Thesis (Ph.D.) - Bogazici University. Institute of Environmental Sciences, 2021., 2021.) İçağasıoğlu, Elif.; Bilgin, Raşit.; Furman, Andrzej.
Mytilus galloprovincialis is an ideal model organism for studying adaptation, as it can inhabit highly variable environments. We examined its acclimation to chronic and gradual long-term salinity stress. Gene expression, pathway and gene set enrichment analyzes were used with RNA-Seq with de novo transcriptome. In our results, low salinity was observed to be correlated with high energy expenditure. Cholinergic ciliary stimulation and calcium signalling were involved. Volume regulation was enhanced by nitrogen metabolism and alterations of membrane permeability. Arachidonic acid metabolism and Na+/K+ pump were inversely regulated with salinity in this context. Genes involved in the synthesis of serine, proline, glycine, ornithine and betaine were also regulated. Protein turnover and nucleotide metabolism were also inversely regulated with salinity. In addition to these regulations, some of the observed metabolic regulations are associated with cancereous cells, as well. Parallel to energy requirement, aerobic and anaerobic respiration genes were parallely regulated, as well as genes of reciprocally regulated processes of glycolysis and gluconeogenesis. Although there are many types/causes of cancer, there are common adaptations that support survival and proliferation, such as apoptosis suppression and the aforementioned metabolic regulations. In addition, in our study, parallel with these metabolic regulations, p53 and p63 originated apoptosis were triggered with participation of TP53 apoptosis effector (PERP), TLRs and TNFSF14. Understanding genes and pathways that triggers apoptosis in this context in our study, and investigating their projections in humans, may be important in our understanding of cancer and in developing therapeutic and protective products such as vaccines.
Biogeneration of activated carbon in the treatment of phenolic compounds
(Thesis (Ph.D.)-Bogazici University. Institute of Environmental Sciences, 2006., 2006.) Aktaş, Özgür.; Çeçen, Ferhan.
This study aimed to clarify the effect of adsorbability, desorbability, biodegradability and activated carbon type on the extent of bioregeneration in the treatment of phenolic compounds in activated sludge systems combined with activated carbon. Bioregenerabilities of activated carbons preloaded with phenol, 2-chlorophenol and 2-nitrophenol were studied. For this purpose, four different activated carbon types; thermally activated and chemically activated powdered carbons (PAC), and their granular countertypes (GAC) with similar physical characteristics were used. Thermally activated carbons were better adsorbers for phenolic compounds than chemically activated ones. However, apparently higher adsorption irreversibility was calculated in the case of thermally activated carbons. The results suggested that, rather than the physical form, carbon activation type and chemical surface characteristics played a more important role on adsorbability of phenolic compounds and its reversibility. Also, adsorption and its reversibility were highly dependent on the type of the target compound. Bioregeneration of chemically activated carbons was also higher than thermally activated ones. This showed that bioregeneration was controlled by the reversibility of adsorption. The results suggested that carbon activation type was of crucial importance for bioregeneration. PAC and GAC countertypes showed comparable bioregeneration efficiencies indicating that carbon size was not an effective factor. Oxidative polymerization of phenol and 2-chlorophenol was a plausible explanation for lesser bioregeneration of thermally activated carbons. However, bioregeneration efficiencies of thermally activated carbons were much higher than their total desorbabilities. This indicated the presence of exoenzymatic bioregeneration. Bi-solute experiments showed that competition for adsorption sites greatly determined the extent of adsorption reversibility and bioregeneration. Cometabolic biodegradation of 2-chlorophenol and 2-nitrophenol in the presence of phenol resulted in efficient bioregenerability of activated carbons, when they were loaded with non-growth substances together with a growth substrate.
Elucidation of the photocatalytic removal pathways of humic substances: progress towards mechanistic explanations
(Thesis (Ph.D.)-Bogazici University. Institute of Environmental Sciences, 2005., 2005.) Uyguner, Ceyda Senem.; Bekbölet, Miray.
The objective of this research was to characterize the spectroscopic properties ofhumic and fulvic acids of different origins as model compounds to represent the naturalorganic matter in aquatic systems. The photocatalytic oxidation of model humic and fulvic acids was carried out using TiO2 Degussa P-25 as the photocatalyst. The degradationkinetics was assessed based on pseudo first order and Langmuir Hinshelwood (L-H)kinetic models. The related data for aquatic and terrestrial humic substances werecomparatively presented in terms of UV-vis parameters such as Color436, Color400, UV365, UV300, UV280, UV254 and total organic carbon (TOC) removal. Furthermore, the molecularand structural characteristics of the humic acid molecule relative to changes duringphotocatalytic oxidation were monitored by spectroscopic techniques.On the basis of their diverse chemical and physical properties such as molecular weight, molecular size, elemental composition and source of origin, substantial differenceswere observed in photocatalytic removal efficiencies of humic and fulvic acids. For all ofthe humic substances, higher removal rates were achieved in terms of UV254 valuescompared to that of Color436. Moreover, humic acids exhibited higher pseudo first order removal rates with respect to that for fulvic acid. The declining trend of the specified UVvisparameters, the related changes in the fluorescence spectra (initial increase of thefluorescence intensities, formation of new fluorophores, shift of the spectra to lowerwavelength region and decline of intensity after long photocatalytic irradiation times), decrease of TOC content during degradation, the spectral changes in FTIR and NMRindicated the oxidative degradation of humic substances.Considering the complexity and polydispersity of the humic macromolecules, theywere fractionated into well defined subcomponents of known molecular sizes usingultrafiltration through membranes in the range of 100-1 kDa. The effect of photocatalyticoxidation on the molecular size fractions of humic substances were also evaluated on acomparative basis by UV-vis and fluorescence spectroscopy. As confirmed by the spectroscopic evaluation of the molecular size distributiondata, photocatalytic degradation of humic acid leads to the formation of lower molecularsize (small fractions) and higher UV-absorbing compounds. For fractions less than 10 kDa,UV254 absorbing moieties in treated humic acid samples become higher than that of rawhumic substances designating the generation of new species during photocatalysis.Based on the comparison between the synchronous scan fluorescence spectra ofthe molecular size fractions of raw and oxidized humic substances, it could be concludedthat oxidative cleavage of the molecule leads to a blue shift of the spectra which isindicative to the formation of new fluorophores in each size fraction. It is assumed thatoxidative degradation of the macromolecule occurs through an unselective pathway, by thereaction of .OH radicals with the various moieties within each fraction.
Evaluation of natural organic matter-metal oxide adsorption isotherms under influential structural concepts
(Thesis (Ph.D.)-Bogazici University. Institute of Environmental Sciences, 2006., 2006.) Süphandağ, Şerif Altan.; Bekbölet, Miray.
The adsorption of molecules onto a surface is a necessary prerequisite to any surface mediated chemical process. Therefore, the mechanism of binding of humic acids to TiO2 surface has to be addressed in order to improve the understanding of photocatalytic degradation. From the fundamental point of view, natural organic matter (NOM) for water scientists can be perceived as very complex entities both in terms of chemistry and comprehension. Especially the fulvic (FA) and humic acids (HA), the soluble portions of NOM, are often considered as oligomeric and polymeric materials. In literature, there are ongoing discussions regarding the high molecular mass is due to aggregation of small units, as in micelles, or due to covalently bound units, as in polymers. The essence of this thesis is to evaluate the adsorption under the light of these two debatable approaches and bring reasonable interpretations of the observed isotherm patterns through the use of proposed structures. In this dissertation the isotherms of humic acid (HA) on titanium dioxide are analyzed at acidic, neutral, and basic pH. Combined effects of pH and increasing ionic strength were evaluated in order to asses the effect of changing solution matrix on the molecular structure of humic acid.|Keywords: humic acid, titanium dioxide, adsorption, natural organic matter, metal oxides
Projections for changes in climatology and extreme events of the Cordex-Australasia domain :|a dynamical downscaling approach
(Thesis (Ph.D.) - Bogazici University. Institute of Environmental Sciences, 2021., 2021.) Turp, Mustafa Tufan.; Yenigün, Orhan.; Kurnaz, M. Levent.
Climate change, which is one of the most vital threats to humanity today, will affect many countries on a regional and local scale in terms of common and country-specific areas. In order to adapt to the changing climate, the impacts of climate change in the future should be addressed well. For this reason, joint projects are developed that lead to the production of high resolution climate data in order to accurately determine the impacts of climate change in different parts of the world. In this thesis, within the scope of CORDEX, which is the most prominent of these joint projects today, changes in temperature and precipitation climatology of the Australasia region as well as changes in extreme climate events were examined. For Australasia, one of the least studied regions under the umbrella of CORDEX, the mean air temperature and precipitation changes for three different periods (i.e., 2016 - 2035, 2046 - 2065, 2081 - 2100) were analyzed under three different scenarios (i.e., RCP2.6, RCP4.5, RCP8.5 using global circulation models/global climate models with the approach of multi-model ensemble mean. Later, by using RegCM4.6 regional climate model, low resolution data of HadGEM2-ES and MPI-ESM-MR global climate models were dynamically downscaled to 50 km x 50 km horizontal resolution. Before the future projections were applied in the study, the most suitable Planetary Boundary Layer (PBL) scheme and convective parameterization of the RegCM4.6 model for the region were determined. Accordingly, the RegCM4.6 model was employed using the BATS landuse scheme with the Holtslag PBL scheme and the mixed convective parameterization which is the Tiedtke scheme over lands and the Emanuel scheme over oceans. With RegCM4.6 driven by HadGEM2-ES and MPI-ESM-MR outputs, mean, minimum and maximum temperatures and total precipitation of Australasia have been examined under the RCP4.5 and RCP8.5 scenarios for the periods of 2011-2040, 2041-2070, and 2071-2099 with respect to the reference period of 1971 - 2000. In another part of the study, using the NEX-GDDP dataset with a horizontal resolution of 0.25° x 0.25°, the temperature and precipitation extreme indices for the Australasia region were computed via the RCP4.5 and RCP8.5 scenario outputs of the ACCESS1-0 and MPI-ESM-LR models. While very hot days, tropical nights and heatwaves are used as temperature extremes, very heavy precipitation days, simple daily intensity and consecutive dry days are used for precipitation extremes. The changes in extreme climate events have been analyzed for 2016-2035, 2046-2065, and 2081-2100 with respect to the reference periods of 1981-2000. The results of the analysis show that there will be increasingly higher temperatures in Australasia towards the end of the century. It is concluded that the mean temperature increase expectation of approximately 1.5 - 3 ℃ may be around 5 ℃ at the end of the century and this value can reach up to 7 ℃ for the maximum temperature. It appears that the expected warming may be greater as we approach the end of the century and move from the most optimistic to the most pessimistic scenario. On the other hand, the change in precipitation varies greatly depending on the period and sub-region. Average ±20 % change in precipitation may occur as 50 % or more increases or 30 % or more decreases in some places. In addition to the change in mean temperature and precipitation, it is clear that there will be an increase in temperature and precipitation extremes for the Australasia region. These results indicate that Australasia will have a future in which hot days and nights, heatwaves are more frequent, and the days with heavy precipitation are more common. In conclusion, it is certain that changes in both mean values and extreme climate events pose a very high risk in terms of human health, ecosystems and ecosystem services, habitats and limited agricultural areas in the region.
Agricultural decision-making in Turkey from climate change perspective :|a new road map for the period of 2021-2050
(Thesis (Ph.D.) - Bogazici University. Institute of Environmental Sciences, 2020., 2020.) An, Nazan.; Yenigün, Orhan.; Kurnaz, M. Levent.
The expectation that it can affect basic life resources and particularly food security on a global, regional, and local scale with its impact on the ecosystem has made climate change one of the most urgent issues on the global agenda. Extreme weather events due to climate change may degrade food quality, affect access to food and raise food prices, markedly affecting agricultural productivity. Many countries have already been faced the global impacts of climate change, therefore studies on the effects that may occur on ecosystems are of great importance. As one of the regions that may be most affected by climate change, the Mediterranean Basin is at risk in terms of agricultural production due to temperature increases and precipitation regime changes, and what’s more the increase in the frequency and severity of extreme weather events due to climate change. As a country located in the Mediterranean Basin, Turkey may also suffer from climate change. This situation poses a risk in terms of crop production value and export income, particularly for products with high commercial value grown in Turkey. Therefore, the study has focused two crops of the country i.e., hazelnut and grape with the high commercial value. In the first stage, the climate data for different phenological periods and different variables for each crop was obtained from the regional climate model, RegCM4.4 with the MPI-ESM-MR global climate model under the RCP8.5 pessimistic scenario for the baseline of 1991-2012 and the future period of 2021-2050. In the second stage, the change in hazelnut yield was analyzed by statistical approach, panel data method, and the change in grape yield was analyzed using the crop growth simulation model, STICS. At the last stage, how the climate conditions of hazelnut (88 locations) and grapes (96 locations) will change in the future has been examined by using membership function. However, considering the crop production values of these two crops and export revenue contribution to the national economy, the possibility of new locations where these crops may grow in the future has been analyzed in 923 locations throughout Turkey. Accordingly, at this stage of the thesis, climate suitability index was calculated for hazelnut and grape, and climatic suitability conditions were determined according to 5 classification ranges. In brief, it has been observed that climate change may have a negative impact on both hazelnut and grape yields in the future and it is predicted that there may be significant reductions in climatic suitability conditions in the locations where these two crops grow.
Dynamic simulation model for long term comprehensive environmental analysis of GAP
(Thesis (Ph.D.)- Bogazici University. Institute of Environmental Sciences, 1999., 1999.) Saysel, Ali Kerem.; Yenigün, Orhan.; Barlas, Yaman.
Integrated development projects based on water resources development, aiming hydropower production and agricultural modernization have many potential impacts on social and natural environments. Southeastern Anatolian Project (GAP), located in Southeast Turkey, comprising 10% of Turkish lands, targeting irrigation schemes on 1.7 million hectare fertile lowlands and 7400 MW hydropower production on Euphrates and Tigris would have many social and environmental consequences. In this study, potential environmental problems suggested by GAP, questions related with utilization of water resources, land degradation, agricultural pollution and land use are analyzed in systems perspective, focusing on the integrity of environmental, social and economic issues. With this aim, GAP S 1M, a dynamic simulation model is developed to trace long term trajectories of selected parameters, representing the relevant aspects of GAP's social, economic and natural environment. Based on a "systemic" problem definition, GAPSIM simulates the development rate of irrigation schemes, hydropower production with respect to changing irrigation releases, water availability on farmlands, crop selection and production, salinization, erosion, pesticide and fertilizer consumption, rangeland and forest quality, urbanization and population dynamics in GAP during 1990-2030 period, which comprises water facilities construction process. GAPSIM is validated, first "structurally", according to the validation tests suggested by the literature and then, model "behavior" is calibrated with respect to data available for the period 1990-1998. GAPSIM provides a dynamic simulation platform where several scenarios and policy analyses concerning GAP environment can be executed in order to arrive at an improved understanding of GAP as a socio-environmental system. Scenario and policy runs on GAPSIM reveal that, increased intensity of the most evapotranspirant crop cotton on GAP fields may cause significant water scarcity, which hinders the development rate of irrigation into new acres and inhibits crop yields by decreased water delivery to individual farms.
Improvement of biogas production by fungal treatment during the conversion of agricultural biomass into energy and digestate
(Thesis (Ph.D.) - Bogazici University. Institute of Environmental Sciences, 2019., 2019.) Akyol, Çağrı.; İnce, Bahar Kasapgil.
In this PhD study, the advantage of highly-cellulolytic white-rot fungus Trametes versicolor and anaerobic rumen fungus Orpinomyces sp. was taken by aerobic pretreatment and bioaugmentation approaches in lignocellulose-based anaerobic digestion (AD) trials, respectively. Selected cereal crop materials (i.e. wheat, rye, barley, triticale) were harvested at different stages and subjected to AD with cow manure as the co-substrate. In all AD tests, early-harvested barley was found to be the highest methane-yielding crop material. Changes in the quantity of selected key functional enzyme groups responsible for lignocellulose degradation and biomethanation were further determined in AD using quantitative real time PCR (qPCR). 16S rRNA gene amplicon sequencing revealed a more diverse microbial community in fungal-treated anaerobic digesters. Comparatively more unique microbiome of biogas reactors upon fungal treatment synergistically affected VFA production, cellulose degradation and eventually methane yield in an affirmative way. Following the AD tests, anaerobic digestates were collected on crop-basis and composted. All compost piles exhibited same abiotic profiles. Based on 16S and 18S rRNA gene amplicon sequencing, similar predominant bacterial and fungal genera detected that were mostly composed of lignocellulose degraders. In the last step, each final compost product was amended to agricultural fields where the crops were planted, and changes in soil microbiome was monitored using 16S rRNA gene amplicon sequencing. Proteobacteria was the most abundant bacterial phylum; whereas a shift in the predominance from Actinobacteria to Acidobacteria was observed following the compost amendment. In addition, there was a remarkable increase in the relative abundance of Bacteroidetes upon compost amendment.
Sustainability assessment of selected dairy farms using social multi criteria approach
(Thesis (Ph.D.) - Bogazici University. Institute of Environmental Sciences, 2019., 2019.) Kabasakal Güzeloğlu, Leyla.; Saysel, Ali Kerem.; Özertan, Gökhan.
Turkish dairy industry is being modernized and there are many successful examples. Big farms are supported while ecologic and social factors can often be overlooked. Objective of the research is to quantify sustainability at dairy farm level and compare farms with different management practices. The study examined current dairy production practices on farms assessing resource and energy uses as well as management and industry structure. Based on literature and stakeholders, a sustainability assessment framework was developed. Feed management, herd management, manure management and social organization are the main components in the framework and encompass environmental, social and economic dimensions. Dairy farms were selected by purposive sampling method. Dairy farms are categorized based on the processor they sell raw milk to; industrial milk processors, co-operatives and directly to consumers. Qualitative and quantitative data is collected from eighty farms via questionnaire. Based on the questionnaire; resource, energy, water and labor criteria were quantified using both qualitative and quantitative data. Sustainability assessment was conducted using Social Multi Criteria Evaluation methodology. A snapshot of the farms was taken and their performances based on farm management and milk production practices were compared from a sustainability standpoint. NAIADE is used for final comparison of the farms. Results indicate that small cooperative member farms are more sustainable. Using the same framework, larger studies with a larger sample size are encouraged to be conducted to see if general farm population reflects results of this study. Results of the assessment aim to start discussing sustainability at farm level.
Phylogeography of the large mouse-eared bats in Turkish thrace and Anatolia
(Thesis (Ph.D.) - Bogazici University. Institute of Environmental Sciences, 2020., 2020.) Çelik, Yalın Emek.; Furman, Andrzej.
The main objective of this study is to determine the exact number of species/subspecies within the Large Mouse-eared Bat Complex that inhabit Anatolia and the Turkish Thrace. In this study we also explore the historical relationships among these taxa, and how their geographical distribution changed over time. Defining precise methods for identification of these species/subspecies in the field and in laboratory settings is among the aims of the study. We also focus on the discrepancy in the information acquired from the nuclear and mitochondrial DNA in terms of species identification and try to explain the processes that cause this discrepancy. The results of our study reveal that in the study area, there are two distinct species one of which is further divided into two evolutionarily significant units. Besides the previously accepted two taxa, there is a separate unit residing in Anatolia that is morphologically similar to the Myotis myotis in the west but genetically isolated from this ancestral population. We conclude that some of the alleged subspecies in previous studies do not exist, but Anatolia is occupied by a genetically isolated branch of the greater form that might be defined as a different species/subspecies with the previously suggested name, M. (m.) macrocephalicus. This study also highlights the importance of these findings that redefine the species distribution, with regard to conservation studies. A mathematical method including morphological measurements is also suggested for differentiation of these species in the field.
Quantification of multi-class antibiotics by UHPLC-MS/MS in animal manure and fate of antibiotics during rapid composting
(Thesis (Ph.D.) - Bogazici University. Institute of Environmental Sciences, 2020., 2020.) Karaca, Serap.; Yenigün, Orhan.
Massive amounts of animal waste are generated from livestock raising and proper management of this waste is critical for the elimination of manure pollutants including various gaseous, nutrients, pathogens, and antibiotics. A comprehensive multiresidue method for the analysis of 33 antibiotics from 7 prevalent classes was comparably investigated for both dairy and poultry manure. Following salting-out-assisted extraction with Acetonitrile (MeCN), the antibiotics were quantified with Ultrahigh-Performance Liquid Chromatography Tandem Mass Spectrometry (UHPLC-MS/MS) without a clean-up step. Although the physicochemical properties of selected antibiotics were quite different, the apparent recovery from dairy and poultry manure samples were 86–121% and 89–113%, respectively. Rotary drum composting was performed in closed systems with controlled aeration for the reduction of detected antibiotics and volume of manure. Two identical reactors were operated up to 20 days. After the characterization of manure samples, proper compositions for rapid composting were prepared by blending of dairy (D), broiler (B), and layer-hen (L) manures. The performances of composting process for DB and DL manure mixtures as well as B and D manures were evaluated. Time to attain the peak composting temperature (68-73°C) was reduced and higher peak temperatures were achieved in mixed manures compared to the composting of D manure alone. While the composting with high aeration rate (17±3m3.h-1) caused a decrease in composting temperature, the elevated temperature achieved with low aeration rate (3.6±0.2 m3.h-1) did not improve antibiotic reduction, and high aeration reduced the half-lives of antibiotics regardless of manure blending indicating the importance of biotic processes.
Recover of silver and neodymium from aqueous solutions by using microalgae
(Thesis (Ph.D.) - Bogazici University. Institute of Environmental Sciences, 2019., 2019.) Tunalı, Merve.; Yenigün, Orhan.
Electronic waste is one of the fastest growing streams of waste due to the increase in electronics production. Electronic waste consists of valuable elements that many governments and companies wish to extract from the waste. Although the increase in the usage of electronic devices is inevitable, eco-friendly and easily operated recovery methods for the valuable elements can be developed. In this study, characterization of electronic waste were carried out by using three different digestion methods; USEPA 3051, USEPA 3050B and Modified Microwave Digestion Method to define focus elements. The recovery of selected elements was carried out by using green microalgae, Chlorella vulgaris. Results showed that silver and neodymium were found as major precious metal and rare earth element, respectively. Biosorption capacities were found as 151.7 mg/g for silver, and 296.8 mg/g for neodymium. Bioaccumulation capacities refer to 161.6 mg/g for silver and 239.7 mg/g for neodymium. When there were multi-elements in the solution, the uptake capacities decreased and uptake of selected element can be limited via changing the process parameters. Variations in functional groups were observed that suggests binding of elements to the microalgae. Silver and neodymium were seen on algal surfaces as particles and scattered, respectively. Pseudo-second order kinetics fitted better both to biosorption and bioaccumulation for silver and neodymium. Freundlich isotherm model and linear model was found suitable for biosorption and bioaccumulation, respectively. In the context of sustainability, this study supports the achievement of United Nations Sustainable Development Goals by following Goals: 3, 9, 11, and 12.
Sonolytic, sonocatalytic and photocatalytic destruction of pharmaceuticals and personal care products in water
(Thesis (Ph.D.)-Bogazici University. Institute of Environmental Sciences, 2019., 2019.) Savun, Başak.; İnce, Nilsun.
Pharmaceuticals and personal care products are used for health and cosmetic reasons and discharged readily to sewage treatment facilities to be transported to freshwater systems due to their low biodegradability. Ultrasound is an excellent tool for the destruction of such refractory chemicals, but the method is energy-intensive and ineffective for carbon-mineralization. Hence, combination of ultrasound with solid particles, or other processes (e.g. adsorption, homogeneous/heterogeneous AOP’s) is expected to improve the efficiency. The present study encompasses a thorough investigation of single ultrasound and combinations with adsorption, catalysis and photolysis for the destruction of PPCPs in water. The probe chemicals were salicylic acid, methylparaben and caffeine, while the catalysts were zero-valent iron (ZVI), sepiolite, TiO2, nanoparticles of sepiolite-SDS, and sepiolite-TiO2. The study also includes the use of an experimental design method for the analysis and evaluation of the operating parameters/factors, characterization of sonolytic and sonocatalytic systems, and determination of the individual and interaction effects of the operating parameters on the process efficiency. A summary of findings is as follows: i) ultrasound-assisted advanced Fenton reaction is much more effective than unassisted Fenton, via preventing H2O2 addition, which inhibits the mineralization process; ii) sepiolite is a good adsorbent and catalyst particularly when the surface is modified by sonication or when it is converted to a nanocomposite with sodium-dodecyl-sulfate (SDS); iii) Photocatalytic and sonocatalytic activity of TiO2 is significantly enhanced by modification of the catalyst surface to produce sepiolite/TiO2 nanoparticles.
On the aquatic toxicity of diverse chemicals: Development of novel in silico models tow ards selected aquatic organisms under the framework of reach regulation
(Thesis (Ph.D.) - Bogazici University. Institute of Environmental Sciences, 2018., 2018.) Önlü, Serli.; Türker, Melek.
Environmental hazard and risk assessment of chemicals are crucial for aquatic species within the direction of the European Regulation on the Registration, Evaluation, Authorization and Restriction of Chemicals (REACH). In consideration of ethical concerns, animal welfare and sustainability, as well as the need for aquatic toxicity data, in silico models, such as validated quantitative structure-toxicity relationships (QSTRs), are of great importance. In the present study, an activity-independent rational approach towards selecting an optimal geometry optimization method for improved QSTR modeling was proposed for the first time. Different QSTR and interspecies models towards three representative aquatic species (algae, fish, and planarian) were developed using the rational approach recommended. QSTR models on the prediction of cytotoxicity to rainbow trout liver cell line (RTL-W1), toxicity to Dugesia japonica, and an interspecies quantitative toxicity relationship between Daphnia magna and D. japonica were reported for the first time. The presented QSTR models have contributed to the literature by providing notable prediction coverage for environmentally significant chemicals, such as contaminants of emerging concern and high production volume chemicals. Furthermore, the first predicted aquatic toxicity and cytotoxicity data were provided for a great majority of the chemicals addressed in “The List of Chemicals with no Ecotoxicological Data” announced by the Scientific and Technological Research Council of Turkey (TÜBİTAK). The developed models are promising as potential tools in toxicity assessment, screening and prioritization of chemicals in a scientific and regulatory frame.
The phylogeographic history, taxonomy and conservation of two cave-dwelling bat species : Miniopterus schreibersii and myotis capaccinii (Chiroptera: vespertilionidae)
(Thesis (Ph.D.) - Bogazici University. Institute of Environmental Sciences, 2018., 2018.) Gürün, Kanat.; Bilgin, Raşit.
Miniopterus schreibersii and Myotis capaccinii are two cave-dwelling bat species with subcosmopolitan distributions, which are well-suited for phylogeographic studies at large geographic scales. In this study, the social and genetic structure of Miniopterus schreibersii was investigated using nuclear microsatellite and mitochondrial DNA markers, and the taxonomy and phylogeography of Myotis capaccinii was examined using mitochondrial DNA data, using samples from the entire circum-Mediterranean range of these species. Local genetic structuring previously detected among populations of Miniopterus schreibersii using mitochondrial markers was not observed for microsatellite markers, indicating male-biased dispersal. Some support was found for the fifth paradigm of postglacial expansions in Europe, which states that Anatolia might have been a primary refugium during the last glacial maxima. Regarding Myotis capaccinii, all analyses revealed the existence of three haplogroups, B, C1 and C2. The divergence of haplogroup B from C haplogroups was dated to 350,000 years BP and divergence of C1 and C2 to 130,000 years BP, indicating isolation and differentiation during multiple glacial periods. Individuals from haplogroups B and C1 were found sympatrically in the same cave, suggesting they might represent distinct species. Similarly, the C1 – C2 divergence might indicate subspecific differentiation. However, analyses of nuclear markers and phenotypic characters are required to make further subspecific and specific recommendations. Species distribution models predicted a northward movement of potentially suitable areas for Myotis capaccinii in the near future due to climate change, thus the implementation of proper environmental measures is of utmost importance for the conservation of this species complex.
Remediation of DNAPLs in saturated porous media: Cosolvent flushing and sherwood correlation
(Thesis (Ph.D.) - Bogazici University. Institute of Environmental Sciences, 2018., 2018.) Aydın, Derya.; Copty, Nadim.
The contamination of the subsurface by the accidental release of organic contaminants in the form of non-aqueous phase liquids (NAPLs) is a widespread and challenging environmental problem. However, there is lack of cost effective technologies for the remediation of groundwater systems contaminated with NAPLs. A key process influencing the effectiveness of NAPL remediation is the interphase mass transfer which is the transfer of components across the interface separating the aqueous and NAPL phases. This study evaluates the use of cosolvent flushing for the removal of NAPLs from saturated porous media. Intermediate-scale laboratory experiments were conducted to investigate the impact of cosolvent content, flow velocity, and pumping pattern on cosolvent enhanced NAPL dissolution. Results demonstrated the importance of the flushing solution content and the flow characteristics on NAPL removal. The experimental results were also modeled using multiphase flow simulator. The model results highlighted the significance of the interphase mass transfer in NAPL remediation and the need to model this process as a non-equilibrium kinetic process. To further elucidate the factors influencing the interphase mass transfer mechanism, a series of controlled dissolution experiments from pooled NAPL were also conducted. The interpretation of the experiments was performed using a 2D pore network model in addition to a simplified 1D analytical solution. Results showed that the analytical solution which ignores lateral transport, under-estimates the interphase mass transfer coefficient. Based on the estimated mass transfer coefficients, improved non-lumped Sherwood correlations were developed. These correlations can be used in future modeling studies involved pooled NAPL configurations.
Phylogeography and evolutionary history of whiting (Merlangius merlangus) and picarel (Spicara spp.) along the Turkish coastal waters
(Thesis (Ph.D.) - Bogazici University. Institute of Environmental Sciences, 2018., 2018.) Şalcıoğlu, Aslı Şükriye.; Bilgin, Raşit.
In this study, the effects of the Turkish Straits System (TSS) on the evolutionary history and phylogeography of Spicara flexuosa and Spicara maena, and Merlangius merlangus were investigated. The results of the study indicated that the distinction of the three taxa under Spicara is possible with three different mtDNA markers, e.g. (16S, CO1, cyt-b). S. maena and S. flexuosa were also analyzed using a partial fragment of the nuclear IRBP gene. Molecular results showed that Spicara flexuosa was significantly more common in the Turkish coastal waters, when compared to S. maena. Morphological measurements revealed that the S. maena samples were smaller than the S. flexuosa samples. An absence of genetic structure between subpopulations from Turkey indicate the connectivity of the Spicara flexuosa populations, suggesting that the TSS is a corridor for gene flow for this species. Considering Merlangius merlangus, the mitochondrial DNA (CO1, cyt-b) genes and nuclear DNA (RAG1) gene were used. The results confirmed the existence of two subspecies in the sampling sites used in this study, based on mitochondrial DNA results, one in Turkish coastal waters and Greece (M. m. euxinus), and the other (M. m. merlangus) in Atlantic. High levels of genetic differentiation was observed along the Turkish coastal waters based on the cyt-b gene, suggesting that TSS potentially represents a barrier to dispersal for this species. As the whiting populations in the Black Sea were found to belong to different stocks when compared to those in the Aegean, separate conservation strategies are necessary for their protection.

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