The world is increasingly urbanizing with approximately 54% of the world population livingin cities (Langemeyer, 2015). This number is expected to rise to 66% by 2050 (UN, 2014),which means that urbanized areas will expand in size with an additional 2.5 billion new urbaninhabitants (Langemeyer, 2015). Studies show that urban expansion has the effect ofdecreasing, fragmenting, and isolating natural patches by altering the size, shape, andinterconnectivity of the natural landscape (Ricketts, 2001; Alberti, 2005). The consequentloss and degradation of urban and peri-urban green/blue space and elements couldadversely affect ecosystem and its services as well as human health and well-being.Through literature review, the concepts of urban ecosystem services and green-blueinfrastructures are introduced, as well as the main design principles for green-blueinfrastructures. The thesis also briefly introduces urban policies and implementation throughcase study with a focus on Malmö city. Meanwhile, the thesis discusses how the planninginstruments of Green Space Factor and Green Points are used in the Bo01 project and howthey contributed to promote ecosystem services in built environment.Through literature review and case study, the aim of this thesis is to collect design solutionsthat can be used as inspiration and guidance to promote urban ecosystem services throughgreen-blue infrastructures in built environments at different scales.

The world is increasingly urbanizing with approximately 54% of the world population livingin cities (Langemeyer, 2015). This number is expected to rise to 66% by 2050 (UN, 2014),which means that urbanized areas will expand in size with an additional 2.5 billion new urbaninhabitants (Langemeyer, 2015). Studies show that urban expansion has the effect ofdecreasing, fragmenting, and isolating natural patches by altering the size, shape, andinterconnectivity of the natural landscape (Ricketts, 2001; Alberti, 2005). The consequentloss and degradation of urban and peri-urban green/blue space and elements couldadversely affect ecosystem and its services as well as human health and well-being.Through literature review, the concepts of urban ecosystem services and green-blueinfrastructures are introduced, as well as the main design principles for green-blueinfrastructures. The thesis also briefly introduces urban policies and implementation throughcase study with a focus on Malmö city. Meanwhile, the thesis discusses how the planninginstruments of Green Space Factor and Green Points are used in the Bo01 project and howthey contributed to promote ecosystem services in built environment.Through literature review and case study, the aim of this thesis is to collect design solutionsthat can be used as inspiration and guidance to promote urban ecosystem services throughgreen-blue infrastructures in built environments at different scales.

Antibiotic resistance (AR) is a critical and looming threat to human health that requires action across the One Health continuum (humans, animals, environment). Coordinated surveillance within the environmental sector is largely underdeveloped in current National Action Plans to combat the spread of AR, and a lack of effective study approaches and standard analytical methods have led to a dearth of impactful environmental monitoring data on the prevalence and risk of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in aquatic environments. In this dissertation, integrated surveillance approaches of surface water and wastewater systems are demonstrated, and efforts are made towards standardizing both metagenomic- and culture-based techniques for globally comparable environmental monitoring. A field study of differentially-impacted watersheds on the island of Puerto Rico post-Hurricane Maria demonstrated the effectiveness of metagenomics in defining direct impact of anthropogenic stress and human fecal contamination on the proliferation of ARGs in riverine systems. The contribution of treated wastewater effluents to the dissemination of highly mobile and clinically-relevant ARGs and their connection to local clinical settings was also revealed. At the international scale, a transect of conventional activated sludge wastewater treatment plants (WWTPs), representing both US/European and Asian regions, were found to significantly attenuate ARG abundance through the removal of total bacterial load and human fecal indicators, regardless of influent ARG compositions. Strong structural symmetry between microbiome and ARG compositions through successional treatment stages suggested that horizontal gene transfer plays a relatively minor role in actively shaping resistomes during treatment. Risk assessment models, however, indicated high-priority plasmid-borne ARGs in final treated effluents discharged around the world, indicating potentially increased transmission risks in downstream environments. Advancements were also made toward standardizing methods for the generation of globally representative and comparable metagenomic- and culture-based AR monitoring data via two comprehensive and critical literature reviews. The first review provides guidance in next-generation sequencing (NGS) studies of environmental AR, proposing a framework for experimental controls, adequate sequencing depths, appropriate use of public databases, and the derivation of datatypes that are conducive for risk assessment. The second review focuses on antibiotic-resistant Enterococcus spp. as robust monitoring targets and an attractive alternative to more widely adopted Gram-negative organisms, while proposing workflows that generate universally equivalent datatypes. Finally, quantitative metagenomic (qMeta) techniques were benchmarked using internal reference standards for high-throughput quantification of ARGs with statistical reproducibility. / Doctor of Philosophy / Antimicrobials have contributed to the reduction of infectious diseases in humans and animals since the early 20th century, increasing productivity and saving countless lives. However, their industrial-scale application across human, animal, and agricultural sectors over the last several decades, especially the use of antibiotics, have engendered the proliferation of antibiotic resistance (AR). AR occurs when changes in bacteria cause the drugs used to treat infections to become less effective and has become one of the leading public health threats of the 21st century. The global spread of AR through the transmission and evolution of antibiotic resistant bacteria (ARB; known colloquially as "superbugs") and antibiotic resistance genes (ARGs) across the One Health continuum (i.e., humans, animals, and the environment) is resulting in increased hospitalization, length of hospital stays, suffering, death, and overall health-care associated costs globally. This dissertation demonstrates the use of metagenomics, the sequencing of all genetic material (e.g., DNA) recovered from a microbial community, for the comprehensive monitoring of ARB and ARGs in aquatic environments, a key pathway for the dissemination of AR into and out of human populations. In order to impede the proliferation of AR, surveillance systems are currently in place to track the spread and evolution of ARB and ARGs in humans and livestock, as well as agri-food sectors. However, the surveillance in natural and built environments (i.e., rivers and domestic sewage) has significantly lagged due to the lack of standard monitoring targets and methodologies. It is also a goal of this dissertation to suggest guidance for the collection of metagenomic- and culture-based AR monitoring data to generate universally comparable results that can be included in centralized databases. Riverine systems are ideal models for tracking input of antibiotic resistance to the natural environment by human activity. After Hurricane-Maria, many of Puerto Rico's wastewater treatment plants (WWTPs) went offline, discharging raw sewage to local surface waters. In a cross-sectional study of watersheds impacted by WWTPs, the abundance of ARGs was directly correlated to increases in local population density. Also, highly mobile and clinically-relevant ARGs were found directly downstream of WWTPs across the island. We found that many of these ARGs corresponded well to forms AR endemic to the region. WWTPs are the primary engineering controls put in place to curb the spread of human and animal waste streams and can help to reduce AR. An international transect of conventional activated sludge WWTPs representing US/Europe and Asia were sampled to garner a mechanistic understanding of the fate or ARGs through treatment. Although WWTPs remove total bacteria, human fecal indicators, and much of the abundance of ARGs, mobile and clinically-relevant ARGs are discharged around the world in large quantities. Consideration is needed in certain regions of iv the world where the managing of human waste streams is the first line of defense against the dissemination of resistance to local communities. Two comprehensive critical literature reviews were conducted to evaluate the various methodologies for generating and analyzing metagenomic- and culture-based AR monitoring data. These reviews address the need for experimental rigor and disclosure of extensive metadata for inclusion in future, centralized databases. The articles further provide guidance with respect to universally comparable datatypes and efficient workflows that will aid in the scale-up of the collection of environmental monitoring data within a global surveillance framework. Finally, a study was conducted to benchmark the use of internal DNA reference standards for the absolute quantification of ARGs (i.e., on a ARG copy per volume of sample basis). The statistical framework for ARG detection and its implications for wastewater-based surveillance systems of AR are also discussed.

Streams and rivers are a vital part of our ecosystem. They are imperiled by human ecological activities such as urbanization, industrialization, and agriculture which discharge excess nitrate and other pollutants into our waterways. Here, this dissertation seeks to understand the physical and biogeochemical processes which attenuate pollutants in stream corridors. The focus is hyporheic zones which form the interface between surface water and groundwater below and adjacent to stream channels, and riparian zones which form the interface between channels and adjacent uplands, both of which can attenuate pollutants. In this context, soil-pipes can dominate subsurface hydraulics. This research first employed MODFLOW and MT3D-USGS to model transient hyporheic hydraulics and nitrate transport in a length of riparian/riverbank soil to probe the effects of soil pipes on hydraulics and denitrification due to peak flow events in the channel. Findings showed that inserting just one soil pipe 1.5 m in length caused a ~75% increase in both hyporheic exchange and denitrification. A rough upscaling showed soil pipes could remove up to ~3% of nitrate along a 1-km reach. Next, the ability of soil pipes to bypass the often championed ability of riparian buffers to remove nitrate migrating from uplands to the channel was evaluated. This effort also employed MODFLOW and MT3D-USGS to simulated hydraulics and nitrate removal along a length of riparian soil. Findings showed that soil pipes increased flow of nitrate to the banks by five orders of magnitude in some cases. We posited a non-dimension parameter which governs when nitrate bypass is significant. In addition to soil pipes, dune bedforms can also enhance hyporheic exchange, primarily in the stream/riverbed. Again employing MODFLOW but now pairing with the transport code SEAM3D to simulate microbially-mediated aerobic metabolism of dissolved organic carbon and dissolved oxygen, the combined effects of dune translation and microbial growth and death were explored. Major findings include that neglecting microbial growth can lead to inaccurate modeling of biogeochemistry, and that aerobic metabolism increased with celerity. The results herein bolster knowledge of natural pollutant attenuation in stream and river corridors, and have implications for pollutant mitigation strategy and stream credit allocation. / Doctor of Philosophy / Streams are a vital part of our ecosystem. They are imperiled by human ecological activities such as urbanization, industrialization, and agriculture which discharge nitrate and other pollutants into our waterways. Here, this dissertation seeks to understand the physical and biological processes which attenuate pollutants. The hyporheic zone is the interface between surface water and groundwater below the bed and adjacent to stream banks, and can attenuate pollutants. Transient peak flow events such as a storm or snow melt raise the stream water levels, causing the water pressure in the stream channel to temporarily outweigh the water pressure in the soil pore spaces adjacent to the stream channel. This drives water into the banks subjecting it to pollutant attenuation processes. Soil pipes (long cylindrical void spaces created by decayed plant roots) are prevalent along stream banks, and they dominate subsurface hydraulics. This dissertation implemented a numerical study on a chunk of riparian soil to probe the effects of soil pipes on hydraulics and denitrification. Findings showed that inserting just one – 1.5 m soil pipe caused a ~75% increase in both water flow volume into the bank and nitrate removal. Riparian buffers are the vegetated strips adjacent to stream channels and have long been championed as stalwarts of pollutant removal. Soil pipes undermine this by acting as a bypass mechanism. A numerical study was again performed on a chunk of riparian soil to quantify the effects soil pipes on riparian bypass of nitrate. Findings showed that soil pipes increased flow of nitrate to the banks by five orders of magnitude in some cases. This means that a buffer enhancement strip with fine roots that prevent the formation of soil pipes should be installed along riparian buffers. In addition to soil pipes, dune bedforms can increase flowrate of water into the hyporheic zone. This dissertation modeled the combined effects of dune translation and microbial growth and death. Major findings include that neglecting microbial growth can lead to inaccurate modeling of biogeochemistry, and that biodegradation increases with increased dune velocity. The results herein bolster knowledge on natural pollutant attenuation in streams, and have implications in terms of pollutant mitigation strategy and stream credit allocation.

Evaluation of the sources and cycles of water quality contaminants in watersheds is critical for effective surface water resource management. In particular, iron (Fe) and manganese (Mn), commonly found in rocks and sediments, have adverse impacts on water quality. However, controlling Fe and Mn in surface water systems is often complex and requires careful consideration of the hydrologic and biogeochemical factors that influence the speciation and mobility of these metals. This dissertation investigates the sources and cycles of Fe and Mn in surface waters designated for human use. Here, I present the findings from three field- and laboratory-based studies conducted at sites in western Virginia, United States. The first study examines the impacts of reservoir-derived and watershed-derived metals on water quality along the 180 km reach of the Roanoke River downgradient from Leesville Dam. The results from this study showed strong temporal influences on river water quality immediately downgradient of the dam, resulting from seasonal reservoir dynamics. Further downgradient in the Roanoke River, water quality was strongly tied to hydrologic conditions resulting from influences generated in the watershed. The second study investigated the effects of increasing dissolved oxygen (DO) concentrations in the hypolimnion of stratified drinking water reservoir on Fe and Mn oxidation and removal. Results from a whole-ecosystem experiment showed that increasing DO concentrations through hypolimnetic oxygenation was effective for preventing the accumulation of soluble Fe in the water column. Although Mn oxidation increased under well-oxygenated conditions, soluble Mn still accumulated in the hypolimnion. Results from a laboratory experiment demonstrated that the oxidation of Mn was strongly tied to the activity of Mn oxidizing microbes. The third study examined the relative contribution of external and internal metal loadings to the exchange of metals between sediments and the water column and the source/sink behavior of a seasonally stratified reservoir under varying hydrologic conditions in the inflows and outflows and redox conditions in the reservoir hypolimnion. Results from this study showed that redox conditions strongly influenced the exchange of metals between the sediment and aqueous phase, but had little effect on the source/sink behavior of the reservoir, while external tributary loadings had little effect on internal redox cycles, but was a strong indicator for whether the reservoir behaved as a net metal source or sink. Overall, the findings from these studies exemplify the value of characterizing the hydrologic and biogeochemical drivers of Fe and Mn cycles for managing the water quality effects of these metals in surface water supplies. / Ph. D.

The Central Appalachian region is home to several resource-extraction industries, a host of globally unique aquatic wildlife species, and region-wide poverty. These overlapping circumstances make solving environmental issues in the region challenging. Of particular focus is the coal mining industry, both because of its prevalence and because of controversial methods of practice such as mountain top mining. One of the primary concerns in the region is the extirpation of sensitive aquatic macroinvertebrate species. Several studies have suggested the primary driver of this loss of biodiversity is due to increased conductivity in streams impacted by these mining practices. The reality is that several pollutant sources coexist in these Central Appalachian watersheds. Because of geographic isolation, many headwater communities lack proper sewerage and discharge directly into nearby waterways, compounding potential effects of upstream mining activities. Additionally, several legacy sites exist throughout the Appalachian region, both underground and surface mining in nature. To best mitigate ecological impacts of all of these pollutant types, relative contributions of each must be understood, as well as the nature of the pollution contributed by each. As a contribution towards this region-wide need for better information on pollution, the studies comprising this dissertation seek to better understand the composition of these different pollutant sources and their in-stream contributions to conductivity. The first paper found that these sources are indeed distinct in their inorganic ion make-up: surface coal mining was found to contribute primarily Ca, K, Ni, Se, and SO₄⁻², while untreated household waste (UHW) was primarily associated with P. HCO₃⁻ Mn, and Si were found to be associated with a legacy underground discharge. The second and third scientific studies included here analyzed conductivity's effect on Virginia Stream Condition Index (VSCI) versus other water quality and habitat parameters as well as the effect of specific ion suites on VSCI score. Findings indicated that excellent habitat extends species resilience against elevated conductivity, with passing VSCI scores found at conductivity in the 600-800 µs/cm range in cases of excellent habitat metric scores. Meanwhile, VSCI score suppression was highly related to surface mining-related inorganic ions (Ca, K, Mg, Ni, and SO₄⁻²), but also negatively correlated with ions related to UHW (P and Na). These results indicate the need for quantification of biological responses to specific ions in order to initiate targeted mitigate of pollutants in Central Appalachian watersheds. / Ph. D.

Increases in reactive nitrogen from human actions have led to negative impacts on surface water (SW) and groundwater (GW) quality, and it is important to better understand denitrification processes in aquatic systems. The hyporheic zone has unique biogeochemical conditions, and is known to attenuate contaminants originating from SW and traveling through the hyporheic zone, together with necessary reactants. However, the ability of the hyporheic zone to attenuate contaminants from deeper upwelling GW plumes as they exit to SW is less understood. I used MODFLOW and SEAM3D to simulate hyporheic flow cells induced by riverbed dunes and upwelling GW together with mixing dependent denitrification of an upwelling nitrate (NO3-) plume. My basecase model scenario entailed dissolved organic carbon (DOC) and dissolved oxygen (DO) advecting from SW and DO and NO3- advecting from GW, which is typical of water in agricultural land uses. I conducted a sensitivity analysis to determine controls on mixing dependent denitrification. Mixing dependent denitrification increased with increasing hydraulic conductivity, decreasing lower bottom flux, as well as increasing DOC in SW and NO3- in GW. Non-mixing dependent denitrification also occurred when there was SW NO3-, and I found its magnitude was much greater than mixing dependent denitrification. Nevertheless, potential for hyporheic zones to attenuate upwelling NO3- plumes seems to be substantial, though highly variable depending on biogeochemical reaction rates as well as geomorphic, hydraulic and biogeochemical conditions. Stream and river restoration efforts may be able to increase both mixing and non-mixing dependent reactions by increasing hyporheic zone residence times. / Master of Science

Restoring hydrologic connectivity between the channel and floodplain is a common practice in stream and river restoration. Floodplain hydrology and hydrogeology impact biogeochemical processing and potential nutrient removal, yet rigorous field evaluations of surface and groundwater flows during overbank floods are rare. We conducted five sets of experimental floods to mimic floodplain reconnection. Experimental floods entailed pumping stream water onto an existing floodplain swale, and were conducted throughout the year to capture seasonal variation. Each set of experimental floods entailed two replicate floods occurring on successive days to test the effect of varying antecedent moisture. Water levels and specific conductivity were measured in surface water, shallow soils, and deep soils, along with surface flow into and out of the floodplain. Total flood water storage increased as vegetation density increased and or antecedent moisture decreased. Hydrologic flow mechanisms were spatially and temporally heterogeneous in surface water, in groundwater, as well as in exchange between the two and appeared to coexist in small areas. Immediate propagation of hydrostatic pressure into deep soils was suggested at some locations. Preferential groundwater flow was suggested in locations where the pressure and electrical conductivity signals propagated too fast for bulk Darcy flow through porous media. Preferential flow was particularly obvious where the pressure signal bypassed an intermediate depth but was observed at a deeper depth. Bulk Darcy flow in combination with preferential flow was suggested at locations where the flood pressure and electrical conductivity signal propagated more slowly yet arrived too quickly to be described using Darcy's Law. Finally, other areas exhibited no transmission of pressure or conductivity signals, indicating a complete lack of groundwater flow. Antecedent moisture affected the flood pulse arrival time and in some cases vertical connectivity with deeper sediments while vegetation density altered surface water storage volume. Understanding the variety of exchange mechanisms and their spatial variability will help understand the observed variability of floodplain impacts on water quality, and ultimately improve the effectiveness of floodplain restoration in reducing excess nutrient in river basins. / Master of Science

The pollution of streams and rivers is a growing concern, and environmental guidance increasingly suggests stream restoration to improve water quality. �Solute retention in off channel storage zones such as hyporheic zones and floodplains is typically necessary for significant reaction to occur. �Yet the effects of two common restoration techniques, in stream structures and inset floodplains, on solute retention have not been rigorously compared. �We used MIKE SHE to model hydraulics and solute transport in the channel, inset floodplain, and hyporheic zone of a 2nd order stream. �We varied hydraulic conditions (winter baseflow, summer baseflow, and storm flow), geology (hydraulic conductivity), and stream restoration design parameters (inset floodplain length, and presence of in stream structures). �In stream structures induced hyporheic exchange during summer baseflow with a low groundwater table (~20% of the year), while floodplains only retained solutes during storm flow conditions (~1% of the year). �Flow through the hyporheic zone increased linearly with hydraulic conductivity, while residence times decreased linearly. �Flow through inset floodplains and residence times in both the channel and floodplains increased non linearly with the fraction of bank with floodplains installed. �The fraction of stream flow that entered inset floodplains was one to three orders of magnitude higher than that through the hyporheic zone, while the residence time and mass storage in the hyporheic zone was one to five orders of magnitude larger than that in floodplain segments. �Our model results suggest that in stream structures and inset floodplains are complementary practices. / Master of Science

Increased reactive nitrogen from human activities negatively affects surface water (SW) quality. The hyporheic zone, where SW and groundwater interact, possesses unique biogeochemical conditions that can attenuate contaminants (e.g., denitrification), including mixing-dependent reactions that require components from both water sources. Previous research has explored mixing-dependent denitrification in the hyporheic zone but did not address the effects of varying SW depth as would occur from storms, tides, dam operation, and varying seasons. We simulated steady and unsteady hyporheic flow and transport through a riverbed dune using MODFLOW and SEAM3D, and varied SW depth, degree of sediment heterogeneity, amplitude and frequency of sinusoidal fluctuations, among others to determine these effects. We found that increasing steady state surface water depth from 0.1 to 1.0 m increased non-mixing dependent aerobic respiration by 270% and mixing-dependent denitrification by 78% in homogeneous sediment. Heterogeneous hydraulic conductivity fields yielded similar results, with increases in consumption due to variation in correlation length and variance of less than 5%. Daily SW fluctuation, including variation of amplitude, period, and sinusoidal versus instantaneous changes had significantly less impact than longer-term trends in SW depth. There is potential for the hyporheic zone to attenuate NO3- in upwelling groundwater plumes. Restoration efforts may be able to maximize the potential for mixing-dependent reactions in the hyporheic zone by increasing residence times. / Master of Science / Increased nitrogen in runoff from human activities negatively affects surface water quality. The hyporheic zone is where surface water and groundwater interact, and the mixing between the waters can help to this nitrogen to undergo reaction (denitrification), potentially stopping the contaminant from spreading. Previous research has explored this idea, but has not addressed the impact of varying surface water depth, as would realistically occur due to storms, tides, dam operation, and varying seasons. We simulated both constant and fluctuating surface water conditions on a riverbed dune to see the effects on hyporheic flow and denitrification. Test variables included the surface water depth, the degree of sediment heterogeneity, the amplitude and frequency of surface water fluctuations. We found that increasing the steady-state surface water depth had the most dramatic increase on the amount of reaction undergone. This trend was also seen in heterogeneous sediment. Any daily-scale surface water fluctuations, including runs that varied the amplitude, period, and sinusoidal vs instantaneous changes in surface water depth, had significantly less impact than longer-term trends in surface water depth.