Species have complex and contextual relationships with their environment; both the relative contributions of life-history stages to population growth and the effect of environmental factors on each stage can be different among co-existing species. Timing and extent of reproduction, survival, and mortality determine population growth, species distributions, and assemblage patterns. I evaluate the role of habitat (intact, degraded) and microsite (shrub, leaf litter, bare sand) on population dynamics of Florida scrub herbs. Isolated overgrown shrubs and extensive bare sand areas in degraded scrub were expected to decrease seed predation, reduce competition of herbs with shrubs, and provide larger habitat for recruitment. I provide evidence that habitat and microsite variation influenced demography of five endemic and two common native species through effects on seed removal, emergence, and establishment. Habitat and species affected seed removal: endemic species with large seeds were removed in higher frequency in degraded habitat, likely by vertebrates, while species with small seeds were removed in higher frequency in intact habitat, by invertebrates. There was no evidence of differences in individual seed production between habitats for the two common species, C. fasciculata and B. angustifolia. Invertebrates were primarily responsible for seed removal of both species, although peak season of removal and microsite varied with species. Removal of seeds, emergence, and establishment increased with seed density. Matrix modeling indicated that population growth of C. fasciculata was greater in degraded habitat and greatest in litter microsites, and population growth of B. angustifolia was similar between habitats and greatest in bare sand. Contrasting responses among species to environmental factors in intact and degraded scrub indicated that natural disturbances are not ecologically equivalent to anthropogenic iv disturbances. Idiosyncratic species dynamics in common environments suggest that understanding relationships between life-history traits and environmental conditions will be required to facilitate restoration

The rapid spread of antibiotic resistance is a major global health concern, jeopardizing the successful treatment of bacterial infections. Natural environments are potential hotspots for the emergence and spread of antibiotic resistance genes (ARGs). Among these potential hotspots, aquatic ecosystems are of particular concern, as they receive wastewater containing antibiotic-resistant bacteria and ARGs originating from both human and animal sources. Several key questions remain to be addressed. What is the fate of ARGs in receiving water bodies? What are implications of environmental ARGs for human health? How does wastewater discharge impacts aquatic microbial communities with regard to the overall ecosystem well-being? The objective of this work was to investigate the impact of wastewater, seasonal variations, and the riverine compartment on the prevalence of selected ARGs and the composition of natural microbial communities in a near-pristine river, and to specifically assess the effect of antibiotics on riverine microbial communities. Quantitative real-time PCR was used to monitor the abundance of three indicator ARGs (sul1 and sul2, conferring resistance against sulfonamide antibiotics, and intI1, a marker for anthropogenic pollution) upstream and downstream from a wastewater treatment plant (WWTP). Furthermore, the impact of WWTP effluent on the riverine microbial community was examined through 16S rRNA amplicon sequencing. Wastewater was the main source of all three target genes and significantly altered the microbial community in the river. The surface water compartment served as a dissemination route for ARGs, with increased prevalence even 13 km downstream of the WWTP, particularly during the summer season when the proportion of wastewater in the river was high. Notably, riverbed biofilms served as a local reservoir for ARGs only at the discharge point, with little abundance of target genes further downstream. The sulfonamide antibiotic sulfamethoxazole (SMX) was persistent in both near-pristine and wastewater-impacted river water when introduced at a concentration of 12.5 µg/L, but had neglectable effects on the microbial community diversity. Interestingly, concentrations as high as 100 µg/L SMX induced a short-term increase in microbial activity in both surface water and biofilm compartment, as revealed by bulk and nanoscale measurements. Altogether, this work underscores the fundamental role of wastewater treatment in combating the environmental dissemination of antibiotic resistance.:Summary 1 Zusammenfassung 5 1 Introduction 9 1.1 Rundown of the global antibiotic resistance crisis 9 1.1.1 History of antibiotics 9 1.1.2 Emergence of antibiotic resistance 9 1.1.3 Integrons as vehicles for antibiotic resistance 10 1.1.4 Risks related to environmental antibiotic resistance 12 1.2 Fate of antibiotic resistance genes in the aquatic environment 14 1.2.1 Genetic indicators for antibiotic resistance 14 1.2.2 River surface water compartment as dissemination route for antibiotic resistance 15 1.2.3 River biofilm compartment as reservoir for antibiotic resistance 17 1.3 Impact of antibiotics on aquatic microbial communities 18 1.4 Fate and effect of sulfamethoxazole in surface waters 20 2 Scope of the thesis 22 3 Main findings and scientific implications 24 3.1 Fate of antibiotic resistance genes after wastewater discharge into a near-pristine river 24 3.1.1 Wastewater is the primary source for aquatic antibiotic resistance 24 3.1.2 Drought increases the antibiotic resistance prevalence in surface waters 25 3.1.3 Riverbed biofilms serve as local reservoirs for antibiotic resistance genes 26 3.2 Anthropogenic pollution is the key driver for microbial community alteration 26 3.3 Sulfamethoxazole increases the microbial activity of aquatic microbial communities 27 4 Conclusions and future perspective 29 5 References 31 6 Publications 43 6.1 Publication 1 43 6.2 Publication 2 56 6.3 Publication 3 69   7 Appendix 94 7.1 Declaration of independent work 94 7.2 List of publications and conference contributions 95 7.2.1 Publications 95 7.2.2 Conference contributions 96 7.3 Contribution of Co-authors 97 7.4 Curriculum vitae 101 7.5 Acknowledgements 104 7.6 Supplementary Material 105 7.6.1 Supplementary Material for Publication 1 105 7.6.2 Supplementary Material for Publication 2 118 7.6.3 Supplementary Material for Publication 3 125

<p> A study of two shallow fringing reefs off the coast of Zanzibar Island was conducted. The study site was Grave Island, 1 km off the shore of Zanzibar town. The comparison site was Chumbe Island, 10 km upcurrent of the town, adjacent a less densely inhabitated coast. The major anthropogenic stress on these reefs could be considered nutrient loading from sewage discharge.</p> <p> Studies of the sea urchin Diadema setosum, indicated mean densities at Grave Island of 6.4 urchins/m^2 and 1.2 urchins/m^2 at Chumbe Island. Urchin densities comparable to those at Grave Island have been related to overfishing and reduced coral recruitment. Coral associate densities were also considered with a mean density of 87/m^2 at Grave Island and 31/m^2 at Chumbe Island. High coral associate densities have been linked to structurally and physiologically weakened coral.</p> <p> Transect studies were conducted and suggested there were significantly reduced coral cover and reduced amounts of live coral at Grave Island (cf Chumbe Island). As well, coral species diversity was significantly lower at Grave Island than at Chumbe Island. Lowered species diversity suggests an unstable community structure, and reduced coral cover may indicate a faltering reef.</p> <p> Stable Isotope studies were conducted on tissue samples from both sites. They showed no significant difference.</p> <p> This study reflects the poor health of Grave Island. The high abundance of urchins and filter feeders, combined with reduced coral cover and diversity, suggest high nutrient loading on these reefs. The high abundance of urchins and associates also suggest coral mortality will be high and recruitment low. If these trends continue, it is unlikely the reef at Grave Island will be able to survive.</p> / Thesis / Bachelor of Science (BSc)

<p>Frenchman's Bay is a shallow coastal lagoon (0.84 km2) located near the eastern limits of the Toronto urban area. Wholesale land clearance in the 1850's and subsequent industrialization and urbanization of the watershed have had severely impacted wetland habitats and degraded sediment and water quality. Prior to implementation of remediation work, a detailed sedimentologic and magnetic property study was conducted to determine the impacts of post-colonial land use changes in Frenchman's Bay. 11 vibrocores (2-4.5m length) were extracted from the lagoon and 3 5 magnetic susceptibility profiles were collected using a probe driven 1-2 m in the lagoon floor. The core lithofacies were logged in detail and magnetic susceptibility (K, x.) and remanence parameters (NRM, SIRM, Bcr) were measured at 2 cm intervals. Magnetic property and lithofacies data were integrated with geochemical analyses (TOC, C03) and 210Pb dating of core in order to reconstruct the lagoon lithostratigraphy and the thickness of the post-colonial 'anthropogenic layer'. </p> <p>The stratigraphic succession in the lagoon consists of a thick upper sequence of marly gyttja and peat-rich silty marls overlying Holocene laminated marls. The postcolonial layer (Unit 1) is recognized as an uppermost high magnetic susceptibility (x = ~200-300 xl0-8 m3/Kg) gyttja layer that extends to 1-1.5 m depth. The base of the unit has a 210Pb age of 1850 (±55.6), corresponding with the main phase of land clearance and onset of industrialization of the harbour. Titanomagnetite, maghemite and magnetite spherules are the primary magnetic minerals, indicating soil erosion and coal burning as the predominant sources of magnetic particles. The underlying Unit 2 consists of peaty marls with abundant plant fragments recording a more extensive marsh. Unit 3 consists of more carbonate-rich laminated sands (magnetic susceptibility x = 6000 x10-8 m3/Kg) deposited in a low energy oligotrophic lagoon. The basal layer (Unit 4) consists of high magnetic susceptibility massive pebbly muds, which record a pre-lagoon phase of higher water levels in post-glacial Lake Iroquois (ca. 13,500 Ka). </p> <p> Isopach mapping of the magnetostratigraphic units clearly identifies that the anthropogenic layer (Unit I; post-1850) is thickest within a central basin which has acted as trap for sediment carried into the lagoon by several streams. The total volume of impacted anthropogenic sediment is estimated at 4 x105 m3. Isopach maps also identify two thin(< 2 m) wedges of sand (9.6 x104 m3) near the north and southern shores of the bay that records periodic overwash and growth of the beach barrier. </p> <p>The major environmental changes in the lagoon since it inception (ca. 2. 7 Ka include: 1. The formation of a shallow coastal embayment following water level rise from a mid-Holocene low-stand in Lake Ontario (Unit 4); 2. Development of a spit and beach barrier by eastward longshore transport (Unit 3); 3. Closure of the lagoon and development of a stabilized marsh habitat with low sedimentation levels (Unit 2); 4. Destruction of marsh habitats and eutrophication of the lagoon coinciding with land clearance (post-1850's) and an increased in the influx of sediments eroded from the catchment area. </p> / Thesis / Master of Science (MS)

Though the water in eastern Georgian Bay is oligotrophic, some of the coastal embayments and wetlands have begun to show signs of water quality impairment that is thought to be related to human development along the shoreline. The primary objective of my thesis is to provide environmental agencies with the resources to effectively manage water quality in the coastal zone of eastern Georgian Bay. First, I evaluate the ability of the Lakeshore Capacity Model (LCM), developed for inland Precambrian Shield lakes, to predict the trophic status of coastal embayments. Finding that the LCM does not accurately predict trophic status, I develop the Anthro-geomorphic Model (AGM), which uses the level of human development and the degree of mixing between the embayment and open waters of Georgian Bay to predict embayment trophic status. Second, I explore the spatial association between densities of building, dock and road development and Water Quality Index (WQI) scores, an index designed to evaluate wetland condition, for wetlands in the Township of Georgian Bay. I found an inverse relationship between WQI scores and the density of these stressor variables inside wetland catchments, which indicates that these stressors have a negative impact on wetland water quality. I then created a series of mapping products that present building, dock and road densities, along with WQI scores for 61 wetlands in the Township of Georgian Bay, to determine how wetland water quality is spatially associated with densities of these stressor variables. I found that regions with high densities of building, dock and road development were associated with wetlands of lower quality, whereas wetlands in areas that had low densities of development were of higher quality. I used this information to identify areas of conservation priority for management in the Township of Georgian Bay. The results from this thesis will provide environmental managers with resources to protect the valuable coastal waters of eastern Georgian Bay. / Thesis / Master of Science (MSc) / A number of coastal embayments and wetlands of eastern Georgian Bay show signs of water quality impairment thought to be caused by cottage development. The objective of my thesis is to develop and evaluate models designed to measure the impact of human development on water quality in these coastal zones. First, finding that the Ontario Lakeshore Capacity Model, developed for Muskoka lakes, does not accurately predict trophic status in embayments, I develop the Anthro-geomorphic Model, which uses building density and basin morphometry to predict embayment trophic status. Second, I explore the appropriateness of using development densities (building, dock and road) to quantify anthropogenic stress in coastal wetlands. This thesis provides the scientific basis for choosing management practices to protect the coastal waters of Georgian Bay.

Carbon (C) is an essential element for all life. However, modern livestock keeping and usage of carbon through burning of fossil fuels are resulting in increased concentrations of carbon dioxide and methane in the atmosphere, two important greenhouse gases (GHG).  Rising concentrations of  GHGs in the atmosphere  is one of the world’s most pressing issues  and  is evidently resulting in rising global temperatures. Nations are fighting to reach net zero emissions of carbon dioxide, and Sweden has set out to have net zero emissions by 2045. To reach this goal, system changes are needed over all sectors in Sweden. The aim of this study is therefore to provide a holistic picture of anthropogenic carbon flows, sources and sinks in Sweden to contribute to a better understanding of the functioning of the Swedish anthropogenic  carbon system. This is done by quantifying the most significant  anthropogenic  carbon sources, flows, and sinks, and visualise them in substance flow charts. The results from this study will thus provide insight into the functioning of the Swedish anthropogenic carbon system.  Through the practical usage of Substance Flow Analysis, this study identifies and quantifies anthropogenic  carbon flows between the sectors set out by  the 2006 IPCC Guidelines for National Greenhouse Gas Inventories; (i) Agriculture, Forestry and Other Land Use (AFOLU), (ii) Industrial Processes and Product Use (IPPU), (iii) Energy, and (iv) Waste. The study also regards imports, exports, extractions from the lithosphere, and emissions to the atmosphere. Furthermore, the study analyses and visualises how carbon flows between different activities within each above-mentioned sector.  The major identified carbon flows occur in the Energy sector, the IPPU sector, and the AFOLU sector. In the Energy sector,  transportation  and  electricity production  &amp;  domestic heating  are  the main contributing activities to emissions of carbon, and in the IPPU sector, industrial processing is subjected to the largest carbon flows. The carbon flows related to  the  transportation,  electricity production  &amp; domestic heating and  industrial  processing activities depend largely on fossil carbon. Targeting these activities with  measures to reduce fossil fuels could potentially have  positive trade-off effects on the Swedish  anthropogenic  carbon system.  The forestry activity in the AFOLU sector  act as an important carbon sink, through capturing significant amounts of carbon each year.  The  result  from this study  provides  a holistic  visualisation  of the  Swedish carbon flows, sources and sinks that occur from anthropogenic activities. It  can be used as tool to describe the relation between different sectors and activities, and it contributed to an understanding of the functioning of the Swedish anthropogenic carbon system. / Kol (C) är en väsentlig beståndsdel för allt liv. Modern  boskapshållning och användning av kol genom förbränning av fossila bränslen leder dock till ökade koncentrationer av koldioxid och metan i atmosfären, två viktiga växthusgaser (GHG). Stigande koncentrationer av växthusgaser i atmosfären är en av världens mest akuta frågor och leder till stigande globala temperaturer. Nationer världen över kämpar för att nå nettonollutsläpp av koldioxid och Sverige har satt som mål att ha nettonollutsläpp till 2045. För att nå detta mål krävs flera systemförändringar inom alla sektorer i Sverige Syftet med denna studie är därmed att ge en helhetsbild av antropogena kolflöden, källor och sänkor i Sverige, vilket kan bidra till en bättre förståelse för  det antropogena kolets kretslopp i det  svenska  systemet. Detta görs genom att kvantifiera de viktigaste antropogena kolkällorna, flödena och sänkorna, och visualisera dem i ämnesflödesscheman.  Resultaten från denna studieger  därmed  insikt i  det svenska  antropogena kolkretsloppet. Genom tillämpning av ämnesflödesanalys identifierar och kvantifierar denna studie  antropogena kolflöden mellan de sektorer som anges i 2006 års IPCC:s riktlinjer för nationella inventeringar av växthusgaser; (i) Jordbruk, skogsbruk och annan markanvändning (AFOLU), (ii) Industriella processer och produktanvändning (IPPU), (iii) Energi och (iv) Avfall. Studien omfattar även import, export, utvinning från litosfären och utsläpp till atmosfären. Vidare analyserar och visualiserar studien hur kol flödar mellan olika verksamheter inom varje ovan nämnda sektor. De största identifierade kolflödena förekommer inom energisektorn, IPPU-sektorn och AFOLU-sektorn. Inom energisektorn är transporter  samt  elproduktion och uppvärmning de huvudsakliga bidragande aktiviteterna  till utsläpp av kol, och inom IPPU-sektorn  står industrier  för de största kolflödena. Kolflödena relaterade till transporter, elproduktion och uppvärmning,  samt  industriell bearbetning beror till stor del på fossil energi. Riktade åtgärder för att minska användningen av fossila bränslen inom dessa  aktiviteter  kan potentiellt ha positiva effekter  på det svenska  antropogena kolkretsloppet. Skogsbruk i AFOLU-sektorn fungerar som en viktig kolsänka genom att fånga upp betydande mängder kol varje år. Resultatet från denna studie ger en holistisk visualisering av de svenska kolflöden, källor och sänkor som uppstår från antropogen verksamhet. Den kan användas som ett verktyg för att beskriva relationen mellan olika sektorer och verksamheter och bidra till en förståelse för det svenska antropogena kolets kretslopp.

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