This Ph.D. Thesis is focused mainly on the biology of two typical European predatory fishes, European catfish (Silurus glanis) and perch (Perca fluviatilis). Catfish is a typical apex predator, whereas perch is a smaller species that plays role of a mesopredator. Although, catfish is the third largest freshwater fish in the world, only few studies dealing with this species have been revealed thus far. The main reason is connected with capturing of the species that is inefficient by standard ichthyologic methods. Studies, that have been revealed recently, focused mainly on expansions of catfish to the West and South Europe. Catfish is unwanted in these localities due to a potential negative impact on native fish community, thus its reduction is desirable. In contrast, catfish occurrence is important in native localities where it plays a key role as a biomanipulative species (I). Catfish is a true generalist, which is a typical feature for large-bodied apex predators connected with high energy consumption of their bodies. The second typical feature is a wide diet plasticity and thus good adaptability to new food sources. It is associated with distribution of various food sources among individuals within the population (II). By contrast, perch is one of the most studied fish in the world and hundreds of studies with IF are revealed every year. However, the more information about biology of perch have been known, the more questions have been arisen. Several phenomena are revealed also in this thesis. For instance, crucial impact of juvenile perch on the entire ecosystem is described. High predation pressure on zooplankton may induce piscivory in primarily zooplanktivorous fish (III). Further, juvenile perch utilize hypoxic pelagic zones as a refuge against predation (IV). The last surprising phenomenon is described in the study dealing with both species, catfish and perch. Their coexistence may lead in strong discrimination of one species caused by special predation that was supposed to be implausible (V).

Lake-rich thermokarst landscapes, such as Old Crow Flats (OCF) in northern Yukon, Canada have been identified as amongst the most vulnerable to climate change. This has raised concerns of the Vuntut Gwitchin First Nation (VGFN) and Parks Canada (Vuntut National Park) about the ecological integrity of this significant wetland. The influence of climate change on the hydroecological conditions of thermokarst lakes are complex and vary across the landscape, thus long-term hydroecological monitoring is essential to adequately assess the ecological integrity of the aquatic ecosystem and how it is changing over time. In a genuine interdisciplinary and collaborative approach, this thesis establishes an integrated approach using isotope hydrology, aquatic ecology, and paleolimnology to develop a robust long-term aquatic monitoring program that has already been adopted by Parks Canada. In collaboration with Parks Canada, 14 of 58 lakes that were previously studied during the International Polar Year from 2007-09 were selected to represent monitoring lakes. Lakes were sampled in early June and late August/early September 2010-11. Water samples for analysis of hydrogen and oxygen isotope composition and chemistry (i.e., ions and nutrients) were collected to track hydrological and limnological conditions. Artificial substrates were deployed in June and accrued algae were collected at the end of the ice-free season to assess community composition and abundance. Sediment coring was conducted in a culturally-significant lake (Zelma Lake – OCF06) to reconstruct long-term baseline hydroecological conditions over the past three centuries. Radiometric dating techniques (137Cs, 210Pb) were used to develop a sediment core chronology. Baseline hydroecological conditions were reconstructed through analyses of loss-on-ignition, bulk organic carbon and nitrogen elemental and isotope compositions, and pigments. Meteorological data and a multi-year evaporation pan experiment were used to develop a robust isotope framework, which provides the basis for interpreting five years (2007-11) of lake water isotope measurements and deriving knowledge of hydrological conditions for the monitoring lakes. Using this framework and the coupled-isotope tracer method, isotopic compositions of input water (δI) and evaporation-to-inflow (E/I) ratios were calculated and provide key hydrological information for each sampling interval. δ¬I values distinguish snowmelt- and rainfall-sourced lakes, with δP representing a threshold between the two isotopic-based hydrologic regimes. A Mann-Kendall test showed that three lakes (OCF11, 26, and 49) displayed significant increasing trends in δI values indicating a potential transition from snowmelt-sourced to rainfall-sourced isotope-based hydrologic-regimes. E/I ratios >0.5 signifies lakes that are evaporation-dominated with positive water balances and E/I ratios >1 indicates lakes that are evaporation-dominated with negative water balances. Six lakes in OCF (OCF06, 19, 37, 46, 49, and 58) surpass the 0.5 threshold and three of these lakes (OCF06, 19, and 46) crossed the significant evaporation threshold (E/I > 1) during dry climatic conditions. Multi-proxy paleolimnology analysis conducted on Zelma Lake reveals different hydroecological transitions during the past ~330 years that include: phase 1 (~1678-1900) characterized by stable hydroecological conditions; thermokarst expansion (~1900-1943) marked by decreases in productivity; phase 2 (~1943-2007) distinguished by increasing productivity; and a post drainage phase following rapid drainage in 2007 characterized by further increases in productivity. The stratigraphy of Zelma Lake shows that hydroecological conditions in dynamic landscapes such as OCF are complex and require multi-proxy paleolimnological analysis. In particular, organic matter, δ13Corg, and pigment concentrations are important parameters to consider when interpreting past hydroecological conditions, thermokarst expansion, and lake drainage events.

Amphibians are the most threatened taxon on the planet. Declines have been associated with over-exploitation, habitat loss, pollution, and pathogenic diseases, but of these factors, pollution and disease have been relatively under-studied. Here, I investigated: 1) the impacts of commonly used pesticides on aquatic communities, 2) the effect of these pesticides on amphibian susceptibility to the pathogenic chytrid fungus, Batrachochytrium dendrobatidis (Bd), and 3) whether there are non-amphibian hosts of Bd and 4) how to best quantify the survival of Bd through ontogeny of the host. In my first research chapter, I quantified the effects of environmentally relevant concentrations of the mot commonly used synthetic fungicide in the US, chlorothalonil, on 34 species-, 2 community- and 11 ecosystem-level responses in a multitrophic-level system. Chlorothalonil increased mortality of amphibians, gastropods, zooplankton, algae, and a macrophyte (reducing taxonomic richness), reduced decomposition and water clarity, and elevated dissolved oxygen and net primary productivity. These ecosystem effects were indirect but were predictable based on changes in taxonomic richness. A path analysis suggests that chlorothalonil-induced reductions in biodiversity and top-down and bottom-up effects facilitated algal blooms that shifted ecosystem functions. In my second chapter, I investigated how a wide range of ecologically relevant concentrations of chlorothalonil affected four species of amphibians (Osteopilus septentrionalis, Rana sphenocephala, Hyla squirella and H. cinerea). I also evaluated the effects of chlorothalonil on liver tissue, immune cell density, and the stress hormone, corticosterone. Chlorothalonil killed nearly every amphibian at the expected environmental concentration (EEC) and, at concentrations to which humans are commonly exposed (up to the EEC), it was associated with elevated corticosterone levels and changes in immune cells. Three species (O. septentrionalis, R. sphenocephala, and H. cinerea) showed a non-monotonic dose-response, with low and high concentrations causing significantly greater mortality than intermediate concentrations and controls. Corticosterone exhibited a similar non-monotonic dose response and chlorothalonil concentration was inversely associated with liver tissue and immune cell densities. These studies on chlorothalonil emphasize the need to re-evaluate its safety and to further link anthropogenic-induced changes in biodiversity to altered ecosystem functions. In my third research chapter, I investigated the effects of chlorothalonil and atrazine, one of the most commonly used herbicides in the US, on amphibian susceptibility to Bd, a leading cause of amphibian extinctions. Relative to controls, atrazine monotonically reduced Bd growth in culture and on tadpoles. In contrast, chlorothalonil non-monotonically reduced Bd growth in culture and on tadpoles, with low and high concentrations causing significantly greater mortality than intermediate concentrations and controls. This study is one of only a handful of studies to document a non-monotonic dose response of an invertebrate (Bd) to a pesticide. Although both pesticides reduced Bd growth on tadpoles and in culture, neither eliminated Bd entirely, and because we know little about the long-term effects of the pesticides on hosts (e.g., immunosuppression), I do not recommend using these chemicals to control Bd. In my fourth research chapter, I investigated whether there are non-amphibian hosts for Bd. Non-amphibian hosts could explain how Bd is able to persist in the environment after amphibians are extirpated, and the extreme virulence and distribution of Bd. In laboratory and field studies, I found that crayfish, but not mosquitofish, were hosts for Bd. I found that crayfish could be infected with Bd, could maintain that infection long term (at least 3 months) and could transfer that infection to susceptible amphibians. I also revealed that exposure to water that previously held Bd caused significant crayfish mortality and gill recession, suggesting that Bd releases a chemical that can cause host pathology in the absence of infection. Most efforts to conserve and restore amphibian populations challenged by Bd have been unsuccessful, but managing alternative hosts offers a new and potentially more effective approach to managing Bd. Likewise, identifying the specific pathology-inducing chemical released by Bd might facilitate the development of new strategies to reduce the risk posed by this pathogen. The fifth and sixth research chapters are aimed to improve the quality and efficiency of Bd research. During amphibian development, Bd infections transition from the mouthparts of tadpoles to the skin of post-metamorphic frogs but this transition has never been quantified and thus researchers might be sampling the wrong parts of amphibian bodies to detect Bd. I showed that Bd abundance in O. septentrionalis mouthparts declined from Gosner stages 35-42 and increased on epidermis from Gosner stages 38-46. Assuming our findings are general across species, I recommend sampling mouthparts of amphibians less than Gosner stage 41 and hind limbs of amphibians greater than Gosner stage 41. This should provide researchers with guidance on where to sample to maximize detection of Bd. I also investigated whether Trypan blue dye could be used to determine the viability of Bd. I showed that the proportion of zoospores stained with Trypan blue dye matched the proportion of known dead zoospores added to cultures. In contrast, all of the zoosporangia stage (including known dead zoosporangia) of Bd stained blue. These results demonstrate that Trypan blue can be used to determine the viability of Bd zoospores but not zoosporangia. I recommend using Trypan blue to report the number of live zoospores to which hosts are exposed and to help determine whether factors have lethal or sublethal effects on Bd. My work demonstrates that managing exposure to contaminants and biological reservoirs for Bd might provide new hope for imperiled amphibians. Further exploring how pesticides and pathogens are contributing to amphibian declines will allow us to formulate crucial management and conservation plans to begin remediation.

Freshwater ecosystem degradation in the Amazon and Orinoco river basins is increasing due to rising human population numbers, and large water development projects. Therefore, monitoring ecosystem condition in these rivers of high biodiversity is of global conservation importance. This dissertation evaluated the potential of using river dolphins as indicators of ecosystem condition in large tropical rivers of South America. First, population estimates of river dolphins were obtained by line-strip transect surveys and mark-recapture methods on photo-identifications. Using this information, I identified critical habitat, hotspots, and areas of concern for river dolphins, as well as the relationship between dolphin density and group size estimates with ecological features. Second, I evaluated the relationship between dolphin estimates and human stressors. Higher densities of dolphins occurred in rivers with low indices of overall freshwater degradation, such as rivers with high water quality and the lowest human population numbers. Thus, dolphin density estimates seem to be good indicators of freshwater ecosystem degradation in the Amazon and Orinoco basins. These top predators not only are indicator species, but also have the potential to act as flagship and sentinel species, indicating freshwater ecosystem degradation and stimulating conservation action. This dissertation highlights the large changes in the Amazon and Orinoco that are approaching fast. Indicator, flagship and sentinel species can become science-based conservation tools not to only document freshwater ecosystem degradation, but to raise awareness about broader implications of human stressors on biodiversity and river systems.

Lake-rich thermokarst landscapes, such as Old Crow Flats (OCF) in northern Yukon, Canada have been identified as amongst the most vulnerable to climate change. This has raised concerns of the Vuntut Gwitchin First Nation (VGFN) and Parks Canada (Vuntut National Park) about the ecological integrity of this significant wetland. The influence of climate change on the hydroecological conditions of thermokarst lakes are complex and vary across the landscape, thus long-term hydroecological monitoring is essential to adequately assess the ecological integrity of the aquatic ecosystem and how it is changing over time. In a genuine interdisciplinary and collaborative approach, this thesis establishes an integrated approach using isotope hydrology, aquatic ecology, and paleolimnology to develop a robust long-term aquatic monitoring program that has already been adopted by Parks Canada. In collaboration with Parks Canada, 14 of 58 lakes that were previously studied during the International Polar Year from 2007-09 were selected to represent monitoring lakes. Lakes were sampled in early June and late August/early September 2010-11. Water samples for analysis of hydrogen and oxygen isotope composition and chemistry (i.e., ions and nutrients) were collected to track hydrological and limnological conditions. Artificial substrates were deployed in June and accrued algae were collected at the end of the ice-free season to assess community composition and abundance. Sediment coring was conducted in a culturally-significant lake (Zelma Lake – OCF06) to reconstruct long-term baseline hydroecological conditions over the past three centuries. Radiometric dating techniques (137Cs, 210Pb) were used to develop a sediment core chronology. Baseline hydroecological conditions were reconstructed through analyses of loss-on-ignition, bulk organic carbon and nitrogen elemental and isotope compositions, and pigments. Meteorological data and a multi-year evaporation pan experiment were used to develop a robust isotope framework, which provides the basis for interpreting five years (2007-11) of lake water isotope measurements and deriving knowledge of hydrological conditions for the monitoring lakes. Using this framework and the coupled-isotope tracer method, isotopic compositions of input water (δI) and evaporation-to-inflow (E/I) ratios were calculated and provide key hydrological information for each sampling interval. δ¬I values distinguish snowmelt- and rainfall-sourced lakes, with δP representing a threshold between the two isotopic-based hydrologic regimes. A Mann-Kendall test showed that three lakes (OCF11, 26, and 49) displayed significant increasing trends in δI values indicating a potential transition from snowmelt-sourced to rainfall-sourced isotope-based hydrologic-regimes. E/I ratios >0.5 signifies lakes that are evaporation-dominated with positive water balances and E/I ratios >1 indicates lakes that are evaporation-dominated with negative water balances. Six lakes in OCF (OCF06, 19, 37, 46, 49, and 58) surpass the 0.5 threshold and three of these lakes (OCF06, 19, and 46) crossed the significant evaporation threshold (E/I > 1) during dry climatic conditions. Multi-proxy paleolimnology analysis conducted on Zelma Lake reveals different hydroecological transitions during the past ~330 years that include: phase 1 (~1678-1900) characterized by stable hydroecological conditions; thermokarst expansion (~1900-1943) marked by decreases in productivity; phase 2 (~1943-2007) distinguished by increasing productivity; and a post drainage phase following rapid drainage in 2007 characterized by further increases in productivity. The stratigraphy of Zelma Lake shows that hydroecological conditions in dynamic landscapes such as OCF are complex and require multi-proxy paleolimnological analysis. In particular, organic matter, δ13Corg, and pigment concentrations are important parameters to consider when interpreting past hydroecological conditions, thermokarst expansion, and lake drainage events.

Thesis (M.Sc. (Zoology)) -- University of Limpopo, 2019 / Freshwater ecosystems in South Africa are losing their quality and quantity over time due to pollution mainly from mining, agriculture, industries, deforestation, sewage systems, construction of dams, channel modification and over extraction of water. The Dwars River, a tributary of the Olifants River, is of no exception, as recent studies indicated an increase in nutrient input possibly from agriculture. The Dwars River is an important source of water for nearby communities (Ga-Mampuru). The aim of the study was to assess water and sediment quality of the Dwars River using macroinvertebrates as bioindicators of pollution. Water and macroinvertebrates sampling were done seasonally from July 2017 to May 2018. The water quality results indicated that non-toxic constituents such as salinity and EC (Electrical Conductivity) were above permissible limits stipulated by the DWAF (1996) guidelines. More sensitive taxa were found upstream, despite high concentrations of some nutrients and metals in the water column. The high abundance and distribution of macroinvertebrates observed upstream was confirmed by the Canonical Correspondence Analysis (CCA), South African Scoring System (SASS5) and Average Score Per Taxon (ASPT) results during the study. Site 1 was dominated by the most sensitive taxa and this could be due to high dissolved oxygen content and increased heterogeneity of the area. Site 4 was dominated by the most tolerant taxa, according to the CCA, SASS score and ASPT results. This could possibly be due to the nutrients and heavy metals washed from upstream, which get adsorbed by the sediment. The results for species abundance, diversity and richness indicated that Ephemeroptera was the most abundant, while Diptera was the most diverse. Ephemeropterans are known to be indicators of good water quality. Site 1 had the highest number of families and orders while site 4 had the least families and orders. Ephemeroptera, Plecoptera and Tricoptera (EPT) taxa richness and Shannon diversity (H’) index values are high upstream and decrease downstream. Overall, the SASS5 indices, CCA and physicochemical results indicated that the water quality in the Dwars River is deteriorating in most impacted sites / National Research Foundation (NRF) and VLIR

Nature and humans are intrinsic parts of the same system, called a social-ecological system (SES), wherein freshwater ecosystems form one of the important bases of the survival of all life. Human activities, such as land use and overconsumption, impact on freshwater systems; and freshwater systems also impact on the urban systems through which they flow. Changes in one part of the system, be it human or ecological, will impact on the other. If a freshwater ecosystem’s resilience is negatively affected and fails to retain its functional integrity, it will increase the vulnerability of the SES. Disregarding this connection can have a significant impact on the quality of an urban system. Throughout its history since 1855, the City of Tshwane SES has moved through different eras of change, which have altered the quality of the connection between the Apies River and the urban infrastructure through which it flows. These eras have been identified as: a) First era (1855–1909) Apies River as a natural system; b) Second era (1910–1970) Apies River becoming a hidden, polluted and disconnected freshwater system; and c) Third era (1971–2016), the era of attempts at beautification and to regenerate the Apies River freshwater system. The main goal of this study is to understand how changes in the connection between the built infrastructure in the City of Tshwane and the Apies River have affected the resilience of the Apies River’s system as an integral part of the Tshwane SES. The study achieved this by identifying the different changes, the drivers of change, and the effects that these changes have had on the resilience of the Apies River. This was carried out using the method of a historical narrative. It was concluded that the Apies River gained specific resilience but lost its general resilience and therefore its adaptive capacity. The main drivers behind the loss of general resilience of the Apies River system were: a) the lack of a local government structure to supply proper infrastructure and service delivery to the people of Pretoria, followed by an inflexible and largely unresponsive local government system lacking tightness of feedback and therefore not detecting the signals of crossing a threshold in time; and b) a lack of ecological awareness or the necessary understanding of how freshwater ecosystems function, in order to integrate natural freshwater ecosystems as a functional part of the urban infrastructure. / Dissertation (ML (Arch))--University of Pretoria, 2015. / National Research Foundation (NRF) supported this study as part of the program: Resiliency Strategies for Aspirational African Cities, through the research Grant no. 78649. Opinions expressed and conclusions arrived at, are those of the author and cannot necessarily be attributed to the NRF. / Architecture / ML (Arch) / Unrestricted

This dissertation thesis was focused on improving the methodology to detect fish with modern sonar systems in lakes and reservoirs. The first part of the thesis is aimed to the vertical beaming acoustics with a key focus on the acoustic dead zone and its practical solution. The second part deals with the fish orientation in reservoir?s open waters and its consequences in horizontal beaming acoustics. The last one dedicates to the DIDSON multi-beam sonar and its reliability in detection and sizing of fish.