Dissertations / Theses on the topic 'Aquatic ecosystems'

Benthic algae a re one of the most important primary producers i n lotic ecosystems, and changes i n their community structure and function (e.g., metabolism) will influence other organisms at higher trophic levels or even the entire aquatic ecosystem through bottom-up effects. Since they are known to be sensiti ve to changes i n ambient conditions, benthic algae and especially diatoms have been widely used as i ndicators of environmental changes in aquatic ecosystems, particular ly i n E urope , through developi ng diatom-based indices. However, these indices have not been widely used i n other continents. Applications of such i ndices in Asia and Oceania first require testi ng to see whether the y can perform as reliable bioindicators across time and space, considering that aquatic systems are constantly changing in terms of their ambient environment such as water physical and chemical conditions. Nevertheless, few studies have been carried out to compare the environmental influences on benthic algal communities among different geographic regions, nor the influences at different spatial scales (e.g., catchment, reach, and habitat). F urthermore, few studies have considered how diatom indices perform compare with other commonly used bioindicators of aquatic ecosystem health.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
Griffith School of Environment.
Science, Environment, Engineering and Technology
Full Text

The present study examines the cycling of elements in the biosphere. The first chapter proposes a theoretical framework for this cycling based on both metal/ligand theory and mass balance studies. Empirical modelling serves as an alternative and complement to mass balance studies in predicting the export of elements from watersheds. Watershed output (export per unit area per unit of time) is predicted using atmospheric deposition rates, an element bonding strength index, the watershed area and a forest classification (deciduous vs coniferous). Finally the last chapter examines, in a speculative fashion, the partitioning of elements between the atmosphere and hydrosphere as a function of element behaviour and discusses the ecological consequences of human activity on this partitioning.

There is an increasing interest in dynamical food web modeling, and recent advances of computational biology provide new algorithms and tools for modern systems ecology. In this work stochastic individual-based models are used for simulating food web dynamics in two case studies: the Kelian river, in Borneo, Indonesia and a marine ecosystem in Gulf of Guinea. The two cases present effects from human perturbations. In both cases, we constructed food webs, based on real databases. We parameterized the stochastic dynamical model for the system models and performed sensitivity analysis (and community response indicators) in order to quantify the relative importance of system components. The main aims are to understand the importance of functional diversity of aquatic ecosystems and relations between the dynamics of species and the whole community in perturbed ecosystems due to human activities (pollution due to gold mining activity and human settlements in the case of the Kelian river ecosystem and the impact of Fish Aggregation Devices on skipjack tuna communities in the case of the Gulf of Guinea ecosystem). In Kelian river case, our results suggest that invertebrate shredders are indicators of human impact on the river. In downstream sites our results show that the river is more polluted and the relative importance of grazers and shredders decrease. The primary producers disappear downstream as consequence of mine activity and human waste. In the marine system case study, we analyzed the effects of association between tunas and FADs, and compared this to the behavior of free tuna individuals. The results suggest that skipjack tuna is affected by the use of FADs as fishing strategy on them. Some individual species show more sensibility to variation of population size of tuna. These two studies contribute to better understand how functional diversity is related to human impact. This kind of approach may help in shaping systems-based conservation and marine fisheries management strategies. Keywords: food web, aquatic ecosystems, stochastic model, sensitivity analysis

There is an increasing interest in dynamical food web modeling, and recent advances of computational biology provide new algorithms and tools for modern systems ecology. In this work stochastic individual-based models are used for simulating food web dynamics in two case studies: the Kelian river, in Borneo, Indonesia and a marine ecosystem in Gulf of Guinea. The two cases present effects from human perturbations. In both cases, we constructed food webs, based on real databases. We parameterized the stochastic dynamical model for the system models and performed sensitivity analysis (and community response indicators) in order to quantify the relative importance of system components. The main aims are to understand the importance of functional diversity of aquatic ecosystems and relations between the dynamics of species and the whole community in perturbed ecosystems due to human activities (pollution due to gold mining activity and human settlements in the case of the Kelian river ecosystem and the impact of Fish Aggregation Devices on skipjack tuna communities in the case of the Gulf of Guinea ecosystem). In Kelian river case, our results suggest that invertebrate shredders are indicators of human impact on the river. In downstream sites our results show that the river is more polluted and the relative importance of grazers and shredders decrease. The primary producers disappear downstream as consequence of mine activity and human waste. In the marine system case study, we analyzed the effects of association between tunas and FADs, and compared this to the behavior of free tuna individuals. The results suggest that skipjack tuna is affected by the use of FADs as fishing strategy on them. Some individual species show more sensibility to variation of population size of tuna. These two studies contribute to better understand how functional diversity is related to human impact. This kind of approach may help in shaping systems-based conservation and marine fisheries management strategies. Keywords: food web, aquatic ecosystems, stochastic model, sensitivity analysis

Mammals in freshwater aquatic systems play important roles as ecosystem engineers, trophic transfer agents, and apex predators, thus acting as indicators of freshwater ecosystem function. Watersheds inhabited by semi-aquatic mammals have increased links between adjacent terrestrial and aquatic ecosystems compared to watersheds where they are not present. Semi-aquatic mammals not only exert top-down influences on streams, but are affected by bottom-up forces from the riparian system itself. The goal of this study was to identify variables that correlate with the presence of beaver (Castor canadensis), muskrat (Ondatra zibethicus), mink (Neovison vison), and river otter (Lontra canadensis), including their interactions, resulting in a better understanding of the areas where these semi-aquatic mammals occur and their effects on the riparian system. The objectives of this study were (1) to identify variables related to the probability of detection, initial occupancy, colonization, and extinction of the 4 semi-aquatic mammals in southern Illinois; and (2) to test if the reintroduction of river otter has changed stream food webs. To address my first objective, I sampled 120 bridge sites in 2 periods (winter: Jan-Feb; and spring: Mar-Apr) during 2012–2014 in 11 major watersheds in the southern third of Illinois (44,526 km2) to estimate multi-season occupancy. Each survey unit was a 400-m stream segment visited twice by 2 observers for a total of 4 observations per site per period. Observers recorded all mammal signs found, including sign species and type. Sites were Intensive Basin Survey Sites sampled by Illinois Department of Natural Resources (IDNR) and Illinois Environmental Protection Agency (IEPA), allowing data collected by the state to be available for explanatory variables for mammal occupancy. Data collected by the Illinois Natural History Survey (INHS) also were available for a subset of sites. I collected local- and landscape-scale habitat and weather variables for each site. I developed hypotheses regarding occupancy of sites based on land-cover, human disturbance, and stream attributes for each species. I developed additional hypotheses regarding prey availability and water quality for river otter and mink. Sites used in each analysis were dependent on data available to address the hypotheses of interest. Beaver and muskrat were present at ≥100 of 103 sites for ≥1 observation. Naïve occupancy was high (≥82%) every year for both species. Detection probabilities for beaver and muskrat were best predicted by survey period. Beaver detection remained fairly constant across survey periods except for a decrease in winter 2014, whereas muskrat detection was generally lower during winter and higher during spring. Beaver were more likely to occupy larger streams than smaller streams during the initial survey period. Sites that lacked a dominant land-cover had a lower probability of beaver colonization than sites dominated by agriculture or woody vegetation at the landscape scale. In addition, the probability that a site would be colonized by beaver during the study increased with availability of water within 1 km of the surveyed segment, increased stream density, sites at larger streams, and river otter presence during the previous period. The probability of site extinction decreased as stream size, stream density within 1 km, and water availability within 500 m of the survey segment increased. Occupancy of muskrat during the initial survey period was negatively predicted by % forest in the 1-km riparian area, channel incision, and amount mercury in the sediment. Colonization by muskrats was lower during the long spring to winter intervals than the short winter to spring intervals, and was positively related to the amount of organic carbon in the sediment. The probability of site extinction by muskrat increased with increasing % forest within the riparian area around the stream segment, decreasing 1-km stream density, and when land-cover within 1 km of sites was dominated by agriculture or woody vegetation. Multi-season occupancy of river otter and mink were assessed in 2 separate analyses that used either land-cover and management variables or prey availability and riparian community composition, respectively. In the first analysis, river otter and mink were present at ≥84 of 103 sites. Naïve occupancy was higher every year for mink (≥88.3%) than for river otter (≥55.3%). Detection of river otter and mink in the first analysis increased as substrate availability increased. Occupancy of river otter during the initial survey period was predicted by large stream size, low % developed area within 250 m of the surveyed segment, and proximity to nearest river otter reintroduction point. Probability of colonization by river otter varied by survey period and was higher at sites with larger streams, higher stream density, lower % developed area, and within a known river otter population area. Site extinction by river otter in the first analysis varied by survey period and was linked to increased organic carbon in the sediment, and decreased road density within 1 km of the surveyed segment. River otter harvest was not found to affect site colonization or extinction. Mink occupancy during the initial period was negatively associated with water availability within 100 m of the survey segment. Site colonization by mink varied by month and increased with increasing developed area within 100 m of the surveyed segment, increasing channel incision, and decreasing rainfall. Probability of site extinction for mink increased as stream size and developed area within 500 m of the surveyed segment increased, and when woody vegetation was the dominant land-cover type within 1 km of the surveyed segment. The second analysis of multi-season occupancy of river otter and mink used 77 sites, 81.8% of which had ≥1 river otter detection in the study and 98.7% of which had ≥1 mink detection. Naïve occupancy differed between years but gradually increased for river otter and remained high (≥93.5%) for mink. Increasing substrate availability increased the probability of river otter detection, whereas mink detection varied by survey period. Occupancy during the initial survey period was higher in sites closer to the reintroduction points for river otter. Probability of colonization of river otter was positively associated with macroinvertebrate IBI and fish species richness, sites with high fish species richness of fish families preferred by river otter also had reduced otter extinction probability. No tested variables predicted initial occupancy for mink, but mink were more likely to colonize sites with increased fish richness and when muskrat were present during the previous period. Mink had decreased probability of extinction in sites with increasing mussel community index. My results indicate that semi-aquatic mammals in Illinois were affected by a riparian habitat, water availability, and stream community variables at both the landscape and local scale. I found high occupancy of mink, beaver, and muskrat across the entire landscape of southern Illinois, and my results suggest that the geographic range of river otter continues to expand. Relationships of occupancy of these semi-aquatic mammals to measurements of urban areas and human disturbance were not consistent across all species. Mink and river otter occupancy were both predicted by aspects of prey availability, indicating the importance of predator-prey relationships in occupancy dynamics of riparian predators. Hypotheses regarding predator pressure and changes in environmental variables were used to test the effects of river otter reintroduction on stream communities. For this objective, I used structural equation models. I compared fish and macroinvertebrate communities from before (1982-1995) and after (2005-2013) reintroduction of river otter, which occurred in 1994–1996. Fish and macroinvertebrate community data for 35 sites located throughout 6 major watersheds in southern Illinois (25,550 km2) were obtained from state agencies. Changes in stream communities were evaluated using 4 metrics (species richness, species dominance, skewness in size distribution of prey, and proportion of individuals in the size class preferred by river otter). Neither the inclusion of river otter site use nor change in stream quality, measured by change in % forest, improved models over the simple model which only included fish and macroinvertebrate communities. Overall, I found no evidence that river otter presence or change in forest cover affected stream fish and macroinvertebrate communities.

Crayfish are keystone species and ecosystem engineers that affect the structure and function of aquatic ecosystems. Whilst ecological impacts are caused by crayfish in their native range, non - native crayfish species typically have a greater ef fect on some other aquatic organisms and ecosystem processes (Chapter 2). Crayfish are extremely successful invaders that often cause declines in native cra yfish (Chapter 3). Of the 7 non - native crayfish species in the UK, the signal crayfish ( Pacifastacus leniusculus ) is currently the most widespread (Chapter 3). Field and laboratory data, however, suggest that in parts of the UK signal crayfish are being outcompeted by more recently introduced virile crayfish ( Orconectes cf. virilis ) (Chapter 4). Non - native crayfish also threaten native crayfish through disease, notably crayfish plague ( Aphanomyces astaci ), transmission. Whilst non - native North American crayfish are largely resistant to A. astaci , infection in susceptible native European species is usually lethal. Within this study 23 signal crayfish populations were screened for A. astaci and 13 were infected (Chapter 5). Virile crayf ish from the UK were also infected with A. astaci , and therefore should also be considered as a transmission pathway for this pathogen in the UK (Chapter 6). Whilst the majority of studies on crayfish symbionts are focused on A. astaci , crayfish host a wid e range of micro and macro - parasites. One group of particular interest are branchiobdellidans (Annelida: Clitellata). Two species of these ectosymbionts, Xironogiton victoriensis and Cambarincola aff. okadai , were recently discovered on invasive signal cra yfish in the UK (Chapter 7). Owing to their abilities to survive for extended periods off the host and reproduce rapidly both species have a high invasion potential in the UK (Chapter 8). Laboratory experiments show that signal crayfish infested with X. victoriensis were less aggressive and poorer foragers than uninfested c rayfish , therefore these symbionts may influence signal crayfish invasion dynamics (Chapter 9).

Black carbon (BC), the incomplete combustion product from biomass and fossil fuel burning, is ubiquitously found in soils, sediments, ice, water and atmosphere. Because of its polyaromatic molecular characteristic, BC is believed to contribute significantly to the global carbon budget as a slow-cycling, refractory carbon pool. However, the mass balance between global BC generation and accumulation does not match, suggesting a removal mechanism of BC to the active carbon pool, most probable in a dissolved form. The presence of BC in waters as part of the dissolved organic matter (DOM) pool was recently confirmed via ultrahigh resolution mass spectrometry, and dissolved black carbon (DBC), a degradation product of charcoal, was found in marine and coastal environments. However, information on the loadings of DBC in freshwater environments and its global riverine flux from terrestrial systems to the oceans remained unclear. The main objectives of this study were to quantify DBC in diverse aquatic ecosystems and to determine its environmental dynamics. Surface water samples were collected from aquatic environments with a spatially significant global distribution, and DBC concentrations were determined by a chemical oxidation method coupled with HPLC detection. While it was clear that biomass burning was the main sources of BC, the translocation mechanism of BC to the dissolved phase was not well understood. Data from the regional studies and the developed global model revealed a strong positive correlation between DBC and dissolved organic carbon (DOC) dynamics, indicating a co-generation and co-translocation between soil OC and BC. In addition, a DOC-assistant DBC translocation mechanism was identified. Taking advantage of the DOC-DBC correlation model, a global riverine DBC flux to oceans on the order of 26.5 Mt C yr-1 (1 Mt = 1012 g) was determined, accounting for 10.6% of the global DOC flux. The results not only indicated that DOC was an important environmental intermediate for BC transfer and storage, but also provided an estimate of a major missing link in the global BC budget. The ever increasing DBC export caused by global warming will change the marine DOM quality and may have important consequences for carbon cycling in marine ecosystem.

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Dissertacao (Mestrado)
IPEN/D
Instituto de Pesquisas Energeticas e Nucleares - IPEN-CNEN/SP

Thesis (Ph. D.) -- University of Maryland, College Park, 2006.
Thesis research directed by: Marine-Estuarine-Environmental Sciences. Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.

This dissertation addressed questions pertaining to mercury (Hg) fate and transport in aquatic ecosystems by applying stable Hg isotopes as a tracer. Mercury poses a public health burden worldwide. In parts of the developing world, Hg-use during artisanal and small-scale gold mining (ASGM) is pointed at as the source of elevated Hg in the environment. However, Hg from other sources including soil erosion associated with land cover and land-use change (LCLUC) may also contribute to local Hg pollution.

Stable Hg isotope profiles of sediment cores, surface sediments, and soils from two aquatic ecosystems in Amapá, Brazil, one downstream artisanal gold mining (AGM) and one isolated from AGM were assessed. Although previous studies attributed elevated environmental Hg levels in this area to AGM, stable Hg isotopic evidence suggests elevated Hg downstream of AGM sites is dominantly from erosion of soils due to LCLUC.

In contrast, the impact of Hg-use during small-scale gold mining (SGM) in the Southern Andean Region of Portovelo-Zaruma, Ecuador on Hg in the trans-boundary Puyango-Tumbes River was also investigated. By comparing preliminary isotopic Hg signatures from river sediment along the Puyango-Tumbes to soil and sediment from upstream locations along the Puyango tributaries, we suggest Hg-use during SGM in this region is likely responsible for elevated Hg downstream and into Peru. Technical and policy challenges in measuring and responding to gold mining-related cumulative impacts were also reviewed in the context of Portovelo-Ecuador.

Together, the findings not only answer questions of critical importance to preventing Hg pollution in two of the world's most vulnerable ecosystems but also provide information that can be used to better target interventions to reduce environmental Hg levels and subsequent human exposures. Furthermore, the validation and application of the stable Hg isotope method to trace Hg pollution from ASGM in different aquatic ecosystems represents a critical step to the application of stable Hg isotopes to trace pollution in other complex natural environments and to address public health-related questions.

Робота публікується згідно наказу ректора від 21.01.2020 р. №008/од "Про перевірку кваліфікаційних робіт на академічний плогіат у 2019-2020 навчальному році". Керівник проекту: доцент кафедри екології, к.б.н., Білик Тетяна Іванівна
The object of research is the pollution of aquatic ecosystems with phosphates. The subject of research is the reduction of the impact of phosphates on aquatic ecosystems due to the improvement of wastewater treatment systems. The aim of the work was to analyze the prospects for reducing water pollution by phosphates and their impact on aquatic ecosystems due to the improvement of wastewater treatment system. Research methods: analytical, chemical, statistical methods of data processing. Relevance. In recent years, the amount of phosphates in the wastewater entering the treatment facilities of the city of Kyiv - Bortnytsia aeration station, has increased significantly. To date, it reaches almost 30 mg / l, with a standard discharge 8.0 mg / l. At this concentration of phosphates in the incoming water, the old treatment technologies do not allow to reach the established norms for wastewater, which causes eutrophication and death of aquatic organisms. The solution to this problem is to improve wastewater treatment systems and limit the use of phosphorus-containing detergents. Scientific novelty: an analysis of ways to reduce the impact of phosphates on aquatic ecosystems. Practical significance: the results of the study are prepared for implementation in a comprehensive program aimed at protecting aquatic ecosystems and reducing the content of phosphates in water bodies of Ukraine. Personal contribution of the author: elaboration of scientific literature on the topic of work, analysis of data of the Institute of Hydrobiology of the National Academy of Sciences of Ukraine and Kyivvodokanal, preparation for the implementation of research results.

Estrogens are steroidal hormones that can affect the endocrine system at very low levels. Impacts of natural and synthetic estrogens on environment are under arising concern, since they are systematically discharged into environment and impacts on ecosystems and accumulation via food webs are not fully known. Natural and synthetic estrogens originating from households enter the sewage systems and are conveyed to wastewater treatment plants (WWTP). Because current WWTPs are not designed to remove these compounds, they are then discharged into the environment. Other significant source of estrogens is e.g. livestock waste. Combined and synergetic effects with other chemicals make the evaluation of the impacts of estrogens very complex. Furthermore, analysis costs are high which reduce the capabilities of environmental authorities and researchers of conducting extensive monitoring programs. Environmental fate modelling is a fast and cost-effective tool to evaluate the environmental fate of chemical compounds (degradation, advection etc.), which are influenced by several complex processes. Using models, the impacts can be predicted before the chemicals are discharged in the environment making it an important tool in assessing environmental impacts of chemicals such as estrogens. The main objective of this thesis was to investigate the occurrence, concentration, fate and estimated environmental impacts of the synthetic estrogen 17-alpha-ethinylestradiol (EE2) and the natural estrogens 17-beta-estradiol (E2) and estrone (E1). These estrogen compounds were included in the European Commission watch list of compounds posing a significant risk to the aquatic environment. The secondary aim was to evaluate the suitability of environmental fate models in predicting the fate of sewage derived estrogens in aquatic ecosystems. Research methods included literature review and a case study where FATEMOD modelling software was used to estimate the fate of estrogens in the selected study site Lake Pyhäjärvi located in Tampere, Finland. The modelling part was conducted in collaboration with Finnish Environmental Institute. Two separate models representing parts of Lake Pyhäjärvi were constructed. The modelling process involved the compartmentalization of the environment including the attribution of parameters describing environmental compartments, the attribution of properties of the estrogens and the transport and transformation processes linked to the evaluated compounds and study site. These properties, parameters, etc. were found from available literature and databases. Based on the literature review conducted, estrogens are found in trace amounts (ngL⁻¹) in WWTP effluents, and usually natural estrogens are detected in higher concentrations than synthetic estrogens. However, synthetic estrogens are more persistent in the environment and cause impacts at lower levels. Although several studies report on the concentration of estrogens in WWTP effluents and receiving waterbodies, the detected concentrations vary significantly, and number of samples and replicates are low due mostly to the costs of analysis. Predicted no-effect concentrations used in risk assessment of aquatic organisms vary between 0.1–6 ng L⁻¹ and for example estrogens has been detected in the water of Lake Pyhäjärvi in concentrations of 0.4–0.6 ngL⁻¹ for E1 and 0.064 ngL⁻¹ for EE2, while E2 was below limit of detection (rapid transformation of E2 into E1 can occur in the environment). Impacts on aquatic ecosystems have been consistently observed with for example the feminization and other abnormalities occurring in fish, and reproduction changes in zooplankton, mussels and snails. Results from the FATEMOD models were promising, leading to the conclusion that the software can be seen as a useful tool for evaluating the fate of estrogens in aquatic ecosystems, although more accurate input data, especially regarding to degradation processes of estrogens in cold climate is still needed
Estrogeenit ovat steroidihormoneja, jotka voivat vaikuttaa endokriiniseen järjestelmään hyvin pieninä pitoisuuksina. Luonnollisten ja synteettisten estrogeenien ympäristövaikutukset ovat herättäneet lisääntynyttä huolestuneisuutta, sillä niitä johdetaan systemaattisesti ympäristöön ja niiden vaikutuksia ekosysteemeihin ja kertyvyyttä ravintoketjuissa ei täysin tunneta. Kotitalouksista lähtöisin olevat luonnolliset ja synteettiset estrogeenit siirtyvät viemäriverkostojen kautta jätevedenpuhdistamoille, joista ne kulkeutuvat ympäristöön, sillä nykyisiä puhdistamoita ei ole suunniteltu tällaisten yhdisteiden poistamiseen. Merkittävä estrogeenien lähde on myös esimerkiksi karjanlanta. Yhteisvaikutukset muiden kemikaalien kanssa tekevät estrogeenien ympäristövaikutusten arvioinnista hyvin hankalaa. Lisäksi analyysikustannukset ovat korkeita, mikä vähentää ympäristöviranomaisten ja tutkijoiden mahdollisuutta suorittaa laajoja tarkkailuohjelmia. Mallintaminen on nopea ja kustannustehokas työväline kemikaalien ympäristökohtalon (hajoaminen, kulkeutuminen jne.) arvioimiseen, mihin vaikuttaa useat monimutkaiset prosessit. Malleja hyödyntämällä vaikutuksia voidaan ennustaa ennen kuin kemikaaleja johdetaan ympäristöön, mikä tekee malleista tärkeän työvälineen kemikaalien, kuten estrogeenien, ympäristövaikutusten arvioimisessa. Tämän diplomityön päätavoitteena oli tutkia synteettisen estrogeenin 17-alfa-etinyyliestradiolin (EE2), sekä luonnollisten estrogeenien 17-beta-estradiolin (E2) ja estronin (E1) esiintyneisyyttä, pitoisuuksia, ympäristökohtaloa ja arvioituja ympäristövaikutuksia. Nämä estrogeenit sisältyvät Euroopan komission luetteloon tarkkailtavista aineista, jotka voivat aiheuttaa vesiympäristölle merkittävän riskin. Tavoitteena oli myös tutkia ympäristökohtalomallien soveltuvuutta jätevesien sisältämien estrogeenien ympäristökohtalon ennustamiseen. Tutkimusmenetelmät sisälsivät kirjallisuuskatsauksen ja tapaustutkimuksen, jossa FATEMOD-mallinnussovellusta käytettiin estrogeenien ympäristökohtalon mallintamisessa valitulla tutkimuspaikalla Tampereen Pyhäjärvellä. Mallinnusosuus suoritettiin yhteistyössä Suomen ympäristökeskuksen kanssa. Osasta Pyhäjärveä laadittiin kaksi erillistä mallia. Mallinnusprosessi sisälsi ympäristön osittelun mukaan lukien ympäristöosien parametrien määrittämisen, estrogeenien ominaisuuksien määrittämisen, sekä estrogeeneihin ja tutkimuspaikkaan liittyvien kulkeutumis- ja muuntumisprosessien määrittämisen. Nämä ominaisuudet, parametrit ym. kerättiin käytettävissä olevista kirjallisuudesta ja tietokannoista. Suoritetun kirjallisuuskatsauksen perusteella estrogeeneja löydetään pieninä (ngL⁻¹) pitoisuuksina jätevedenpuhdistamoiden purkuvesistä ja yleensä luonnollisia estrogeeneja korkeampina pitoisuuksina kuin synteettisiä. Synteettiset estrogeenit ovat kuitenkin ympäristössä pysyvämpiä ja vaikuttavat pienempinä pitoisuuksina. Vaikka useita tutkimuksia on raportoitu estrogeenien pitoisuuksista jätevedenpuhdistamoiden purkuvesissä ja vesistöissä, havaitut pitoisuudet vaihtelevat merkittävästi ja näytemäärät ovat vähäisiä johtuen korkeista analyysikustannuksista. Riskien arvioinnissa käytetyt ennustetut haitattomat pitoisuudet (PNEC, predicted no-effect concentration) estrogeeneille ovat 0.1–6 ngL⁻¹ ja esimerkiksi Pyhäjärvestä on mitattu pitoisuuksia 0.4–0.6 ngL⁻¹ E1:stä ja 0.064 ngL⁻¹ EE2:sta, kun E2 oli määritysrajojen alapuolella (nopea muuntuminen E2:sta E1:ksi voi tapahtua ympäristössä). Vaikutuksia vesistöjen ekosysteemeihin on havaittu usein esimerkiksi kalojen naisistumisina ja muina poikkeavuuksina sekä muutoksina eläinplanktonin, etanoiden ja simpukoiden lisääntymisessä. Tulokset FATEMOD-malleista olivat lupaavia ja ohjelma voidaan nähdä käyttökelpoisena työkaluna mallintaa estrogeenien ympäristökohtaloa vesiekosysteemeissä. Tästä huolimatta vielä tarvitaan kattavampia lähtötietoja erityisesti liittyen estrogeenien hajoamisprosesseihin kylmissä ilmastoissa

The environmental health of aquatic ecosystems depends amongst others, on the chemical pollution coming from activities in the catchment's area. In the Swan River Estuary, Western Australia, the chemical pollutants of concern released into the river are petroleum hydrocarbons and sodium pentachlorophenate (NaPCP). Decreased water quality causes a loss of biotic diversity especially amongst fish populations. The health of aquatic ecosystems can be monitored by fish health, especially fish located at higher levels in the food chain. Pink snapper (Pagrus auratus), an endemic Western Australian fish species, was tested for its potential as a bioindicator of aquatic environmental health. This thesis presents data on the responsiveness of pink snapper to the contaminants of concern, using biomarkers such as serum sorbitol dehydrogenase (SDH), mixed function oxygenase (MFO), metabolic enzymes such as citrate synthase (CS), cytochrome C oxidase (CCO) and lactate dehydrogenase (LDH) and the histological alteration such as hepatic cell lesions (hyperplasia and hypertrophy), and glycogen and lipid droplets. The metabolic enzymes CCO and LDH as well as the hepatic MFO induction and histopathology were proven to be the most suitable biomarkers for use for routine monitoring of the Swan River Estuary using pink snapper as a bioindicator. However, CS activity and hepatic cell lesions (hyperplasia and hypertrophy) did not respond to exposure to contamination and are therefore not suited as biomarkers of effects in pink snapper. The first phase of the study aimed at investigating the responsiveness of juvenile pink snapper to an MFO inducer. Polychlorinated biphenyl isomer # 126 was selected as a model MFO inducer for this study. In the initial experiment, MFO activity was measured as a biomarker of exposure, and serum SDH activity was assessed as a biomarker of liver damage.MFO and SDH activities were of special interest as these biochemical tools have not previously been validated for any Western Australia fish species. Juvenile pink snapper were injected intraperitoneally (i.p.) with 0, 10, 100, 500, 1000 microgram PCB-126 per kilogram. Fish were sacrificed 10 days postinjection, and liver and blood were collected for MFO and SDH analysis, respectively. Doses of 10 and 100 microgram PCB-126 per kilogram caused the highest MFO induction, while doses of 0 and 1000 microgram PCB-126 per kilogram did not result in higher MFO activity relative to carrier-injected (peanut oil) control fish. SDH activities were not significantly different among treatments indicating that hepatocellular damage was not responsible for the reduced MFO activity at the highest dose. Metabolic enzymes in pink snapper exposed by NaPCP were studied in the second phase of the experiment. The aim of this second experiment was to test the responsiveness of pink snapper to contaminants known to cause metabolic perturbations in vertebrates. Juvenile pink snapper were intraperitoneally (i.p.) injected with 0, 5, 10, 20 mg per kilogram. Oxidative enzymes were assessed by measuring CS and CCO activities and glycolytic enzyme was assessed by measuring LDI-1 activity in liver and white muscle tissues. CS activity remained unchanged in both the white muscle and in the liver. CCO activity was significantly enhanced in liver in all treated fish relative to control fish, but not in the white muscle. LDH activity was also higher in liver in all treated fish as compared to control fish, while in white muscle, LDH activity significantly increased at the highest dose injected.The use of a suite of biochemical markers is useful in determining the effects of xenobiotic exposure of aquatic organisms, because it provides a holistic approach with biomarkers at different levels of biological organization. For the third and final phase of the study the suite of biomarkers selected were MFO, metabolic enzyme (CS, CCO and LDH) activities, and histological alternations in combination with physiological indices. The aim of this last experiment was to investigate if a modified liver metabolic activity would alter the MFO induction potential. To test if altered liver metabolism would influence liver detoxication capacities, juvenile pink snapper were i.p. injected with peanut oil (control), or pentachlorobiphenyl # 126 (PCB 126), with sodium pentachlorophenate (NaPCP), or combination of PCB 126+NaPCP. Relative to controls, ethoxyresorufin-O-deethylase (EROD) activity was induced in the PCB 126 and PCB 126+NaPCP fish, but not in the NaPCP group. In the liver, CCO activity was enhanced by the treatments while CS activity remained unchanged and LDH activity was increased in the NaPCP treatment only. In the white muscle, only the PCB 126+ NaPCP treatment enhanced CCO activity, with all other enzymatic activities remaining unchanged. Low serum sorbitol dehydrogenase (sSDH) activity and histopathology of the liver indicated no significant alteration of cellular structure, albeit the lipid droplet size was increased in the PCB 126 and in the PCB 126+NaPCP treatments.It is concluded that the hepatic metabolic changes correspond to histopathological observations, but an altered metabolic capacity does not influence the metabolism of xenobiotics by liver enzymes, as measured by EROD activity. These experiments answered the need to identify a suitable fish species for routine monitoring of the aquatic environment in Western Australia. It also identified the most suitable biochemical markers of exposure and effects, and the suitability of the pink snapper as a bioindicator. Finally, the experiments investigated interactions between biomarkers and provided new knowledge useful to scientists using MFO and/or metabolic enzymes in field or laboratory toxicology.

Radionuclides are widely used in energy production and medical, military and industrial applications. Thus, understanding the behaviour of radionuclides which have been or may be released into ecosystems is important for human and environmental risk assessment. Modelling of radionuclides or their stable element analogues is the only tool that can predict the consequences of accidental release. In this thesis, two dynamic stochastic compartment models for radionuclide/element transfer in a marine coastal ecosystem and a freshwater lake were developed and implemented (Paper I and III), in order to model a hypothetical future release of multiple radionuclides from a nuclear waste disposal site. Element-specific mechanisms such as element uptake via diet and adsorption of elements to organic surfaces were connected to ecosystem carbon models. Element transport in two specific coastal and lake ecosystems were simulated for 26 and 13 elements, respectively (Papers I and III). Using the models, the concentration ratios (CR: the ratio of the element or radionuclide concentration in an organism to the concentration in water) were estimated for different groups of aquatic organisms. The coastal model was also compared with a 3D hydrodynamic spatial model (Paper II) for Cs, Ni and Th, and estimated confidence limits for their modelled CRs. In the absence of site-specific CR data, being able to estimate a range of CR values with such models is an alternative to relying on literature CR values that are not always relevant to the site of interest. Water chemistry was also found to influence uptake of contaminants by aquatic organisms. Empirical inverse relationships were derived between CRs of fish for stable Sr (CRSr) and Cs (CRCs) and water concentrations of their biochemical analogues Ca and K, respectively (Paper IV), illustrating how such relationships could be used in the prediction of more site-specific CRCs and CRSr in fish simply from water chemistry measurements.

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 4: Manuscript.

Thesis (Ph. D.)--Florida State University, 2009.
Advisor: Yang Wang, Florida State University, School of Arts and Sciences, Dept. of Geological Sciences. Title and description from dissertation home page (viewed Oct. 21, 2009). Document formatted into pages; contains ix, 88 pages. Includes bibliographical references.

The traditional procedures for the ecotoxicological risk assessment are general, schematic and simplified and, for these reason, they are powerful tools for regulation purposes. Anyway, they don't take into account the actual consequences on natural communities, the interactions among populations within the community or the indirect effects of a contamination. The need of more "ecological realism" into them is thus felt. Recently, the application of the vulnerability concept, instead of sensitivity, and the use of biological characteristics (traits) of organisms for predicting it represent steps towards the introduction of more ecological realism in ecotoxicology. In the present work the traditional ecotoxicological procedures were used in different compartments in the same area, considering the stress given by plant protection products. Then, based on the previous step, some innovative aspects were applied on the soil compartment. Natural communities were investigated for assessing the actual consequences of the stress and possible indirect effects on the food web. The recent trait-based and vulnerability approaches were applied and the results compared each other. A vulnerability analysis procedure to a mixture of plant protection products for soil community was also developed.

Results from this study enables a better understanding of groundwater surface water interactions in the TMG, particularly regarding aquatic ecosystems. It has also highlighted the necessity to do proper impact assessments before proceeding with bulk abstraction from this important aquifer. The results also demonstrated the importance of differentiating between real groundwater and non-groundwater discharge contributions to surface hydrology and where these interface areas are located.

RESUMO A Ãgua constitui o recurso de maior importÃncia para o homem, no entanto parece nÃo existir nenhuma preocupaÃÃo do ser humano em preservÃ-la, uma vez que as atividades diÃrias estÃo prejudicando cada vez mais, a qualidade deste recurso. Este trabalho teve por objetivo analisar a estrutura da comunidade fitoplanctÃnica e a qualidade da Ãgua de ecossistemas aquÃticos do Estado do Cearà (Brasil). Foram realizadas coletas mensais nas estaÃÃes chuvosa e seca, entre 2004 e 2007, nos seguintes ecossistemas: estuÃrios dos rios CauÃpe, MundaÃ, Cearà e Malcozinhado; lagoas de Jijoca, PecÃm, Uruaà e Maraponga; bicas do Ipu e das AndrÃas e aÃudes Favelas, da Corte e Campus do Itaperi. Os resultados mostraram mudanÃa significativa na estrutura da comunidade fitoplanctÃnica, influenciada principalmente pelos nÃveis de precipitaÃÃes pluviomÃtricas. As Bacillariophyceae foram predominantes nos ecossistemas analisados, exceto nos aÃudes Favelas, da Corte e do Campus do Itaperi, que apresentaram elevados nÃveis de eutrofizaÃÃo, com dominÃncia de Cyanophyceae, Zygnematophyceae e Chlorophyceae, respectivamente. As espÃcies raras, a grande maioria, formaram um grupo totalmente isolado daquelas consideradas dominantes, abundantes e pouco abundantes, constituÃdas por um nÃmero reduzido de espÃcies, confirmando a grande influÃncia sazonal da regiÃo, sobre a comunidade fitoplanctÃnica. Os ecossistemas apresentaram grande variaÃÃo na diversidade, riqueza e equitabilidade das espÃcies, no entanto a diversidade foi maior durante a estaÃÃo chuvosa. Com base nos teores de O2 e CO2 dissolvidos, amÃnia total, nitrito, fosfato, bem como, nos Ãndices do estado trÃfico do fosfato e/ou da transparÃncia da Ãgua e na presenÃa de bioindicadores, os estuÃrios dos rios MundaÃ, CauÃpe e CearÃ, a lagoa da Maraponga e os aÃudes Favelas, da Corte e Campus do Itaperi foram classificados como ambientes eutrÃficos; o estuÃrio do Rio Malcozinhado e as lagoas do PecÃm e de Uruaà como mesotrÃficos; e a lagoa de Jijoca e as bicas do Ipu e das AndrÃas como oligotrÃficos. Foram registrados diversos bioindicadores de Ãguas eutrofizadas e/ou poluÃdas, destacando-se a presenÃa de Cyanophyceae potencialmente tÃxicas nos diversos ecossistemas, com blooms no estuÃrio do Rio Cearà e no aÃude Favelas, nÃo sendo registrada uma biomassa significativa nos outros ambientes, mesmo naqueles que apresentaram elevado estado trÃfico, como o aÃude do Campus do Itaperi, com ocorrÃncia de bloom de Chlorophyceae e, no aÃude da Corte, cujo bloom foi de Zygnematophyceae, mostrando que na anÃlise de sanidade dos ecossistemas aquÃticos, a anÃlise conjunta dos parÃmetros biolÃgicos e fÃsico-quÃmicos do ecossistema à de suma importÃncia para um parecer ambiental adequado.
Water is the most important resource for humans, though it s eems there is no concern of human beings in preserving it, because daily activities increasingly under mine the quality of this resource. This study aimed to analyze the phytoplankton community structure and water quality in aquatic ecosystems of Cearà State (Brazil). Monthly collections were made during the rainy and dry seasons between 2004 and 2007 in the following ecosystems: the CauÃpe, MundaÃ, Cearà and Malcozinhado river estuarie s; the Jijoca, PecÃm, Uruaà and Maraponga lakes; the Ipu and Andreas waterspouts and the Favelas, Corte and Campus do Itaperi dams. The results showed significant changes in phytoplankton community structure, mainly influenced by levels of rainfall. The Bacillariophyceae were predominant in the ecosystems studied, except in the Favelas, Corte and Campus do Itaperi dams, which showed high levels of eutrophication, with dominance of Cyanophyceae, Zygnematophyceae and Chlorophyceae, respectively. Rare species, the great majorit y, formed a group totally isolated from those considered dominant, abundant and little abundant, consisting of a small number of species, confirming the major seasonal influence of the region's on the phytoplankton community. Ecosystems showed great variation in diversity, richness and evenness of species, however, diversity was highest during the rainy season. The following environments were classified according to the concentration of dissolved O 2 and CO2, total ammonia, nitrite, phosphate, as well as on trophic status indices of phosphate and/or water transparency and on the presence of bioindicators: the MundaÃ, CauÃpe and Cearà river estuaries, Maraponga lake and the Favelas, Corte and Campus do Itaperi dams as eutrophic environments; the Malcozinhado river estuary and PecÃm and Uruaà lakes as mesotrophic environments; and Jijoca lake and the Ipu and AndrÃas waterspouts as oligotrophic environment. Several bioindicators of eutrophic and/or polluted waters were recorded, in partic ular the presence of potentially toxic cyanobacteria in various ecosystems, with blooms in the Cearà river estuary and Favelas dam, while significant biomass was not recorded in other environments, even those showing a high trophic status, such as the Campus do Itaperi dam, with a Chlorophyceae bloom, and the Corte dam, with a Zygnematophyceae bloom, showing that the joint analysis of biological and physicochemical parameters of the ecosystem is of paramount importance for an appropriate environmental assessment of the health of aquatic cosystems.

Understanding the pathways of contaminant transfer within trophic networks is of paramount importance to weigh up forces driving ecological changes and to plan focused intervention strategies targeted to environmental conservation. The subject developed in this PhD dissertation aligns with this goal and encompasses the combination of different modelling approaches with experimental data to interpret the effects of bioaccumulation and bioremediation phenomena on species. Toxic agents adversely influence substance and energy fluxes at the ecosystem level affecting in turn the number of inter- and intra-specific interactions both at the community and population levels. Furthermore, the environmental stochasticity and the diversity of food webs along with the specificity of action of different bioaccumulative compounds greatly increase the complexity of this field of research. Current challenges in ecotoxicology focus on the need to find reliable predictive tools able to turn toxicity data of biota into powerful estimation methods and to asses the long-term effects of chemical exposure on species. In this context, predator-prey relationships are crucial to characterize the contamination patterns and to predict how chemicals transfer and accumulate within food webs. Food web members exhibit different levels of bioaccumulation in function of their trophic role, in a way that trophic links cannot be considered equal for all species in bioaccumulation phenomena. However, marine ecosystems are not just ensembles of macro-species, but complex multiscale networks. Microbial marine communities are metabolically involved in bioremediation processes and also represent an active compartment in the lower trophic levels of food webs. Thus, microbial degradation of persistent organic chemicals may play a key factor in changing the fate of these compounds within ecosystems and in reducing the contaminant uptake that leads to bioaccumulation in marine species. The work of research carried out during my PhD studies has been centred on the bioaccumulation and bioremediation modelling problems with specific interest on polychlorinated biphenyls (PCBs) contamination of the Adriatic food web. Notwithstanding a number of specific experimental studies on PCBs concentrations in different Adriatic species have been carried out over the last decades, to the best of our knowledge, a comprehensive PCBs bioaccumulation model for the Adriatic food web was still missing prior to the work presented in this thesis. The contributions of this PhD dissertation are structured by publication. Chapter 1 introduces the main content and includes an unpublished review of experimental PCBs concentration data in Adriatic species over the last two decades, along with an overview of the most important modelling approaches for bioaccumulation and bioremediation. In Chapter 2, we present a computational framework to model the bioaccumulation of organic chemicals in aquatic food webs, and to discover the toxic keystones, i.e. the species with a key role in the trophic transfer of contaminants. The approach is applied to reconstruct the first PCBs bioaccumulation model of the Adriatic food web, parametrized with a subset of the concentration data reviewed in Chapter 1. The framework integrates different modelling and analysis techniques, the first being the reconstruction of a trophic network from biomass data. Then, we use the estimated biomass flows and concentration data to derive the PCBs bioaccumulation network. Network reconstruction is performed using linear inverse modelling (LIM), an efficient technique for estimating food webs from empirical data. This step allows us to infer concentration values and contaminant flows for all species and remarkably, also for species with no input data associated. The estimated concentrations highlight the occurrence of PCBs biomagnification, which we show depending mainly on the trophic structure. The second main part of the framework is dedicated to the problem of identifying the toxic keystones, for which we propose the application of network analysis tools, typically employed in the trophic context. To this aim, we define a new network index, sensitivity centrality, able to capture not just direct and indirect effects in the PCBs network, but also the dynamics of bioaccumulation. Indeed, the index is based on the sensitivity analysis of a differential equation model derived from the bioaccumulation network. We compare sensitivity centrality with established network centrality indices, by evaluating the impact of successive species extinctions on global network properties, where such extinctions are performed following the importance ordering of the different indices. This analysis demonstrates that the introduced index can better identify the species with the highest impact on the total contaminant flows and on the efficiency of contaminant transport within the food web. In Chapter 3, we propose a novel computational framework of analysis to investigate multiscale effects of bioremediation processes at the ecosystem level. We integrate the bioaccumulation model presented in Chapter 2 with the genome-scale metabolic network of Pseudomonas putida KT2440 (iJN746), which we extend to simulate the aerobic PCBs degradation under arbitrary scenarios of contaminant removal. We use a reaction-based ecological/microbial network representation by combining ecological and metabolic modelling techniques, namely LIM and flux balance analysis. In this way, we describe in a unique framework PCBs flows among species, metabolites concentrations and reactions fluxes in the microbial metabolism. We investigate the tradeoff between PCBs uptake and growth of P. putida at different oxygen levels, by using a bi-level flux balance analysis approach. We study the interdependence between PCBs and toluene uptake, which is a natural degradation pathways in P. putida, by performing a phenotypic phase plane analysis. We apply this framework to study how different bioremediation strategies can impact PCBs concentration in species, thus enabling an ecosystem level analysis. Finally, we evaluate also the effect of bioremediation on indices of species centrality in the PCBs bioaccumulation network. To sum up, the aims and contributions of this PhD thesis are: Provide a review of PCBs concentration data in the Adriatic ecosystem and of modelling methods for bioaccumulation and bioremediation. Reconstruct the first PCBs bioaccumulation model of the Adriatic food web and investigate species having a central role in the trophic transfer of contaminants. Integrate the Adriatic bioaccumulation model with a genome-scale metabolic model for PCBs biodegradation in order to enable multiscale ecosystem analyses. References chapter 2: M. Taffi, N. Paoletti, P. Lia'², S. Pucciarelli, and M. Marini. Bioaccumulation modelling and sensitivity analysis for discovering key players in contaminated food webs: The case study of PCBs in the Adriatic Sea. Ecological Modelling, 2014. chapter 3: M. Taffi, N. Paoletti, C. Angione, S. Pucciarelli, M. Marini, and P. Lia'². Bioremediation in marine ecosystems: a computational study combining ecological modelling and flux balance analysis. Frontiers in Genetics, 5(319), 2014. v

Due to the complex nature of aquatic food webs, the interaction between abiotic and biotic factors that govern ecosystem dynamics is often elusive. Recent advancements in both the collection of reliable field data and the development of ecological models have enabled researchers to gain insights into these more complex interactions. In this study the relationship between physical and ecological processes has been explored by applying a process based coupled physical and ecological model (DYRESM-CAEDYM) to the data sets of three aquatic ecosystems. In the first, the role of zooplankton in the nutrient cycles of Lake Kinneret, Israel was quantified. The model was parameterized and calibrated using an extensive field data set. It was found that the excretion of dissolved nutrients by zooplankton accounted for up to 58% of phytoplankton demand and that this value varied seasonally in response to patterns of stratification and mixing. In the second ecosystem, Mono Lake, USA, results from model simulations were studied to determine the significance of the transport of nutrient rich hypolimnetic water via the benthic boundary layer (BBL) on lake productivity. Model results indicated that although on average the impact of BBL transport on Mono Lake ecology was not large, significant nutrient fluxes were simulated during periods when BBL transport was most active. The timing of these fluxes in the context of seasonal changes were found to be critical to specific aspects of food web dynamics. In the final application, the ecological gradients of the primary salt ponds of Shark Bay, Australia were studied with specific focus on the role of zooplankton as a determinant of ecosystem dynamics. Model results indicated that zooplankton grazing was responsible for reduced water column particulate organic matter and increased light available for the development of microbial mats. However, no direct 8 link between zooplankton grazing and observed changes in planktonic algal species composition or nutrient limitation across the salinity gradient of the ponds was found. Results from this study demonstrate the potential of a lake ecosystem model to extract useful process information to complement field data collection and address questions related to the relationship between physical and ecological processes in aquatic ecosystems.

The effects of pollutant burdens on natural cyclic patterns in aquatic ecosystems have been studied, to test the hypothesis that a parameter or parameters describing the pattern of variation in a single determinant, such as DO or pH, may be used to describe the status of a body of water more meaningfully than results from single spot measurements. In this study the background water quality in a Scottish and a Ghanaian lake was assessed, then rafts were built on the lakes (Myrtle Dam and Weija Lake respectively) creating three small lakes to test the effects of pollutant loads (e.g. organics and nutrients) on them. Laboratory investigations to study the behaviour of the pollutants on DO or pH cycles were carried out, and then a dynamic DO model was developed to describe the cyclic behaviour of DO. Finally, the model was used to investigate the effects of added pollutant burdens on the DO cycles. Water quality assessment of Myrtle Dam and Weija Lake by using the Weighted Water Quality Index proved that Weija Lake has doubtful quality with WQI 51, which needs improvement. Myrtle Dam WQI of 73 shows that the lake waters are unpolluted (or recovered from pollution). It is also well oxygenated at the surface and receives no toxic discharge. The raft experiments for Myrtle Dam and the Weija Lake have been used to demonstrate that, in the raft tubes, organic loadings do have effects on the oxygen cycles, and showed that there are two effects. One is that, with a small organic loading, the mean DO value dropped, then increased as the organic loading was consumed. The second is that the amplitude of the DO cycle increased as the organic loading increased from 2.5 to 5.0 mg L^-1 TOC for Myrtle Dam, and decreased for Weija Lake as the organic loading increased from 2.5 to 5.0 mg L^-1 TOC. The laboratory experiments in both Ghana and Aberdeen proved to be useful in explaining the effects of nutrients and trace elements on the DO cycles. It was evident that the higher the algal concentration, the greater was the DO cycle and 30% v/v (c.a. 254 mg L^-1 chlorophyll 'a' content ≍ 17 g L^-1 biomass aqueous algal suspension) proved to be the most suitable concentration for investigations, because, with higher organic loadings, the 100% aqueous algal suspension proved to be too concentrated and caused total deoxygenation.

This thesis presents models applicable for aquatic ecosystems. Geographical Information Systems (GIS) form an important part of the thesis. The dynamic mass balance models focus on nutrient fluxes, biotic/abiotic interactions and operate on different temporal and spatial scales (site, local, regional and international). The relevance and role of scale in mass balance modelling is a focal point of the thesis.

A mesocosm experiment was used to construct a model to estimate the nutrient load of phosphorus and nitrogen from net cage fish farming (i.e., the site scale). The model was used to estimate what feeding conditions that are required for a sustainable aquaculture scenario, i.e., a zero nutrient load situation (a linkage between the site scale and the regional scale).

A dynamic model was constructed for suspended particulate matter (SPM) and sedimentation in coastal areas (i.e., the local scale) with different morphometric characteristics and distances to the Sea. The results demonstrate that the conditions in the Sea (the regional and international scale) are of fundamental importance, also for the most enclosed coastal areas.

A foodweb model for lakes was transformed and recalibrated for Baltic Sea conditions (i.e., the international scale). The model also includes a mass balance model for phosphorus and accounts for key environmental factors that regulate the presuppositions for production and biomasses of key functional groups of organisms. The potential use of the new model for setting fish quotas of cod was examined.

For the intermittent (i.e., regional) scale, topographically complex areas can be difficult to define and model. Therefore, an attempt was made to construct a waterscape subbasin identification program (WASUBI). The method was tested for the Finnish Archipelago Sea and the Okavango Delta in Botswana. A comparison to results from a semi-random delineation method showed that more enclosed basins was created with the WASUBI method.

[Truncated abstract] Estimating internal biogeochemical fluxes is essential to the understanding of the dynamic of aquatic ecosystems. Different ecological approaches have been used to gain insight into the internal cycling, but success has been limited. A critical point is the identification of the characteristic scales of patterns and the underlying processes affecting the behaviour of biological and chemical species. Failing to capture these scales leads to misinterpretation of field and numerical data. In this study, key aspects in the design of ecological surveys are identified to ensure that the internal biogeochemical processes are well represented. In the first part of this thesis, a 1D reaction-diffusion-advection equation is used to investigate the formation of patterns and relevant time and spatial scales. This is used to define an approach for the determination of a critical domain size that allows differentiation of the role of local and internal cycling from advective fluxes across the open boundaries in a shallow coastal ecosystem. By using a 3D numerical model, in conjunction with an extensive field data set, it is shown that domain sizes must be larger than this critical value in order to capture the patterns generated within the system. For smaller domains, transport processes control the evolution of the system across the boundaries misleading the interpretation of the internal ecological dynamics. The study of the influence of boundary fluxes on ecological patchiness was motivated by the need to define the size of the domain necessary for the assessment of the impact of a sewage outflow on a coastal regime. The quantification of biogeochemical processes has proven to be difficult to achieve especially under conditions of high spatial and temporal hydrodynamic and biogeochemical variability. In the second part of this thesis, a Lagrangian experimental design is employed to estimate biogeochemical rate coefficients in situ. A set of four drogues and a cross-transect sampling design is used to capture the patchy distribution of phytoplankton and nutrient species, and high transport and mixing rates. ... Total chlorophyll from both models shows similar behavior when the variability in the 3D model, expressed as Chlamax/Chlamin, is low. When Chlamax/Chlamin is high, the difference between the biomass predicted by the two models reaches 30% due to the generation of localised patches. Comparison of the 1D and 3D results highlights the need of using models that are able to resolve the spatial complexity to some extent, as the use of averaged properties may produce misleading results. This is especially important in the presence of patches with differential physiological and biogeochemical characteristics, and nonlinear processes, in which case biomass average is not necessarily linearly related to the averaged environment.

Body size is a fundamental property of organisms that underpins the structure and function of aquatic communities. Human impacts such as climate or fishing can significantly alter the size structure of ecological communities. This thesis aimed to understand further the effect of those impacts on properties of size-based indicators in real communities, by examining trends at levels of organisation or scales that have not been studied in detail before. To do this, various quantitative approaches were developed that allowed 1) trends in size-based indicators to be decomposed into contributions of constituent parts, and 2) significance of indicators and trends in indicators to be appropriately assessed. Results revealed important features of community size structure that should be considered when assessing trends in indicators. A study of the response of body size to warming in a diatom community did not support the commonly held idea that reduced body size is a universal response to warming at either the species or community levels. Results further demonstrated that overall community trends in body size are not wholly representative of the responses of the components that made up the community. This was further supported by results from decomposing a size-based fisheries indicator, where the overall trend in the indicator was an average of wildly diverging contributions of both species and geographic locations. The methods developed also allowed finer structure of the size spectrum in the North Sea fish community to be examined, and found empirical evidence of biologically meaningful deviations in the overall size structure over time. Finally, the methods developed for assessing significance provided a useful tool for analysing the components of size-based indicators and their response to human pressures, and offer a solution for detecting significant trends in indicators calculated from trawl survey sampling data that has applications for management of marine systems.

The global increase in livestock and poultry production observed in the last decades has led to an increase in animal waste generated. The animal waste contains high levels of nitrogen and may carry antibiotics that can disturb important microbial activities such as denitrification in terrestrial and aquatic ecosystems. Disturbances of microbial denitrification can have detrimental consequences to environmental health. In the terrestrial environment, denitrification is an important source and sink of N2O, a potent greenhouse gas in the atmosphere. In aquatic ecosystems, denitrification is a dominant NO3- removal pathway, contributing to prevent eutrophication. The overall goal of this dissertation is to evaluate the impacts of animal waste and potential antibiotic exposure on microbial communities responsible for denitrification in terrestrial and aquatic ecosystems. To achieve this goal, a combined approach of measuring activity rates and performing a molecular characterization of the microbial communities was used. In Chapter 2, the microbial community changes associated with the impacts of acute antibiotic exposure on denitrification were evaluated in soil microcosms. Antibiotic exposure caused a significant increase in N2O production from denitrification. This increase was paralleled with a greater ratio of fungi:bacteria abundance and lower abundances of particular taxa with N2O reduction capacity. In Chapter 3, the impacts of animal manure and antibiotic contamination on N2O fluxes and the abundance of denitrification genes were investigated in soil mesocosms. N2O fluxes in soils treated with manure fertilizer and tetracycline were considerably higher than in control soils. The manure fertilization and antibiotic exposure had diverse effects on different bacterial taxa responsible for N2O production. In Chapter 4, the denitrification activity and microbial community structure in tidal creek sediments impacted by wastewater discharge from a poultry processing plant were evaluated through a field survey and a microcosm experiment. Denitrification rates were inhibited in the location affected by the wastewater discharge. This decrease in denitrification activity was associated with changes in the microbial community structure, such as a lower relative abundance of bacterial taxa carrying denitrification genes and lower abundance of N2O reducing bacteria. In Chapter 5, the abundance and diversity of antibiotic resistance genes were evaluated in a tidal creek impacted by wastewater discharge from a poultry processing plant. The numbers of antibiotic resistance genes were higher in the location closer to the wastewater discharge, suggesting an historic antibiotic exposure associated with the activity of the poultry processing plant. Overall, this work provides new knowledge of the impacts of animal waste and antibiotics on N2O emissions in terrestrial ecosystems and microbial NO3- removal in aquatic ecosystems. This dissertation emphasizes the functional importance of microbial communities to ecosystem health and their responses to anthropogenic disturbance.

The environmental health of aquatic ecosystems depends amongst others, on the chemical pollution coming from activities in the catchment's area. In the Swan River Estuary, Western Australia, the chemical pollutants of concern released into the river are petroleum hydrocarbons and sodium pentachlorophenate (NaPCP). Decreased water quality causes a loss of biotic diversity especially amongst fish populations. The health of aquatic ecosystems can be monitored by fish health, especially fish located at higher levels in the food chain. Pink snapper (Pagrus auratus), an endemic Western Australian fish species, was tested for its potential as a bioindicator of aquatic environmental health. This thesis presents data on the responsiveness of pink snapper to the contaminants of concern, using biomarkers such as serum sorbitol dehydrogenase (SDH), mixed function oxygenase (MFO), metabolic enzymes such as citrate synthase (CS), cytochrome C oxidase (CCO) and lactate dehydrogenase (LDH) and the histological alteration such as hepatic cell lesions (hyperplasia and hypertrophy), and glycogen and lipid droplets. The metabolic enzymes CCO and LDH as well as the hepatic MFO induction and histopathology were proven to be the most suitable biomarkers for use for routine monitoring of the Swan River Estuary using pink snapper as a bioindicator. However, CS activity and hepatic cell lesions (hyperplasia and hypertrophy) did not respond to exposure to contamination and are therefore not suited as biomarkers of effects in pink snapper. The first phase of the study aimed at investigating the responsiveness of juvenile pink snapper to an MFO inducer. Polychlorinated biphenyl isomer # 126 was selected as a model MFO inducer for this study. In the initial experiment, MFO activity was measured as a biomarker of exposure, and serum SDH activity was assessed as a biomarker of liver damage.
MFO and SDH activities were of special interest as these biochemical tools have not previously been validated for any Western Australia fish species. Juvenile pink snapper were injected intraperitoneally (i.p.) with 0, 10, 100, 500, 1000 microgram PCB-126 per kilogram. Fish were sacrificed 10 days postinjection, and liver and blood were collected for MFO and SDH analysis, respectively. Doses of 10 and 100 microgram PCB-126 per kilogram caused the highest MFO induction, while doses of 0 and 1000 microgram PCB-126 per kilogram did not result in higher MFO activity relative to carrier-injected (peanut oil) control fish. SDH activities were not significantly different among treatments indicating that hepatocellular damage was not responsible for the reduced MFO activity at the highest dose. Metabolic enzymes in pink snapper exposed by NaPCP were studied in the second phase of the experiment. The aim of this second experiment was to test the responsiveness of pink snapper to contaminants known to cause metabolic perturbations in vertebrates. Juvenile pink snapper were intraperitoneally (i.p.) injected with 0, 5, 10, 20 mg per kilogram. Oxidative enzymes were assessed by measuring CS and CCO activities and glycolytic enzyme was assessed by measuring LDI-1 activity in liver and white muscle tissues. CS activity remained unchanged in both the white muscle and in the liver. CCO activity was significantly enhanced in liver in all treated fish relative to control fish, but not in the white muscle. LDH activity was also higher in liver in all treated fish as compared to control fish, while in white muscle, LDH activity significantly increased at the highest dose injected.
The use of a suite of biochemical markers is useful in determining the effects of xenobiotic exposure of aquatic organisms, because it provides a holistic approach with biomarkers at different levels of biological organization. For the third and final phase of the study the suite of biomarkers selected were MFO, metabolic enzyme (CS, CCO and LDH) activities, and histological alternations in combination with physiological indices. The aim of this last experiment was to investigate if a modified liver metabolic activity would alter the MFO induction potential. To test if altered liver metabolism would influence liver detoxication capacities, juvenile pink snapper were i.p. injected with peanut oil (control), or pentachlorobiphenyl # 126 (PCB 126), with sodium pentachlorophenate (NaPCP), or combination of PCB 126+NaPCP. Relative to controls, ethoxyresorufin-O-deethylase (EROD) activity was induced in the PCB 126 and PCB 126+NaPCP fish, but not in the NaPCP group. In the liver, CCO activity was enhanced by the treatments while CS activity remained unchanged and LDH activity was increased in the NaPCP treatment only. In the white muscle, only the PCB 126+ NaPCP treatment enhanced CCO activity, with all other enzymatic activities remaining unchanged. Low serum sorbitol dehydrogenase (sSDH) activity and histopathology of the liver indicated no significant alteration of cellular structure, albeit the lipid droplet size was increased in the PCB 126 and in the PCB 126+NaPCP treatments.
It is concluded that the hepatic metabolic changes correspond to histopathological observations, but an altered metabolic capacity does not influence the metabolism of xenobiotics by liver enzymes, as measured by EROD activity. These experiments answered the need to identify a suitable fish species for routine monitoring of the aquatic environment in Western Australia. It also identified the most suitable biochemical markers of exposure and effects, and the suitability of the pink snapper as a bioindicator. Finally, the experiments investigated interactions between biomarkers and provided new knowledge useful to scientists using MFO and/or metabolic enzymes in field or laboratory toxicology.

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Os organismos planctônicos são a base das cadeias alimentares no ecossistema aquático e os herbívoros zooplanctônicos, em particular, são importantes para o fluxo de energia nos ecossistemas aquáticos, sendo um elo entre os produtores primários e níveis tróficos mais elevados. Este estudo se propôs a ampliar o conhecimento da herbivoria do zooplâncton sobre o fitoplâncton em uma lagoa marginal ao rio Paranapanema. Foi realizado um experimento in situ, com instalação de enclosures com paredes de polietileno fechados no fundo que permitiram a realização de quatro tratamentos: 0% da densidade natural de zooplâncton (apenas fitoplâncton), 50 % (metade da densidade natural), 100% (densidade natural) e 150% (densidade acima da natural). A variação da densidade do zooplâncton foi conseguida por meio de filtração da água por rede de abertura de malha de 50μm. Água da lagoa também foi coletada. Todos os tratamentos foram realizados em tréplica. O experimento durou 18 dias. As coletas foram realizadas a cada seis dias (quatro coletas). A temperatura foi obtida em campo e água foi coletada para análise de oxigênio dissolvido, saturação, pH, condutividade elétrica, concentrações de fósforo total, nitrogênio total, material em suspensão total, material em suspensão orgânico, material em suspensão inorgânico, clorofila-a e feofitina-a. Foram coletadas também amostras de zooplâncton e fitoplâncton que foram contadas e identificadas, normalmente, até ao nível de espécie. Rotifera teve sua abundância relativa alterada em todos os tratamentos, com o favorecimento de Keratella cochlearis e Polyarthra vulgaris provavelmente porque o enclosure as protegeu de predadores. Cladocera foi dominado em todos os tratamentos por Bosmina freyi e B. hagmanni, bioindicadores de eutrofização...
The planktonic organisms are the basis of food chains in the aquatic ecosystems, and the grazer zooplankton, specifically, are very important to energy flow in the aquatic ecosystems, being a link between primary producers and higher trophic levels. The aim of this study is enhance the knowledge of zooplankton grazing over phytoplankton in a lateral lake by Paranapanema River, Brazil. The experiment was conducted in situ, with installation of enclosures of polyetilene walls, closed at the bottom, which allowed the manipulation of four treatments: 0% of the natural density of zooplankton (phytoplankton only); 50% (half of natural density); 100% (natural density) and 150% (a higher density than the natural). The zooplankton density range was obtained by water filtration in zooplankton web with 50μm mesh. The water of the lake was collected either. All the treatments were made using three replications each one. The experiment was carried out for 18 days. The samplings were made each six days (four samplings). The water temperature was measured at field, and a water sample was collected for dissolved oxygen, saturation, pH, conductivity, and concentrations of total phosphorus, total nitrogen, total suspended matter, organic suspended matter, inorganic suspended matter, chlorophyll-a and pheophytin-a analyses. Samples of zooplankton and phytoplankton were also taken. They were counted and identified until specie level, mostly. Rotifera had its relative abundance changed in all treatments, showing the increasing of Keratella cochlearis and Polyarthra vulgaris, probably because the enclosures protected them from predators. Cladocera dominated all treatments by Bosmina freyi and B hagmanni, which are bioindicators of water euthophication. The absolute abundance of this group was the one that best responded... (Complete abstract click electronic access below)

Anthropogenic impacts such as fishing and eutrophication are significant challenges to the sustainable management of aquatic ecosystems. This study used two ecosystem modelling techniques to investigate the effects of fishing and eutrophication on aquatic ecosystems in Western Australia. Firstly, a qualitative modelling technique called ‘loop analysis’ or ‘qualitative modelling’ was used to characterise the dynamics of the seagrass ecosystem in Shark Bay, Western Australia (Chapter 2). A qualitative model based on differential equations, was developed to represent the dynamics of the seagrass ecosystem, particularly interactions among tiger sharks, megafauna (e.g. dugongs), and megafauna prey (Fig. 2.2). Although the model structure generated some uncertainty about model predictions and model stability, it was possible to assess the stability of the model and to determine the response signs of model variables by applying data and magnifying loops. Qualitative modelling analyses indicated a strong top-down control by tiger sharks and suggested that this controlling effect occurred in four stages. A step-by-step increase in tiger sharks (States 1 and 2) led to a habitat shift by the megafauna out of seagrass meadows and into safer, deeper channel habitat. A step-by-step decrease in tiger shark numbers led to the megafauna returning to seagrass meadows, leading to a decrease of megafauna prey in this habitat (steps 3 and 4). Thus, tiger sharks influenced the use of seagrass habitats by megafauna species through direct and behaviourally mediated impacts. Further, megafauna responses to tiger shark predation risk established alternating predation pressure on different prey groups within seagrass habitats. Curiously, despite the fact that only some megafauna species (e.g. dugongs) are major components of diet of the adult tiger sharks, the perceived predation risk created by the high abundance of of tiger sharks in summer appears sufficient to cause megafauna species to leave (or under-utilise) feeding habitats in seagrass meadows. Thus, the modelling results suggest that the abundance of tiger sharks exerts an important top-down, regulatory influence on the other ecosystem components. This regulatory system has the potential to become imbalanced if there is a decrease in the abundance of adult tiger sharks in Shark Bay, as has occurred tiger shark populations in other areas worldwide. Targeting of tiger sharks by fishers in the waters of Northern Australia and Indonesia has increased steadily during the last years and impact the tiger shark stock in Shark Bay if, as has been hypothesized, there is single common stock. A qualitative trophic model suggested that the activities of recreational fishermen within Shark Bay reduce prey availability for juvenile tiger sharks, an impact which might adversely affect the tiger shark population and, thus, the dynamics of this seagrass ecosystem. Evidence of the ecological importance of tiger sharks and the potential impact of a population decline emphasises the need to sustain the tiger shark population in Shark Bay. In the second part of this study, a quantitative modelling technique, Ecopath with Ecosim and Ecospace, was applied to the ecosystem of the Peel-Harvey Estuary, Western Australia. A key impact on this ecosystem is the the Dawesville Channel, an artificial entrance channel was constructed in the mid-1990s to increase the flushing and reduce nutrient concentrations in the estuary. Ecopath was used to analyse the impact of the Dawesville Channel on the estuarine ecosystem. A large dataset was collected for model development, a process that uncovered significant data gaps (e.g. missing data on detritus pool and dietary information and indicated important areas for further research (Chapter 3). Two identical Ecopath models (comprising 30 living functional groups) were otherwise developed for the Peel-Harvey Estuary to describe the state of the ecosystem before (‘pre DC’) and after (‘post DC’) the opening of the Dawesville Channel (Chapter 4). Modelling found that, in addition to changes in the community structure of plants, fish and invertebrates, the entire ecosystem of the Peel-Harvey Estuary has declined drastically in total biomass since the opening of the Dawesville Channel, as has the biomass at each trophic level and in the size of flows between the functional groups. Changes in flows and transfer efficiencies suggested a change in the functioning of the ecosystem in which consumption has become a more important and more efficient flow since the opening of the channel. Analysis of network and system statistics indicated that food web structure had also changed, with more linkages in the ‘post DC’ model and thus a more web-like structure than in the ‘pre DC’ model. Modelling also identified changes in cycling processes and suggested that the ecosystem in the ‘post DC’ model was not able to keep carbon within the system, even though: (i) the food web has developed more linkages and (ii) with less primary production and less cycling, the size of the ecosystem has decreased drastically since the channel opening. Overall, the results of the Ecopath modelling indicated that the Dawesville Channel has markedly impacted the features, functioning and services of the Peel-Harvey Estuary (Chapter 4). Several indices were applied that suggested that both the ‘pre DC’ and the ‘post DC’ models were highly immature. Ecopath was also applied to investigate the impact of the Dawesville Channel on ecosystem services. Ecopath modelling indicated that all ecosystem services had declined, such as provisioning services (catches), regulating services (CO2-Fixation) and supporting services (nutrient cycling, primary production and biodiversity). Unfortunately, it was not possible to locate data relating to cultural services (tourism) for the ‘pre DC’ model. To support the reliability of the Ecopath and Ecosim predictions, model uncertainty and the sensitivity of the parameter settings were assessed in detail (Chapter 5). Overall, the results of this analysis indicated that the parameter settings for the ‘pre DC and ‘post DC’ models were robust and did not lead to uncertainties regarding modelling results and predictions. However, the vulnerability settings are crucial for Ecosim and Ecospace and need to be treated with caution. Ecosim was applied to identify: 1) the impact and effectiveness of the selective reduction of different primary producers and 2) the impacts of fishing on target and non-target species on the ecosystem model (Chapter 6). The application of Ecosim requires fitting a model to time series data; for this study, the sourcing and fitting of time-series data indicated the importance and uncertainty of vulnerability settings. Three categories of vulnerabilities were identified: (a) vulnerabilities that did not have any effect on time series fitting (category 1); (b) interactions in which the lowest sums of squares occurred at low vulnerability settings (v=1 or 2, category 2); and settings that had a drastic impact on model fitting (category 3). The Ecosim simulations indicated that fishing affected almost all functional groups in the model, not just the target species. The recreational fishing sector also had a very strong impact on many functional groups, particularly Blue Swimmer Crabs and other invertebrate groups like bivalves and gastropods. The commercial fishing sector affected functional groups less than the recreational sector, but affected a range of estuarine fish groups including non-target fish species. Thus, the results of this study suggest that it may be not advisable to close those fleets completely as some aspects of the estuary ecosystem appear to benefit from increasing fishing pressure. Some fish groups and some target species responded positively to the closure of certain fleets, while others – particularly waterbirds and other top predators – did not (Table 6.8). Ecosim analyses highlighted the need for more data to ensure sustainable management, but suggested that the coexistence of fleets might be a better solution for sustaining catches and group biomasses in the future. Ecosim modelling indicated that selective plant removal is a reasonable management tool for this estuary. However, nutrient reduction and, thus, the permanent reduction of microscopic algae appears to be more ecologically and economically worthwhile (Fig. 6.12). Removing aquatic plant groups showed no significant longterm change in biomasses and the magnitude of short-term effects was much higher than for long-term effects. The Ecosim simulations demonstrated that only a permanent reduction in microscopic algae led to a reduction in total biomass. Reducing phytoplankton might be worthwhile because, although blooms of Nodularia spumigena no longer occur in the estuary because the salinities are too high (Huber, 1985), the estuary now contains several phytoplankton species (e.g. Heterosigma akashiwo) that cause blooms in other ecosystems (Guiry & Guiry, 2010). While the effects of phytoplankton blooms on the ecosystem depend on the size (i.e. the biomass) of the bloom, even blooms that only double the biomass of microscopic algae can have drastic long-term effects. This study supports the conclusion that a reduction in phytoplankton through management of nutrient input in the estuarine catchment represents the only ecological and economical management scenario that provides long-term sustainability for this ecosystem (Chapter 6). Ecospace modelling represents biomass dynamics over two-dimensional space and time. For this study, a model with fours habitats (shallow mud, deep sand, rocks and plant habitat) was developed. By applying Ecospace, the effects of reducing plant habitat and the effectiveness of two Marine Protected Areas were investigated, with specific consideration of waterbirds (Chapter 7). The Ecospace simulations suggested that waterbirds and piscivorous waterbirds were impacted by fishing and would benefit slightly from an introduction of a MPA, in particular a MPA at Point Grey. Further, the results of this Ecospace scenario indicated that waterbirds would profit from the reduction of plant habitat, whereas piscivorous waterbirds showed a small decline in biomass after removal of aquatic plants. Under the current fishing effort, the total biomass of the system and of the fish community increased. Thus, while the major prey groups of piscivorous waterbirds increased in biomass, but piscivorous waterbirds did not benefit from increased prey biomasses in the model, presumably because of the competition for fish. Ecospace modelling indicated that the catches would also increase drastically and, thus, that piscivorous waterbirds were in direct competition with the fishing sectors and other piscivorous predators (e.g. dolphins and sharks) and were out-competed for fish. The modelling suggest that the sustainable management of the fishing sectors is essential for bird conservation. A MPA at Peel Inlet led to lower catches under the current fishing scenario and catches declined even further under lower fishing effort. In contrast, after introducing a MPA at Point Grey, the total catch only declined when the fishing effort was lessened. The Ecospace simulations indicated that an MPA at Point Grey increased the biomasses of functional groups and target species and also raised the total biomass of the system; however, these effects strongly depend on fisheries management (Chapter 7). Overall, the qualitative and quantitative modelling methods applied in this study improved our understanding of the dynamics and functioning of the Shark Bay and Peel-Harvey ecosystems (Chapter 8). Both approaches produced robust and reliable results. If precise quantitative predictions are required for a management scenario, Ecopath with Ecosim is the appropriate method to choose, as this approach can deliver detailed changes in biomass and catches. In contrast, qualitative modelling only indicates the direction of change, which might not always satisfy management needs. However, qualitative models are the ideal method when management decisions have to be made fast and when a detailed data set of the ecosystem is not available.

Understanding the drivers and patterns of biological diversity has been a central tenet for ecologists over the past century. Aquatic ecosystems appear to be particularly sensitive to biodiversity declines and thus comprehending the causes of these biodiversity losses has become a pressing issue. The objectives of this thesis are twofold. First, I wanted to investigate the effect of phosphorus, a surrogate for productivity in aquatic ecosystems, on the diversity of two taxonomic groups across broad spatial and temporal scales. Secondly, I wanted to quantitatively assess the use of biodiversity indicators in aquatic ecosystems, with particular emphasis on the role of body size. In the first chapter of this thesis, I took a palaeolimnological approach to investigate how the species richness of subfossil diatoms and cladocera varies in response to phosphorus. From both our spatial and temporal analyses, a significant decline in species richness of diatoms and cladocera was observed as phosphorus increased. When subdivided according to habitat preference, only the littoral species richness showed a decline in species richness. We attribute this decline in species richness in the littoral taxa to the interplay of nutrients on littoral habitat heterogeneity. At low levels of phosphorus, the littoral zone is thought to be more productive and harbor a greater abundance of submerged macrophytes and is thus able to maintain a more diverse community. The second chapter of this thesis investigated the efficiency of cross-taxon congruence as a method for estimating biodiversity in aquatic ecosystems. I approached this subject by performing a spatial field study coupled to a meta-analysis of the published literature. The field survey and meta-analysis show that organisms of similar size tended to exhibit more congruent diversity patterns. I argue that this pattern arises because organisms of similar body size have similar life history traits and thus similar biodiversity responses to environmental gradients. I demonstrate that cross-taxon biodiversity indicators are most effective when estimating the diversity of communities of most similar body size. Overall, this research has expanded our understanding of patterns, drivers and similarities of biodiversity across trophic levels in aquatic ecosystems.
Au cours du siècle dernier, plusieurs écologistes ont tenté de comprendre les caractéristiques ainsi que les facteurs qui contrôlent la diversité biologique. Les écosystèmes aquatiques semblent être particulièrement sensibles au déclin de la biodiversité et donc en découvrir les causes devient alors une question pertinente. Cette thèse possède deux objectifs. Tout d'abord, je souhaite étudier l'effet du phosphore, un substitut de productivité dans les écosystèmes aquatiques, sur la diversité de deux groupes taxonomiques à travers de grandes échelles spatiales et temporelles. Deuxièmement, je désire évaluer, de façon quantitative, les indicateurs de biodiversité dans les écosystèmes aquatiques, et ce, en mettant l'emphase sur le rôle de la dimension des organismes. Dans le premier chapitre de cette thèse, j'ai utilisé une approche paléolimnologique pour étudier comment la richesse spécifique des diatomées et des cladocères fossilisés varie en fonction du taux de phosphore. Grâce à mes analyses temporelles et spatiales, j'ai noté une baisse significative de la richesse spécifique des diatomées et des cladocères avec une augmentation du phosphore. De plus, lorsque les communautés étaient divisées par leurs préférences d'habitat, seules les richesses spécifiques littorales ont démontré un déclin en fonction du phosphore. J'attribue ce déclin de la richesse spécifique dans les groupes littoraux à l'effet des nutriments sur l'hétérogénéité des habitats littoraux. À de bas niveaux de phosphore, la zone littorale est plus productive et peut accueillir de grandes abondances de macrophytes qui fournissent plus de niches écologiques pour les espèces, donc une plus grande diversité.Le deuxième chapitre de cette thèse porte sur l'utilisation de la richesse spécifique d'une communauté d'organismes pour estimer la richesse spécifique d'une autre. Cette méthode de substitution est utilisée pour estimer la biodiversité dans les écosystèmes aquatiques. J'ai abordé ce sujet en effectuant une étude spatiale jumelée à une méta-analyse des écrits. Mon analyse spatiale et ma méta-analyse illustrent que les groupes taxonomiques ayant des dimensions similaires ont tendance à présenter des patrons de diversité plus conformes. Je suppose que les organismes de tailles similaires démontrent plus de similarité en ce qui concerne leurs traits de vie et à leurs patrons de diversité lors de gradients environnementaux. Je démontre que les indicateurs utilisés pour prédire la biodiversité sont plus efficaces lorsque leurs tailles sont plus similaires. Conséquemment, cette recherche a permis d'agrandir nos connaissances des patrons, des processus et des similitudes de la richesse spécifique dans les écosystèmes aquatiques.

This thesis uses a range of different size spectra to compare contrasting benthic habitats in the aquatic realm. Temporal and spatial variation in benthic size spectra were investigated across a full salinity gradient (i.e. from freshwater, through estuarine to marine) in the River Yealm, south Devon, in order to gauge the influence of large differences in taxonomy and evolutionary history. Abundance and biomass size spectra showed a similar pattern among sites in all seasons but winter, suggesting that the size structure of benthic communities may be similar in sites with very different community compositions. A subsequent study comparing size spectra across salinity by employing artificial substrata suggested that substratum type also had little effect on the size structure of these benthic communities. A technique was developed for obtaining microbial size distributions for benthic communities and showed that microbial size structures were also similar between the marine and freshwater sites within the Yealm system. A final study demonstrated that the shape of size spectra was clearly affected by metal contamination. Size spectra across a salinity gradient -(i.e. from freshwater to lower estuary) in the highly contaminated Fal system were very different to those in the uncontaminated Yealm, due mostly to the low macrofaunal abundance in the former. This thesis is the first to assess patterns in benthic size spectra across a full salinity range in the same system. It is hoped that it will provide a base line for further studies in this exciting research area in macroecology and that biomass spectra might also prove useful as metrics for biomonitoring.

A study of fluctuating asymmetry (FA) in two species of fish; the Swan River goby (Pseudogobius olorum) and the mosquitofish (Gambusia holbrooki) was undertaken at wetlands in Perth, Western Australia. Although significant levels of FA were recorded, no clear relationships between FA and the concentrations of pollutants were found. Physicochemical stress, ecological stress and genetic factors were hypothesized to be causative factors of the FA detected. A laboratory investigation based on the experimental effects of temperature, conductivity and food availability on G. holbrooki collected from Lake Jandabup and Lake Carabooda revealed significant correlations between these factors and FA in fish from both wetlands. However, the response of FA to experimental treatments differed between fish from the two water bodies. The differing results appeared to be the result of different genetic composition arising from adaptation to differing conditions within each wetland. Multicomparison tests of FA in G. holbrooki collected from wetlands of differing pH, colour and nutrient status revealed no significant differences in FA among locations, however high levels of FA were detected in fish from Kogolup Lake, Mussel Pool, Lake Jandabup and Bibra Lake. Whether low pH or other stresses were the causative factors could not be determined. Fluctuating asymmetry appeared to be influenced by nonspecific, complex stresses occurring within the wetlands and so does not appear to be a useful bioindicator with respect to specific pollutants events. The lack of significant differences in levels of FA in G. holbrooki from Perth wetlands and those of G. affinis from heavily polluted waterbodies in Bangkok, Thailand appeared to be the result of local adaptation of the Thai fish to heavily polluted environments. However, FA in fish from the most highly polluted site in Thailand ranked most highly. In addition, the FA of fish (pooled) from all Perth wetlands was significantly lower than those of all sites in Thailand. The lack of differences of FA in G. holbrooki collected before and after an application of a herbicide (glyphosate) in the Canning River may have been due to the small pre-treatment sample size, the presence of other factors obscuring the impacts of the herbicide, or the low persistence of the herbicide in environment. Detection of high levels of FA and deformity in particular characters appeared to be a function of fitness, stage, time of development as well as low canalization of these characters. High levels of FA detected in some meristic characters appeared to be the result of low canalization. Deformities were detected in fish in the natural environment but were lower in number and level. The reasons why deformities occurred in different characters at different wetlands were not known. Possibly different stressors were present or the fish were adapted to different conditions. The finding that physico-chemical and ecological factors may have a greater influence on FA than pollutants supports the results of previous studies. Improvement in the ecological status of degraded wetlands is recommended and suggestions as to further research needed on FA as an bioindicator for developmental stability are provided.