Ph.D. / South Africa is the highest produce-producing and therefore the highest pesticide consumer on the African continent. Although greatly beneficial to the industry, indiscriminate and over usage of these agrochemicals pose a risk to the aquatic ecosystems through non-point source pollution. Data on these risks are limited in the developing countries such as Africa since limited environmental monitoring of pesticides is undertaken. This is due to technical, logistical and economical constraints in determining the links between exposure and effect on non-target organisms. Methods that are able to screen for and monitor pesticides that could pose a risk according to site-specific scenarios are therefore necessary. Economical and easy-to-use predictive models incorporated into Preliminary Risk Assessments (PRA’s) are useful in this regard and have been developed and applied globally to assist in estimating the probability of risks of pesticides associated with aquatic ecosystems. Currently no such risk assessment model is applied in South Africa for this purpose. The main aim of the present study was to present and assess the suitability of selected PRA models as preliminary screening tools for estimating potential pesticide exposure and associated effects within aquatic ecosystems. To achieve this, the primary objectives were to apply and validate these models for assessing predicted risks and to relate these to actual ecological hazards by monitoring the exposure and effects of selected pesticides that were identified as potentially posing a risk. It was hypothesised that the data determined by these models would elucidate the association between potential risks of pesticides and actual environmental impacts and could therefore be applied and validated for South African conditions. A framework was thus developed using multidisciplinary approaches to predict the risks of agricultural pesticides to non-target aquatic organisms and to validate these risks in an area known to have a high pesticide usage, namely the Crocodile (west) Marico catchment. This area is representative of a typical farming community in the subtropical central area of South Africa. It is a catchment area that exhibits high urban and agricultural usage, which has compromised the overall ecological integrity of the aquatic systems. The focus of the study was on the Crocodile (west) and Magalies Rivers and the associated irrigation canal network systems. The present study was based on integrating multidisciplinary techniques following the implementation of a tiered approach for assessing the ecological risks of selected pesticides known to be used within the Crocodile (west) Marico catchment. Tier 1 starts with the PRA assuming a relatively worst-case scenario by identifying pesticides most commonly used (through surveys) and estimating exposures posing a potential risk to the aquatic environment using the PRIMET (Pesticide Risks In the tropics to Man, Environment and Trade) model. The second tier can establish a more realistic characterisation of risk for the pesticide application scenarios of interest by using models such as PERPEST (Predicting the Ecological Risks of PESTicides), PEARL (Pesticide Emission Assessment of Regional and Local Scales), TOXSWA (TOXic substances in Surface Waters), or SSDs (Species Sensitivity Distributions). Higher tiers then include comparing the results from the PRA model predictions to the actual hazards of pesticides and can determine if these risk models are valid under South Africa conditions. This can be achieved using a combination of laboratory- and field-based monitoring assessments in the form of a triad approach (using chemical, toxicological and ecological assessments) to construct several lines-of-evidence (LoEs). The risk assessment process ends with a summary and integration of the data based on the multiple LoEs gathered during monitoring using a weight-of-evidence (WoE) approach.

The Reserve concept, introduced in the National Water Act, has led to an increasing use of biomonitoring techniques to assess the current ecological status of rivers in South Africa. The ecological status of a river provides vital information necessary to establish the amount and quality of water needed by the aquatic ecosystem. If the amount and quality of water is inadequate, then the water resource will not be able to provide the necessary goods and services to their respective water users. The biomonitoring of rivers gained impetus with the establishment of the River Health Programme (RHP) and its various objectives. The RHP led to the development and refinement of a range of biomonitoring indices to assess various components of the aquatic ecosystem. The components used to assess the current ecological status of a river include the physical habitat, riparian vegetation, water quality, as well as the macro-invertebrate and fish communities. The Mvoti River, in the vicinity of Stanger, is subjected to extensive water abstraction, which is then utilised for irrigation, industrial use, urban water requirements and various domestic uses by informal settlements. Previous studies on the river indicated that it is in a severely degraded state, especially below the confluences of the Nchaweni and Mbozambo rivers. Thus, this assessment of the current ecological status of the Mvoti River was undertaken to possibly identify the main causes of the degraded state. The study was undertaken during the high (February) and low flow (August) periods in 2005. Selected monitoring sites included sites used in previous studies on the Mvoti River as well as sites on the Nchaweni and Mbozambo tributaries. The methodology for this study was to implement the various indices used in the RHP for the different ecosystem components. The habitat indices implemented in this study were the Habitat Quality Index (HQI) and Integrated Habitat Assessment System (IHAS). Physicochemical water analyses were done during each sampling period to assess the water quality against the South African Water Quality Guidelines. The biotic indices used included the South African Scoring System 5 (SASS5) index to assess the macro-invertebrate community and the Fish Assemblage Integrity Index (FAII) to assess the fish community. Additionally, the newly developed EcoStatus indices for the fish and macro-invertebrate communities were implemented on the available fish and macro-invertebrate data. These indices were developed mainly to be used in Reserve determination assessments, where the assessments are built around the integration of all ecosystem components into a single value for the ecological status. The fish index is termed the Fish Response Assessment Index (FRAI) and the macro-invertebrate index the Macro-invertebrate Assessment Index (MIRAI)…. Multivariate statistical analyses were performed on the water quality as well as the macroinvertebrate and fish communities to establish any temporal and spatial trends together with any dominating water quality variables responsible for species composition at the different sites. PRIMER and CANOCO computer software were used to construct hierarchical clusters and NMDS plots for the biotic communities, while RDA and PCA bi-plots were used to represent the water quality variables and their effects on the biotic community structure. The Mvoti River is in a seriously degraded state and this degradation was particularly evident during the low flow period below the Sappi Stanger mill and the Stanger Sewage works effluent discharge points. The degraded state of the river is caused by the multitude of impacts on the river, which includes the local land-use, upstream land-use and effluent discharges in the vicinity of Stanger. The water quality in the vicinity of Stanger was in a poor state during the low flow, while the high flow was only slightly better. The upstream site is in a fair condition but, after the Nchaweni and Mbozambo rivers enter the Mvoti River, the water quality decreases. The variables found to be problematic included microbiological variables, chlorides and electrical conductivity in the Mvoti River. High nutrient values were found together with very high electrical conductivity in especially the Nchaweni River tributary. The lower Mvoti River contains very little habitat of good quality to support the biotic communities. The habitat is generally degraded due to the destruction of the riparian zone and the dominance of alien vegetation in the form of reeds. This, together with land-use and water abstraction activities, has caused high sediment loads in the lower Mvoti River which are continually moving. The IHAS and HQI results indicated the habitat in the lower Mvoti River is in a modified condition. The statistical analysis of the macro-invertebrate data showed that a definite spatial variation existed while no significant temporal variation was identified. There is a difference in the community structure between the Mvoti River and its tributaries, with the tributaries containing a very poor diversity. This lowered species diversity was attributed to the effects of, specifically, chlorides on the community structure but the origin of the chlorides could not be linked specifically to the Sappi Stanger mill’s activities. The SASS5 was similar with the Mvoti River sites having slightly higher scores, placing it in either a B or C class while most of the tributaries had a Class D. The community structure in the tributaries responded to nutrients and chlorides and these variables reduced the numbers of sensitive species and allowed hardy taxa to flourish. The results of the MIRAI index provided the same categories as identified by the SASS5 index. The fish community structure showed the same spatial differences identified in the macroinvertebrate communities, with the tributary sites containing different community structures than those found in the Mvoti River. The Mvoti River fish community is in a modified state with the majority of fish sampled being tolerant with very few sensitive species present. The FAII scores for the Mvoti River was a Category C, while the tributary sites scored a Category D or lower. The fish community is affected by the poor water quality, habitat and flow modifications in the lower Mvoti River. The FRAI index provided the lower Mvoti River and its tributaries with the same categories as identified with FAII. Overall, the Mvoti River is in a seriously degraded state with even the reference site being subjected to impacts that could potentially be harmful to the ecosystem. The ecological state of the river decreases as it moves past Stanger and is subjected to the impacts from the Nchaweni and Mbozambo rivers in the form of nutrients and salinity concentrations. The impacts on the Mvoti River have a multitude of different sources and if the aquatic ecosystem is to improve, only a collective effort will be of any value. / Prof. V. Wepener

M.Sc. / Water resources in South Africa are scarce and need to be protected and managed in a sustainable way for future generations. Food supply is a great priority worldwide and the pressure to produce enough food has resulted in the expansion of irrigation and the steadily increasing use of fertilizers and pesticides to achieve higher yields. Rivers are impacted by agriculture through increased suspended sediment loads (which affects primary production, habitat reduction and introduction of absorbed pollutants), elevated nutrient inputs (which may increase the abundances of algae and aquatic plants), salinization and pesticide runoff (which eliminates species intolerant to these conditions and therefore impacts on the normal production of the river system). Aquatic biota plays an integral part in the functioning of aquatic ecosystems. Biological monitoring is used to assess ecosystem health and integrity. Biological communities reflect the overall integrity of the river ecosystem by integrating various stressors and therefore provide a broad measure of their synergistic effects. The research area falls within the Lower Vaal Water Management Area (WMA), which lies in the North-West and Northern Cape Provinces. The lower Vaal River and the Harts River (one of the tributaries of the Vaal) are the river systems under investigation in this study. Farming activities ranges from extensive livestock production and rain fed cultivation to intensive irrigation enterprises at Vaalharts (such as maize, cotton and groundnuts). The Vaalharts is the largest irrigation scheme in South Africa. Salinity is of concern in the lower reaches of the Harts- and Vaal Rivers, due to saline leachate from the Vaalharts irrigation scheme. Agricultural inputs are known to affect aquatic communities and chemicals (e.g. pesticides, herbicides, fertilizers) are extensively used in the Vaalharts irrigation scheme. At present there are no data on the effect of these chemicals on the aquatic biota of the lower Harts- and Vaal Rivers. The aims of this study were to assess the diatom- and macroinvertebrate community structures, ecosystem integrity and macroinvertebrate feeding traits (functional feeding groups – FFGs) in relation to land use.

No description available.

Devido à importância do uso de bioindicadores para avaliação da qualidade ambiental e às vantagens do emprego de macroinvertebrados bentônicos para este fim, estes organismos foram utilizados para avaliar a qualidade da água da bacia do alto Atibaia (SP) em oito pontos de amostragem: 3 no rio Atibainha, 3 no rio Cachoeira e 2 no rio Atibaia. Foram amostrados o canal, a margem deposicional e a margem erosional, sendo coletadas três unidades amostrais em cada ambiente de cada ponto, com auxílio do amostrador Hess (rede de 500 μm e área de 678,9 cm2) ou pegador Petersen modificado (área de pegada de 325 cm2). Foram coletadas amostras de sedimento com pegador Petersen modificado em aço inox para análise de granulometria, resíduos totais, voláteis e fixos e umidade. Este trabalho está dividido em três capítulos. No primeiro, a análise da fauna evidenciou que os pontos de cabeceira e à jusante dos reservatórios dos rios Atibainha e Cachoeira tenderam a apresentar riqueza e diversidade menores que os pontos de localização intermediária. Já nos pontos situados no rio Atibaia, a fauna respondeu à deterioração da qualidade da água, refletindo um gradiente ambiental. No segundo capítulo, visando à utilização de técnicas de avaliação rápida para facilitar a análise e interpretação de dados, foram aplicadas vinte e uma métricas biológicas. Dentre todas as métricas testadas, as que evidenciaram o gradiente ambiental presente na bacia estudada, com restrito coeficiente de variação no ponto referência foram riqueza e diversidade de famílias, densidade total, riqueza de EPT e ETO, porcentagem de Táxons de Diptera (exceto Tanytarsini) e não insetos, BMWP “JUNQ” e IBBJ. No terceiro capítulo, com a finalidade de contribuir para a elaboração de um plano de monitoramento de avaliação rápida para a bacia do Alto Atibaia (SP), concluiu-se que, com a metodologia empregada, a margem erosional seria o habitat que melhor corresponderia à media ou somatória para o ponto, pelo menos durante o período de estiagem. / Due to importance of the use of bioindicators to assess environmental quality and the advantages of employing benthic macroinvertebrates for this purpose, these organisms were used to assess the water quality of the Atibaia river basin (SP) in eight sites: 3 in the Atibainha river, 3 in the Cachoeira river, and 2 in the Atibaia river. Channel, depositional margin and erosional margin were sampled. Three replicates were collected in each habitat using a Hess sampler (678.9 cm2, 500μm mesh) or modified Petersen grab (325 cm2). Sediment samples were collected with a stainless steel modified Petersen grab for analysis of granulometry, humidity and total, volatile and fixed residues. This study is divided in three chapters. In the first, the fauna showed that headwater and downstream reservoir sites of Cachoeira and Atibainha rivers presented lower richness and diversity than intermediate sites. In the sampling sites of the Atibaia river, the fauna responded to the water quality decline, reflecting an environmental gradient. In the second chapter, aiming the utilization of rapid assessment techniques to facility data analysis and interpretation, twenty one biological metrics were applied. Metrics that evidence the environmental gradient of the basin, with restricted variation coefficient, were richness and diversity of families, total density, richness of EPT and ETO, percent of Diptera taxa and noninsects, BMWP “JUNQ” and IBBJ. In the third chapter, aiming to contribute to the development of a rapid assessment monitoring plan for the Atibaia river basin, according to the methodology employed, it was concluded that the erosional margin was the habitat that showed the best correspondence with the average or sum of the sites, at least during the dry season.

Devido à importância do uso de bioindicadores para avaliação da qualidade ambiental e às vantagens do emprego de macroinvertebrados bentônicos para este fim, estes organismos foram utilizados para avaliar a qualidade da água da bacia do alto Atibaia (SP) em oito pontos de amostragem: 3 no rio Atibainha, 3 no rio Cachoeira e 2 no rio Atibaia. Foram amostrados o canal, a margem deposicional e a margem erosional, sendo coletadas três unidades amostrais em cada ambiente de cada ponto, com auxílio do amostrador Hess (rede de 500 μm e área de 678,9 cm2) ou pegador Petersen modificado (área de pegada de 325 cm2). Foram coletadas amostras de sedimento com pegador Petersen modificado em aço inox para análise de granulometria, resíduos totais, voláteis e fixos e umidade. Este trabalho está dividido em três capítulos. No primeiro, a análise da fauna evidenciou que os pontos de cabeceira e à jusante dos reservatórios dos rios Atibainha e Cachoeira tenderam a apresentar riqueza e diversidade menores que os pontos de localização intermediária. Já nos pontos situados no rio Atibaia, a fauna respondeu à deterioração da qualidade da água, refletindo um gradiente ambiental. No segundo capítulo, visando à utilização de técnicas de avaliação rápida para facilitar a análise e interpretação de dados, foram aplicadas vinte e uma métricas biológicas. Dentre todas as métricas testadas, as que evidenciaram o gradiente ambiental presente na bacia estudada, com restrito coeficiente de variação no ponto referência foram riqueza e diversidade de famílias, densidade total, riqueza de EPT e ETO, porcentagem de Táxons de Diptera (exceto Tanytarsini) e não insetos, BMWP “JUNQ" e IBBJ. No terceiro capítulo, com a finalidade de contribuir para a elaboração de um plano de monitoramento de avaliação rápida para a bacia do Alto Atibaia (SP), concluiu-se que, com a metodologia empregada, a margem erosional seria o habitat que melhor corresponderia à media ou somatória para o ponto, pelo menos durante o período de estiagem. / Due to importance of the use of bioindicators to assess environmental quality and the advantages of employing benthic macroinvertebrates for this purpose, these organisms were used to assess the water quality of the Atibaia river basin (SP) in eight sites: 3 in the Atibainha river, 3 in the Cachoeira river, and 2 in the Atibaia river. Channel, depositional margin and erosional margin were sampled. Three replicates were collected in each habitat using a Hess sampler (678.9 cm2, 500μm mesh) or modified Petersen grab (325 cm2). Sediment samples were collected with a stainless steel modified Petersen grab for analysis of granulometry, humidity and total, volatile and fixed residues. This study is divided in three chapters. In the first, the fauna showed that headwater and downstream reservoir sites of Cachoeira and Atibainha rivers presented lower richness and diversity than intermediate sites. In the sampling sites of the Atibaia river, the fauna responded to the water quality decline, reflecting an environmental gradient. In the second chapter, aiming the utilization of rapid assessment techniques to facility data analysis and interpretation, twenty one biological metrics were applied. Metrics that evidence the environmental gradient of the basin, with restricted variation coefficient, were richness and diversity of families, total density, richness of EPT and ETO, percent of Diptera taxa and noninsects, BMWP “JUNQ" and IBBJ. In the third chapter, aiming to contribute to the development of a rapid assessment monitoring plan for the Atibaia river basin, according to the methodology employed, it was concluded that the erosional margin was the habitat that showed the best correspondence with the average or sum of the sites, at least during the dry season.

It is unclear whether accounting for the number of rare taxa or differentiating live (cells with visible chloroplasts) and dead (empty cells) diatoms would enhance the accuracy and precision of diatom-based stream bioassessment. My dissertation research examines whether the number of rare taxa and percentage (%) live diatoms can be used as indicators of human disturbance in streams/rivers. To address my objectives, I analyzed two datasets collected at different spatial scales. The large scale dataset was collected over the course of five years and included more than 1300 sites and over 200 environmental variables from 12 Western US states (US EPA's Environmental Monitoring and Assessment Program). The small scale dataset included 25 streams from the Oregon Coast Range. My findings revealed that rarity definition is important in bioassessment. Rural taxa richness (number of taxa with high occurrence and low abundance) was the only rarity metric that distinguished least disturbed (reference) sites from the most disturbed (impacted) ones. Neither of the other two rarity metrics, satellite (taxa with low occurrence and abundance) and urban (taxa with low occurrence and high abundance) taxa richness, was able to do that. Results from regression tree analysis revealed that rural taxa richness increased with human disturbance, but it was significantly higher at impacted sites only in the Mountains ecoregion (t-test, p0.05). Percentage live diatoms distinguished reference from impacted sites only in the Mountains ecoregion (t-test, p=0.02) and somewhat in the Plains (t-test, p=0.05). However, % live diatoms exhibited opposite patterns in the two ecoregions. They increased with disturbance in the Mountains and decreased in the Plains. The results from the small scale study in the Oregon Coast Range revealed similar species compositions between live and live+dead diatom assemblages (non-metric multidimensional scaling) and similar relationships with their environmental variables (linear fitting). Both assemblages correlated well with in-stream physical habitat conditions (e.g., channel dimensions, substrate types, and canopy cover). Both rural taxa richness and % live diatoms can be used as indicators of human disturbance in streams/rivers, especially in the Mountains ecoregion, dependent on specific assessment objectives.

The utilisation of rainwater tanks and bore wells are very common in many parts of rural Australia and Papua New Guinea. In Australia, on-site collection and storage of potable water for domestic use is carried out by approximately 30.4 percent of the rural population while 90% of the population in Papua New Guinea access water from on-site collection and storage of potable water. Few studies have monitored the quality of such water supplies on a seasonal and event associated basis. The aim of this study was to evaluate the microbiological and physio-chemical properties of the on-site domestic water supply systems and various factors that may influence characteristics of the water. It aimed to evaluate the relationship of microbiological and physio-chemical characteristics in the water supply systems. 14 rainwater tanks, 4 bore well and 10 reticulated water supply sites in Hawkesbury District, NSW Australia were investigated. Characteristics of the sites physical situation and natural environmental condition were considered to be similar to on-site water supply situations in Papua New Guinea. The results and techniques of the study will be used as a model in Papua New Guinea in the assessment of water quality issues. As the study showed that the quality of water in rainwater tanks was below WHO guideline recommendations on numerous instances, it was proposed that water treatment and maintaining the cleanliness of roof catchments, gutters and tanks should be addressed for domestic use systems. A protocol for sampling, assessment and data interpretation of faecal indicator bacteria populations in domestic catchment supply systems was developed and demonstrated / Master of Science (Hons)

Rapid bioassessment techniques used for aquatic macroinvertebrate and plants in wetlands were tested in New South Wales, Australia. Wetlands surveyed ranged from coastal wetlands in the North and Central parts of the State, to tableland wetlands west of Sydney. Wetlands varied in dominant vegetation, hydrology, substrate and level of human impairment. Different options for sampling (mesh size, live-picking times, quadrat size, number of samples or quadrats) and analysis (taxonomic resolution, transformations, biotic indices, multivariate and univariate analyses) are compared to determine optimal sampling effort and evaluate the effects of errors or variability. Results show that, for wetlands of New South Wales, sampling procedures developed and tested in streams and other regions of Australia may not be the most efficient. Using the data from 21 wetlands in New South Wales, a number of analytical techniques were evaluated for the effects of errors. Results show that species-level multivariate analysis is more sensitive in detecting less obvious differences between wetlands (i.e., small effect sizes), while family-level analyses are more appropriate for large effect sizes. A modified waterplant index was developed that is simpler and has a wider application than the other Australian options available. Inherent problems in each index tested were addressed. The results show that the process of summarising a large amount of information into a single value will result in the loss of both information and variability between samples and this cumulative effect of error may effect the assessment of wetland condition. The practical outcome of this thesis is a set of standardised steps to assess wetland quality using biological assemblages. The results show that protocols and indices for rivers are not directly transferable to palustrine, vegetation dominated wetlands. I present protocols that are more appropriate to wetlands and recognise that each protocol would need to be adapted for each wetland type. Despite the need for flexible protocols, I promote the need for a standard approach to wetland sampling and the need for consideration of the effects of errors in sampling designs. This study highlights the need for more research on the response of specific stressors to wetlands flora and fauna. The results from this study also show that wetland macroinvertebrates and plant communities can be used as surrogates in multivariate analyses for detecting large differences between wetlands (wetland types) but that impact assessment requires more detailed investigations including species identification and careful consideration of the choice of reference and control sites. In conclusion I emphasise the need for scientific rigour in the use of biological indicators and consideration of the effects of errors and implications to sampling designs. / Doctor of Philosophy (PhD)

The focus of this research was to develop bacterial community indicators of stream sanitary and ecological condition. The first study compared substrate utilization patterns between centrifuged and uncentrifuged split samples. We found a shift in the relative proportion of each group of bacteria following centrifugation, with a marked increased in the fecal coliform group and relatively fewer heterotrophic and total coliform bacteria. Centrifuged samples consistently responded faster and oxidized more substrate than did their uncentrifuged counterparts. Substrate utilization patterns of centrifuged sub-samples from 19 sites showed better separation between Willamette Valley and Cascade ecoregions than did the uncentrifuged sub-samples in ordination space. We recommend developing microtiter plates with substrates specific types of environmental stress. The second study determined the minimum volume of water needed and the maximum time and temperature that bacteriological water samples captured on a membrane filter can be held in guanidine isothiocyanate buffer (GITC) prior to DNA extraction for community fingerprint analysis. We found 100 ml water samples yielded more information than the 50 ml or the 250 ml water samples and observed a marked decrease in information for samples that were held at room temperature for more than 24 hours. We concluded that 100 ml samples were optimal for bacterial community DNA fingerprint analysis. Furthermore, we recommended transporting filtered water samples held in GITC on ice and keeping the samples frozen until DNA is extracted for further analysis. The third study addressed questions of sampling error and response variability of two PCR-based indicators, bacterial community-level Terminal-Restriction Fragment Length Polymorphisms and Bacteroidetes ruminant and human specific fecal source tracking markers. We found the T-RPLP and Bacteroidetes markers to show very little sampling error, and suggested collecting a single 1-liter water sample. A high turbidity scenario resulting in higher fecal pollution and lower bacterial species richness explained why decreased TRF richness was strongly associated with high fecal coliform density, turbidity, and human Bacteroidetes detection. We propose that in times of increased turbidity, a disturbance in the bacterial community occurs, reducing bacterial richness and increasing a few types of stress-resistant fecal bacteria. / Graduation date: 2004