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.

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 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

Traditional public health bacterial indicators of water quality and the Biolog�� system were evaluated to compare their response to other indicators of stream condition with the state of Oregon and between ecoregions (Coast Range, Willamette Valley, Cascades, and Eastern Oregon). Forty-three randomly selected Oregon rivers were sampled during the summer low flow period in 1997 and 1998. Testing included heterotrophic plate counts (HPC), total coliforms, fecal coliforms, E. coli, and Biolog�� GN plates. Statewide, HPC correlated strongly with physical habitat and chemistry indicators while fecal coliforms and E. coli were highly correlated only with the river chemistry indicators. Total coliform bacteria did not correlate with either of the above environmental indicators. Dividing the sites by ecoregion, Eastern Oregon was characterized by high HPC, fecal coliforms, E. coli, nutrient loads, and indices of human disturbance, whereas the Cascades ecoregion had correspondingly low counts of these indicators. The Coast Range reflected statewide results and the Willamette Valley presented no consistent indicator pattern. Attempts to separate ecoregions with the Biolog system were not successful nor did a statistical pattern emerge between the first five principle components and the other environmental indicators. Our research has shown that traditional public health microbial indicators may, however, be useful in measuring the effects of anthropogenic stress over large spatial scales. / Graduation date: 2000

The Environmental Monitoring and Assessment Program (EMAP) site selection protocol was used to generate a random sample of streams throughout the state of Oregon. One hundred and forty-six selected streams were sampled during the summer, low-flow period of 1997. Traditional microbial public health indicators, including heterotrophic plate counts (HPC), total coliforms (TC), fecal coliforms (FC) and E. coli, were enumerated using the membrane filtration technique. Nearly 17% (3.4-23.6%, 95% C.I.) of streams exceeded the current state of Oregon standard for water-contact recreation. Levels of bacteria were also shown to differ significantly by ecoregion. The Cascades ecoregion had low levels of all types of bacteria. The Willamette Valley, Columbia Plateau and Snake River Basin had high levels of one or more groups of bacteria measured. Twenty-six sites were resampled and FC and E. coli estimates were not significantly different for the different sampling dates. Biolog GN plates were used to provide a measure of the functional diversity of microbial communities for the same streams as above. Two groups were formed based on inoculum density and Biolog GN plates were analyzed using principal component analysis (PCA). The first few principal components explained nearly half of the variation of the data in both groups. Principal components were correlated with the average carbon source utilization, levels of coliform bacteria, and ecoregions. These results indicate that patterns produced by Biolog GN plates may be useful in the assessment of ecological condition of freshwater streams. Subsequent publications will explore the relationships between the pattern of substrate utilization of Biolog GN plates with other indicators of ecological function. / Graduation date: 1999

Thesis (doctoral)--Swedish University of Agricultural Sciences, 2004. / Thesis documentation sheet inserted. Appendix reproduces three papers and manuscripts co-authored with R.K. Johnson and two papers co-authored with R.K. Johnson and L. Sandin. Includes bibliographical references. Also issued electronically via World Wide Web in PDF format; online version lacks appendix.

Thesis (M.S.)--Eastern Illinois University, 2009. / Includes bibliographical references (leaves [117]-125).

M. Tech. Water care / Free-living amoebae are important predators that feed on bacteria, fungi and algae by phagocytosis. However, a number of bacteria have become resistant to, and are able to survive, grow and exit Free-living amoebae. Free-living amoebae are ubiquitous organisms that have been isolated from various man-made and environmental water systems. Some of these free-living amoebae host amoeba-resistant bacteria such as Legionella spp. Vibrio cholerae and Mycobacterium species which are regarded as human pathogens. The objective of this study was to establish amoebal enrichment and co-culture techniques in order to isolate and identify amoebae and amoeba-resistant bacteria from seeded and environmental water samples. The aim of the study was to introduce and establish amoebal co-culture and amoebal enrichment techniques in South Africa, to provides South African laboratories with baseline information on the efficiency of culture-based methods as well as analytical requirements like incubation temperature, media preparation and storage conditions for amoebal enrichment and co-culture techniques for the detection and isolation of amoebae and amoeba-resistant bacteria from environmental water systems.