Water is a scarce and precious resource in South Africa. Not only is the quality and quantity of water available limited by climatic conditions but these resources are often impacted by domestic and industrial effluents, as well as run-off from agriculture. Monitoring the aquatic environment helps to determine the impact of various pollutants. Chemical monitoring, important as it is, can only at best give a "snapshot" of water quality at a particular moment in time. Biomonitoring in particular forms a vital part of monitoring programmes as it gives a time integrated reflection of a particular pollutant or group of pollutants on the ecosystem. Although diatoms have long been studied in South Africa, as well as being used in the past to indicate water quality, the current suite of bioindicator organisms used in this country has not until recently included diatoms, or any autotrophic organisms for that matter. This body of work is presented with the aim of facilitating the use of diatoms as bioindicators of water quality in South Africa. Methods for the collection, preparation and analysis of diatoms have been collated and standardized. A number of European and other indices have been tested in diverse localities for use in indicating recent and historical water quality. The impact of diffuse mine effluent on diatom community structure has also been discussed. A new species common in impacted waters (i.e. a potential indicator species for these conditions) has been described and a guide to the common diatoms of South Africa is presented which, it is hoped, will be of use to those who wish to commence with a study of South Africa's diatom flora. The results of this study show that diatom indices are successful in reflecting both current and past water quality in South Africa. This result justifies the inclusion of diatoms with the current suite of bioindicator organisms as well as in national monitoring initiatives such as the River Health Programme. Concluding comments underline the importance of using diatoms as indicators, not only of water quality, but also as indicators of aquatic microorganism biodiversity, or loss thereof. The need for continued research in the fields of diatom ecology and taxonomy is also highlighted. / Thesis (Ph.D. (Environmental Science))--North-West University, Potchefstroom Campus, 2007.

Diatoms have been proven to be reliable indicators of water quality in many countries of the world particularly Europe. The potential use of diatoms as indicators of water quality in South Africa was tested in the studies in this document. This study evaluates the potential use of diatom based indices by testing it against a macroinvertebrate index (SASS 5) and evaluating the variation in the index scores of the two indices due to changes in chemical water quality and habitat. It was concluded that the diatom monitoring system performs well as bioindicator of water quality. It was also concluded that it should be used as a complementary system to the much used SASS 5 invertebrate index. This conclusion was made due to the fact that diatoms react more directly to changes in water quality than macroinvertebrates (SASS 5), and macroinvertebrates react more readily to changes in habitat than diatoms. A further part of the study was to assess whether aut-ecological or diversity based diatom indices performed best in South African conditions. This study found that the ecological indices were more sensitive to changes in water quality than the diversity indices. The diatom based indices that performed best as water quality indicators were the specific pollution sensitivity index (SPI) and the biological diatom index (BDI). A standard method for the sampling, preparation and enumeration for diatoms to be used for index score generation is also suggested to ensure the comparability of diatom based index data to facilitate use of such bio monitoring data for management purposes. The main focus of the study was to eliminate some of the obstacles for the use of diatoms as bio indicators of water quality in South Africa. It is believe that this aim has been accomplished in the study. / Thesis (Ph.D. (Environmental Science))--North-West University, Potchefstroom Campus, 2008.

In a semi-arid country like South Africa, the availability and quality of water has always played an important part in determining not only where people can live, but also their quality of life. The supply of water is also becoming a restriction to the socio-economic development of the country, in terms of both the quality and quantity of what is available. Thus different monitoring techniques should be put in place to help inform the process of conserving this precious commodity and to improve the quality of what is already available. Water quality monitoring has traditionally been by the means of physico-chemical analysis; this has more recently been augmented with the use of biomonitoring techniques. However, since the biota commonly used to indicate aquatic conditions are not always present in wetlands; this study tested the use of diatoms as bio-indicators in wetlands. Diatom samples were collected from thirteen wetlands in the Western Cape Province, and cells from these communities were enumerated and diatom ?based indices were calculated using version 3.1 of OMNIDIA. These indices were useful for indicating water quality conditions when compared to the measured physico-chemical parameters. In addition, most diatom species found were common to those found in riverine environments, making the transfer of ecological optima possible. The objective of the study was to provide a preliminary diatom-based index for wetlands, however, given the relatively small study area and the strong bias towards coastal wetlands it was deemed inadvisable to construct such an index, instead several indices are recommended for interim use until further research that more comprehensively covers wetlands in South Africa has been conducted. It is thus the recommendation of this study that more data is collected for comparison to other wetlands and that in the interim, indices such as SPI be applied for routine biomonitoring of these environments. / Thesis (M.Sc. (Botany))--North-West University, Potchefstroom Campus, 2010.

A Holocene lake sediment record spanning 7300 years from Wishart Lake, in the Turkey Lakes Watershed central Ontario, was produced to determine the main drivers of long-term change in the lake ecosystem. The mid-Holocene sediments are dominated by benthic diatoms, around 4000 yrs BP, diatoms in the genera Cyclotella and Tabellaria increase. Comparisons with nearby pollen records show that changes in local vegetation and diatom assemblages occurred synchronously, suggesting a response to nutrient changes caused by vegetation succession. The most recent sediments, dated using activity of 210Pb and the Ambrosia pollen rise, show increases in planktonic Cyclotella spp., particularly around the Ambrosia rise (1880 AD). Thus, the diatom changes in the recent sediments suggest a response to multiple stressors. However, due to some buffering capacity in watershed soil, recent acidification of the lake has not taken place despite nearby industrial air pollution, tracked since 1980 by an on-site monitoring program.

A Holocene lake sediment record spanning 7300 years from Wishart Lake, in the Turkey Lakes Watershed central Ontario, was produced to determine the main drivers of long-term change in the lake ecosystem. The mid-Holocene sediments are dominated by benthic diatoms, around 4000 yrs BP, diatoms in the genera Cyclotella and Tabellaria increase. Comparisons with nearby pollen records show that changes in local vegetation and diatom assemblages occurred synchronously, suggesting a response to nutrient changes caused by vegetation succession. The most recent sediments, dated using activity of 210Pb and the Ambrosia pollen rise, show increases in planktonic Cyclotella spp., particularly around the Ambrosia rise (1880 AD). Thus, the diatom changes in the recent sediments suggest a response to multiple stressors. However, due to some buffering capacity in watershed soil, recent acidification of the lake has not taken place despite nearby industrial air pollution, tracked since 1980 by an on-site monitoring program.

Graduation date: 1980

Phytoplankton dynamics and chemical characteristics of the euphotic zone were measured from 1998-2000 (an El Niño/La Niña cycle) at the 5 major stations along Line P. Near-shelf and offshore stations exhibited low seasonality in chlorophyll and moderate seasonality in particulate organic carbon (POC) production. During the 1998 El Niño, June was characterized by low chlorophyll and POC productivity due to nitrate depletion. In contrast, during the 1999 La Niña, and in 2000, higher POC productivity and nitrate occurred in June. During 1999, chlorophyll and POC productivity were similar to 1998 in late summer. Near-shelf biomass was highest in June and lowest in Feb. for the near-shelf stations. High nitrate, low chlorophyll (HNLC) stations had the highest chlorophyll in Feb. followed by June. The coccolithophore assemblage was usually numerically dominated by Emiliania huxleyi, particularly in June. Along the transect, coccolithophore abundance was much higher in June during the 1998 El Niño than in the 1999 La Niña, with Aug./Sept. abundance of both years being very low. Higher abundances were measured along the transect in June and the late summer of 2000 with sporadic ‘blooms’ of >1000 cells ml⁻¹ at some stations. Particulate inorganic carbon (PIC) production was high along the transect during June 1998, and low during both winters, June 1999 and during late summers of 1998 and 1999. There was an increase in diatom biomass and >20 µm POC production during the 1998 El Niño, specifically in the farthest offshore HNLC stations, yet diatoms were rarely found to dominate total phytoplankton biomass or production. However, there were some sporadic examples of anomalously high diatom biomass (carbon and abundance) as well as >20 µm POC production, specifically at P12 in Aug./Sept 2000. The same major diatom species were found throughout Line P (near-shelf, P16, and HNLC). Integrated silica production measured by ³²Si ranged from 0.2 to 4.7 mmol Si m⁻² d⁻¹ between 1999-2000. Silicic acid and nitrate were never limiting at all stations in Feb. and generally increased in concentration along Line P during all seasons.

The quest to discover simple, sensitive and global bioindicators of nutrient enrichment and ecological health continues. The present study is the first to address this quest in Hervey Bay by investigating links between key physico-chemical water quality parameters and two diatom forms. Free floating in the water column as phytoplankton, and attached to seagrass leaves and artificial substrates as microalgal epiphytes, diatoms are assessed for their abundance and diversity along an environmental gradient. Relationships between Secchi depth (Zsd), light attenuation coefficient (Kz) and minimum seagrass compensation depth (Zc) are established for the recovery, growth and survival of aquatic plants following disturbance, with equations derived specifically for this region to allow conversions from Zsd to Kz. These relationships allow predictions to be made and provide a management tool to meet water quality targets and combat elevated nutrient and sediment loads that result from anthropogenic activity and affect all marine life, from microalgae to marine mammals. Environmental links, identified as drivers of change to biodiversity, focus research effort and provide predictive management tools. Consequently, catchment and coastal activities such as dredging, construction and canal development, with the potential to increase nutrient and sediment loads, can be managed and scheduled at times least likely to adversely impact near shore ecosystems and therefore improve the balance between growth and sustainability. Seasonal and zone differences were significant for many of the water quality parameters monitored in Hervey Bay during 1994. Water clarity measures consistently showed significant differences between near and offshore zones (Secchi depth; P<0.01, turbidity; P<0.05 and TSS; P<0.01) as well as oxygen (P<0.01), soluble reactive phosphate (SRP, P<0.05), oxides of nitrogen (NOx, P<0.01), chlorophyll a (Chl a, P<0.01) and pH (P<0.01). Some default trigger values for water quality targets listed by ANZECC/ARMCANZ (2000) for concentrations of key indicators, a threshold for risk of adverse biological effects, were exceeded in dry and flood periods during the 1993 to 1995 survey. The community structure of phytoplankton and seagrass epiphytes were examined by monitoring changes to and 35 seagrass epiphyte species coincident with changes in some key water quality parameters along a water quality gradient. Chl a, Secchi depth (Zsd), soluble reactive phosphate (SRP) and pH were found to be the best subset of water quality parameters to maximise the rank correlation with phytoplankton communities whereas NOx and temperature maximised the rank correlation with the Halophila ovalis seagrass epiphyte communities. These parameters statistically link key water quality parameters to changes in phytoplankton and seagrass epiphyte density and assemblage structure and are supported as significant drivers of change in biodiversity research. Evidence for nitrogen limitation was found in the post flood surveys for phytoplankton and the growth and assemblage structure for seagrass systems and their epiphytes. Seasonal and zone differences in phytoplankton assemblage structure were most apparent with some site influence detected. Cylindrotheca closterium dominated the phytoplankton assemblage structure at the near shore zone while Thalassionema nitzschioides and Chaetoceros sp. differentiated the river from the Waste Water Treatment Plant (WWTP) creek site. Rhizolsolenia and Guinardia sp. were found in significantly higher concentrations at offshore sites (P < 0.01) and Thalassionema nitzschioides (P < 0.01), Thalassiosira sp. (P < 0.01) and Pseudonitzschia sp. (P < 0.05) were found in significantly higher abundance in the near shore zone A Trichodesmium bloom was examined and post flood changes to the phytoplankton assemblage structure associated with increased nutrient loads, reduced water clarity (Secchi depth, TSS and turbidity) and changes to pH and salinity were assessed. The results of analyses of variance provided support to multivariate statistical analyses to identify phytoplankton as a useful and sensitive bioindicator of environmental change. Post flood phytoplankton cell density increased and species diversity rose from 10 to 38 species at the Mary River mouth however, the changes to cell density and assemblage structure were not reflected in Chl a concentrations. The Mary River mouth experienced growth of mainly small phytoplankton species (< 20 µm) while Pulgul Creek, a source of WWTP effluent, experienced a disproportional increase in the larger phytoplankton species (>20µm). The increase in phytoplankton cell density at offshore sites occurred for both large and small species. Phytoplankton species dominance changed at each site during the postflood period. C. closterium remained the dominant species but increased from 34 to 648 cells/mL at Pulgul Creek however, C. similis, the second most dominant species was replaced by Pseudonitszchia sp., whose cell density rose from 2.0 to 320 cells/mL. A recent study also found that Cylindrotheca closterium, Skeletonema costatum, and Cyclotella choctawhatcheeana had strong positive relationships with coastal nutrients and suggested these species be used as potential reliable indicators of eutrophication (Toming and Jaanus, 2007). Some Pseudonitszchia sp. and dinoflagellate species have previously been noted as toxic and Chaetoceros sp. are associated with gill damage and fish kills. Rhizosolenia sp. and the Guinardia species G. flaccida and G. striatula, were indicators for the offshore relatively pristine sites, which may conversely, determine these species as indicators of environmental health in this waterway. Specificity of epiphyte attachment to particular seagrass species were detected and microalgal epiphyte assemblages on Halophila ovalis were identified as useful bioindicators of environmental gradients as this seagrass species is located at intertidal, shallow and deep water sites for a substantial part of the year. H. ovalis also recorded the highest average annual epiphyte loads (3873 ± 1882 cells/mm2) with the diatoms Diatoma vulgare and Cocconeis scutellum representing 19.6% and 17.2% of the total epiphyte cover. Highest cell density was recorded in autumn, followed by summer and winter: spring recorded the lowest epiphyte cover. Micro-algal epiphyte load was assessed as dry weight (g/m2), Chl a (µg/L) and cell density (cells/mm2) on artificial seagrass deployed along a water quality gradient. Equations were derived to describe percentage light transmission as a function of each measure of epiphyte load which allows transformation of data from one unit of expression to another and hence, allow comparison of past, current and future studies. Water column light attenuation was evaluated along a water quality gradient and linked to Secchi depths (Zsd) to derive equations that describe this relationship where for Hervey Bay, when Zsd < 4.26m, Kz = -1.2 ln Zsd + 1.74 and when Zsd ≥ 4.26m, Kz=1.37/Zsd. Species succession, diversity and seagrass growth were monitored for the first time during a recovery phase and limits for the seagrass compensation depth (Zc), were established on a seasonal basis for five seagrass species at four locations within intertidal, shallow and deep water zones in Hervey Bay and the Great Sandy Straits. Conceptual models for each site were constructed to describe habitat characteristics and include nutrient concentrations for SRP, NOx and ammonia (NH4+), Chl a, phytoplankton density, epiphyte density and light requirements measured as light attenuation, total suspended sediment, turbidity and Secchi depth at each location. The study provides a descriptive model for light attenuation and establishes (1) an annual and seasonal baseline water quality data set that characterises the waterways of Hervey Bay and the Great Sandy Straits (2) identification of phytoplankton species in Hervey Bay and their response to post flood changes in water quality (3) phytoplankton density and diversity along an environmental gradient with links established to Chl a, Secchi depth, SRP and pH (4) seagrass epiphyte assemblage structure along an environmental gradient with links established to NOx and temperature (5) conversion factors for epiphyte load expressed as dry weight, Chl a and cell density (6) functions to convert Secchi depth to light attenuation coeffiecients (Kz) (7) seagrass species succession at intertidal, shallow and deep water sites during a recovery growth phase in Hervey Bay (8) seagrass compensation depths (Zc) for five seagrass species at four locations and (9) habitat characterisation for seagrass recovery in Hervey Bay. Identification catalogues for phytoplankton and seagrass epiphytes were prepared with light and electron micrographs to assist future identification studies of diatoms in this region and for other similar biogeographical areas. The management of water quality to reach specific targets requires the capacity to predict seagrass compensation depth (Zc) as a function of water quality. Seasonal and annual light attenuation measurements are derived as a function of water quality at intertidal, shallow and deep water habitats during the colonisation of Zostera Capricornii, Halodule uninervis, Halophila ovalis, Halophila spinulosa and Halophila decipiens.

Mire pools – shallow water-bodies in peat-forming wetlands – are a characteristic feature of New Zealand’s subalpine and alpine landscapes (>1000 m a.s.l.), yet have been the subject of few biological studies to date, particularly of their algal communities. This research focuses on these subalpine systems, and on their diatom communities. Despite the established paradigm of ubiquitous dispersal in micro-organisms, recent taxonomic studies have confirmed a distinctive endemic component in the freshwater diatom flora of the New Zealand / Tasmania / East Australian region. In this study, I examined benthic diatom communities from >320 freshwater sites throughout New Zealand and showed that over 20% of species may be confined to this region. The endemic diatom species had highest densities in stable, unproductive environments, particularly in high-altitude mire pools and tarns. In most cases, non-endemic taxa coexisted with endemic species. This raised questions about (1) the special characteristics of mire pools and tarns (since endemism might be expected in areas that have unique environmental characteristics), and (2) the mechanisms that have allowed existing endemic taxa to withstand displacement by common cosmopolitan taxa, which, by definition, are successful colonisers. I addressed these questions using two years of data from four subalpine mire pools (Bealey Spur wetland, near Arthur’s Pass, South Island). Physico-chemical data showed that water chemistry of these pools may differ from that of many Northern Hemisphere mire systems with respect to the relationship between pH and dissolved ions (especially calcium). This may be due to a combination of high pH rainfall, high rainfall quantities that limit the acidification effects of humic substances, and possibly vegetation differences. Therefore, some endemic taxa may be confined to these habitats because of the characteristic properties of the pools. I investigated the effects of disturbances in these stable environments. In the largest pool endemic species were shown to decline as wind-induced substrate disturbance increased. Endemic species also declined in two pools following small-scale experimental substrate disturbances. In all cases, non-endemic species remained unchanged. The distinctive species Eunophora cf. oberonica was responsible for much of the observed decline in endemic species abundances, which was evidently due to destruction of their specialised habitat within the cyanobacterial mats that made up the pool substrates. I explained pool-specific responses of diatom communities to disturbances by drawing on recent theory of invasibility as an intrinsic environmental property. I further investigated species coexistence by examining several general patterns of interspecific coexistence described for macroscopic organisms (e.g., abundance – occupancy, abundance – persistence). Patterns in mire-pool diatom communities were generally similar to those in larger organisms, and did not differ with respect to geographical range size (endemics vs. non-endemics), except at the scale of single pools. At this scale, endemic taxa, in particular E. cf. oberonica, can persist as dominant species. All the community analyses were underpinned by detailed taxonomic studies, from which I assessed over 40% of the more common species in the pools to be either endemic or likely to be endemic. Two species occurring in the study area are formally described as new species. Overall, this work highlights the vulnerability of this hidden component of New Zealand’s biodiversity to disturbances and environmental changes.

Thesis (Ph. D.)--Ohio State University, 2006. / Title from first page of PDF file. Includes bibliographical references (p. 211-226).