The ecologist Garrett Hardin (1968) introduced a useful concept called the tragedy of the commons, which describes how ecological resources become threatened or lost. The term “commons” is based on the commons of old English villages and is symbolic of a resource that is shared by a group of people. If every person were to use each resource in a sustainable fashion it would be available in perpetuity. However, if people use more than their share they would only increase their personal wealth to the detriment of others. In addition, an increase in the population would mean that the size of each share would have to decrease to accommodate the larger number of people. As a result, resources are threatened by personal greed and uncontrolled population growth. Freshwater is an example of a common resource that is under threat in South Africa where the average annual rainfall is less than 60 percent of the global average (Mukheibir & Sparks 2006). The increasing demands for freshwater as well as its eutrophication are major concerns with regards to estuarine health, environmental resource management and human health. The correct management of water is necessary to ensure that it is utilised in a sustainable manner. The National Water Act (No. 36 of 1998) has provided the rights to water for basic human needs and for sustainable ecological function; the Basic Human Needs Reserve and Ecological Reserve are both provided as a right in law. The amount of water necessary for an estuary to retain an acceptable ecological status, known as the Estuarine Ecological Reserve, is determined through the implementation of procedures (rapid, intermediate or comprehensive) compiled by the Department of Water Affairs and Forestry (1999) in its Resource Directed Measures (RDM) for the Protection of Water Resources. The impact of restricted flow on estuaries can be reduced by manipulating the water released from impoundments, the regulation of water abstractions within the river catchment or both (Hirji et al. 2002). The reserve assessment method is designed to evaluate ecosystem requirements by employing groups of specialists from different disciplines. In South Africa, this includes hydrologists, sedimentologists, water chemists and biologists (including microalgae specialists). The use of microalgae in ecological assessments has largely been based on research that was initiated at the Nelson Mandela Metropolitan University (formerly University of Port Elizabeth) and subsequently at Rhodes University (Grahamstown) and the University of KwaZulu Natal (Durban). The microalgal research can be divided into two main focus areas; phytoplankton and benthic microalgae

Biodiesel from microalgae is a viable alternative for replacing the global demand for petro-diesel. High biomass and lipid production are key desirable characteristics needed in a species to be used for biodiesel production. It has been demonstrated in literature that the increase in salinity can increase the lipid content of microalgae, but lower the growth rate of a species. Therefore the effect that salinity has on the growth and lipid content of ten microalgal species, isolated from a warm temperate solar saltworks, was investigated. The microalgae were cultivated at a temperature of 22°C and at salinities ranging from 17 to 70 psu. It was found that growth and lipid production for all species were influenced to some degree by the salinity. Growth rates greater than 0.6 d-1 showed a decrease with higher salinity. Most (71 percent) of the growth rates that exceeded 0.6 per day were exhibited by cultures exposed to normal salinity (35 psu). This shift is a good indication that salinity inhibits/slows down growth and that the species in general prefer lower salinity conditions. Growth rates ranged from 0.17 ± 0.05 to 1.19 ± 0.17 d-1. Lipid content for the diatoms (2.78 ± 0.36 to 10.86 ± 4.59 percent DW) were lower than expected, whereas the lipid content for the green flagellates (3.10 ± 1.56 to 22.64 ± 1.19 percent DW) was on par with that reported in literature. To bring results into perspective a production model was developed to simulate a production scenario at the Swartkops Saltworks. Lipid and productivity results obtained in this study were used to estimate how much oil and biomass can be produced within the ponds of the Swartkops Saltworks. The model showed that although microalgae cultivation for biodiesel is technically feasible, at present it is not economically viable to do so.

An ecological reserve study by the Department of Water Affairs on the Great Brak Estuary stated that there was a need to determine how much nitrogen and phosphorus was flowing through the estuary as well as how effective the macroalgae were at removing N and P. The objective of this study was to investigate the physico-chemical characteristics in the estuary and the influence of these on the submerged macrophytes and macroalgae. A nutrient budget for the estuary was developed in order to quantify the contribution of the submerged macrophytes and macroalgae relative to other contributing sources. The Wolwedans Dam located 3 km upstream from the estuary has reduced the amount of freshwater flow to the estuary by as much as 56 percent. The estuary has been allocated 2 x 106 m3 per annum of freshwater (ecological reserve) that is used to breach the mouth once or twice a year in spring or summer. Even though this water has been made available it is not sufficient to flush the estuary. Reduced flushing has led to an accumulation of organic matter and degradation in the water quality. Physico-chemical measurements between September 2010 and July 2012 showed that dissolved oxygen values were generally below 6 mg l-1. The average NH4+ concentration in the estuary was 7 μM and increased with depth to 12 μM at 2 m depths. Concentrations >45 μM were found in February and April 2011 at the 5 m deep hole at 3.4 km upstream. Negative correlations between dissolved oxygen and NH4+ during November 2010, February 2011, April 2011 and July 2011 (r = -0.68; -0.67; -0.63; -0.96) indicated that remineralisation of organic matter had occurred. Soluble reactive phosphorus (SRP) followed a similar trend to the NH4+ and was generally below 1 μM in the water column for most months, and had peaks at 1.0 km and 3.4 km in the bottom water. The abundance of submerged macrophytes and macroalgae below the N2 bridge were mostly influenced by mouth state and river inflow. During the closed phase the dominant macroalga Cladophora glomerata had an area cover ranging from 3000 to 6000 m2 while Zostera capensis and Ruppia cirrhosa covered an area of 2000 to 3500 m2 and 1500 to 2900 m2, respectively. After an artificial breach in February 2011, water drained out of the estuary leaving the alga stranded on the marshes and as the flood tide entered the macroalga was once again redistributed in the lower reaches. The alga utilised the available nutrients in the water column and expanded its area cover from 35000 m2 in February 2011 to 64000 m2 in March 2011. However, after the floods in June 2011, Cladophora glomerata had been washed out of the system while the submerged macrophytes responded positively extending their area cover. By comparing the artificial breach with the natural breach, and the effect on the estuary, an important observation was highlighted. Increasing the current allocated ecological reserve, and using a larger volume of water to breach the mouth artificially, would result in better scouring of sediment and associated organic matter out of the estuary. This would enable better oxygenation of the water column, reduce remineralisation and minimise algal blooms.

The present study was undertaken in the temporarily open/closed Mngazi and permanently open Mngazana estuaries, located on the subtropical east coast of South Africa. The results from this research will assist decision makers in the freshwater management of these systems. Intertidal and subtidal benthic chlorophyll a concentrations, water column chlorophyll a, nutrients and several physico-chemical parameters were measured between June 2002 and November 2003. The objective of this study was to determine if the presence of freshwater in the estuaries had an effect on the microalgae of both estuaries. Five sites were sampled in the Mngazi Estuary and 14 sites were sampled in the Mngazana Estuary. The average water column chlorophyll a was significantly higher (p<0.05) in the Mngazana Estuary (surface 7.8 ± 0.7 μg.l-1, bottom 6.4 ± 0.7 μg.l-1) compared to the Mngazi Estuary (surface 4.9 ± 1.2 μg.l-1, bottom 7.3 ± 1.5 μg.l-1). There was no evidence of an REI (river-estuary interface) zone in areas where the water column chlorophyll a concentrations were high even during open mouth conditions in the Mngazi Estuary. The REI is that area where salinity is less than 10 ppt and is characterized by high water column productivity. Even though both systems received some freshwater during the summer periods, this was not enough to stimulate phytoplankton growth and nutrient availability seems to be the major factor limiting phytoplankton in these systems. Flagellates and diatoms were the dominant phytoplankton groups in both estuaries during the entire sampling session. The relative abundance of the different phytoplankton groups did not show differences between sites. The relative abundance of flagellates was in most cases greater than 60% and diatoms made up the remainder. The average benthic chlorophyll a was higher in the Mngazana Estuary (intertidal 24 ± 6 μg.g-1 subtidal 15.2 ± 3 μg.g-1) compared to the Mngazi Estuary (intertidal 15.3 ± 4.3 μg.g-1 subtidal 5.4 ± 1.6 μg.g-1). Regions with high benthic chlorophyll a concentrations had high sediment organic content. Sediment organic content was higher in the Mngazana Estuary (1 percent - 8 percent) compared to the Mngazi Estuary (4 percent – 6.8 percent). The sites situated on the Main Channel had on average significantly higher (p<0.05) benthic chlorophyll a biomass compared to Creek 1 and Creek 2 in the Mngazana Estuary. Peaks in benthic chlorophyll a concentrations occurred in the intertidal sediments in Creek 1 (50.4 ± 13.4 μg.g-1) and Creek 2 (57.4 ± 1.4 μg.g-1) in the Mngazana Estuary, the peaks occurred in winter during a period of low freshwater inflow into the estuary. Microphytobenthic biomass measured in the Mngazi Estuary is among the lowest values reported in the literature for temporarily open/closed estuaries. Statistical 4 analysis showed no significant difference between benthic chlorophyll a during the different mouth conditions and sampling sessions in the Mngazi Estuary. Microalgal responses in the Mngazana Estuary were similar to those observed in other permanently open marine dominated estuaries. In the temporarily open/closed Mngazi Estuary microalgal characteristics were different to that of other temporarily open/closed estuaries probably because the estuary was only sampled in the open and semi-closed state.

The ecological position of micro-algae at the base of the aquatic food web makes them critical components of aquatic ecosystems. Their short generation time also makes them useful biological indicators because they respond quickly to changes in environmental condition, enabling timely identification and assessment of water quality changes. The inclusion of micro-algae as indicators in water resource regulation and management in South Africa has started recently, their more extensive use in biomonitoring and ecotoxicology programmes for water resource management would contribute to the South African policy if water resource protection. The standard algal growth inhibition assay with the species Pseudokirchneriella subcapitata is currently used for monitoring toxicity of in-stream and industrial wastewater discharges to freshwater micro-algae. The relevance of the data generated by standard toxicity bioassays has been questioned, since micro-algae in particular are extremely variable in their sensitivity to a range of contaminants and these standard species used may not occur in the local aquatic environment. As a result, international regulatory agencies, have recommended algal growth inhibition tests be changed from a single standard species to tests with a number of species. One recommendation, in addition to the use of standard toxicity tests, is the use of species isolated from the local environment which may be more relevant for assessing site specific impacts. This study investigated the value and application of locally isolated South African freshwater micro-algae in toxicity tests for water resource management and was carried out in three phases. The first phase involved isolating micro-algae from South African aquatic resources. Micro-algae suitable for toxicity testing were identified and selected using as set of criteria. Three (Scenedesmus bicaudatus, Chlorella sorokiniana and Chlorella vulgaris) out of eight successfully isolated species satisfied the prescribed selection criteria and these were selected as potential toxicity test species. The second phase focused on refining and adapting the existing algal toxicity test protocol (the algal growth inhibition assay) for use on the locally isolated algal species. The refinement of the test protocol was achieved by exposing the locally isolated species to reference toxicants in order to assess and compare their growth and sensitivity to the toxicants under the prescribed toxicity test conditions with that of the standard toxicity test species (Pseudokirchneriella subcapitata) and a commercial laboratory species (Chlorella protothecoides). During this phase, one of the three local species (Scenedesmus bicaudatus) was eliminated as a potential toxicity test species due to inconsistent growth. The third phase of the study involved assessing the sensitivity of the two remaining species (C. vulgaris and C. sorokiniana) to a range of toxicants (reference toxicants, salts, effluents and a herbicide) and comparing it to that of the standard toxicity test species P. subcapitata and C. protothecoides. The toxicants were selected based on their relative importance in the South African context, as well as the practicality of using these local micro-algae to routinely determine the impact of these toxicants on local aquatic resources. The growth of the four micro-algae was stimulated by the selected effluents. The standard toxicity test species P. subcapitata was ranked the most sensitive and of the four species to two reference toxicants and two inorganic salts. Chlorella sorokiniana was ranked the most sensitive of the three Chlorella species to two reference toxicants and two inorganic salts. The herbicide stimulated the growth of C. vulgaris while inhibiting the growth of the other species. Pseudokirchneriela subcapitata and C. sorokiniana showed high intra-specific variability in growth, which made it difficult to determine the effective concentrations of the herbicide and therefore compare the sensitivity of the species. This varied response of micro-algal species to toxicants may result in the biodiversity shifts in aquatic ecosystems, and also supports the recommendation of using a battery of different species to support more informed decisions in water resource management.