Thesis (MSc)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: A 2010 Food and Agriculture Organization (FAO) report indicated that 85% of the world´s fish stocks overexploited. This highlights the importance of commercial aquaculture as a sustainable alternative to capture fisheries. Growth rates for international aquaculture production are slowing, although an average annual increase of 12.6% occurred in Africa between 1970 and 2008. Sub-Saharan Africa accounted for 0.50% of the total world aquaculture production in 2008. The South African aquafeed industry recognized the need for aquaculture research in alternative feed ingredients to ensure a more sustainable future. With routine use of antibiotics in aquaculture, antibiotic resistance have emerged, and novel strategies are needed. Currently, alternative feed ingredients and practical substitution of antibiotics are two of the major challenges faced in aquaculture. The use of plant proteins is preferred over animal proteins such as fish meal. By developing sustainable aquafeeds, that have both nutritional and health benefits, the gastrointestinal tract (GIT) microbiota of the host should be considered. The fish GIT is an open system and acts as a route of infection for pathogenic bacteria. A comparative study was done to determine the structure of the GIT microbiota in Mozambique tilapia (Oreochromis mossambicus) and rainbow trout (Oncorhynchus mykiss). Tilapia and trout are important freshwater aquaculture species in South Africa. Tilapia is a warmwater herbivorous fish with a long coiled GIT, whereas trout is a coldwater carnivore and its GIT is short and compartmentalized. Tilapia was reared in recirculation systems with lower water pH and trout in flow-through systems with higher water pH. Tilapia diets consisted of plant-based protein, whereas trout diets contained animal-based proteins. To understand the role of the autochthonous bacteria in the GITs of these fish, we determined community structure along the length of the respective GITs. A highly reproducible DNA fingerprinting technique, automated ribosomal intergenic spacer analysis (ARISA), was used that targeted the intergenic spacer region (ITS) in bacteria. Community analysis based on operational taxonomic units (OTUs) was used to statistically compare the microbiota in different segments. The different GIT compartments in trout also showed distinct bacterial community structures. However, the degree of variation between identical segments between different fish was shown, and consequently, individual microbiotas was not seen. ARISA was further used to determine if formulations containing dietary phytogenics will modify the GIT microbiota. The GIT of fish plays a role in food digestion, while the resident GIT bacteria are important contributors to disease control and nutrient utilization. During two feeding trials tilapia was fed 16 and trout six different diets. Microbial diversity was lower in the GIT of tilapia as compared to trout and no significant shifts in community structure were detected in both species. With a high-throughput DNA sequencing technique, we followed a metagenomic approach to classify the autochthonous microbiota of tilapia and trout on a phylogenetic level. Pyrosequencing was used to define a core microbiota that would enable comparative feeding studies to be carried out. The proposed microbiota of tilapia consisted of genera from the Proteobacteria (5), Firmicutes (1), Actinobacteria (1), Fusobacteria (1) and Cyanobacteria (2). The microbiota of trout comprised genera of the Proteobacteria (3), Firmicutes (3) and Actinobacteria (1). Three genera from the Proteobacteria were common in tilapia and trout, confirming the dominance of this group in the GIT of freshwater fish. The variability and distribution of Lactobacillus in the GITs of both species was determined. Culturing of lactic acid bacteria (LAB) from the GIT of tilapia proves to be difficult and this was confirmed by the low-abundance of particularly Lactobacillus. A number of other LAB genera were identified that confirmed LAB as part of the autochthonous microbiota in freshwater cultured fish. The detection of secondary bacterial fish pathogens as part of the resident microbiota was also established. The use of 454 pyrosequencing in this study, gave a deeper insight into the structure of bacterial communities in the GITs of tilapia and trout. This research is novel and based on our knowledge, the first study to determine the core microbiota in two South African aquaculture species. Data based on community diversity and structure can be used as a basis for further studies. One important study would be to determine the effect environmental stressors would have on the core microbiota. / AFRIKAANSE OPSOMMING: Volgens `n 2010-verslag van die FAO (Food and Agriculture Organization) is 85% van die wêreld se visbronne oorbenut. Dit beklemtoon die belangrikheid van kommersiële akwakultuur as `n alternatief tot visvangste. Internasionaal neem die groeitempo van akwakultuur produksie af, alhoewel groei in Afrika tussen 1970 en 2008 jaarliks met `n gemiddeld van 12.6% toegeneem het. In 2008 was lande suid van die Sahara verantwoordelik vir 0.50% van die wêreld se akwakultuur produksie. Die Suid-Afrikaanse akwavoer industrie het die behoefte raakgesien vir akwakultuur navorsing in alternatiewe voerbestanddele om 'n meer volhoubare toekoms te verseker. Die roetine gebruik van antibiotika in visboerderye het bygedra tot die ontstaan van weerstandbiedende organismes, en daarom is nuwe strategieë nodig. Tans is alternatiewe voeding en die praktiese vervanging van antibiotiese stowwe belangrike uitdagings in akwakultuur. Die gebruik van plantaardige proteïne in viskos word verkies bo dierlike proteïene soos vismeel. Deur die ontwikkeling van volhoubare viskos, wat beide voedingswaarde en voordele vir die gesondheid van visse inhou, moet die mikrobiota in die spysverteringskanaal (SVK) van die gasheer oorweeg word. Die SVK van visse is `n oop sisteem en dien sodoende as `n infeksie kanaal vir patogeniese bakterieë. `n Vergelykende studie is uitgevoer om SVK mikrobiota struktuur te bepaal in Mosambiek tilapia (Oreochromis mossambicus) en reënboogforêl (Oncorhynchus mykiss). Tilapia en forêl is twee belangrike varswater spesies in Suid-Afrikaanse akwakultuur. Tilapia is `n warmwater herbivoor met `n lang, gekronkelde SVK. In teenstelling is forêl `n kouewater vis met `n kort SVK, wat uit verskillende segmente bestaan. Tilapia is in hersirkulasie waterstelsels met `n lae pH gekweek terwyl forêl in deurvloei waterstelsels met `n hoër pH gekweek is. Tilapia diëte het plantaardige proteïne bevat tewyl forêl diëte proteïne vanaf dier-afkoms bevat het. Om die rol van SVK bakterieë beter te verstaan is populasie struktuur bepaal langs die lengte van die SVK. Geoutomatiseerde ribosomale intergeniese spasie analise (ARISA) is `n herhaalbare DNS vingerafdruk tegniek wat die intergeniese spasies gebied (ITS) in bakterieë teiken. Analise gebaseer op operasionele taksonomiese eenhede (OTEs) is gebruik om die mikrobiota van SVK segmente statisties te vergelyk. Die SVK kompartemente in forêl het ook duidelike bakteriële populasie strukture getoon. `n Groot variasie tussen identiese segmente van verskillende vise is waargeneem en individuele mikrobiota kon nie uitgesonder word nie. ARISA is gebruik om die effek van plantaardige dieet formulasies op die SVK mikrobiota te toets. Die SVK van visse speel `n rol in voedselvertering, terwyl die natuurlike SVK bakterieë `n belangrike rol speel in siektebeheer en die benutting van voedingstowwe. Twee voedingsproewe is op tilapia en forêl uitgevoer, met onderskeidelik 16 en 6 verskillende diëte,. Mikrobiese diversiteit was laer in die tilapia SVK in vergeleke met die SVK van forêl en geen beduidende verskuiwings in populasie struktuur is in beide visse waargeneem nie. `n Hoë deurvloei DNS-volgorde bepalings tegniek, gekombineer met `n metagenomiese benadering is gebruik om die mikrobiota van tilapia en forêl op `n taksonomiese vlak te bepaal. “Pyrosequencing” is gebruik om `n kern microbe populasie te identifiseer ten einde vergelykende studies te vergemaklik. Die voorgestelde kern mikrobiota in tilapia het bestaan uit genera van die Proteobakterieë (5), Firmikute (1), Aktinobakterieë (1), Fusobakterieë (1) en Sianobakterieë (2). Die voorgestelde kern mikrobiota van forêl het bestaan uit genera van die Proteobakterieë (3), Firmikutes (3) en Aktinobakterieë (1). Drie genera van die Proteobakterieë het algemeen in tilapia en forêl voorgekom, wat die oorheersing van hierdie groep in die SVK van varswatervisse bevestig. Die veranderlikheid en verspreiding van Lactobacillus in die SVKs van beide visse is bepaal. Dit is moelik om melksuurbakterieë (MSB) uit die SVK van tilapia te isoleer en `n lae voorkoms van Lactobacillus is waargeneem. Ander MSB genera is ook geïdentifiseer wat MSB as deel van die plaaslike mikrobiota in varswater gekweekte visse bevestig. Verder is daar ook vasgestel dat sekondêre patogene deel uitmaak van die plaaslike mikrobiota. In hierdie studie het 454 “pyrosequencing” `n dieper insig gegee oor die struktuur van bakterie-populasies in die SVK van tilapia en forêl. Hierdie navorsing is oorspronklik en volgens die literatuur die eerste studie wat `n kern mikrobe populasie in twee Suid-Afrikaanse akwakultuur spesies waargeneem het. Data wat gebasseer is op populasie diversiteit en struktuur kan gebruik word as basis vir verdere studies. Een so `n studie kan die effek van omgewings stresfaktore op die kern mikrobiota in hierdie vise bepaal.

During the last decades marine aquaculture has steadily expanded and diversified to include a wider range of commercial species. Despite the intense effort towards understanding the biological requirements of farmed species, several issues remain to be addressed. Mariculture success is restricted by a number of production bottlenecks including limited seed supply, caused mainly through a combination of compromised productivity in broodstock paired with high mortalities during the early life stages. Productivity and survival success is often dependent on the successful recreation of natural environmental conditions. While in a commercial setting a concerted effort is generally made to simulate key environmental stimuli there remains a lack of understanding of the significance of many potential signals. The overarching aim of this thesis was to investigate the effects of some of the overlooked environmental stimuli on fish performance in enclosed facilities and where possible relate this to the natural setting from which the species have been removed. The studies contained in this text are focused on the effects of anthropogenic noise, light spectral composition and substrate on the performance of broodstock and juvenile development of two valuable commercial marine species Atlantic cod (Gadus morhua) and turbot (Scophthalmus maximus). The aim of Chapter 3 was to test if artificial sound can act as a stressor in Atlantic cod and thereafter to examine if chronic sound disturbances can compromise broodstock spawning performance in land-based facilities. Results showed that anthropogenic noises in a land-based marine farm are within the auditory thresholds of cod and other fish species. Juvenile cod exposed to 10 min of artificial noise (100-1,000 Hz) from 10 to 20 dB 1 re µPa above background sound levels presented a typical acute stress response with a 4 fold elevation of plasma cortisol levels within 20 min, with a return to basal levels after 40 min, while the intensity of the stress response (in terms of amplitude and return to normal levels) appeared to be correlated to the noise level applied. When a similar artificial noise of 35 dB 1 re µPa above background sound level was applied to a broodstock population daily on a random schedule during the spawning season, it significantly impacted on reproductive performances in comparison to a control undisturbed population with notably a reduction in fertilisation rate that correlated with increased egg cortisol contents. Overall, these studies confirmed, for the first time, that artificial noise mimicking anthropogenic sounds generated in marine land-based facilities trigger a typical acute stress response if a similar sound exposure is then applied in a chronic manner it resulted in reduced broodstock spawning performances. Overall this work provides novel evidence on the potential of anthropogenic noise to act as stressor in fish. The possible implications for both captive and wild stock are discussed. In chapter 4 the effects of light spectrum and tank background colour on Atlantic cod and turbot larval performance from hatch until the end of metamorphosis were investigated. In both species larvae exposed to shorter wavelengths (blue and green spectrums) showed significantly enhanced growth in terms of standard length, myotome height, eye diameter and condition factor in comparison to larvae exposed to longer wavelengths (red). Larvae performances in the colour background experiment differed between species. Atlantic cod larvae reared in a red tank background displayed the best growth and survival, while larvae in blue tank background had a significant positive effect on final survival rate. In contrast, turbot larvae survival rates were the highest in the red tank background colour with the lowest growth parameters, while larvae in the blue tank background displayed the best growth. In both species, white tank background colour resulted in the lowest final survival rate. These results highlight the biological relevance of light spectrum and background colour in marine larvae performance and survival, demonstrating the importance of considering the light composition of the light units used in the hatcheries for larval rearing. Subsequently in chapter 5 the effects of light spectrum in juvenile turbot growth, appetite, stress response and skin pigmentation were investigated. Two sets of experiments were performed with post-metamorphosed (1 g) and on-growing (100 g) turbot. Results demonstrated that short wavelength treatments had a significant positive effect on growth parameters (total length and wet weight), food intake and feeding response. Light treatments caused a positive correlation between plasma glucose and cortisol levels with significant differences between the short and long wavelength treatments. Skin pigmentation was affected by the light treatments, showing a relationship between wavelength and brightness (negative) and darkness (positive). Blue light treatment resulted in brighter and lighter skin colouration, while red light had the opposite effect: darkening of the skin. Overall these results confirm that turbot juveniles performance is enhanced by exposing them to a similar photic environment than the one from the natural ecological niche. Light spectrum intervenes in skin pigmentation and the possible mechanisms behind the variations are discussed. In general chapter 5 provides background knowledge of the possible implications of light spectrum in fish juveniles performance and possible commercial applications. The final two experimental chapters turned focus back on the optimisation of broodstock environmental management and subsequent effects on their productivity. In Chapter 6 the importance of crepuscular light simulation was investigated in Atlantic cod broodstock spawning performance. No significant impact could be observed in terms of egg production and quality in association with dawn/dusk simulation compared to abrupt lights on/off. This suggests, at least for Atlantic cod, that crepuscular light simulation is not a key factor affecting spawning performance during the spawning window. The possible implications of twilight on gamete quality prior ovulation are discussed. In Chapter 7 the effect of a “breeding nest” containing a substrate (i.e. sand) in turbot broodstock spawning performance was investigated. Behavioural observation recorded active occupancy of the nests with the suggestion of social structuring as specific individuals (females) occupied the nest preferentially. However no fertilised, naturally released eggs were collected from the overflow during the spawning seasons. This would suggest that the presence of a nest is not enough to induce natural spawning behaviour in turbot in itself however the elective occupancy suggests that nests and/or their substrate was a physical enrichment that was valued by the fish which should be explored further. Overall the studies contained in this thesis highlight further the importance of considering noise and light as crucial environmental factors in marine aquaculture. Results from the different chapters offer a possible application within the enclosed facilities that might contribute to the success of the industry. Present findings contribute towards the understanding of the effects of environmental signals in fish and provide further insight to guide further lines of research on the involvement of light spectrum on fish physiology.

Thesis (PhD)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: Aquaculture has proven to be a viable operation in multi-used irrigation reservoirs (also referred to as farm dams) in the Western Cape province (WCP) of South Africa. Many studies found that the fitness-for-use of these reservoirs for both net cage culture of fish and irrigation of crops is feasible. However, practising intensive fish farming in existing open water bodies can increase the nutrient levels of the water through organic loading, originating from uneaten feeds and fish metabolic wastes. Under such conditions the primary (irrigation) and secondary (drinking water and recreation) usage of the dam could be compromised by deteriorating water quality. Rainbow trout (Oncorhynchus mykiss) farming is done in Mediterranean climatic conditions of the WCP. This type of climate presents short production seasons with fluctuating water quality and quantity. The study investigated the dynamics of water physico-chemical parameters and assessed the long term impact of rainbow trout farming on irrigation reservoirs. Furthermore, associated land-use in the catchment of such integrated aqua-agriculture systems is described, and mitigation to minimise the impact of fish farming evaluated. The investigation concluded with assessing the contribution of aquaculture to rural and peri-urban communities. The aim is to present an integrated, socio-ecologically balanced farming system for irrigation reservoirs with associated aquaculture activities. A total of 35 reservoirs, including both fish farming and non-fish farming ones, were selected as research sites. They were located in three geographical regions namely, Overberg (Grabouw/Caledon), Boland (Stellenbosch/Franschhoek) and Breede River (Ceres/Worcester). Reservoirs were <20 ha in surface area and the volume ranges from 300 000 to 1 500 000 m3. Water samples were collected monthly and seasonally for the different investigations and analysed for a range of water quality parameters, including: transparency (Secchi disc), temperature, dissolved oxygen (DO), pH, sodium (Na), potassium (K), calcium (Ca), magnesium (Mg), iron (Fe), chloride (Cl), carbonate (CO3), bicarbonate (HCO3), manganese (Mn), copper (Cu), zinc (Zn), boron (B), total phosphorous (TP), orthophosphate (PO4), total ammonia nitrogen (TAN), nitrate-nitrogen (NO3-N), nitrite-nitrogen (NO2-N), aluminium (Al), total suspended solids (TSS), total dissolved solids (TDS), alkalinity, hardness and sulphate. Phytoplankton samples were also collected, genera identified and biomass calculated. The water quality data were analysed in terms of surface and bottom strata in both fish farming and non-fish farming reservoirs based on repeated measurements at the same site location at different times using the procedure General Linear Models of Stastical Analysis System (SAS, 2012). Values p<0.05 were considered as statistically significant. A Principal Component Analysis (PCA) biplot was used to graphically depict all the sites and measured water quality variables with the purpose of trying to see whether the fish farming and non-fish farming ones showed any groupings and how the sites were related to the measured variables. Structured questionnaires and informal discussions were used to collect additional information on the water use, production data and socio-economic effects on fish farmers. Categorical data gathered from the interviews (21 aquaculture projects) were analysed for frequency of occurrence using the Statistical Product and Service Solutions (SPSS) computer programme (SPSS Systems for Windows, Version 12.0). Results are presented in publication form with research chapters focusing on the subject areas of water quality impact, catchment land-use, potential mitigation measures and aquaculture contribution. Results for the water quality analyses indicated that as a collective, the farm reservoirs’ overall minimum, mean and maximum values for the physico-chemical parameters were fit-for-use for trout farming. The depth of the reservoirs ranged from 1.2 - 21.6 m with the low value taken during the summer season. Values lower than 5.0 m can cause management problems for floating cages that require a minimum of 4.0 m for net suspension and 1.0 m of free space below for adequate lateral flow. The Secchi disc reading of the reservoirs ranged from 10 – 510 cm. Higher transparencies were recorded after the winter rains when sand, silt and clay settled. Trout feeding is dependent on visibility and transparencies of more than 50 cm are required for good feeding conditions. The dissolved oxygen (DO) ranged from 0.3 – 16.4 mg/L with values below 5.00 mg/L recorded during summer when extraction and temperatures were high and provided conditions unable to sustain trout farming. The situation reverses with the onset of winter when the dams fill and DO rises above 5.00 mg/L as required for trout farming. The phosphorous (P) levels ranged from 0.001 – 0.735 mg/L. Higher concentrations were recorded during the winter turnover phase when bottom and surface waters mixed. Concentration above 0.01 mg/L can cause eutrophication of the water bodies. Total ammonia nitrogen (TAN) ranged from 0.015 - 6.480 mg/L. Higher concentrations were recorded during summer when temperatures were high and depths were low. TAN can be toxic to fish when the pH and temperature are high. The generally low least square means (LSM) for TAN were indicative of minor environmental impact of trout farming operations conducted during the colder, winter rainfall months. Trout farming coincided with conditions where the water temperatures were low, dam levels were high and dams were overflowing. The difference in bottom and surface water quality of reservoirs and the site location were found to be more important than the absence or presence of fish farming. The difference in bottom and surface water is directly linked to the ecological status of the sediment, which serve as nutrient sinks. In monomictic dams found in Mediterranean areas, mixing occurs during the winter turnover phase. Nutrients are released due to surface and bottom water mixing, brought about by torrential rains and wind turbulence. The concentration of organic material in the sediment and bottom waters is a function of the nutrient loading over time, irrespective whether the non-point sources were fish farming or agricultural activities and therefore it is difficult to partition causes and effects. In cases where reservoirs were already eutrophic due to past agricultural practices, implementing aquaculture could exacerbate the poor water quality status of the reservoir. There was a statistically significant difference between fish farming and non-fish farming for phosphorous, Secchi disc, total suspended solids and nitrite-nitrogen (p<0.05) and no statistically significant difference between fish farming and non-fish farming for dissolved oxygen, total ammonia nitrogen and nitrate-nitrogen (p>0.05). There was a statistically significant difference between surface and bottom waters for P and TAN (p<0.05). One reason for higher P and TAN concentrations in bottom waters is the accumulation of both in the sediment and subsequent release in the water column when the water mixes. A two-dimensional scatter plot was generated using the score for the first two principal components. The first two principal components accounts for 40 and 17 % of the total variance respectively, and the two groups of fish farming and non-fish farming did not separate well based on the first two principal components. The occurrence and distribution of phytoplankton biomass fluctuated with dam water levels and nutrient concentrations. The prevailing phytoplankton communities are important to fish farmers for two reasons: 1. It leads to fluctuations in dissolved oxygen concentrations via users (respiration and decomposition) and producers (photosynthesis). 2. It could lead to algal taint of fish flesh when geosmin-producing phytoplankton species are present. The frequency of occurrence indicated that the Group Chlorophyta (including genera, Chlamydomonas, Closterium, Oocystis, Scenedesmus, Staurastrum, Tetraedron, etc) had the most occurrences (n=371) with Chrysophyta (including genera, Dinobryon, Mallomonas, Synura, etc) the least (n=34). There was a statistically significant difference between genera occurrence and season (p<0.05). The geographical location of sites had no significance influence on the frequency of phytoplankton occurrence. There was no direct link between water quality and production yield (p>0.05). The fish yield of farms were linked mainly to the quality of fingerlings and the feed conversion ratio (FCR) achieved (p<0.05). Land-use patterns in the catchment where fish farming dams were located have shown that the dams are multiple-used systems. The ecological integrity of the farm dam ecosystem is dependent on the base volume. The dam is primarily for irrigation and fish farming can be compromised when higher demand for water is required during the dry season. The dams receive about 20 % of its water from rainfall and the rest from runoffs. Farmers could not provide accurate extraction rates making it difficult to predict water levels for future fish production. Four potential mitigation measures to reduce nutrient loading were described namely, feed management (quantity, frequency, type, etc.), feeding method (demand feeders, hand feeding), feed ingredients (formulation) and floating gardens. Both feed management procedures and demand feeders were evaluated as to the efficiency of reducing feed wastage and optimising FCR’s. The small-scale fish farmers were producing approximately 6 tons and had an average FCR of 1.96:1 ± 1.15. If farmers could improve their FCR’s by 0.1 (i.e. from 1.96 to 1.86), it would translate into a reduction of 100 kg feed for every ton of fish produced and result in 5% decrease in nutrient loading. The results of the water analysis and visual assessment of faecal length and colour showed no statistically significant difference between treatments for the guar-gum based binder (p>0.05). In addition, the level of binder did not influence digestibility of the experimental diets. The floating garden study indicated that it was feasible to construct a low cost raft system that is easy to manage and can produce plant crops as a hydroponic system in conjunction with fish farming cages. The lettuces grown on farm dam water provided support for the premise that the water quality can be improved via extraction of nutrients for crop production. For the production of 3.5 kg/m2 lettuce, a ratio of 1.09 plants/fish equal to 1.84 g feed/day/plant would reduce the accumulation of soluble nutrients around floating net cage farming system. The socio-economic evaluation of the contribution of fish farming to the welfare of rural and peri-urban farming communities supported the notion that aquaculture can lead to the upliftment of participating communities. Seventy-one percent (71%) of the respondents indicated that their motivation for exploring aquaculture is to supply fish to the wholesale market in order to generate income. Sixty-one percent (61%) of the respondents conducted the sales themselves or co-opted family members to assist them. The contribution of aquaculture provided direct benefits through improvement in household income, subsistence food supply and skills development. Indirect benefits included providing an information hub for other emerging farmers, elevation of the fish farmer’s status in the community through greater wealth and knowledge creation and promoting sector diversification through new products and technology. The three main constraints to the promotion and growth of aquaculture were listed as lack of government support, insufficient market intelligence and access, and limited choice in the availability of suitable candidate aquaculture species. Irrigation reservoirs in the WCP have a history of enrichment through external sources supplying water via agricultural runoff (fertilisers and pesticides), catchment runoff (leaf litter and organic debris) and stormwater effluent (grey and black water). The incorporation of aquaculture into such dams adds extra nutrients to the water column and management is crucial to limit the nutrient loading and ensure environmental sustainability. Such an approach will ensure that commercial land-based crop farmers’ irrigation regime and water distribution operations would not be negatively affected. Therefore future research needs should focus on; firstly the prevention and minimisation of pollution deriving from aquaculture through improved production management and technology transfer, secondly the monitoring and evaluation of the catchment ecosystem as a continuum with all the external factors affecting the ecology of farm dams and thirdly, evaluating the sediment processes and dynamics as sinks for nutrient accumulation. / AFRIKAANSE OPSOMMING: Akwakultuur het getoon dat dit ‘n lewensvatbare inisiatief is vir meerdoelige-gebruik van besproeiingsdamme (ook genoem plaasdamme) in die Wes-Kaap provinsie (WKP) van Suid-Afrika. Vele studies het bewys dat die geskiktheid-vir-gebruik van die reservoirs haalbaar is vir beide visproduksie sowel as besproeiing van landbougewasse. Nieteenstaande, die beoefening van intensiewe visboerdery in bestaande buitelug watersisteme kan lei tot ‘n toename in nutriëntvlakke van die water as gevolg van organiese belading afkomstig van ongevrete voere en metaboliese afvalstowwe van die vis. Onder sulke omstandigthede kan die primêre- (besproeiing) en die sekondêre (drinkwater en rekreasie) gebruik van die dam in gedrang kom weens ‘n afname in waterkwaliteit. Reënboogforel (Oncorhynchus mykiss) boerdery word beoefen in die omliggende Mediterreense klimaat van die WKP. Die tipe klimaat verskaf kort produksie-seisoene met wisselvallige water kwaliteit en kwantiteit. Die studie het die dinamika van water se fisies-chemiese parameters ondersoek en het die impak van forelboerdery op besproeiingdamme oor die langtermyn beskryf. Verder het die studie die geassosieerde landgebruik in die opvangsgebied met geïntegreerde akwa-landbou sisteme beskryf, asook moontlike toetrede (mitigasie maatreëls) geëvalueer wat die impak moontlik kan verlaag. Die ondersoek is afgesluit deur die bydrae wat akwakultuur lewer aan landelike en semi-stedelike gebiede, te beskryf. Die hoofdoel is die daarstelling van ‘n geïntegreerde, sosio-ekologiese gebalanseerde sisteem vir besproeiingdamme met gesamentlike akwakultuuraktiwiteite. ‘n Totaal van 35 besproeiingsdamme, insluitend die met visboerdery en nie-visboerdery, is gekies as navorsingspersele. Dit is hoofsaaklik geleë in drie geografiese gebiede naamlik, Overberg (Grabouw/Caledon), Boland (Stellenbosch/Franschhoek) en Breederivier (Ceres/Worcester). Die reservoirs is almal < 20 ha in oppervlakarea en die volumes het gewissel van 300 000 – 1 500 000 m3. Watermonsters is maandeliks sowel as seisoenaal versamel vir die onderskeie ondersoeke en ontleed vir ‘n reeks van parameters, insluitend: sigbaarheid (Secchi disc), temperatuur, opgeloste suurstof (OS), pH, natrium (Na), kalium (K), kalsium (Ca), magnesium (Mg), yster (Fe), chloor (Cl), karbonaat (CO3), bikarbonaat (HCO3), mangaan (Mn), koper (Cu), sink (Zn), boor (B), totale fosfor (TP), ortofosfaat (PO4), totale ammoniak stikstof (TAN), nitraat-stikstof (NO3-N), nitriet-stikstof (NO2-N), aluminium (Al), totale gesuspendeerde vaste stowwe (TGV), totale opgeloste vaste stowwe (TOV), alkaliniteit, hardheid en sulfate. Phytoplanktonmonsters is ook versamel, genera geïdentifiseer en die biomassa bepaal. Die waterkwaliteitsdata is ontleed in terme van oppervlak- en bodemstrata vir beide visboerdery en nie-visboerdery reservoirs en was gebaseer op herhaalde metings by dieselfde perseel op verskillende tye deur gebruik te maak van die Algemene Liniêre Model van Statistiese Analitiese Sisteem (SAS, 2012). Waardes p<0.05 is oorweeg as statisties beduidend. ‘n Hoofkomponentanalise bi-stipping (HKA) is toegepas om die persele en veranderlikes grafies voor te stel en te bepaal of die visboerdery en nie-visboerdery s’n enige groeperinge vorm asook hoe die persele assosieer met die veranderlikes. Gestruktureerde vraelyste en informele besprekings is onderneem om inligting in te samel op watergebruik, produksie-data, en die sosio-ekonomiese invloed wat akwakultuur bied aan visboere. Kategoriese data wat deur die onderhoude (21 akwakultuurprojekte) ingesamel is, is ontleed vir die frekwensie van aanwesigheid deur die gebruik van Statistiese Produk en Dienste-oplossings (SPDO) rekenaarprogram (SPSS Systems for Windows, Version 12.0). Die resultate vir die verskeie ondersoeke is beskryf en saamgestel in publikasie-vorm met die navorsingshoofstukke wat gefokus het op die areas van waterkwaliteitsimpak, opvangsgebied landgebruik, toetrede-meganismes en die bydrae van akwakultuur. Die resultate vir die waterkwaliteitsanalises het getoon dat gesamentlik die reservoirs se oorhoofse minimum, gemiddelde en maksimum waardes vir die verskillende fisies-chemiese parameters geskik is vir forelboerdery. Die diepte van die reservoirs het gewissel van 1.2 - 21.6 m, met die laagste waarde aangeteken gedurende die somermaande. Waardes laer as 5.0 m kan bestuursprobleme vir drywende hokstelsels versoorsaak want ‘n minimum van tenminste 4.0 m vrye spasie onder die hokke word benodig vir voldoende laterale vloei. Die Secchi-skyf lesing (sigbaarheid) van die reservoirs het gewissel van 10 – 510 cm. Hoër sigbaarheidswaardes is aangeteken na winterreëns wanneer sand-, slik- en klei deeltjies uitgesak het. Forel voer op sig en sigbaarheid van > 50 cm word benodig om goeie voeding te handhaaf. Die OS het gewissel van 0.3 – 16.4 mg/L met waardes onder 5 mg/L aangeteken gedurende somer wanneer wateronttrekking en temperature hoog was. Dit het gelei tot ongunstige toestande vir forelboerdery. Die situasie swaai om met die begin van winter wanneer die damme vol reën en die OS bo 5 mg/L styg soos benodig vir forelboerdery. Die P-vlakke het gewissel van 0.001 – 0.735 mg/L. Hoër waardes is aangeteken gedurende die winteromkeerfase wanneer die bodem en oppervlak se water meng. Konsentrasies bo 0.01 mg/L kan tot eutrofikasie van watersisteme lei. TAS het gewissel van 0-015 – 6.480 mg/L. Hoër konsentrasies is aangeteken gedurende die somer wanneer temperature hoog is en damvlakke laag. By hoë pH’s en temperature kan TAS toksies wees vir vis. The algemene lae kleinste kwadaat gemiddelde (KKG) waarde vir TAS het getoon dat daar ‘n klein impak op die omgewing was wanneer forelboerdery bedryf word gedurende die koue, winter reënvalmaande. Forelboerdery val saam met omstandigthede wanneer die watertemperature laag is, damvlakke hoog en die reservoirs oorloop. Die verskil in die bodem- en oppervlak water in die besproeiingsdamme en die ligging van die perseel is vasgestel om meer belangrik te wees as die teenwoordigheid of afwesigheid van visboerdery. Die verskil in die bodem en oppervlak is toe te skryf aan die toestand van die sediment waar nutriënte kan opgaar. In monomiktiese damme soos gevind in Mediterreende areas, vind vermenging plaas gedurende die winteromkeerfase. Nutriënte word vrygestel a.g.v. die vermenging van die oppervlak en bodem se water wat dan veroorsaak word deur harde reën en windturbulensie. Die konsentrasie van organiese materiaal in die sediment en bodem water is ‘n funksie van die nutriëntlading met tyd, ongeag of dit afkomstig was vanaf visboerdery of landbou-aktiwiteite. Dit is dus moelik om die spesifieke oorsaak van besoedeling af te baken. In gevalle waar die reservoirs alreeds eutrofies is a.g.v. aangewese landbouaktiwiteite, kan die toestand van die waterbron vererger indien akwakultuur toegepas word. Daar is ‘n statistiese noemenswaardige verskil tussen visboerdery en nie-visboerdery vir P, Secchi-skyf, totale gesuspendeerde vaste stowwe en nitrite-stikstof (p<0.05), en geen statistiese noemenswaardige verskil tussen visboerdery en nie-visboerdery vir OS, TAS en nitraat-stikstof (p>0.05). Daar is ‘n statistiese noemenswaardige verskil tussen oppervlak- en bodem water vir P en TAS (p<0.05). Een moontlike rede vir hoër P en TAS konsentrasies in die bodemwater, is die akkumulasie van beide parameters in die sediment en gevolglike vrystelling in die waterkolom wanneer die water gemeng word. ‘n Twee dimensionele spreidingstipping is geprodueer deur die waardes te gebruik van die eerste twee hoofkomponente. Die eerste twee hoofkomponente dra by 40 % en 17 % van die totale variansie onderskeidelik, en die twee groepering van visboerdery en nie-visboerdery het nie duidelik getoon nie. Die voorkoms en verspreiding van phytoplankton biomassa het gewissel met die verandering in damvlakke en nutriëntkonsentrasies. Die aanwesige phytoplanktongemeenskappe is belangrik vir die visboer vir twee redes: 1. Dit kan wisselende OS-vlakke versoorsaak deur die verbruik (respirasie en dekomposisie) en produksie (fotosintese) daarvan. 2. Dit kan lei tot alge na-smake van vis wanneer geosmin-produserende phytoplankton spesies aanwesig is. The frekwensie van voorkoms het getoon dat die Groep Chlorophyta (insluitend die genera, Chlamydomonas, Closterium, Oocystis, Scenedesmus, Staurastrum, Tetraedron, ens.) die meeste voorkom (n=371), met Chrysophyta (insluitend die genera, Dinobryon, Mallomonas, Synura, ens.) die minste (n=34). Daar is ‘n statistiese noemenswaardige verskil tussen genera voorkoms en seisoen (p<0.05) vir phytoplankton. Die geografiese ligging van die perseel het geen noemenswaardige invloed op die frekwensie van phytoplankton voorkoms nie. Daar is geen statistiese noemenswaardige verbintenis tussen waterkwaliteit en visproduksieopbrengste nie (p>0.05). Die visopbrengste by plase is hofsaaklik afhangende van die kwaliteit van die vingerlinge en die voeromsettingsverhouding (VOV) wat bereik is (p<0.05). Die landgebruikspatrone in die opvangsgebied waar visboere gesetel is, het aangedui dat die besproeiingsdamme meeldoelige sisteme is. Die ekologiese integriteit van die plaasdam-ekosisteem is afhanklik van die basisvolume. Die dam is hoofsaaklik daar vir die besproeiing en visboerdery kan in gedrang kom wanneer daar ‘n hoër aanvraag vir water gedurende die droë seisoen is. Die damme het omtrent 20 % van die water vanaf reënval ontvang en die res van aflope. Boere kon nie akkurate inligting verskaf van waterontrekking nie wat dit moeilik gemaak het om te voorspel wat die beskikbare watervlakke in die toekoms sou wees vir visproduksie. Vier potensiële toetrede meganismes om die nutriëntlading te verminder, is beskryf naamlik voedingsbestuur, (kwantiteit, frekwensie, tipe, ens.) voermetodes (aanvraagvoeder, handvoeding), voerbestandele (formulasies) en drywende tuine. Beide voedingsbestuur prosedure en aanvraagvoeders is geëvalueer as ‘n metode om die voervermorsing te verminder en die VOV te verbeter. Die kleinskaalse visboere het ongeveer 6 ton produseer met ‘n gemiddelde VOV van 1.96:1 ± 1.15. Indien die visboere hul VOV’s met 0.1 kan verbeter (bv. van 1.96 tot 1.86), sal dit beteken dat daar ‘n vermindering van 100 kg voer bewerkstellig word vir elke ton vis geproduseer. Dit kan ook lei tot ‘n vermindering van 5 % in die nutriëntlading. Die resultate van die wateranalises en die visuele waarneming van faeceslengte en kleur het geen statistiese noemenswaardige verskil tussen die behandelinge vir die guar-gom binder getoon nie (p>0.05). Verder, die hoeveelheid van die binder het nie die vertering van die eksperimentele diëte beïnvloed nie. Die studie op die drywende tuine het getoon dat dit haalbaar is om ‘n lae-koste sisteem te bou wat maklik is om te bestuur en gewasse kan produseer soos in ‘n hidroponiese sisteem tesame met visproduserende hokstelsels. Die kropslaaie se groei het getoon dat die waterkwaliteit van besproeiingsdamme kan verbeter word deur die opname van nutriënte wanneer plante verbou word. Vir die produksie van 3.5 kg/m2 kropslaaie, sal ‘n verhouding van 1.09 plante/vis of 1.84 g voer/dag/plant die akkumulasie van opgeloste nutriënte rondom die hokstelsels verminder. Die sosio-ekonomiese evaluasie van die bydrae van visboerdery tot die welvaart van die landelike en semistedelike plaasgemeenskappe ondersteun die feit dat akwakultuur verbetering kan bewerkstellig, veral onder deelnemende gemeenskappe. Een-en sewentig persent (71 %) van die respondente het getoon dat hul oorweging vir die bedryf van akwakultuur is om vis te voorsien aan die grootmark en daarvolgens geld te maak. Een-en-sestig persent (61 %) van die respondente het aangedui dat hulself die vis verkoop of vir familie-lede vra om met die verkope te help. Die bydrae van akwakultuur het direkte voordele aan die deelmers voorsien deur ‘n verbetering in huishoudelike inkomste, voedselvoorsiening vir selfgebruik en die ontwikkeling van vaardigthede. Indirekte voordele sluit in dat die deelmers ‘n bron van inligting geword het vir opkomende boere, hul status in die gemeenskap het verbeter omdat hul kennis verbreed het en dit het verder gelei tot diversifisering in die sektor a.g.v. die skepping van nuwe produkte en tegnologie. Die drie hoof struikelblokke wat die groei en bevordering van akwakultuur belemmer is o.a., ‘n tekort aan staatsondersteuning, onvoldoende markinligting en toegang en ‘n beperkte keuse in spesies vir boerdery. Besproeiingsdamme in die WKP het ‘n geskiedenis van verryking deur eksterne bronne wat water voorsien vanaf landbou-afloop (bemestingstowwe en pesbestrydingsmiddels), opvangsgebied-afloop (blare en ander organiese debris) en stormwateruitlaat (gruis- en swart water). Die implementering van akwakultuur in sulke damme voeg addisionele nutriënte tot die waterkolom en bestuur is krities om die lading te verminder en te verseker dat omgewingsvolhoubaarheid behou word. Indien die regte praktyke en bestuur toegepas word, sal dit beteken dat die kommersiële boer se besproeiing en waterverspreiding nie negatief beïnvloed word nie. Vervolgens moet toekomstige navosingsbehoeftes fokus op eerstens, die voorkoming en vemindering van besoedeling afkomstig van akwakultuur deur verbeterde produksie-bestuur en tegnologie-oordrag, tweedens, die monitoring en evaluering van die opvangs-ekosisteem as ‘n kontinuum met al die eksterne faktore wat die ekologie van die plaasdam kan beïnvloed en laastens, die ondersoek en evaluering van die sediment se prosesse en dinamika as ‘n sisteem wat nutriënte ophoop.

The effect of parasitism on the individual, and on a population, is one of the least understood and poorly studied areas of fish ecology. Parasites compete for maternal energetic reserves required for the production of viable eggs and offspring; thus parasites can directly influence population dynamics by lowering the number of offspring that survive to produce. The goal of this work was to explore the effect of parasitism on the reproductive potential of fish. Traditional measures of somatic energy reserves and body condition were examined along with newer measures of fatty acids present in eggs to approximate reproductive potential. Eighty female common snook, Centropomus undecimalis, were collected during spawning season (mid April to mid October) from four spawning aggregations along the southeastern coast of Florida and examined for a suite of biological, reproductive, and parasite infection measures. General linear models were used to model somatic indices, body condition, fatty acid composition and the ratios of fatty acids in eggs as a function of parasite infection parameters, host age, capture location, capture month and year. All fish were included in the somatic indices and body condition analysis while a subset of 40 fish were used in the analysis on fatty acid composition and the ratios of fatty acids in eggs. / Includes bibliography. / Dissertation (Ph.D.)--Florida Atlantic University, 2015. / FAU Electronic Theses and Dissertations Collection

Many studies have investigated the impacts of marine cage fish farming on seabed sediments. Most of these studies have focused on organic loading or toxic chemicals used for the treatment of disease, normally for a single or a small number of sites over short time periods. Only very rarely has there been the opportunity to use large data sets consisting of a large number of fish farm sites over a long time scale. In Scotland, localised nutrient impacts have been well documented for marine cage salmon farms, but mixed effects of nutrient and chemicals such as SLICE (the active ingredient of which is emamectin benzoate) have not been investigated in the long term. The aim of this project was to investigate the ecological impacts on sediments from farming activities using very large spatial and temporal data to investigate the long term effects of nutrient and chemical waste. This was achieved using a metadata set collected from 403 sampling stations at 31 fish farms on the west coast of Scotland over a 9 year period. Data consisted of sediment macrofauna, carbon and nitrogen levels, redox potential, particle size for sediment characterisation and sediment concentrations of SLICE. The data was analysed for trends using statistical and multivariate analysis to look for changes in sediment community and related conditions, and the relationships between these parameters were investigated. At sampling stations that were less than 50 metres from the sea cages, 72% of the macrofauna communities were correlated with regard to their species composition and abundance. A significant relationship between the concentration of SLICE and sediment characteristics was represented as: SLICE= 0.000644*(median size particle size) + 0.0311*(C %) – 0.00213*(redox potential) + 1.453. Annelids were the most sensitive to the presence of emamectin benzoate, with the sipunculid Phascolion strombi, the echinoderm Ophiura affinis, and the custaceans Iphinoe, Diastylis and Iphimedia also showing sensitivity. During the data period, there was a clear change in species composition associated with improved seabed conditions. This correlated with biomass changes at the relevant sites, where there was a consequent decrease in nutrient input and SLICE usage. The statistical comparison of the AMBI and ITI indices indicated a 68.9% correlation, but they differed in their ability to indicate levels of organic disturbance. AMBI was shown to correlate more closely with conditions and thus a more reliable index when working with large databases. Univariate and multivariate analysis indicated that a combination of abundance (N), Shannon Wiener (H’) and AMBI, as biological indices for describing the status of the ecological level associated with the carbon percentage and redox potential of sediments gave the most reliable representation of environmental change over a series of sampling stations. In conclusion, the overall results suggest that, in the long-term, sampling stations which contained significant levels of SLICE had a higher impact status than those affected only by nutrient inputs. The accuracy of multiple regression models were increased by adding biotic and abiotic parameters, though fish biomass at the sites were not considered be as important factor for the prediction of impacts. However, this model could be sensitive to natural environmental conditions and variations. In light of these results and conclusions, recommendations can be made both for updating the existed environmental regulation of marine fish farms and in the development of meaningful models to relate sediment conditions to accurate estimations of overall environmental impacts.

Thesis (PhD (Conservation Ecology and Entomology))--University of Stellenbosch, 2011. / ENGLISH ABSTRACT: Water storage in reservoirs forms an integral part of the agricultural landscape in the Western Cape Province, South Africa. A few large reservoirs serve primarily as a drinking and industrial water supply, while on private farms, small reservoirs provide irrigation water for the dry summer period. Protection of water quality to secure irrigation and drinking water quality, and the extension of water use efficiency are priority issues in the Western Cape. In the current study, the suitability of rainbow trout (Oncorhynchus mykiss) cage farming as a non-abstractive water use was investigated. The current study concentrated on the identification, and where possible quantification of aquaculture impacts, the identification of successful sites and a description of requirements in which net-cage aquaculture has none or a very low negative impact on water quality (e.g. <15 % change from previous water quality conditions for phosphorus concentrations). In order to study the effects of 5 t trout cage production units in reservoirs <15 ha in area, the general ecology of the irrigation reservoirs was assessed. Sixteen reservoirs without aquaculture production (reference reservoirs) were compared to 26 reservoirs with aquaculture production (production sites with varying production histories). Catchment characteristics were also monitored. Water from different depths (0 m, 2 m, 6 m and near bottom) was tested for physical and chemical qualities as well as nutrient concentrations. Phytoplankton and zooplankton biomass and species composition was monitored. In addition to the general phytoplankton findings, cyanophytes were evaluated for their contribution to algal taint problems that emerged at a number of production sites. Sediments were tested for total phosphorus content and phosphorus release capacity. Indicators and minimum conditions to avoid the most common production problems were formulated. In order to determine long-term production success, which prevents trophic level changes of reservoirs, a mass balance approach (nutrient budget) was employed to indicate the limits for nutrients that can be added. The phosphorus balance indicated long term trends for reservoirs with and without aquaculture. The detailed mass balance approach was compared to a “ready to use” carrying capacity model that estimated the maximum fish load each reservoir could support. The anthropological input of phosphorus into the reservoirs causes a decreasing water quality in the studied reservoirs and this development was also reported for lowland rivers. Twenty percent of the studied reservoirs are in a condition that could be an immediate threat to fish or water bird health (e.g. free ammonia concentrations and pH). Harmful algal blooms were not observed. Aquaculture production evoked changes in water chemistry and ecology in most of the studied reservoirs. Adverse effects of aquaculture sites versus non-aquaculture sites were: increased phytoplankton biomass and species shifts towards sizes >80 μm. The increased phytoplankton abundance influenced pH maxima to values >9 at mid-day. The high pH fluctuations were greatly influenced by the naturally low alkalinity and hence low calcium buffering capacity of Western Cape waters. The deoxygenation of the hypolimnion during stagnation (summer) occurred faster in reservoirs of certain character, greatly dependent on elevation and surface area, with consequent acidification of the hypolimnion, as well as ammonia and total phosphorus (TP) accumulation. In this context, a diversity of each reservoir with and without aquaculture production, with a similar ratio of undisturbed reservoirs to reservoirs with influence of e.g. agriculture, were compared to each other. When grouping the respective differences from the average reference reservoir (i.e. no trout production), a low impact on water quality was manifested at four sites (15 %) with <15 % increase of bottom TP and ammonia, while eight sites (31 %) showed medium effects (59 % mean increase), and a high impact was found at 54 % of the sites (312 % mean increase). In reservoirs without aquaculture, the extent of incoming phosphorus (which could represent an influence by runoff from agricultural land) was very high. However, in small reservoirs (<5 ha), these values were exceeded by the incoming phosphorus from aquaculture practices. In the case of small reservoirs where the carrying capacity was clearly surpassed, effects caused by aquaculture were severe and the assimilation of waste by the system was not possible (in extreme cases aquaculture waste delivered 60 to 90 % of all incoming phosphorus – two to nine times the phosphorus brought in by rivers and runoff). With regards to sediment, only indirect conclusions could be drawn. Aquaculture production increased hypolimnetic anoxia and the latter was shown to increase potential phosphorus release from sediments. This implies that not only will aquaculture increase the phosphorus concentration of surface waters directly, but it will also increase internal loading. The sedimentation rate was increased with cage aquaculture which affects a hypothesized area of approximately 0.2 to 1.0 ha depending on reservoir hydrology. The composition of the sediment increased organic components which can impact on sediment processes. It can be postulated that increased sedimentation of aquaculture waste and extended anoxic conditions impact on macrozoobenthos. Hydrological and nutrient mass exchange of the reservoirs indicated that no annual increase of phosphorus was achieved with low nutrient input (good inflowing water quality) or good water exchange (>5 times per year), and sometimes with extraction of hypolimnetic water during the stagnation period (summer). A model developed by Beveridge (1984) showed similar results to the mass balance approach and can therefore serve as a more ready model to determine suitable stocking rates. The small (man-made) reservoirs in the Western Cape are in a eutrophication process which far exceeds the speed of natural eutrophication (trophic states indicating highly eutrophic or hypertrophic conditions after approximately 10 to 20 years following construction of the reservoirs) and this process is triggered by agricultural practice (indicated by literature – not a subject of this study). However, it is concluded from the data of this study that trout-cage aquaculture duplicated the total phosphorus already present (independent of continuation of the projects, the phosphorus introduced was trapped in the closed systems the reservoirs represent) in only 1 to 2 years of production - which means a significant acceleration of the eutrophication process already in place. There are positive exceptions where trout-cage production is possible without negative effects. Careful site selection is the most important step in successful and sustainable trout production. No impact of aquaculture was recorded at four reservoirs (15 % of the investigated reservoirs) which shared the characteristics of good water exchange (>3 times per year) and a minimum surface area of 5 ha. Additionally, criteria that reduced the risk of algal taint included a minimum water depth of 6 to 7 m in a reservoir at its lowest water point (to avoid intermediate mixing during the stagnation period) as well as cold hypolimnetic conditions (<17 °C) to minimize cyanophyte cyst remobilization. Further improvement of food conversion ratio (feeding management) and feed quality are the next (after site selection) two most important components that determine if a reservoir can be utilised for cage production without any long-term changes. There is potential in advances in feed quality, feed management and waste collection systems. These measures (e.g. the cage size could be decreased to efficate feeding management) can increase the number of sustainable sites and achieve multiplication of water use without water quality deterioration. / AFRIKAANSE OPSOMMING: Die stoor van water in reservoirs vorm ‘n integrale deel van die landboulandskap in die Westelike Kaap gedeelte van Suid-Afrika. ‘n Aantal groter reservoirs voorsien primêr water primer vir drinkdoeleindes en vir aanwending deur industrieë, terwyl kleiner reservoirs op private plase gebruik word vir besproeiing gedurende die droë somerperiode. Die beskerming van die waterkwaliteit en die uitbreiding van watergebruik se doeltreffendheid, word bestempel as ‘n prioriteit vir die Wes-Kaap. In die huidige studie is die geskiktheid van forel hokkultuur as ‘n bykomende watergebruik, maar sonder waterverbruik, ondersoek. Die huidige studie fokus op die identifisering en waar moontlik die kwantifisering van die impak van akwakultuur op besproeiingsreservoirs; die identifisering van potensiële reservoirs vir akwakultuur; en die beskrywing van toestande waarin akwakultuur geen of ‘n baie lae negatiewe uitwerking op die waterkwaliteit (bv. < 15 % verandering vanaf oorspronklike waterkwaliteitstoestande vir fosforkonsentrasies) sal hê. Om die impak van 5 t forel hokproduksie eenhede in <15 ha reservoirs te bestudeer, is die algemene ekologie van die besproeiingsreservoirs bepaal. Watermonsters, geneem op verskillende dieptes (0, 2, 6 en naby die bodem), is getoets vir fisiese- en chemiese kwaliteit sowel as vir die nutriëntkonsentrasies. Die biomassa en spesiesamestelling van fitoplankton sowel as zooplankton is gemonitor. Sestien verwysingsreservoirs is vergelyk met 26 produksiereservoirs (met wisselende vlakke van produksiegeskiedenis). Die karakeristieke eienskappe van die opvangsgebied is ook gemonitor. Tesame met die algemene fitoplankton bevindinge, is blougroen alge ook geëvalueer vir hul bydrae tot algae besmettingsprobleme wat voorgekom het by ‘n aantal produksie persele. Sedimente is getoets vir die totale fosforinhoud en fosforvrystellingskapasiteit. Perseelseleksie is geidentifiseer as een van die mees belangrikste faktore vir suksesvolle hokproduksie. Indikatore en minimum toetstande wat vereis word om die mees algemene produksieprobleme te verhoed, is geformuleer. Om die langtermyn produksie sukses te bepaal, wat trophiese vlakke se verandering in die reservoirs verhoed, is ‘n massa balans benadering (nutriënt balans) gebruik. Die fosfor balans het langtermyn tendense aangetoon en in die geval van die produksie reservoirs, is die akwakultuurimpak gekwantifiseer. Die gedetaileerde massa balans benadering is vergelyk met ‘n “gereed om te gebruik” drakapasiteitsmodel wat die maksimum vis wat die reservoir kan onderhou, geskat het. Die antropogeniese toevoer van fosfor na die reservoirs veroorsaak ‘n afname in die waterkwaliteit van die reservoirs wat bestudeer is. Die verskynsel van ‘n afname in waterkwaliteit is ook vir verskeie laagliggende riviere geraporteer. Sowat 20 % van die besproeiingsreservoirs wat bestudeer is, is tans in ‘n toestand wat die onmiddelike gesondheid van vis en watervoëls kan bedreig. Skadelike algebbloei is nie waargeneem nie. Akwakultuurproduksie het negatiewe effekte getoon in ‘n aantal reservoirs. Die nadelige uitwerking van akwakultuur waar digthede te hoog was, is: toename in fitoplankton biomassa en spesiesverskuiwinge. Die toename in fitoplankton teenwoordigheid het die pH maxima beïnvloed tot waardes >9 teen 12 uur middag. Die hoë pH fluktuasies is grootliks beïnvloed deur die natuurlike lae alkaliniteit en gevolglike kalsium bufferkapasitiet van die Wes-Kaap se waterbronne. Die deoksiginasie van die hipolimnion gedurende stagnasie (somer) het vinniger plaasgevind in oorbelaaide reservoirs, met gevolglik ‘n versuring van die hipolymnion, sowel as die akkumelering van ammoniak en totale fosfor. In hierdie konteks word reservoirs met en sonder landbouproduksie, met ‘n gelyke verhouding van onversteurde reservoirs tot reservoirs wat deur landboubedrywighede beinvloed word, met mekaar vergelyk. By vier persele (15 %) is ‘n lae impak vasgestel (<15 % toename in bodem TF en ammoniak), terwyl agt persele (31 %) ‘n medium impak getoon het (59 % gemiddelde toename in bodem TF en ammoniak) en ‘n hoë impak is opgemerk by 54 % van die persele (31 % gemiddelde toename in bodem TF en ammoniak). In reservoirs sonder akwakultuur, was die omvang van fosforinvloeiing baie hoog en is moontlik veroorsaak deur die invloei van afloopwater uit omliggende landbougebiede. Alhoewel in klein reservoirs (<5 ha) was hierdie waardes oorskadu deur die invloeiing van fosfor deur akwakultuur praktyke.In die geval van klein reservoirs, waar die drakrag duidelik oorskry is, was die gevolge, soos veroorsaak deur akwakultuur ernstig, en die assimilasie van afval deur die sisteem nie moontlik nie. In die uiterste gevalle het akwakultuurafval 60 % - 90 % van alle inkomende fosfor gelewer - twee tot nege maal die fosfor wat deur riviere en afloopwater ingevloei het. Wat die sediment aanbetref, kon slegs indirekte gevolgtrekkings gevorm word. Akwakultuurproduksie het hipolimnetiese anoksia laat toeneem en die laasgenoemde verskynsel, het die potensiaal aangedui vir die toename in die vrystelling van fosfor vanaf die sediment. Dit dui daarop dat akwakultuur nie alleen die fosforkonsentrasie in die oppervlaktwater laat toeneem nie, maar sou ook die interne belading laat kon toeneem. Die sedimentasie tempo het toegeneem met die teenwoordigkeid hokkultuur en het ‘n hipotetiese area van ongeveer 0.05 tot 1.00 ha, afhangende van reservoir hidrologie, beïnvloed. Die samestelling van die sediment het toegeneem in teme van die organiese komponente wat die sedimentasie prosesse kon beïnvloed. Dit kan gepostuleer word dat die toename in sedimentasie van akwakultuurafvalprodukte tesame met verlengde anoksiese toestande, ‘n invloed op die makrosoöbentiese organismes het. Hidrologiese en nutriënt massa uitruiling van die reservoirs het aangetoon dat geen jaarlikse toename in fosfor verkry kan word met lae nutrient toelae (kwaliteit van invloeiende water) of met goeie waterverplasing nie, en soms met die ekstraksie van hipoliminetiese water gedurende die stagnasie periode (somer). Die Beveridge model het soortgelyke resultate getoon tot die massabalans benadering en kan daarom dien as ‘n meer aanvaarbare model om gepaste beladingstempo vas te stel. Kleiner mensgemaakte reservoirs in die Wes-Kaap is onderhewig aan ‘n eutrofikasie proses wat die spoed van natuurlike eutrofikasie (trofies verwys na ‘n hoogs eutrofiese of hipertrofiese toestand ongeveer 10 tot 20 jaar na reservoir konstruksie) oorskry. Literatuur (nie ondersoek in die huidige studie) dui aan dat hierdie versnelde eutrofikasie proses meegebring word deur landbouaktiwiteite in die opvangsarea van die reservoirs. Resultate van die huidige studie het getoon dat forelproduksie in hokstelsels, die konsentrasie van total fosfor wat reeds beskikbaar was, verdubbel het. Die toename in fosforkonsentrasie het binne 1 tot 2 jaar na die aanvang van forelproduksie in die betrokke reservoirs, plaasgevind. Daar is egter uitsonderings waar forelproduksie in hokstelsels moontlik was, sonder die gepaardgaande afname in die waterkwaliteit. Die belangrikste stap vir suksesvolle en volhoubare forelproduksie is deeglike perseelseleksie. Daar is geen impak van akwakultuur waargeneem by vier persele (15 %) wat die eienskappe van goeie waterverplasing (>3 keer per jaar) en ‘n minimum oppervlakarea van 5 ha gehad het nie. Bykomend, sluit kriteria wat die risiko van algbesmetting laat afneem, ‘n minimum waterdiepte van 6 tot 7 m in ‘n reservoir by die laagste punt in (om te verhoed dat intermediêre vermenging plaasvind gedurende die stagnasieperiode) sowel as koue hipolimnetiese toestande (<17 °C) om sianobakterieë sist remobilisasie te minimaliseer. Verdere verbetering van die VOH (voeromsettingsverhouding onder voedingsbestuur) en voerkwaliteit is na perseeleleksie, die volgende komponente wat kan aandui of ‘n perseel gebruik kan word vir hokkultuur sonder enige impak. Vordering met voerkwaliteit en voedingsbestuur kan die aantal volhoubare persele laat toeneem en daardeur meer effektiewe watergebruik teweeg bring, sonder die verwante waterkwaliteit verswakking.

Thesis (MScAgric (Conservation Ecology and Entomology)--University of Stellenbosch, 2007. / Small farm dams (< 20 ha) in the Western Cape Province provide adequate water conditions for intensive cage production of rainbow trout (Oncorhynchus mykiss). A major environmental concern of cage aquaculture, however, is the high inputs of nutrients via commercial diets and the subsequent eutrophication of the water source. Eutrophication can result in the degradation of the general water quality (increasing pH levels, oxygen depletion, increased hydrogen sulphide and free ammonia) and shifts in the phytoplankton structure (increased biomass, single species dominance). Deterioration of water quality will affect the success of the fish farming enterprise as well as the performance of irrigation equipment by increasing the risk of clogging and corrosion. Water quality, phytoplankton and zooplankton compositions were monitored at four sites from June 2005 to November 2006 to determine the effects of cage culture on the farm dam environment, its associated biota as well as irrigation water quality. The distribution of nutrients, nitrogen and phosphorus, was mainly influenced by the stratification and mixing regime of the water bodies. Nutrient concentrations increased during the winter mixing period while in the summer months, they seem to settle to the lower part of the water column. Nutrient concentrations of production sites and reference sites were comparable except for the ammonia levels that were significantly higher at the production sites. Phytoplankton corresponded with nutrient availability resulting in high biomass during winter. In terms of biomass, phytoplankton was approximately two times more abundant in production sites compared to reference sites. Assemblage dominance by cyanophytes (Anabaena circinalis, Microcystis spp.) was found more often in production sites, while reference sites were dominated by dinophytes (Ceratium hirundinella, Peridinium spp.). Zooplankton biomass concurred with high phytoplankton biomass in winter. Zooplankton assemblages in production sites sustained much higher biomass. Effects of cage culture on irrigation water quality are evident from increased algal biomass and shifts in species composition. These results indicated that at its present production level, cage culture had impacts on the farm dam environment and irrigation water quality. The most significant evidence was given by increased plankton biomass and single species dominance in production sites. However, these findings can not solely be ascribed to the introduction of aquaculture as various other factors may also contribute to the water quality of these ecosystems.