Macroalgae such as Ulva are living hosts that are known to perform essential roles in marine ecosystems, and are extensively utilised for several aquaculture operations, including in the integrated production of high value goods such as abalone. Intensive aquaculture operations along the coastline release effluent water into the surrounding coastal waters, which has adverse impact on the environment. As a means to bioremediate abalone effluent, several commercial abalone farms in South Africa use Ulva as a biofilter, after which the Ulva may serve as a feed source for the abalone. Advancements in gene sequencing technology has enabled the assessment of large scale 16S rRNA gene libraries of near full-length sequences. However, studies concerning the epiphytic bacterial communities present on macroalgae grown in effluent systems are scarce, and as a result several commercial farmers have become sceptical about utilising effluent grown Ulva as feed. This study addresses the biosecurity implications associated with the use of Ulva as a biofilter and feed within an integrated multitrophic aquaculture (IMTA) system along with the abalone Haliotis midae by assessing the bacterial communities associated with Ulva and its environment. Water and Ulva samples were collected from an integrated abalone farm along the Western Cape of South Africa and assessed via a culture and a non-culture-based approach. Samples were collected from both fertilised seawater tanks and abalone effluent wastewater raceways. The water samples were collected at the inlets and outlets of each tank/raceway and the Ulva was collected from within each system. The culture-based approach utilised three selective media for the isolation and quantification of culturable bacteria, namely Tryptic Soy Agar (TSA, a general growth media), thiosulfate-citrate-bile-sucrose (TCBS) agar (vibrio selective growth media), and Ulvan agar plates, where the primary carbohydrate of Ulva was utilized as the main carbohydrate source. Post isolation, selected bacteria underwent 16S rDNA gene analysis for identification. The non-culture-based approach utilised the next generation Illumina 16S Metagenomic Sequencing platform (MiSeq). Moreover, the Ulva was sequenced using the rbcL gene to identify the species grown in the aquaculture system. Phylogenetic analysis of Ulva suggests that it falls within the U. rigida clade. The sequenced Ulva cultivated at I&J abalone farm shared close similarity with Ulva rigida (KP233772) and Ulva scandinavica (EU484416) on the GenBank database, and hence was referred to with the name of its corresponding molecular synonym, i.e. U. rigida. The culture-based results indicate that bacterial numbers were significantly higher in the raceways receiving abalone effluent water when compared with the Ulva tanks receiving seawater that were fertilized. Bacterial abundance on all three selective media types was higher on the Ulva cultured in the abalone effluent raceways than on the Ulva cultured in the fertilized seawater tanks. Moreover, it was observed that the Ulva has the potential to significantly reduce the bacterial load of abalone effluent water raceways. Rarefaction results from the non-culture-based approach indicate that the Ulva in both the fertilised seawater and abalone effluent raceways had significantly lower bacterial alpha diversity than the water columns themselves. Principal co-ordinate analysis (PCoA) at phylum level showed that bacterial communities on the Ulva and in the water, columns shared similar phyla diversity. Alternatively, PCoA at genus level demonstrated that microbial communities residing on the Ulva (both effluent and fertilised seawater grown Ulva) had significant differences compared with the water samples obtained from both the inlets and outlets of the effluent and fertilised seawater systems. When assessing the differential abundant bacteria on the Ulva, general marine bacteria appear in high abundance and potentially pathogenic bacteria such as Vibrio appear in low abundance. Moreover, the presence of the Ulva within the wastewater seemed to decrease the bacterial abundance of Vibrio within the fertilised seawater tanks as well as the abalone effluent raceways. Despite the presence of potentially pathogenic bacteria within the abalone effluent raceways, the Ulva does not seem to act as a sink for potentially pathogenic bacteria indicating that feeding effluent grown Ulva to abalone is not of significant biosecurity concern. Even though several commercial abalone farmers consider recirculation within aquaculture feed systems high-risk technology, no papers have reported disease outbreaks due to the use of effluent grown Ulva as abalone feed. These results provide a general basis for the dynamic changes in the bacterial community profiles in a commercial abalone farm associated with utilising effluent grown Ulva as a feed additive for abalone. This effort to profile the bacteria associated with Ulva and its environment under fertilised and effluent conditions provides deeper insight on understanding the biosecurity implications of incorporating effluent grown Ulva into abalone feed.

Thesis (MScAgric)--Stellenbosch University / ENGLISH ABSTRACT: Triploidy is the genetic state of containing three sets of chromosomes per cell in stead of two as in diploid organisms. The South African abalone (Haliotis midae) is naturally a diploid organism that sexually matures between four to eight years of age. Early sexual maturity is a disadvantage in cultured abalone stock, as the process of gonad development and spawning is energy demanding, causing energy to be diverted away from somatic growth. This same problem has been extensively experienced in diploid bivalve molluscs, where triploidy has since been applied as a means to prevent sexual maturation from occurring, thereby speeding up the growth process and shortening the time to marketing. Because triploidy was effective in bivalves, it was thought that it could contribute to faster growth in abalone as well. A procedure for the induction of triploidy in the abalone, Haliotis midae, was developed by De Beer (2004) and yielded up to 100 percent triploidy in treated abalone larvae. The next step was to compare the growth of the diploids and triploids to establish whether there was indeed a growth advantage on the part of the triploids, in view of commercial application. By using the same techniques as described by De Beer (2004), three groups consisting of triploid and diploid siblings were produced and subscribed to a comparative growth trial. The groups were spawned in three different seasons. The main objective was to establish whether there was in fact a difference in growth between diploid and triploid siblings, and whether seasonal effects were associated with growth advantages for either triploids or diploids. The two growth parameters measured were shell length and body weight. Measurements commenced at eight months of age, when the abalone could be individually tagged and continued up to the age of 24 months. The over-all results provided no convincing evidence of statistically significant faster growth of triploid juveniles compared to that of diploids up to two years of age. Growth differences were detected between seasons, but could not confidently be ascribed to seasonal environmental effects. The regression of shell length to body weight was similar for diploids and triploids. / AFRIKAANSE OPSOMMING: Triploiede organismes bevat drie stelle chromosome per sel in plaas van twee soos dit normaalweg in diploiede diere voorkom. Die Suid Afrikaanse perlemoen (Haliotis midae) is van nature ‘n diploiede organisme wat tussen die ouderdom van vier tot agt jaar seksueel aktief word. Vroeë seksuele aktiwiteit is ongewens in kommersiële akwakultuur aangesien energie spandeer word aan gonade ontwikkeling in plaas van somatiese groei. Dieselfde probleem is vroeër in die oester bedryf ondervind waar dit deur middel van triploiede induksie aangespreek is. Triploiedie veroorsaak steriliteit en kan gebruik word as ’n metode om steriliteit op groot skaal te induseer. Steriliteit sou dan meebring dat meer energie beskikbaar is vir somatiese ontwikkeling, wat verhoogde groeitempo en n verkorte tyd tot bemarking beteken. Op soortgelyke wyse is dus gepostuleer dat triploiedie in perlemoen ook tot steriliteit kon lei. ‘n Triploiede induksie metode was ontwikkel deur Mathilde de Beer (2004) wat ‘n hoë persentasie triploidie in geinduseerde perlemoen opgelewer het. Die volgende logiese stap was om die groei van diploiede diere met die van triploiede diere te vergelyk om te bepaal of triploiedie wel ’n groei voordeel tot gevolg het met die oog op kommersiële toepassing. Deur van dieselfde tegnieke as De Beer (2004) gebruik te maak, is drie groepe, elk bestaande uit verwante diploiede en triploiede diere, geproduseer en ingeskryf aan n vergelykende groei proef. Die groepe was in drie verskillende seisoene geproduseer. Die hoof doelstelling van die proef was om groeitempo van diploiede en triploiede diere te vergelyk, asook om die invloed van seisoen op groei van diploide en triploide te bepaal. Twee groei eienskappe naamlik skulp lengte en liggaamsmassa is gemeet vanaf ‘n ouderdom van agt maande (wanneer die diere individueel gemerk kon word) tot ‘n ouderdom van 24 maande. Die algehele resultate het gedui op geen betekenisvolle verskil tussen die groei van triploiede en diploiede perlemoen tot op die ouderdom van twee jaar. Verskille het voorgekom in die groei tussen seisoene, maar daar kon nie bewys word dat die verskille die gevolg van seisoenale omgewingseffekte was nie. Diploiede en triploiede het dieselfde skulp lengte tot liggaamsmassa verhouding getoon tot op twee jaar ouderdom.

Thesis (MSc)--University of Stellenbosch, 2004. / ENGLISH ABSTRACT: The species Haliotis midae is the only commercially exploitable abalone species of the six found in the South African coastal waters. This species is under substantial pressure from both legal and illegal harvesters, to such an extent that it could be commercially extinct within four years. Efforts to alleviate the pressures on the natural populations of both illegal and legal harvesting are being made. The genetic management systems for abalone farming and ranching activities should be carefully evaluated. The loss of genetic diversity and the risks of contaminating the gene pools of natural populations in the vicinity of a farm should be minimized. Genetic evaluation studies will be at great importance to acquire the necessary data needed for genetic diversity and differentiation analysis. The aim at this study was to develop species-specific microsatellite DNA markers to assess the genetic diversity and differentiation within and between the brood stock and commercial stock of the Sea Plant Products abalone farm (Hermanus, Republic of South Africa) and natural populations related to the brood stock. The species-specific DNA markers were also used for parentage assignments within the tarm population (first for abalone) and preliminary OTL (quantitative trait loci)-discovery analysis studying growth rate segregation. Samples were taken of the farm's brood stock and commercial stock (Rows 2, 3, 4) as well as from two natural populations (Saldanha Bay and Black Rock) related to the brood stock. Various statistical parameters and software packages were used to assess genetic diversity and differentiation, to infer parentage and to look for OTL's. Eight species-specific microsatellite DNA markers were designed and used for data analysis. Data analysis showed a loss at genetic diversity from the brood stock to the commercial stock caused by the subdivision of the original brood stock into rows and the differential contributions of parents to the offspring. No genetic differentiation (Fst) was detected between the farm and natural populations, except for the offspring of Row2. levels of inbreeding (ns) were high for all loci within the populations. Thirty-eight percent of all studied offspring were confidently assigned to a couple. The preliminary QTldiscovery suggested the segregation of a number of alleles and genotypes with growth rate. The study concluded that the commercial abalone population of the Sea Plant Products abalone farm holds no threat to the disruption of the genetic diversity of the natural populations. It is proposed that the farm implement a rotational breeding program to increase the genetic diversity of the commercial population. Any newly acquired brood stock must be profiled before their introduction into the breeding program to assess the influence of the animals on the current levels of genetic diversity within the farm. The accuracy and reliability of parentage assignments and QTl-discovery need to be optimised by adding more loci and sampling more animals or even by trying and developing new methods. / AFRIKAANSE OPSOMMING: Van die ses perlemoen spesies wat langs die Suid-Afrikaanse kus gevind word, is die spesie Haliotis midae die enigste een wat van kommersiële belang is. Wettige, sowel as onwettige versameling, plaas hierdie spesie onder sulke geweldige druk dat dit dalk binne vier jaar verlore kan wees vir die kommersiële bedryf. Verskeie strategieë word tans geïmplimenteer om hierdie druk te verlig. Die genetiese bestuurstrategieë binne perlemoen plase moet deeglik ondersoek word. Die verlies aan genetiese diversiteit en die moontlikheid vir die kontaminering van die natuurlike populasies in die omgewing van die plaas se geenpoel, moet uitgeskakel word. Genetiese evaluasies sal van groot belang wees om die nodige data vir genetiese diversiteit- en differensiasie-analises te verkry. Die doel van die studie was om spesies-spesifieke mikrosatelliet DNA merkers te ontwikkel wat gebruik sou word om die genetiese diversiteit en differensiasie binne en tussen die broei diere en die kommersiële diere van Sea Plant Products se perlemoen plaas (Hermanus, Republiek van Suid- Afrika) en die natuurlike populasies wat verwant is aan die broei diere, te bepaal. Die spesies-spesifieke DNA merkers is ook vir ouerskap-bepalings binne die plaas se populasie gebruik, asook vir voorlopige OTL (quantitative trait locI) - ontdekking met betrekking tot groeitempo segregasie. Monsters van die plaas se broei diere en kommersiële diere (Ry 2, 3, 4) asook van twee natuurlike populasies (Saldanha Baai en Black Rock) wat verwant is aan die broei diere, is geneem. 'n Verskeidenheid van statistiese parameters en sagteware pakette is vir die genetiese diversiteit- en differensiasie-analises, vir ouerskap-bepalings en vir die opspoor van OTL's gebruik. Agt spesies-spesifieke mikrosatelliet DNA merkers is ontwerp en toe gebruik vir die data analises. 'n Verlies aan genetiese diversiteit vanaf die broei diere na die kommersiële diere is deur die data analises uitgewys. Dit is veroorsaak deur die verdeling van die oorspronklike broei diere in rye en die differensiële bydraes deur die ouers na die nageslag. Geen genetiese differensiasie (Fst) is tussen die plaas se populasie en die natuurlike populasies gevind nie, maar die nageslag van Ry 2 het wel differensiasie getoon. Die vlakke van inteling (Fis) was hoog oor alle lokusse binne alle populasies. Agt-en-dertig persent van die nageslag wat bestudeer is, was suksesvol met 'n ouerpaartjie geassosieer. Die voorlopige OTL-ontdekking studie toon die potesiële segregasie van 'n aantal allele en genotipes saam met groeitempo. Die bevindinge van die studie is dat die kommersiële populasie op die Sea Plant Products perlemoen plaas, geen bedreiging vir die versteuring van die natuurlike populasies se genetiese diversiteit inhou nie. Daar is voorgestel dat die plaas 'n rotasie-basis broeiprogram moet implimenteer om sodoende die genetiese diversiteit van die kommersiële populasie te verhoog. Enige nuwe broei diere se genetiese profiel moet ook voor die tyd ondersoek word om te sien wat se effek hierdie diere op die huidige genetiese diversiteit van die kommersiële populasie sal hê. Die akkuraatheid en betroubaarheid van die ouerskap-bepalings en OTL-ontdekking moet optimiseer word deur of meer lokusse te bestudeer, of meer diere in analises te gebruik of selfs om nuwe tegnieke te probeer of te ontwikkel.

Thesis (Ph.D.)--University of Western Australia, 2004.

Thesis (Ph. D.)--University of Washington, 1998. / Vita. Includes bibliographical references (leaves [239]-246).

Thesis (M.Sc. (Ichthyology & Fisheries Science)) - Rhodes University, 2008.

Thesis (Ph.D.) - University of Queensland, / Includes bibliography.

Thesis (Ph. D.)--Rhodes University, 1995. / "December 1995." Includes bibliographical references.

An adequate supply of diatoms during the weaning stage (generally 5 - 10 mm shell length (SL)) is one of the primary constraints to the commercial culture of the South African abalone, Haliotis midae. Because of the seriousness of the problem, a project aimed at the development of an artificial weaning diet was initiated. Initially, the chemical composition (proximate composition, amino acid, fatty acid and mineral element profile) of juvenile H. midae was analyzed, as a general lack of such information was identified in a review. Due to the lack of knowledge on the nutritional requirements of H. midae, the formulation of the weaning diet was based on the essential amino acid (EAA) pattern of the shucked tissue, and the known nutrient requirements of haliotids. Subsequently, a water stable gel and pellet form of the diet were developed. The best water stability of a gel was obtained with a 1:3 agar/gelatine mixture which retained 70.7 ± 2.7 % of its dry weight after 24 h. Starch based pellets, however, retained 89.0 ± 0.6 % of their dry weight after 24 h. In a comparative growth trial, pellets produced a significantly better increase in SL and weight than gels after only 15 days. This was probably due to the better water stability of pellets, which resulted in a better nutritional quality than in gels. The feeding behaviour on both forms of the diet did not differ. Activity patterns were exclusively nocturnal and feeding frequency was consistently low. The percentage composition of the pelleted weaning diet, on a dry weight basis, was 5 % casein, 15 % gelatine, 15 % fish meal, 10 % Spirulina spp., 2.5 % fish oil, 2.5 % sunflower oil, 21.0 % dextrin, 23.0 % starch, 4.0 % of a mineral and 2.0 % of a vitamin mixture. The correlation coefficient between the EAA pattern of H. midae and the dietary EAA pattern was r⁷= 0.8989. Pellets were fed to juveniles in a 30 day growth trial to study the effect of photoperiod (12, 16, 20 and 23 hours of darkness) on growth and general nutritional parameters. A comparative experiment feeding diatoms was conducted under a 12hL: 12hD light regime at the same time. The SL and weight of the juveniles did not increase significantly with an increase in hours of darkness. The growth of juveniles fed on pellets did not differ significantly from those fed on diatoms. Percentage feed consumption (PFC), percentage feeding rate (PFR), feed conversion ratio (FCR), protein efficiency ratio (PER) and percentage protein deposited (PPD) were determined for the animals fed on pellets. None of the parameters were significantly affected by photoperiod. However, there were trends in that PFC increased with longer periods of darkness, while PPD decreased. The FCRs (0.44 ± 0.04 to 0.60 ± 0.19) and PERs (5.06 ± 1.74 to 6.64 ± 0.77) indicated that juveniles used the feed, and in particular the protein, very efficiently. Photoperiod did not have an effect on the specific activity of the digestive enzymes amylase, protease and lipase. The specific activity of amylase in the juveniles fed on diatoms was significantly higher than in the pellet fed groups. This was surprising as the main carbohydrate of diatoms is the ß-(l-3) glucan chrysolaminarin, and not starch, a ß-(l-4) glucan. Protease specific activity, on the other hand, was significantly higher in the pellet fed groups, indicating an ability to adapt to the high protein content in the artificial diet (35.48 %), compared to diatoms which had a protein content of 5 %. The specific activity of lipase did not differ significantly between groups, probably because of a similar lipid concentration (5 - 10 %) in diatoms and pellets. Finally, the effect of stocking density, ranging from 1250 to 10,000 juveniles/m2, on the growth of juveniles was evaluated. A model of hatchery productivity was developed based on this investigation. Hatchery productivity was defined as the number of juveniles per unit space reared through to the grow-out stage per unit time. The model predicted that maximum productivity would be achieved at a stocking density of 10,000 juveniles/m2. The results have shown that H. midae can be successfully weaned on an artificial diet, as the growth on the diet was not significantly different to growth obtained on diatoms. Long-term growth trials are needed to confirm these results. The importance of standardized experiments on the nutritional requirements and digestibility of abalone was emphasized. The importance of improved artificial diets, optimal culture conditions, as well as the application of biotechnological techniques to further abalone aquaculture was highlighted.

Masters in Public Administration - MPA / Hawston, a small fishing town situated in Greater Hermanus is famous for its lucrative abalone resource. Since the drastic reduction of the abalone quota, which was implemented from 1994-2001, black commercial abalone divers have been on the receiving end of the new fishing legislation. The decimation of abalone by illegal harvesters, and the annual allocation of one and a half ton of abalone to all black commercial divers at present, are serious factors that influence the future of the commercial abalone divers and their counterparts. An abalone quota plays a pivotal role regarding the existence of various groups of people namely the Southern boat assistants, Overberg commercial abalone divers, Hawston fishing community etc. This study attempts to examine the effects of the drastic reduction of the abalone quota on the commercial divers (from 22-ton to one and a half ton), the boat assistants and the Hawston fishing community. The mentioned groups are also engaged in harvesting their allocated crayfish quotas, the research project mainly focuses on the effect of the new quota system on the allocation of abalone and crayfish quotas in Hawston. In essence, this research project seeks to examine the validity or invalidity of the White Paper regarding policies of the new Living Resources Act on commercial abalone divers, the boat assistants and the Hawston fishing community. The researcher has noted the various shortcomings in the White Paper on Marine Resources and the associated indiscrepancies being practiced by the Department of Environmental Affairs. In the study, a qualitative method is used to assess the impact of the implementation of new fishing quotas on various social groups in Hawston (existing and new groups). This was done by means of in-depth interviews. Some of the policy makers at the Department of Environmental Affairs were also interviewed. An evaluation of data gathered through the use of interviews and review of primary and secondary literature, revealed that equitable fishing quota allocation systems are not addressing the needs of the small-scale fishers in Hawston. By means of reports, it was concluded that various factors are infringing on the rights of those excluded from receiving allocation systems and also has the effect of fuelling uncertainty for the future of commercial abalone divers and small scale fishers in Hawston. The primary objective of this study is to investigate if the White Paper Policy on Marine Resources is benefiting the disadvantaged small-scale fishers in Hawston. Most important for the commercial abalone diver in Hawston, is the effect of the decimation of abalone and how legislation in the new quota system will influence their lives.