Masters Theses

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The Masters Theses collection contains digital copies of AUT University masters theses deposited with the Library since 2002 and made available open access. From 2007 onwards, all theses for masters degrees awarded are required to be deposited in Tuwhera Open Theses & Dissertations unless subject to an embargo.

For theses submitted prior to 2007, open access was not mandatory, so only those theses for which the author has given consent are available in Tuwhera Open Theses & Dissertations. Where consent for open access has not been provided, the thesis is usually recorded in the AUT Library catalogue where the full text, if available, may be accessed with an AUT password. Other people should request an Interlibrary Loan through their library.

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Now showing 1 - 17 of 17

Allometry, biomass and litter decomposition of the New Zealand mangrove Avicennia marina var. australasica
(Auckland University of Technology, 2014) Tran, Phan; Leuzinger, Sebastian; Alfaro, Andrea
Accurate estimates for biomass pools and fluxes are the key for assessing the potential of vegetation to counteract anthropogenic carbon emissions. However, such data are laborious to retrieve and still missing for many ecosystems. In this study, I used the harvest method to estimate above- and below-ground biomass, and litter traps and litterbags to measure litterfall and decomposition of the New Zealand mangrove Avicennia marina var. australasica at Mangawhai Harbour, northern New Zealand from April 2013 to March 2014. Total above-ground biomass of A. marina was estimated at 2.69 - 8.88 kg m-2 and below-ground biomass at 11.62 - 14.7 kg m-2. The root-shoot ratio at this site was 1.73. Fine roots contributed most to the biomass stock with almost 50 % of the below-ground and 37 % of the total biomass. Woody biomass made up 32 %, coarse roots 27 %, leaf biomass 3 %, and pneumatophores and seedlings 1 % of the total biomass. More than 70 % of the root mass was located within 40 cm below the surface. Annual litterfall production of A. marina was estimated as 331.94±69.8 - 476.63±66.1 g m-2 y-1, with leaf litter accounting for 66.6 % - 82.3 %. Litterfall production positively correlated with temperature but it did not show any relationship with monthly maximum wind speed nor total rainfall. Leaf litter of A. marina at Mangawhai harbour decomposed rapidly during the first 37-39 days with 50-60 % of the initial dry weight lost. A further ~15-25 % was lost during the following 40 days, after which biomass loss became even slower. Litter decomposition was 96.5 % complete after 332 days with the average (linear) rate of decomposition of -3.99 % per day. From my findings, New Zealand mangroves store a total of 0.2 - 1.1 Mt carbon (C) above-ground and 1.06 - 1.72 Mt C below-ground. This, together with the high carbon density (6 - 9.9kg C m-2), implies that New Zealand mangroves are carbon-rich ecosystems.
An investigation into the reuse of organic waste produced by the New Zealand mussel industry
(Auckland University of Technology, 2004-01-01) Barnaby, Claire; Alfaro, Andrea
Management of organic waste is a major problem for the New Zealand Mussel Industry. Currently most waste is discarded, and this represents a potential loss of both resources and revenue, unless an alternative use for this waste could be developed. Waste types were first identified, then quantified, first seasonally, then annually, to provide an estimate of total industry-wide waste production. Possible uses for this waste were then identified. Little investigative research has been undertaken on identifying alternative uses for mussel industry organic waste. The uses of organic waste as organic fertilizers, and the economic benefit of adding treated waste products to cement mix to improve its compressive strength and thermal insulation, are two primary objectives of this dissertation. The possibility of using mussel shell in agricultural liming as a substitute is also explored. The potential value of pre-grade waste as an organic fertilizer was explored by addition of decomposed tissue to tomato seedlings and by monitoring plant development and condition. Growth of treatment and control seedlings was monitored by counting the number of branches, stem heights, leaf numbers and total biomass. Analyses prove Perna canaliculus pre-grade organic waste has the potential to be exploited as an expensive, effective organic fertilizer, whereas Mytilus galloprovincialis pre-grade organic waste may not. Moreover, there is further potential to develop P. canaliculus pre-grade organic waste into an odourless, chemically stable fertilizer product. The potential value of post-grade waste in cement mixes to improve compressive strength was explored by addition of shell aggregate to cement mix. Analyses indicate that, as an aggregate, mussel shell has little to no structural potential, but does have latent thermal insulating properties. Recommendations are made to: - Separate Perna and Mytilus pre-grade waste products. - Further explore the thermal insulating potential of mussel-shell concrete. - Further explore techniques for treatment of Perna pre-grade waste as a fertilizer. - Further explore the use of crushed mussel shell as a potential limestone or sand substitute for agricultural, construction and engineering purposes. - Explore markets for Mytilus potential export, to reduce pre-grade waste production and problems of resettlement.
Aquatic invertebrate fauna of Matapouri, Northland.
(Auckland University of Technology, 2008) Pohe, Stephen Robert; Alfaro, Andrea; Ball, Olivier J-P
A study of the aquatic invertebrate communities from two locations (Location 1 and Location 2) within the Matapouri catchment in Northland, New Zealand, was conducted to assess community structure in differing local-scale habitats. Four data collection methods were utilised generating 33,058 adult or larval invertebrates. The sampling methods comprised benthic kick-sampling, sticky trapping, light trapping, and emergence trapping. For the sticky trapping and light trapping, sampling was carried out at three different sites (Sites 1–3) within each location. The sites were situated within three habitat types; native forest, native forest-fringe, and raupo wetland. Emergence trapping also commenced within the three sites, at both locations, but was discontinued after two months, due to the equipment being destroyed by consecutive flooding events (method described in Appendix 1). Benthic sampling was carried out within the Forest and Forest-fringe habitats. Benthic sampling, sticky trapping, and light trapping were carried out following a monthly schedule between June and November 2005. Conductivity, pH, and water temperature measurements were taken concurrently with benthic sampling on a monthly basis, while water velocity and substrate measurements were taken once to assist in habitat characterisation. Overall, 71 taxa were recorded by benthic sampling over the six month period, with a mean of approximately 30 taxa per site per month. In comparison with similar studies elsewhere in New Zealand, a figure of around 30 taxa per sample was high. The benthic macroinvertebrate fauna at all sites was dominated by Trichoptera (19 taxa), Diptera (16 taxa) and Ephemeroptera (10 taxa). This pattern of diversity is similar to that reported in other New Zealand studies. However, in contrast to previous studies, the leptophlebiid mayfly genus Deleatidium was not numerically dominant over the rest of the community, and other leptophlebiid genera (Acanthophlebia, Atalophlebioides, Mauiulus and Zephlebia) were equally represented, possibly reflecting niche partitioning between the groups. The genus Nesameletus was not recorded at any site, despite being one of the core mayfly species in New Zealand streams. The rare mayfly Isothraulus abditus was recorded at one of the forest locations. There are no published records of this species from Northland. Although acknowledged as another of the core New Zealand benthic taxa, the hydropsychid caddisfly Aoteapsyche was not recorded during the study. However, another hydropsychid, Orthopsyche, was commonly recorded, and these may be filling a similar niche to the Aoteapsyche genus. In contrast to the Trichoptera, Diptera, and Ephemeroptera, the Plecoptera fauna was relatively depauperate, probably reflecting the warmer climate of the region and lack of temperature-buffered spring-fed streams. Surprisingly, Zelandobius, a core New Zealand genus, was absent but is regularly recorded in Northland. A species of conservation interest, Spaniocercoides watti, currently recognised as a Northland endemic, was recorded in low numbers. There were no apparent trends in diversity or abundance of benthic invertebrates over time. Also, there were no significant differences in species diversity between the two locations. However, in many cases, taxa were more abundant at Location 2. This may have been due to steeper gradients at Location 2, and the consequent effects on substrate size and streambed stability, as all other physical factors appeared similar between locations. Although several significant differences of individual benthic taxa were recorded, no broad effect of habitat (sites) on species diversity was observable. However, at Location 2, abundances were significantly higher at Site 3 (Forest) compared to Site 2 (Forest-fringe). The reasons were uncertain, but may be attributed to higher retention of allochthonous organic materials, trapped by in-stream cover and larger substrates. Investigations of adult stages by sticky traps supported benthic results recording community compositions and abundances dominated by Trichoptera and Diptera. Plecoptera were poorly represented. Location 2 recorded higher abundances of taxa, particularly Ephemeroptera and Plecoptera. Investigations of adult stages by light traps however did not produce any statistically significant differences in abundances between sites, between locations, or between sites across locations, and it is believed to be due to limited sampling replication combined with some biases of light trapping. This study indicates that the aquatic invertebrate community at Matapouri is diverse but also reasonably representative. Several rare or uncommon insects inhabit the catchment. It is therefore important that Iwi and the local Landcare Group, who invited and supported this research, together with the Department of Conservation, continue their efforts in protecting these areas. The resident fauna have the capacity to restock areas downstream, which are intended to be improved and restored through sediment control and riparian management.
Benthic invertebrate assemblages and sediment characteristics
(Auckland University of Technology, 2009) Boyd, Sheree; Alfaro, Andrea; Campbell, Kathleen A.
Cold seep ecosystems in the deep sea are fuelled by chemosynthetic processes based on methane emission to the sediment surface from gas hydrate disassociation, methanogenesis or thermogenic processes. While cold seep ecosystems have been studied in the last three decades worldwide, little is known about New Zealand’s cold seep habitats and associated fauna. A joint German-New Zealand cruise to the Hikurangi Margin in early 2007 enabled biological and sediment sampling to investigate the biological and sedimentological relationships and variability of seeps and their faunal diversity. Multi-disciplinary approaches were employed that included Xray radiography, stratigraphic descriptions, lebensspuren traces analysis, sediment grain size analysis, determination of total organic content, carbonate content and its stable isotopic composition, and analysis of benthic invertebrate assemblages of seep habitats. The results of this study revealed three distinctive habitats and associated fauna based on the sediment characteristics and faunal type. Habitat 1 includes all sites pertaining to Omakere Ridge, a seep-related habitat comprised of layers of very poorly sorted, sandy silt, shell hash and bands of methane-derived authigenic aragonitic carbonate nodules with low total organic content (TOC). Due to the characteristics of the sediments and death assemblages of molluscs, it is inferred that Habitat 1 methane seepage is actively diffusive, waning or dormant. Habitat 2 describes sites that are either non-seep or relic and applies to those at Bear’s Paw and Kaka. Habitat 2 constituted of shell hash overlain with very poorly sandy silt, and low carbonates content and low to medium TOC. Habitat 3 describes non-seep related habitats, and includes all sites of the Wairarapa region and one reference site from Kaka also falls into this category. Sediments for Habitat 3 constituted poorly sorted silt with high TOC and low carbonate content which can be explained by their close proximity to land and converging sea currents. The mineral components of the background siliciclastic sediments for all sites studied originated in the Tertiary mudstone of the East Coast Basin. The characteristics of seep habitats of the Hikurangi Margin were comparable to that of the Northern Hemisphere modern seep counterparts, although the abundance and distributions of seep fauna were low. Results from this research have enhanced our understanding on the spatial and variability of methane fluxes and their affects on the duration of cold seep ecosystems, especially for New Zealand. However, more such studies are essential to increase our understanding of seep sediments and explain disturbance-sediment-benthic invertebrate interactions.
The Bioactive Potential of New Zealand Farmed Abalone (Haliotis iris)
(Auckland University of Technology, 2018) Serpes, Craig; Seyfoddin, Ali; Alfaro, Andrea; Chen, Jack
The pharmaceutical, nutraceutical and cosmeceutical industries are always in search for new bioactive molecules. Though synthetic compounds can be constructed by just studying their intended targets, natural sources can provide an abundance of unique chemical structures that are hard to replicate. These industries utilise the vast biodiversity offered by the ocean, by screening various plants, animals and microbes for bioactive compounds. Marine molluscs, especially those of commercial value, have consistently been shown to contain bioactives. A plethora of bioactives have been isolated from the meat, blood and shell, of commercially viable abalone species. These compounds typically demonstrate antioxidant, antiaging, antihypertensive, antimicrobial or anticancer activities. However, there is a lack of biochemical or pharmacological data on New Zealand endemic black-footed abalone (Haliotis iris) or ‘paua’. So the present study was prompted to primarily determine the bioactive potential of farmed paua. Solvent extraction with either methanol, ethanol, acetone, n-butanol, ethyl acetate, hexane or hot water, was used on grounded paua meat or shell powder. The gravimetrically measured dry yield of these extracts, indicated that a 90 % yield could be achieved for the meat using acetone. For the shell extracts, methanol achieved a yield of 4.5 %. However, neither hot water extracted (HWE)-meat or -shell extracts surpassed 1 %. Fermentation and enzyme hydrolysis processes improved HWE-meat by a factor of 160 or more. FT-IR analysis indicated the presence of uronic acid and the absence of sulphate groups for meat and shell extracts, which were also respectively supported by the carbazole and barium chloride-gelatin methods. The Bradford assay revealed that HWE-meat contained approximately 17.07 mg/ml uncharacterized protein. Fermentation or enzyme hydrolysis broke this down to less than 1 mg/ml. The blood contained only 0.28 mg/ml haemocyanin protein. The DPPH, cupric reducing antioxidant capacity (CUPRAC) and ferrozine assays respectively revealed the free radical scavenging, reducing and metal chelating activities of paua. The solvent-derived meat extracts had weak scavenging activities, but showed low to moderate reducing and metal activities. The measured antioxidant activities of HWE-meat were increased via fermentation or enzyme hydrolysis. The supernatant and pellet of the waste blood, as well as the solventderived shell extracts, demonstrated chelation activity as strong as EDTA (positive control). The blood pellet and supernatant also showed antiaging properties by inhibiting collagenase activity by 59.7 and 61.58 % respectively. HWE-meat and methanol-derived meat extracts were stronger, measuring 71.27 and 68.22 % respectively. Lastly, disc and well-diffusion assays were used to determine the potential antibacterial properties of paua. However, none of the meat, shell or blood extracts had any antibacterial affect against Bacillus cereus, Escherichia coli, Pseudomonas aeruginosa, Proteus mirabilis, Salmonella typhimurium, Staphylococcus aureus, Streptococcus pneumonia and Streptococcus pyogenes. In conclusion, New Zealand farmed paua has antioxidant and anti-collagenase properties which could be utilised in antiaging creams. Additionally, the meat extracts could also be utilised in health supplements. Future studies on these extracts is required to determine if pH adjustments influence activity. Purification and structural elucidation of the bioactive compounds in paua is also required.
Development of an Insect-based Encapsulated Feed for Shrimp Aquaculture
(Auckland University of Technology, 2022) Kyle, Brooke Samantha; Alfaro, Andrea; Masoomi Dezfooli, Sara
The aim of this thesis was to create an innovative shrimp aquafeed with encapsulation technology and varying concentrations of mealworm meal to improve the sustainability of current shrimp aquaculture production. This feed was developed and tested on a non-commercial shrimp species (Palaemon affinis) as a proxy for application of shrimp aquaculture. Laboratory analyses and feeding trials were conducted to compare the encapsulated feed with a commercial feed for P. affinis growth parameters, feed sustainability and effect on water quality parameters. The results indicate that the encapsulated feed had significantly less matrix erosion over 48 hours in seawater than the commercial feed. Additionally, an eight-week feeding trial was conducted to assess the effectiveness of the encapsulated mealworm diets on shrimp. Four diets were used in the feeding trial: a commercial diet (CF) with predominantly fishmeal as the protein source and three encapsulated mealworm diets with varying concentrations of fishmeal: mealworm ratios (F70, F50 and F30). The final weight and length displayed significant differences in shrimp fed higher concentrations of mealworm meal (F50, F30). However, it was discovered that there was a correlation between the weight gain of shrimp and the lipid concentration in the diets suggesting that the weight gain was due to the increased lipids in mealworms rather than the diets themselves. Uniquely, shrimp fed F50 were found to excrete excess lipids in their diets, resulting in no significant difference in bodily lipids in comparison to the lower concentration of mealworm diets. This suggests that shrimp fed slightly elevated levels of lipids than required may be able to discard the excess lipids in their faecal matter. Additionally, feed utilisation, feed ingested, palatability and survival all indicated no significant differences between commercial and encapsulated diets. Overall, the results indicate that an encapsulated mealworm diet can be utilised to enhance water quality parameters in shrimp aquaculture and indicate that alternative, sustainable insect-based protein sources such as mealworms have the potential to replace fishmeal in varying concentrations.
The effects of cryopreservation on the Pacific oyster Crassostrea gigas larval development
(Auckland University of Technology, 2014) Suneja, Shalini; Alfaro, Andrea; Sebatian, Armagan
Aquaculture in New Zealand is an important growing export industry and around 66 % of its total production is exported, which is worth NZ $ 400 million every year. Based on the growth strategy of this industry, the aim is to achieve an annual production of U.S $ 1 billion by 2025. In New Zealand, the Pacific oyster Crassostrea gigas, is a leading cultivated species with significant exports, along with King salmon and the New Zealand GreenshellTM mussel. Pacific oysters are native to Japan, but now are well established in many parts of the world including New Zealand. Most of the culturing for Pacific oyster in New Zealand is conducted using wild seed, the majority of which are gathered in the Kaipara Harbour on the north-western coast of the North Island. However, this source is highly unreliable, for example recent outbreaks of Ostreid herpesvirus-1 (OsHV-1) led to mass mortality of Pacific oyster larvae in 2010 leaving huge losses within this industry. To overcome these natural disasters and seasonal constraints, use of cryopreserved larvae has been suggested by many scientists. With this method of storing, larvae can be thawed to meet hatchery demands at any time. However, the degree of success using cryopreservation technique is highly variable due to lack of optimum protocols which are highly species specific. Furthermore, little is known about the freezing and cooling effects on the viability of larvae and their subsequent development. Previous studies have been focused on high survival rates just after post-thawing but recently the need to study the effect of cryopreservation on the larval quality over a longer time frame has been recognized. Before cryopreservation techniques can be applied to oyster larvae, a good understanding of the basic larval development process is necessary under normal conditions. There is lack of literature available on the detailed larval development under normal hatchery conditions for Pacific oysters. Therefore, the present study is the first to comprehensively describe the various stages of development from D-stage through to settlement of Pacific oyster Crassostrea gigas larvae under hatchery practices. To supplement this project, details of the effect of 2 cryoprotectant solutions (CPA) on the larval development from D-stage through to settlement is provided. To achieve the above aims, we used a multi-technique approach involving light microscopy, scanning electron microscopy, immunochemistry and direct visual observations. The findings indicate that these complementary techniques provide the best approach to investigate the larval stages of Pacific oysters. Both cryopreserved and normal (controls) larvae were assessed for survivability, feeding consumption, shell length, shell morphology, organogenesis and neurogenesis at regular intervals. The methodology of this study included a larval rearing process conducted at Cawthron Aquaculture Park, Nelson. Larval samples were isolated and fixed every alternate day and later transported to Auckland University of Technology on dry ice for further analysis. Raw data for parametric analyses was also supplied by Cawthron Aquaculture Park. Normal larvae (controls) show a linear downfall in survivability with lowest percentage survivability after 19 dpf, when the pediveligers were approaching metamorphosis. Feeding consumption also varied over the total larval period under investigation and was considerably low after 20 dpf. Shell length show a linear increase before showing some constancy near metamorphosis. Shell morphological observations revealed the presence of a prodissoconch I shell at D-stage with flat hinge and a pitted punctuate region further developing prodissoconch II shell characterised by comarginal growth lines at 5 days post fertilisation (dpf). After progressing to umbo (7-15 days old) stage, larvae exhibited well developed umbo and a special feature called postero dorsal notch which is characteristic of the members of Family Ostreidae. Later the larvae developed into pediveligers at day 17-19 and finally secrete dissoconch layer during transition from larval period to spat. D-stage larvae exhibited limited organogenesis with development of alimentary canal. With progression of larval days, a protruding velum with well beating cilia and velum retractor muscles were present. Further development led to appearance to posterior and anterior adductor muscles. An important mantle rejection technique called pseudofeces was also observed. In pediveligers development of functional foot and eye spot occurred along with gill rudiment. During settlement, velum was retracted inside the shell indicating metamorphosis. The larval density during settlement period was quiet low because of accidental exposure to higher dose of UV than normal and secondly it indicates healthy competitive settlement behaviour. During cryopreservation study, larvae were exposed to 2 treatments 10% ethylene glycol + 1% polyvinylpyrrolidone (PVP- 40) + either 0.2 M or 0.4 M trehalose. Three different cooling rates of 0.5, 1, 2˚C min-1 between -10 and -35ºC post-holding were investigated. Results show that there were significant differences in survivability, shell length feeding consumption and organogenesis between controls and both the treatments. Comparison between the treatments (0.2 M and 0.4 M trehalose), revealed that larvae exposed to 0.4 M especially with the cooling rate of 1˚C min-1 performed exceptionally well. Whereas larvae exposed to 0.2 M trehalose exhibit severe abnormalities with 100% mortality by day 15. Feeding consumption was significantly lower than controls and shell size was considerably small. Shell was more or less oblong giving them oval appearance at early umbo stage rather than circular shape. Organogenesis was the worst effective with severe damage to digestive diverticulum and velum. Moreover, larvae at 5-7 days post fertilisation exhibit D-stage instead of progressing towards umbo stage. All the internal deformities were indicative of larval death near future. 0.4 M cryopreservation treatment show somewhat satisfactory results at cooling rate of 1˚C min-1, the survivability and feeding consumption were significantly lower than controls but the survived larvae (658 ± 570) show almost similar development but delayed organogenesis and smaller shell size. This delay of organogenesis and other developmental characteristics were indicative of cryoinjuries sustained at the cellular level. However, the degree of cryoinjury was worse in 0.2 M exposed larvae. These results indicates future potential to cryopreserve Crassostrea gigas larvae using 0.4 M trehalose as cryopreservative agent provided optimum cooling rate which can enhance larval survivability. Finally, documentation of larval development in normal as well as in cryopreserved larvae of Crassostrea gigas in this project increased our understanding of biology of Pacific oyster larvae and fills the existing gap bridging the cryopreservation studies on relevant species. This study is an important step to reduce the commercial hatchery cultivation cost for this species as it will be easier to distinguish healthy larvae from the abnormal ones.
Evaluation and Improvement of Current Computational Tools for Metabolomics Data Analysis
(Auckland University of Technology, 2017) Li, SiMing; Alfaro, Andrea; Kasabov, Nikola
Heavy metal concentrations in the Pacific oyster Crassostrea gigas
(Auckland University of Technology, 2004-01-01) Perera, Percy; Alfaro, Andrea
Heavy metals present in high concentrations in aquatic habitats are bioaccumulated within the tissues of intertidal organisms. The chemical analyses of animal tissues and sediments provide an indication of bioavailability of heavy metals in the environment. Monitoring of the coastal pollution using organisms is widely practiced all over the world.Chemical analysis of the tissues of Pacific oyster, Crassostrea gigas, and river sediments were used in this study to monitor the environmental concentrations, of cadmium, copper, lead and zinc of shallow coastal areas near to the river mouths of Mahurangi, Awaruku, Waiake, Taiorahi and Wairau. All of these river mouths are situated along the northeastern coast of Auckland. Each month, during the period of November 2002 to October 2003, three replicate samples of oysters, and sediments were collected from each of the river mouths for analysis. Three additional replicate samples of oysters were collected separately, in each month in order to calculate the condition index of oysters. Oyster tissues and sediments were analysed with Inductively Coupled Atomic Plasma Emission Spectrometer to detect the concentration levels of cadmium, copper, lead and zinc.The highest level of copper and zinc concentrations in the oyster tissues was observed in the river mouth of Wairau. Wairau river mouth receives water from heavily urbanised and industrialised catchments. A higher concentration of cadmium was observed in the oysters of the river mouth of Mahurangi than in the oysters in the other sites. The reason for this difference could be due to the heavy use of cadmium contaminated fertilizers at the pasture lands situated around the Mahurangi estuary. Therefore, the relationship between the land use of the catchments and the degree of pollution of the estuarine habitats could be established from the data obtained from this study. Higher concentrations of heavy metals were found in the sediments of Waiake, Taiorahi and Wairau compared to the sediments of Mahurangi and Awaruku. Significantly higher level of copper was observed in the sediments of Awaruku. However no clear co-relation was found between heavy metal concentration in oysters and in sediments. Variations of the condition of oysters were closely related to seasonal changes of the life cycle of the oysters. No clear relationship was found between the condition of the oysters and the heavy metal concentration of the river mouth habitats.This study provides evidence that Pacific oysters are good organisms to use as bioindicators of environmental heavy metal levels in shallow coastal waters. The results of this study suggest a clear relationship between the heavy metal concentration in river waters and the land use of the catchment areas of those rivers. The results may be useful in management strategies of the northeastern coastal areas of Auckland.
An investigation of optimal feeding ration and effects of probiotic bacteria on the growth of New Zealand Abalone (Haliotis iris)
(Auckland University of Technology, 2015) Tuterangiwhiu, Te Rerekohu; Alfaro, Andrea; Gutierrez-Maddox, Noemi
Haliotis iris are long-rearing Pāua that take 4-5 years to reach market size (75mm). A clear gap exists within the aquaculture literature regarding the optimal nutrition in the cultivation of New Zealand Haliotis iris. Further, there has been much research across aquatic species to suggest that the use of probiotics can successfully stimulate growth and decrease the time it takes to grow farmed Pāua. The overall aim of this thesis is to first investigate and identify an optimum feeding ration of the currently used formulated feed, which can improve growth and eliminate wastage of nutrients in Haliotis iris. Second, this thesis aims to evaluate the effects of the formulated feed with added probiotic bacteria on the ingestion, digestion, assimilation of Pāua, with the goal to increase growth rates. There are two growth trials in this study, conducted over 10 weeks, both of which used 160 juvenile abalone (20mm). First, the feeding ration trial compared the growth of Pāua samples from three treatment groups, fed on 3 different rations based on bodyweight of formulated feed (1%, 2%, 5%). Formulated feed rations were calculated by taking a percentage of the mean wet weight of all the Pāua in each feeding treatment. The second growth trial compares groups of Pāua fed with a probiotic (2%) and non-probiotic (2%) diet at an optimum feeding ration determined from the first trial. Three multi-strain probiotics were used in this study: Exiguobacterium sp. strain (JHEb1) and Vibrio sp. strain (JH1), and Enterococscus sp. strain (JHLDc). Growth (i.e., shell size, animal wet and dry weights) and survival of abalone were recorded throughout the experiment, with initial measurements at the start of the experiment and every two weeks for a total of 10 weeks. Shell length measurements were obtained by recording the greatest length. Wet weights were measured by lightly drying individual animals using tissues or hand towels for approximately 30 minutes and weighing them to the nearest 0.001g. In addition to these morphological and survival parameters, physiological responses that the abalone exhibited under the probiotic treatment were recorded, with a particular interest in the enzyme functionality and the assimilation of nutrients into the body tissues. For this, biochemical analyses were conducted to identify protein, lipid and carbohydrate contents within the tissue of the experimental animals. The results indicated growth across all treatment groups in both trials as well as a 100% survival rates. For the feeding ration trial the weight gain of the Pāua were higher in the 2% and 5% rations. With regard to shell length, the 1% and 5% groups had greater increase over the 10 week trial. Based on the results of this study, the ideal optimum feeding ration for Haliotis iris is a 2% body weight feed ration. A 2% body weight food ration is enough to sustain the nutritional requirements of Pāua without storing an excess of lipids. The probiotic trial resulted in growth, both weight and shell length, for the probiotic (an average of 8.72g/9.13mm) and non-probiotic treatment (8.91g/11.39mm). However there was no significant difference between the two groups. This suggests abalone that are reared in ideal conditions do not require supplementary probionts to aid their digestive functions. Overall, the conclusions of this research are that probiotics are unlikely to add benefit if used coupled with ideal culturing conditions for the species. It is hoped that the findings of this work will contribute to efforts to minimize the cultivation period of Haliotis iris and will help reduce cultivation costs by making feeding, digestion and assimilation more efficient.
Larval development of the New Zealand mussel Perna canaliculus and effects of cryopreservation
(Auckland University of Technology, 2012) Rusk, Adam Brett; Alfaro, Andrea
The New Zealand green-lipped mussel, Perna canaliculus, is an important aquaculture species. This commercially attractive mussel species contributes over 70% of total aquaculture in New Zealand, with exports in excess of $NZ 220 million. This industry relies heavily on wild-caught spat, which accounts for about 80% of seed requirements in mussel farming. This source of wild spat is unreliable and unpredictable. As a consequence, recent research focus has been directed at successfully rearing larvae to spat within hatchery settings. Previous research has been focussed at achieving high settlement rates, but this is highly variable due to seasonal variations and inconsistent rearing parameters. An alternative approach to utilising seasonally viable larvae is to cryopreserve (freeze) healthy Perna canaliculus larvae and thaw them on demand for hatchery production. This allows a year-round spat supply without the need to condition broodstock for out of season production. However, the success of this method also has been variable, often resulting in low survival rates. Part of the reason for this lack of success is that little is known about the thawing and post-thawing effects on larval viability and subsequent development. Overall, knowledge about the intricate developmental processes involved within the embryo or larval stages is lacking, and no detailed study has characterised these stages of larval development. Therefore, this study is the first to describe, in detail, larval development of Perna canaliculus from embryogenesis through to settlement in a hatchery environment. This project also included the first comprehensive investigation of the effects of cryopreservation for post-thawed trochophore (16 hours post-fertilisation) and D-stage (48 hours post-fertilisation) larvae through subsequent larval development. A multi-technique approach involving visual observations, scanning electron microscopy, histology, and immunochemistry were performed on larval samples collected daily through all stages of larval development over a 21-day rearing period. Cryopreserved and normal larvae were assessed daily through survivability, shell length, feeding consumption, shell morphology, organogenesis, and neurogenesis. Normally reared larvae had decreasing percent survival with the lowest survival values occurring at the pediveliger and post-settlement stage. Feeding consumption also varied over the 21-day rearing time period with a typically high feeding rate up to 15 days post-fertilisation to metamorphosis. Shell length was positively linear with little deviation except near the settlement stage where variations in shell growth were apparent. A low larval density (< 4%) was observed through to settlement and substrate attachment stages, which normally indicates competent settlement behaviour. For these normally reared larvae, embryogenesis was followed to a gastrula stage at 18 hours post-fertilisation, with the appearance of a blastopore, apical sense organ, and enclosing vegetal pole. D-stage larvae had limited organogenesis with the development of an alimentary and nervous systems. Shell morphology on D-stage larvae (2 days old) revealed a flat hinged, pitted punctuate prodissoconch I shell, followed closely by commarginal growth lines within the prodissoconch II shell at 4 days old. The umbo stage (7–17 days old) had further organogenesis development with a protruding beating velum, a well-developed posterior and adductor muscle, velum retractor muscles, and further dissoconch II secretion of the shell with a more rounded umbonate appearance. Neurogenesis had significantly progressed at this stage with paired cerebral, pedal, and visceral ganglia observed. Pediveliger larvae (18 days old) developed a complete nervous system with more innervations and fibres extending throughout the larva. During pediveliger development, a rapid metamorphosis transition occurred with the development of a gill rudiment, eye spot, and functioning foot. The first appearance of a dissoconch shell layer appeared during this transition. Within the cryopreservation study, results showed that there were significant differences in survivability, shell length, and feeding consumption between controls (not cryopreserved) and frozen (cryopreserved) treatments, but no comparable differences were observed among both frozen treatments (cryopreserved at the trochophore stage and cryopreserved at the D-stage) throughout the 21-day development period. At 18 days post-fertilisation, ~23% of control larvae had progressed to competent pediveliger, while <1% of both frozen larvae stages survived. Those larvae that survived were unable to develop to competent pediveliger or post-larvae. Settlement was achieved in ~9% of control larvae at 21 days post-fertilisation with most individuals developing eye spots. Significant differences were observed in neurogenesis between frozen trochophore larvae and controls. Conversely, frozen D-stage larvae did not differ greatly to controls, and differed slightly to trochophore larvae. Characterisation of shell morphology revealed abnormalities to larvae on both frozen treatments. Frozen trochophore larvae showed the greatest shell abnormalities, which suggests that cryo-damage to the shell gland had occurred. Organogenesis was delayed in larvae within both frozen treatments with no larvae within frozen treatments developing an eye spot. However, larvae in controls successfully made the transition to settlement. This delay in organogenesis and overall developmental characteristics were indicative of cryo-injuries sustained at a cellular level. The relevance of this work ultimately fills existing gaps in larval development of Perna canaliculus in normal and cryopreserved larvae. Characterisation of both viable and abnormal larvae through development is of benefit in reducing commercial hatchery costs and understanding the biology of Perna canaliculus larvae.
Nutrient dynamics at Matapouri Estuary, Northern New Zealand
(Auckland University of Technology, 2004) Soliman, Nabil Zaki Gadalla; Alfaro, Andrea
Mangrove forests are an integral part of coastal wetlands in temperate and tropical regions of the world, including New Zealand. These coastal plants act as a shelter, feeding and breeding grounds for marine and terrestrial organisms. Many overseas studies have investigated the importance of mangrove and seagrass habitats in sustaining coastal food chains. In New Zealand, however, only a few studies have addressed the ecology and food web dynamics of these temperate ecosystems. As a first step to investigate the nutrient dynamics of estuarine food webs in temperate estuaries, this study aimed to quantify the nutrient concentrations in the catchment and the estuary of Matapouri, northern New Zealand. Field studies involved the collection of surface fresh and estuarine water (during low and high tides). Plant material (mangrove and seagrass), and sediment samples were collected at various sites within the estuary. Chemical analyses were carried out to determine the concentration of C, N, P and Si macronutrients and Fe and Zn micronutrients during different seasonal rainfall events. The results suggest that mangrove habitats may act as a source of POC, but not DOC for the adjacent aquatic habitats (i.e., seagrass, sand flats, channels), while seasgrass beds contribute more N to the estuarine system than the mangrove forests. The concentrations of N and P nutrients are strongly influenced by both the freshwater inputs and the bio-chemical processes within the estuary. The results obtained point to the freshwater streams as the main source of Si and Fe in the estuary. However, Zn was higher in the estuarine water compared to the catchment freshwater. NO3 -, NH4+, Fe and Zn concentrations showed strong responses to the higher rainfall months reaching their highest level during the winter and early spring seasons. Conversely, P concentrations showed a negative seasonal pattern, which was linked to monthly rainfall events. Mangrove sediments may operate as a sink for the heavy metal Zn in Matapouri estuary. Iron concentration in seagrass leaves exceeded that in mangrove leaves by 65 orders of. magnitude. The study suggests that seagrass plants could be used as a biological indicator of iron concentration in the estuary. The complex dynamics of bio-chemical cycles in Matapouri indicate that each habitat within the estuary has specific nutrient contributions to the estuarine food web system. However, the catchment and oceanic influences must also be considered in the nutrient balance of these coastal environments.
Nutrition and broodstock conditioning of the New Zealand Pipi, Paphies australis
(Auckland University of Technology, 2010) Mamat, Nawwar Z.; Alfaro, Andrea
The New Zealand pipi, Paphies australis, occurs widely around the coast of New Zealand and belonging to the family Mesodesmatidae. Pipi form a part of the recreational bivalve fishery, and there is also an annual restriction of the total commercial harvest. Previous investigations have examined the biological and ecological aspects of pipi in the wild. However, neither of them studied the nutritional requirements of pipi under hatchery conditions. This thesis discusses the feeding requirements of pipi collected from Waiwera Beach and Onehunga Harbour, during their growing and maturing stages. A series of studies on the cell clearance rates, feeding trials, proximate analysis, and broodstock conditioning of pipi clams were conducted over 15 months (September 2008 until December 2009) at the AUT Aquaculture Laboratory. In the cell clearance rates study, the rates for microalgal diets in descending order were Thalassiosira pseudonana > Isochrysis galbana > Chaetoceros muelleri > Tetraselmis suecica > Pavlova lutheri. It is inferred that pipi are capable of filtering a variety of microalgal species while at the same time being a selective filter feeder. The same microalgal species tested in the aforementioned study were fed to pipi of different size classes (spat, juveniles, and adults) in the feeding trials experiment. Three processed diets (baker's yeast, wheat flour, and corn flour) also were tested on the pipi clams. This study was carried out to test the effect of different diets on growth and survivality, and body composition of spat, juvenile, and adult pipi. There were positive relationships between the growth performance (length and weight) and dietary lipid content for spat and juveniles. For adult pipi, the carbohydrate content in the diets was positively related to pipi shell growth. However, proximate analyses of adult pipi at the end of the experiment indicated an overall depletion of carbohydrates in the tissues, while proteins and lipids were accumulated. These results suggest that the gonadal development have initiated during the breeding season. Based on the results of the present study, it is suggested that baker's yeast would be a good substitute of spat and juvenile feeds, and wheat and corn flours would be good substitutes for adult feeds. In the conditioning experiment, broodstock pipi were conditioned with three different diets: exclusively P. lutheri, exclusively corn flour, and a mixed diet composed of P. lutheri and corn flour in 1:1 ration. On days 21 and 28, following the conditioning period, broodstock were induced to spawn by temperature shock treatment. Although both spawning induction trials failed to bring broodstock pipi into spawning condition, maturity was apparent for brooodstock fed the mixed diet of P. lutheri and corn flour, indicating that P.lutheri-corn flour may be a better food source compared to P. lutheri or corn flour alone for pipi broodstock conditioning.
Pharmalogical induction of larval settlement in the New Zealand mussel Perna canaliculus
(Auckland University of Technology, 2009) Young, Tim; Alfaro, Andrea; Robertson, John
The endemic New Zealand green-lipped mussel (Perna canaliculus) is a commercially important species. Although this mussel is extensively cultivated in New Zealand, very little is known about its early larval behaviour. After a brief planktonic stage, the young mussels settle onto specific substrates before undergoing metamorphosis into their adult form. However, the timing of this settlement, and preference for substrata is poorly understood. Chemical stimuli of biological origin that modulate neuronal signalling are thought to mediate this process. Exposure of marine invertebrate larvae to neurotransmitters, their precursors or similar molecules that have the ability to induce larval settlement, have been used in numerous studies to give important insights into the biochemical mechanisms underlying settlement behaviour. In the present study, 16 pharmacologically active compounds were assessed for their effectiveness at inducing larval settlement in P. canaliculus. In the laboratory, mussel larvae were exposed to the chemicals for 48 hours. Among the chemicals tested, potassium chloride, acetylcholine, atropine, epinephrine, L-DOPA, hydrogen peroxide and cyclic adenosine monophosphate induced larvae to settle with minimal acute toxic effects. Exposure of larvae to potassium metabisulphite, sodium metabisulphite, ascorbic acid, caffeine, L-Tryptophan, L-Phenylalanine, and L-Tyrosine induced high levels of larval settlement but were acutely toxic to the mussels. Exposure of larvae to gamma aminobutyric acid had inhibitive effects on the settlement process. These results suggest that such compounds, many of which are present endogenously, are naturally involved in the biochemical signalling pathways of larval settlement. An exploratory meta-analysis was performed on larval settlement responses to various inductive compounds among nine marine invertebrate species, clustering the organisms by similarity of response. This investigation may have identified a novel approach to species clustering; illuminating currently concealed relationships based on the biochemical mechanisms involved in larval settlement behaviours. There also may be considerable applications for using these compounds in aquaculture to provide routine, inexpensive, and effective techniques for inducing synchronous settlement of hatchery-reared larvae. A major concern for the green-lipped mussel aquaculture industry in New Zealand is the limited supply of larvae or juvenile mussel spat for cultivation. To stock farms, the primary source of juvenile mussels comes from ‘beach cast spat’, attached to drifting macroalgae washed up on the foreshore. Considerable effort also is made to catch planktonic larvae on ‘spat catching ropes' suspended in the ocean. In the present study, weakly surface-bound acetylcholine was tested as a spat attractant to determine if the compound has commercial applications in areas other than larval settlement. Results showed no apparent capacity for acetylcholine to modulate chemotaxis in P. canaliculus. The effect of substrate surface charge on the ability of spat to attach showed that mussels have a significant preference for positively charged surfaces. Charged surfaces in the marine environment may modulate the colonisations of particular substrata, and may have commercial applications in promoting or inhibiting biofouling. Another problem suffered in the mussel aquaculture industry is poor retention of mussels on growing ropes. Acetylcholine showed no ability to enhance spat retention in a practical capacity, and neither did alterations of surface charge.
Reproduction and larval development of the New Zealand scallop, Pecten novaezelandiae
(Auckland University of Technology, 2013) de Jong, Neil E.; Alfaro, Andrea; Pook, C.
The New Zealand scallop Pecten novaezelandiae is an important fishery. Wild scallop spat are used extensively to enhance and maintain scallop beds. The current yields of scallops have decreased by over a third in the last decade. A potential solution to increasing the scallop yield and conserving stocks are hatchery grown spat. Most studies related to P. novaezelandiae have concentrated on their ecology and the process and effects of scallop enhancement. This study aimed to fill two gaps in our knowledge of P. novaezelandiae biology by exploring the effects of diet ration on the animal’s gonad maturation and to characterise the larval development from zygote to pedivileger. Wild scallops were collected and maintained in the laboratory for seven days and fed ad libitum. An initial sample of scallops was taken and reproductive condition was compared to that of scallops fed one of three algal diets for thirty days: The diet rations were 0.5g (low), 0.92g (medium) and 1.9g (high) of microalgae per day. The results of the study showed there was a significant increase in the gonadalsomatic index (ANOVA; F3=49.3; p<0.05; n=91), wet gonad weight (Steel, p<0.05), egg size (ANOVA, F3=2.8; p<0.05; n=3773) and colour between the male and female portions of the gonad (p<0.05; n=117). However, colour, wet gonad weight and acini area were not significantly different after 30 days of conditioning. Three lots of scallops were spawned to characterise the key phases of P. novaezelandiae from zygote to pedivileger. Two spawnings characterised P. novaezelandiae from gamete to D-larvae. The embryos were cultured in 900ml of fresh sea water, filtered to one micron for 3 days and sampled randomly. There was 100% mortality by day four. The third spawning saw fertilised eggs placed in a 170L conical tank for three days. The D-larvae were then transferred to six Cawthron Ultra Dense Larval rearing systems (CUDLs), from which larvae were selected every two days for imaging with Light Microscopy and Scanning Electron Microscopy. A strong linear growth for P. novaezelandiae larvae diameter corresponded to 6.5895 × age in days + 74.337. A mean growth of 5.92 µm a day was experienced over 30 days for P. novaezelandiae larvae. A mean (±SE) clearance 65.4±2.59% of the Chlorophyll A was cleared per day over 30 days of feeding. P. novaezelandiae sperm morphology, 2.14 ±0.05 length and 61 ±0.07µm breadth, is similar to the Pecten maximus. Unknown micropores are visible on the nucleus of the sperm. P. novaezelandiae eggs are spawned with irregular shapes and experience meiosis in the first hour. A polar body emerges 15min after fertilisation. The embryogenesis of P. novaezelandiae is similar to other scallop bivalves comprising of a polar lobed, cleavage, cell division, blastula, gastrula and trochophore phases. D-larvae emerge after three days. However, an umbo veliger phase is not obvious and only emerges before around when an eyespot is visible around 23 days post fertilisation [PF]. Approximately 30 days PF a pedivileger emerges. This is the first study in broodstock P. novaezelandiae, and which characterises key growth phases. It is also the first time semi quantitative colour measures have been conducted on the diet concentration of the gonad. Spawning was found to be a barrier to successfully spawning large quantities of scallops.
The reproductive biology of the surf clams Triangle Shell (Spisula aequilatera), Ringed dosinia (Dosinia anus) and deep water Tuatua (Paphies donacina) from the North-East of South Island, New Zealand
(Auckland University of Technology, 2013) Aljadani, Nuha; White, Lindsey; Alfaro, Andrea
Surf clam is an important marine organism which plays vital roles in terms of commercial and ecological roles. Commercial harvesting of them is well established at an international level although still the industry use of them is limited in NZ. To sustainably increase surf clam harvesting at a commercial level, the authorities seek to enhance basic researches, particularly around the reproductive biology of clam species. Thus, throughout this study, the aim is to investigate the gametogenesis and gonadal development of Paphies donacina, Dosinia anus and Spisula aequilatera which the species are economically important in Cloudy Bay environment. To investigate the reproductive biology of the three species, this study employs two different methodologies which are histological techniques and develop a condition index. The study examines samples extracted from Cloudy Bay from Aug, 2012 to Jul, 2013 for each month to determine the seasonal variations in the reproductive biology of the three species. The study uses statistical techniques extensively to generalize the findings from the samples into the Cloudy Bay populations. From the above techniques, the current study has found that there are significant seasonal variations in varying extents in the reproductive cycles of the three species. The findings further have concluded that histological techniques are the most appropriate way to investigate the gametogenesis and gonadal development of surf clams over the condition index. It has been clear that temperature is an important exogenous factor that determines reproductive behaviours of Paphies donacina, Dosinia anus and Spisula aequilatera in Cloudy Bay. In addition, this study provides directions for future studies to extend the knowledge discovered from this research. It is hoped that these findings could minimize the research gaps bound around surf clam investigations in NZ context.
Use of probiotic bacteria to improve the growth of farmed New Zealand abalone (Haliotis iris)
(Auckland University of Technology, 2012) Abass Hadi, Jinan; Gutierrez-Maddox, Noemi; Alfaro, Andrea
Abalone are known to have a very slow growth rate that results in significant financial constraints for its cultivation. Commercially farmed abalone which are given formulated feed consisting of soy flour and seaweed still require 4 to 5 years to attain a market size of (80-100 mm) for shell length. To improve growth in farmed New Zealand abalone (paua), Haliotis iris, potential probiotic isolates were isolated from healthy adult abalone obtained from OceaNZ Blue (Bream Bay, New Zealand) and from farm tanks. The isolates were screened qualitatively according to their ability to hydrolyze feed nutrients (such as proteins, starch, and alginate), produce lactic acid, and resist bile salts. Phenotypic and 16s rRNA techniques were used to identify the potential probiotic isolates. Biochemical analyses to determine which isolate exerted the strongest proteolytic, amylolytic, and alginolytic activities were carried out. This study has developed a multi-strain conglomerate of 2- and 3- probiotic bacterial strains that have been supplemented into a commercial abalone feed to determine if probiotic microorganisms can increase the growth rate of farmed H. iris. The 2-probiotic conglomerate consisted of Exiguobacterium JHEb1 and Vibrio JH1, the 3-probiotic conglomerate consisted of Enterococcus JHLDc in addition to Exiguobacterium JHEb1 and Vibrio JH1. The probiotic feeds were used in a laboratory feeding trial involving abalone juveniles (sized 20-30 mm) to determine if probiotic microorganisms can increase the growth rate of farmed H. iris. Two groups of abalone (in 3 replicates) were fed 2- probiotic supplemented, and 3- probiotic supplemented feed were compared with the control group (3 replicates) administered with un-supplemented feed. Proximate analysis of abalone faeces were performed to determine differences in proteins, carbohydrate, and lipid in all abalone groups and determine if these nutrients were more efficiently metabolized in the presence of probiotic bacteria. A significant growth improvement was obtained with the 3-probiotic supplemented feed that produced a significant shell length increase of 20.9%, wet weight gain of 19.8% and reduced mortality (3.33%) (p<0.05). The 2-probiotic supplemented feed also resulted in significant increase in shell length and survival (p<0.05) but not in weight gain. This study is the first to report of the application of Exiguobacterium JHEb1in abalone. This species was incorporated in both the 2-probiotic and the 3-probiotic feeds. This study is also the first to report that a combination of three probiotic species supplemented into the commercial feed of farmed H. iris increased growth measured by shell length and wet weight.

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