Sample list of PhD Dissertations in Aquaculture and Related Fields 2012

Barbara McLain, University of Hawaii-Manoa, Unpublished Manuscript, Honolulu, HI

Farming shrimp for the future: A sustainability analysis of shrimp farming in ChinaCao, Ling. University of Michigan, 2012. 3519549.

Abstract (summary)

The intensification of the shrimp farming industry has generated much concern over its environmental,

social and economic sustainability. The objective of this dissertation was to conduct a comprehensive

sustainability analysis for Chinese shrimp farming. My results could be utilized to evaluate and

improve shrimp production systems in terms of environmental sustainability, economic profitability, and

social acceptability.

Life cycle assessment was conducted to evaluate environmental performance of differentshrimp farming

systems. Intensive systems had higher environmental impacts per unit production than semi-intensive. The

grow-out stage contributed on average 95% of the overall impacts, mainly caused by feed production,

electricity use and effluents. To produce 1 tonne live-weight of shrimp in China, 38.3±4.3 GJ of energy and

40.4±1.7 tonnes of net primary productivity were required, and 23.1±2.6 kg of SO 2 equivalents (eq),

36.9±4.3 kg of PO4 eq, and 3.1±0.4 tonnes of CO2 eq were generated. Changes in feed composition, farm

management, electricity generating sources, and effluent treatment may result in future improvement.

Mathematical models were developed to study nutrient dynamics and the effects of management strategies

on nutrient dynamics and discharge. Management strategies had significant impacts on nutrient dynamics.

Nutrient loading increased with farm intensity. On average, approximately 701 kg N ha -1 cycle-1 (100

days/cycle) and 176 kg P ha -1 cycle-1were unutilized and wasted. Of them, 120 kg N ha -1 cycle-1 in

dissolved form and 62 kg P ha-1 cycle-1 were discharged with effluents. Moderate stocking density and

reduced water exchange could minimize environmental impacts of pond effluents and achieve high

production.

A socioeconomic survey of 100 shrimp farms was conducted to evaluate system profitability, disease risk,

and changes in quality of life. Production costs per kilogram ofshrimp were highest in intensive systems

($2.70), followed by semi-intensive ($2.10) and polyculture ($1.05) systems. Intensive systems had

significantly higher profits ($9,500 ha -1crop-1 ) than the other two systems (< $7,300 ha-1 crop -1 ). If disease

occurred, an average of 78% and 36% of shrimp would die in the worst and most probable cases,

respectively. Disease had highest influence on the intensive systems. Quality of life of farmers was

significantly improved by shrimp farming.

_____Seafood consumption and use of Asian herbal preparation as a source of exposure to multiple trace elements in the Study of Metals and Assisted Reproductive Technologies (SMART)

Kim, Dongsul. State University of New York at Albany, 2012. 1515734.

Abstract (summary)

As, Cd, Cs, Hg, Pb, and Zn may be associated with in vitro fertilization (IVF) outcomes. Seafood and

Asian herbal preparations are identified as sources of exposure to these essential and non-essential trace

elements in humans. The goal of the study is to assess associations between seafood consumption and the

use of Asian herbal preparations and levels of essential and non-essential trace elements in biologic

specimens collected from couples undergoing IVF. Fifty-nine couples completing a first IVF cycle at the

University of California, San Francisco (UCSF) Center for Reproductive Health were recruited to

participate in the Study of Metals and Assisted Reproductive Technologies (SMART). Of these, 25 women

and 15 men who completed a dietary questionnaire and provided blood and/or urine specimens were

included to the analyses. Urine specimens were analyzed for As, Cd, Cs, and Zn and blood specimens were

analyzed for Cd, Hg, and Pb using inductively coupled plasma-mass spectrometry (ICP-MS). Bivariate

analyses and multiple linear regression analyses were used to assess associations between the levels of trace

elements and various dietary exposures, considering potential confounders. Blood Hg and urine As levels

are higher than reported for the U.S. population. Women have higher blood and urine Cd level than men.

Final multivariable linear regression models are constructed for each element, adjusting for potential

confounders. Several seafood groups are associated with increase in the study elements, including 'any

fish', 'shellfish' and 'mollusks' for blood Hg, 'steak fish' for blood Pb, 'farmed fish' and 'shrimp' for blood

Cd, 'canned fish' for urine As, `any fish', `steak fish' and `canned fish' for urine Cs, and 'canned fish' for

urine Zn. Some seafood groups are associated with decrease in the trace elements, including 'farmed fish'

for blood Pb, 'eel' for blood Cd, 'sashimi' and 'tuna' for urine Cd, and 'raw fish' for urine As. Asian herbal

preparations are not significant sources of exposure to any element. Information from this study can be

used to advise IVF couples or infertile couples on dietary and behavioral choices to maximize the

probability for a successful reproductive outcome.

_______Understanding physiological responses and development of stress biomarker from tilapia treated with vitamin C during chronic stress induced by crowdingAbu Hayat, Md Sharif. Purdue University, 2012. 1529890.Abstract (summary)

Experiments were conducted to investigate: i) the effects of vitamin C as a nutraceutical in modulating

stress and ii) usability of expression of the genes adrenocorticotropic hormone (ACTH) receptor and

corticotropin releasing hormone (CRH) as stress biomarkers. Tilapia (Oreochromis niloticu s) fingerlings

were obtained from a local fish farm and were acclimated in the new environment for four weeks. After the

acclimation period, fish were maintained in two different conditions - controlled and stressed (by crowding;

density > 50 g/l). Within each condition, fish were further divided into two diet groups, each with two

replicates, and were fed vitamin C supplemented (@1000 mg/kg feed) and vitamin C free feed, separately

for fifteen days. Six fish from each group were sampled to assess the physiological parameters - plasma

cortisol, blood glucose, plasma protein, packed cell volume, spleen somatic index, and condition

factor. Fish in the stressed conditions showed significantly higher level (P<0.05) of plasma cortisol and

blood glucose indicating stress, both of which were reduced when fed vitamin C supplemented diet.

Significantly higher (P<0.05) hematocrit concentration was observed in the vitamin C fed group indicating

better adaptation. To fulfill the second objective, reverse transcription-polymerase chain reactions (RT-

PCR) were carried on mRNA collected from brain and head kidney tissues. In all samples, almost equal

expression of β-actin, the housekeeping gene was observed. As for the two genes involved in stress

response pathway, CRH expression was not detected in any of the experimental groups whereas ACTH

receptors were clearly expressed in one of the stressed groups. Therefore, we suggest that instead of CRH,

which may not be an ideal candidate, further research be performed to establish ACTH receptors as a

genetic expression biomarker of stress.

______Nutritional contribution of phytoplankton to the Pacific white shrimp Litopenaeus vannamei

Sanchez Corrales, Dagoberto Raul. Texas A&M University, 2012. 3524942.Abstract (summary)The goal of this study was to characterize the nutritional contribution of microalgae to white-legged shrimp and optimize fish meal (FM) and fish oil (FO) inclusion levels in their diets in the presence of microalgae. Phytoplankton composition was first determined in a typical Peruvian intensive commercial shrimp farm and in a semi-closed greenhouse-covered reservoir. A predominance of 76.3% cyanobacteria was observed for most of 9 months in all shrimp ponds. However, with the fertilization program in a reservoir tank, 60.7% diatoms and 22.8% cyanobacteria predominated. Thus, with the imposed fertilization regimen, the microalgae composition was manipulated to be different than that in commercial shrimp ponds. The microalgae composition was then evaluated along with different dietary levels of FM and squid meal (SM) in a feeding trial to evaluate the potential of phytoplankton to reduce FM and SM levels in shrimp feeds. Six diets were formulated to contain either 5, 10 or 20% SM combined with either 6.5 or 12% FM. Dietary effects on growth and survival were compared in a "clear-water system" (CWS) and a "green-water system" (GWS). Results suggest that 6.5% FM and 5% SM can be used as a cost-effective combination in feeds for shrimp.The effects of different dietary levels of FO and soybean lecithin (LT) on shrimp growth in CWS and GWS were evaluated in another feeding trial to determine if dietary phospholipids and phytoplankton increase the availability of essential fatty acids (EFAs) to shrimp. Six diets were formulated to contain 1, 2 or 3% FO combined with either 1 or 4% LT. Shrimp fed diets containing 1% LT and 1% FO in both systems had significantly lower weight gain and higher feed conversion ratio. Cephalothorax lipids and phospholipids were higher in shrimp fed diets containing 4% LT. Inclusion of 4% LT increased the availability of EFAs, and could contribute to reduce the FO in shrimp diets. The contribution of phytoplankton to shrimp weight gain, varied from 38.8 to 60.6%.This study demonstrated that cost-effective diets could be formulated with reduced inclusion levels of FM and FO considering the contribution of microalgae to the nutrition of shrimp._____

Pond management approaches and effects on trophic dynamicsSherman, Michael Scott. Mississippi State University, 2012. 1530714.AbstractMississippi has an abundance of ponds which provides a number of opportunities for anglers. Several enhancement strategies are used to improve fish production in ponds, including fertilizing and supplemental feeding. These strategies may ignore the potential ecological impacts that may unexpectedly arise, such as prolific plant growth. This study consists of two phases; first, a mesocosm experiment investigating fertilizer application rates (mg P/L) in relation to potential sunfish growth, and second, a replicated pond experiment consisting of four treatments to simulate commonly used enhancement strategies. Mesocosm experiment showed a peak of sunfish growth at the 0.6 mg P/L level and served as a high fertilizer threshold level in pond experiment. Ponds were surveyed to assess treatment effects on each trophic level. The costs associated with each pond management strategy were documented. Results from this research help refine management recommendations to maximize results while minimizing costs to landowners and ecosystems.

_____ Regulation of thyrotropin mRNA expression in red drum, Sciaenops ocellatusJones, Richard Alan. Texas A&M University, 2012. 3532178.

Abstract (summary)The role of thyroid-stimulating hormone (TSH) in the regulation of peripheral thyroid function in non-mammalian species is still poorly understood. Thyroxine (T4 ), the principal hormone released from the thyroid gland in response to TSH stimulation, circulates with a robust daily rhythm in the sciaenid fish, red drum. Previous research has suggested that the red drum T4 cycle is circadian in nature, driven by TSH secretion in the early photophase and inhibited by T4 feedback in the early scotophase. To determine whether TSH is produced in a pattern consistent with driving this T4 cycle, I developed quantitative real time RT-PCR (qPCR) techniques to quantify the daily cycle of expression of the pituitary TSH subunits GSUα, and TSHβ. I found that pituitary TSH expression cycled inversely to, and 6-12 hours out of phase with, the T4 cycle, consistent with the hypothesis that TSH secretion drives the T4 cycle. To examine the potential role of deiodinases in negative feedback regulation of this TSH cycle, I also utilized qPCR to assess the pituitary expression patterns of the TH activating enzyme outer-ring deiodinase (Dio2) and the TH deactivating enzyme inner ring deiodinase (Dio3). Whereas Dio2 was not expressed with an obvious daily cycle,Dio3 was expressed in the pituitary mirroring the TSH cycle. These results are consistent with T4 negative feedback on TSH and suggest that TH inactivation by pituitary cells is an important component of the negative feedback system. To further examine the TH regulation of this Dio3 cycle, I developed an immersion technique to administer physiological doses of T3 and T4 in vivo. Both hormones persist in static tank water for at least 40 hours. Immersion in 200ng/ml T4 significantly increased both plasma T4 and T3within physiological ranges above control at 4.5 hours. Immersion in 100ng/ml T3 increased plasma T 3 within physiological ranges over control by 22 hours while significantly decreasing plasma T4 below control, presumably through inhibition of TSH secretion. T4 also significantly inhibited the expression of the TSH α and β subunits at 4.5 and 22 hours of immersion whereas T3 immersion significantly inhibited the expression of the α and β subunits of TSH by 22 hours. Both Dio2 and Dio3 expression were significantly diminished by T3 and T4 at 22 hours. Inhibition of circulating THs with the goitrogen methimazole significantly increased the expression of TSH. These results indicate that both T4 and T3 are capable of negative feedback regulation of TSH expression in red drum on a time scale consistent with the T4 daily cycle, and further support Dio3 destruction of THs in the pituitary, potentially regulated by circulating T4 , as a critical component of negative feedback on TSH. This study supports the importance of central mechanisms acting through pituitary TSH secretion in regulating thyroid function in red drum.

Molecular characterization of rainbow trout Zar1 and Zar1-like genes: their potential roles in egg qualityLin, Chieh-Hung. West Virginia University, 2012. 1520631.

Zygote arrest 1 (Zar1 ) is a maternal-effect gene that is essential for early embryonic development. Recently, a novel gene called Zar1-like (Zar1l ) was discovered. Functional studies showed that Zar1l plays an important role in regulating oocyte-to-embryo transition in the mouse. The objectives of this study were to characterize the rainbow trout Zar1 andZar1l genes and evaluate the potential roles of these genes in controlling egg quality in rainbow trout. Through database mining, we identified the cDNAs encoding rainbow troutZar1 and Zar1l. The Zar1 cDNA codes for a protein of 333 aa ,and the Zar1l cDNA encodes a protein of 323 aa. The sequences at the C terminus of the two proteins are highly conserved and contain a conserved Zinc-binding domain. Analysis of tissue distribution by RT-PCR showed Zar1 is predominantly expressed in ovary and testis with minor expression in other somatic tissues, while Zar1l is exclusively expressed in ovary. The expression patterns of Zar1 and Zar1l genes during early embryonic development (0h, 7.5h, 10.5h, 19.5h, 2d and 7d post fertilization) were determined by quantitative real-time PCR analysis. Both genes are highly expressed in unfertilized oocytes (0h), but they show different expression patterns. While the expression of Zar1 gene decreases from 0h to 10.5h post fertilization, and then increases in 2d embryos, the Zar1l gene shows continuous reduction of expression during early embryonic development (from 0h to 2d embryos). The expression patterns of Zar1 and Zar1l genes during ovarian development (pre, early, middle, and late vitellogenesis) were also determined by quantitative real-time PCR analysis. Both genes showed high expression in pre-vitellogenesis and reduced expression in early and middle vitellogenesis. In late vitellogenesis, expression of Zar1 gene increases again, but Zar1l gene expression continues to decrease. To determine the role of Zar1 andZar1l genes in controlling egg quality, we analyzed the expression of both genes in eggs of different qualities (Day1, Day7, and Day14 post-ovulation). Both genes showed reduced expression in eggs of low quality. Finally, we performed a yeast-two hybridization screening to identify proteins that interact with Zar1l protein. Five proteins showing interactions withZar1l protein were identified which include Di-N-acetylchitobiase, Serine/threonine/tyrosine-interacting protein (STYX), Ariadne-2 homolog, GH20 HexA HexB-like, and C-type mannose-binding lectin.

______Effects of fish on emergent insects and their transport of methyl mercury from pondsTweedy, Brent Norris. Texas Christian University, 2012. 1510231.

Abstract (summary)Methyl mercury (MeHg) is an environmental contaminant affecting the health of wildlife. It was once thought that only aquatic consumers were at risk of MeHg contamination, but we now know emergent insects transport MeHg from aquatic systems to terrestrial food webs (MeHg flux). Factors regulating MeHg flux in emergent insects are currently unknown. This study tests the hypothesis that fish predation regulates insect emergence and flux of MeHg. The experiment utilized five ponds stocked with fish and five ponds without fish. Floating emergence traps were used to capture emergent insects. Fish significantly suppressed Hg flux in dragonflies and damselflies, significantly enhanced MeHg flux in caddisflies, and did not affect Hg flux in midges. Total MeHg flux was significantly greater in ponds without fish. This is the first study to show that fish have complex direct and indirect effects on insect emergence and the flux of MeHg out of ponds.

________________________Flatfish stock enhancement: Examining conditioning strategies to promote successWalsh, Michelle Lynn. University of New Hampshire, 2012. 3533711.

Abstract (summary)Conditioning is the process of providing individuals reared for stock enhancement with some degree of "wild" experience prior to release. Flatfish trained for "wild" conditions may more easily and successfully transition to natural environments. This dissertation identifies strategies that optimize feeding-related performance of flatfish in the hatchery and subsequently post release in the wild.The influence of live feed conditioning on feeding performance of juvenile winter flounder,Pseudopleuronectes americanus , was investigated. In the hatchery, fish reared on live feeds exhibited significantly higher survival (P < 0.0001) and growth (P < 0.01) than those reared on formulated feed. Once released into cages in the wild, amphipodreared fish had higher mean Stomach Contents Index

and RNA/DNA of all feed types, including wild fish. Wild and worm-reared fish exhibited the most similar survival, baseline RNA/DNA values, overall stomach fullness, and diet composition profiles over time.Pre-release, experimental cage conditioning was conducted for stocking Japanese flounder,Paralichthys olivaceus , in Wakasa Bay, Japan. Recaptured fish were acquired through a cooperative effort between researchers and local fishermen. More conditioned fish were recaptured than non-conditioned fish. Laboratory experiments revealed that conditioned fish had significantly better burying abilities (p < 0.001) and enhanced feeding abilities compared to non-conditioned fish.Video trials were conducted with Japanese flounder to assess the behavior of reared fish directly from hatchery tanks, cage-conditioned, and released-and-recaptured, compared to wild fish. Wild fish buried and attacked most, followed by conditioned, reared-and-recaptured, and non-conditioned fish. Wild and conditioned fish revealed much lower variation in total movement duration, which corresponded with lower levels and variation in prey vertical movement. All fish exhibited a lower number of attacks and off-bottom swimming events, and a lower movement duration when exposed to a moving predator model.The present research provides information that may promote advances in feeding strategies for flatfish stock enhancement. This work is the first to examine flatfish conditioning strategies using market data and to evaluate the behavior of hatchery-reared flatfish that have been cage-conditioned or released-and-recaptured. In addition, evidence of enhanced performance by cage-conditioned flounder is provided.

____________Is Ecosystem-Based Management Necessary for Adaptation to Sea Level Rise in Shrimp Growing Areas of the Mekong Delta?Riccio, Ralph W.. University of Washington, 2012. 1528984.

AbstractThroughout history, society has relied on natural capital provided by the surrounding environment. The most successful societies have been those that have been able to adapt their practices in order to take advantage when changes occur in their environment. In the face of climate change, however, societies around the world are threatened by accelerated environmental change. Ecosystem-Based Management (EBM) has been suggested as a way to increase the resilience of vulnerable communities to impacts of climate change, but may be difficult to implement because information on the connectivity between various parts of a system is frequently lacking. This is especially the case in developing countries. The Mekong Delta of Viet Nam is inhabited by 17.6 million people and is an economically valuable region, producing nearly $2.5 billion USD in shrimp per year for export. With an elevation at or below one meter, the area is particularly vulnerable to climate change impacts including specifically, sea level rise (SLR). The national government of Viet Nam is exploring both hard and soft solutions to protect this highly productive delta. Through this study I explore three case studies to determine the extent to which EBM is necessary to maintain adaptability in shrimp growing areas. From these case studies I conclude that, while there are a variety of initiatives under way that do not acknowledge all components of EBM, those that are most promising are adaptive in nature and can address future uncertainty by maintaining flexibility. However, while these solutions are likely to maintain a greater number of ecosystem services, they sacrifice short-term economic productivity. I discuss lessons learned, limitations of an EBM approach, and provide recommendations for large-scale adaptation to SLR through an integrated mangrove shrimp green belt in the Mekong Delta.

_____Survey of resource use efficiency and estimation of carbon and water footprints in fish farming systems using life cycle analysisHagos, Kifle Woldesilassie. University of Rhode Island, 2012. 3522633AbstractResource use efficiency in fish farming systems is a critical area of concern to stakeholders in the seafood industry. Fish farming systems have varying degrees of efficiency of resource use thus have differential impacts on the environment and/or human health. This study addressed the sustainability in fish farming by measuring resource use efficiencies of five fish farms and eight fish hatcheries using life cycle analysis (LCA). Farm input and output data were analyzed using FoodCarbonScope , and results were reported as carbon dioxide emissions (CO2 e/kg output), energy consumption (MJ/kg), and water use (L/kg) from farm operations. Comparative analyses were made among fish farms and hatcheriesand terrestrial animal food

products (chicken, beef and pork) from published literature. CO2 emissions from five fish farms indicated that cobia cage farm had the highest emissions at 8 kg CO2 e/kg fish output. An Asian sea bass recirculation farm had the lowest emissions at 1.7 kg CO2 e/kg fish output. The high CO2 emissions from the cobia cage farm were due to feed use (60%). Feeds were delivered to the farm in Panama from Chile and Peru, an average of 5,600 km. Feed for the Asian sea bass farm, on the other hand, came from a distance of 880 km. The cobia cage farm consumed the highest energy with 123 MJ/kg and Asian sea bass recirculating system the lowest, at 21 MJ/kg. Feed transport was the main source of energy consumption. Among the three recirculating fish farms, tilapia farm (VA) had the highest water use with 403 L/kg and a sea bream farm (NY) used 39 L/kg.This study confirmed that in fish farming systems, feed production, processing and transport were the main sources of CO2 emissions and energy consumption. Recirculating systems used filtration systems of low water use. Finally, comparing fish and chicken, beef and pork on CO2 emissions we found that chicken was comparable to fish having the lowest emissions followed by pork. On energy consumption fish and chicken were more energy efficient followed by pork and beef. Water use in fish systems is more efficient followed by chicken and pork. Beef used almost 140 times (on average) more water than fish.______The social and environmental effects of shrimp mariculture: Case studies of two coastal villages in EcuadorCrider, Mary C.. Florida Atlantic University, 2012. 1517816.AbstractShrimp mariculture expansion in developing countries has been criticized for its ecological destruction and the resulting social conflicts. In Ecuador, shrimp pond development particularly affects rural, coastal communities. This study addresses the environmental and social effects of shrimp farming in two Ecuadorian villages, Muisne and Bunche. Interview and survey responses indicate that locals have an overall negative view of the industry. In some instances, such as increased class marginalization through reduced access to subsistence collection areas, shrimp farming directly results in conflict. However, the data also demonstrates that ponds are only one of various stressors on mangrove ecosystems. Furthermore, mariculture provides benefits to the community, including increasing employment opportunities, the local economy, and shrimp availability. In spite of these benefits, local negative perception suggests modifications to existing regulations and educational programs are necessary to minimize impacts and help the community understand the multiple factors affecting their ecosystem and livelihoods.

_________A Comprehensive Analysis of Marine Recirculating Aquaculture Effluent Treatment

Guerdat, Todd Cameron. North Carolina State University, 2012. 3520890.

Abstract (summary)The development of marine aquaculture is limited by the cost of coastal land and the inherent limitations in the management of saltwater effluent. Greater oversight of nutrient discharge has brought about the need to develop ecologically-sound wastewater treatment systems for marine aquaculture. To promote further development of marine aquaculture, a renewed focus on the capture and storage and a reduction in the cost of treatment of the saline wastewater is required such that facilities may be located further inland.The Marine Aquaculture Research Center (MARC) was developed for the purpose of promoting marine recirculating aquaculture research and is operated by the Department of Biological and Agricultural Engineering at North Carolina State University. The MARC utilizes recirculating aquaculture systems (RAS) for all ongoing marine aquaculture research inside the facility. All effluent from the ongoing RAS operations is treated in a multi-stage wastewater treatment facility prior to discharge or reuse of the treated effluent. The wastewater treatment system consists of a primary solids removal stage and a dissolved nutrient treatment stage. The primary solids removal stage employs a geotextile bag system using a flocculant-aid to improve solids removal from the waste stream. The dissolved nutrient treatment stage consists of two separate biological treatment systems: a conventional biological filtration system and a constructed treatment wetland system. Each system is separate and was evaluated to determine the treatment performance using marine aquaculture effluent.Geotextile bag systems using flocculant-aids offer a low cost, low energy, highly efficient means for capturing and dewatering waste solids from a RAS effluent. Two separate geotextile bag systems were

evaluated using either freshwater or marine RAS effluents. The results were compiled to provide consistency and determine any potential differences between marine and freshwater systems. Results from the two separate geotextile bag systems were similar and showed excellent nitrogen, chemical oxygen demand (COD), total suspended solids (TSS), and phosphorus removal. The resulting filtrate was high in total Kjeldahl nitrogen (TKN) and soluble reactive phosphorus (SRP).The conventional biological filtration system is a two-stage reactor system operated in series employing an anoxic fixed bed bioreactor (FBBR) and an aerobic mixed bed bioreactor (MBBR), operated in triplicate. The treatment system effectively converted and removed nitrogen at a suitable rate to support the ongoing operations inside the facility. The study provided both realistic TN removal rates as well as operational COD:TN ranges for maximizing the efficiency and performance of the FBBRs.The second dissolved nutrient treatment system was a two-stage constructed treatment wetland system employing a combination of subsurface vertical flow (VF) and free water surface (FWS) flow wetland cells, each operated in triplicate. Variation of treatment performance was observed due to seasonal effects. The constructed treatment wetland system successfully treated the wastewater prior to discharge. A portion of the treated effluent was successfully reused in a 1.5 m3 marine RAS growing Hybrid Striped Bass (Morone saxatillis ).The dissertation presented herein is a series of three separate manuscripts written for the purpose of publication upon the completion of the doctoral degree program. The first manuscript details the work using the geotextile bag systems for the purpose of solids removal and dewatering for RAS. The second manuscript details the denitrification and nitrification processes utilized in the two-stage biological reactor system and the limitation excess organic carbon may impose on the removal of TN. The third manuscript is an evaluation of a constructed treatment wetland system treating the effluent from a marine RAS facility. Each of the studies described in this dissertation provide a unique understanding of the required wastewater treatment processes for marine recirculatingaquaculture.

_________Quantifying the nutrient bioextraction capacity of restored eastern oyster populations in two coastal bays on Long Island, New York

Sebastiano, Daria. State University of New York at Stony Brook, 2012. 1515695.

Abstract (summary)Degradation of coastal areas due to eutrophication is becoming evident on a global scale. Like many estuaries, Jamaica Bay and Great South Bay, NY have been impacted by eutrophication at varying degrees. The eastern oyster, Crassostrea virginica , has been suggested as a way to remediate eutrophication through nutrient bioextraction. Eastern oyster populations were once abundant in both Jamaica Bay and Great South Bay. Overfishing, habitat destruction, and pollution have caused ecological extinction of populations in these regions. The abundance of oysters that once existed in these regions may drive the desire for restoration in these areas. Although appealing, invested individuals must be cautious to start restoration based on historical populations as indicators of potential for restoration. In order to determine the potential of eastern oysters to act as bioextraction tools in these areas a two year aquaculture-based assessment in Jamaica Bay and a five month aquaculture-based assessment in Great Bay were implemented. Our assessments revealed fast growth rates in shell height and tissue growth in these regions. Mean values of shell and tissue growth in the first-year season of growth (mid-June to mid-October) in Jamaica Bay 2010 were approximately 50.40mm and 1.54g, respectively. In 2011 in Great South Bay mean values over the same growth period were approximately 33.64mm and 0.84g. Results also showed high cumulative survivorship by the end of the first growing season. Average cumulative survivorship was 95.5% in Jamaica Bay and 75.5% in Great South Bay. Information from these physiological assessments was combined with a quantification of nutrient assimilation by oyster tissue and shell. Total nitrogen content of aquacultured oysters was of particular interest and was quantified by measuring total nitrogen content in the tissue and shell of oysters after the first growing season. Results reveal the average sized oyster to be approximately .19gN in Jamaica Bay and .11gN in Great South Bay.______

Hemoglobin type, egg buoyancy, and antifreeze glycoprotein production as mechanisms for adaptive variation in Gulf of Maine Atlantic cod (Gadus morhua)Clapp, Amanda R. University of New Hampshire, 2012. 1521548.Abstract (summary)Three physiological traits were examined to compare captive populations of winter- and spring-spawning cod from the Gulf of Maine, as differences in these traits have been observed in other locally-adapted subpopulations. Daily mean neutral buoyancy ofhatchery-spawned eggs was observed at three temperatures (5, 10, and 12°C) and three photoperiods (15:9, 9:15, and 24:0 L: D) at 12°C. Body fluids of larvae held at 0°C for five days were tested for antifreeze glycoproteins (AFGPs) to determine the onset of AFGP production. Juveniles held at 0°C were bled between 20 and 35 days to determine induction time for AFGP production. Hemoglobin type was determined by isoelectric focusing of blood from hatchery-reared adults. No significant differences were found in mean neutral buoyancy (∼1.024 g/mL) or hemoglobin type (mostly HbI-1/2). No AFGPs were detected in larvae. AFGPs were first produced by juveniles on day 30, although no AFGP production differences were found between populations.

__________Moral Economy Meets Global Economy Negotiating Risk, Vulnerability and Sustainable Livelihood among Shrimp Farming Households in Vietnam's Mekong Delta

Vu, Hong Anh. Syracuse University, 2012. 3510004.

Abstract (summary)Market liberalization has enabled Vietnam to make substantial economic improvements, but it has also widened wealth disparities. My dissertation examines the process of social differentiation among shrimp farming households in Vietnam's Mekong Delta. I use the ways these households perceive and experience risk and vulnerability as a lens for understanding their situation. The study finds that farming households across the socio-economic spectrum have experienced intensified risk and livelihood vulnerability even as significant economic gains have been made, turning the country from a net food importer in the late eighties to a major agricultural exporter in the world today. This pattern is rooted in the imbalance resulting from two simultaneous processes: (1) fundamental structural transformations in property and production relations resulting from promotion of an export-led growth model that typically transfers risks in the production process to poorer farming households; and (2) weakening and/or loss of social and physical buffers. The latter includes the breakdown of informal safety nets such as kin and neighbor relations, communal bonds, gender relations and integrated families; and the loss of access to common property resources. While both risk and vulnerability are socially differentiated, households that occupy the lower end of the wealth ladder have to bear a disproportionate share of the risk burden channeled down by commercial shrimp aquaculture engaged in by the rich and better-off. By juxtaposing and contrasting globalization-induced changes with a subsistence economy, this study highlights the ways in which rural households perceive and respond to the structural transformations and changes in their living environment, and the implications thereof for sustainable livelihoods.Vibrant Risks: Scientific Aquaculture and Political Ecologies in China

Huang, Yu. University of Washington, 2012. 3542142.

Abstract (summary)This dissertation examines how the dissemination of science in shrimp aquaculture is intertwined with issues of sustainability and risks in south China. In the Leizhou Peninsula of Guangdong Province, shrimp aquaculture took off in the mid-1980s with the dissolution of collective farming, when farmers were encouraged to become enterprising and independent shrimp farmers who produced an export-oriented commodity. In the early 2000s, after the exposure of illicit drug residues created trade barriers for farmed shrimp from China, the focus of science and technology extension shifted from disease control to food safety. The change from food quantity to quality reflects how the global food regime promotes a discourse of sustainability that is hinged on dynamic growth of limits in response to capitalist crisis.I explore how shrimp farmers have experienced the paradox of being incited to do high-intensity farming on one hand, while assuming a heavy burden of risk on the other. To experience this risk at first hand, I rented a shrimp pond from a village to conduct experimental shrimp farming myself. This was an excellent ethnographic gambit as villagers were eager to teach me the ins and outs of shrimp farming, yielding rich

insight about why they inadvertently face a drive for overproduction but suffer from depreciation of labor values as well as heightened risk of disease. This "treadmill effect" of forever increasing the intensity of farming cannot happen without the involvement of extension agents and scientists. Using methodologies developed in Science and Technology Studies to study laboratory scientists, I adapted these to the study of field science to examine how the science and technology of disease control and food safety standardization might generate new risks. While predicated on excluding the observed pathogens and hazards, these technologies disregarded the vitalities of unobservables. I examine how forms of nonhuman agency emerge from developmental schemes pushing for high-intensity production by looking at the complex dynamics between the biological materiality of the shrimp species themselves, the emergence of new pathogens, and the innovation of pharmaceutical technologies as a means of "crisis management" that mimic the increasingly unstable conditions of global capital accumulation.External costs of aquaculture and the effects on Scottish salmon

Gehring, Tysen. The University of Utah, 2012. 1516540.

Abstract (summary)

TranslateAbstractOver the last century, wild Atlantic salmon populations have been in steep decline. Historically, fish populations have deteriorated primarily from overfishing. In the case of wild Atlantic salmon populations, the decline in the population comes from the result of spreading diseases derived from aquaculture. The crux of this thesis focuses on theaquaculture industry in Scotland, because of the rapid and unique development of theaquaculture industry and the effect it has had on wild salmon populations. This thesis will determine the costs aquaculture have had on wild salmon recruitment, as well as the costsaquaculture has had on related industries (primarily recreational angling). Through the analysis of the thesis, there will be a review of two possible policy actions that can be taken to promote abatement and maximize social welfare of the damages. The two policy actions in question will be the use of a penalty tax and the use of marketable permits by authorities.Evolution of the Peconic Estuary 'Oyster Terrain' Long Island, NY

Kinney, Juliet West. State University of New York at Stony Brook, 2012. 3517544.

Abstract (summary)

TranslateAbstractThis study of the relict 'Oyster Terrain' in the Peconic Estuary of Long Island, NY using multibeam bathymetry, chirp sonar and sample analysis provides a history of estuarine evolution over thousands of years. More than 10,000 relict oyster reefs are exposed as mounds on the seabed within the Peconic Estuary, with more mounds imaged below the sediment surface. The tops of these relict oyster reefs are at water depths of ∼6 m - 18 m and reef thicknesses of up to 6 m suggest active reef building over a few thousand years. At 28 psu, the present estuary is too saline for natural populations of the Eastern Oyster,Crassostrea virginica , to survive although transplanted oysters will grow. Morphological and shell data tell of a time when crowded oyster reefs once dominated the area; however, there has been a natural evolution in the Holocene to an environment where oysters are rare. Shells from relict oyster reefs provide the opportunity for a more detailed environmental reconstruction of this important transition through 14 C dating and geochemical proxies such as 87 Sr 86 Sr (salinity) and 226 226 (submarine groundwater discharge). Reefs persisted in the Peconic Estuary despite rising salinities until ∼1,350 years ago. Relict shells were compared to modern aquaculture shells grown in Peconic oyster farms. Submarine groundwater discharge seems to have dramatically decreased over time within the estuary according to concentrations of 226 Ra recorded in several sample shells. Sr isotope measurements indicate past variability in salinity was also captured in the relict shells. The era of abundant oyster reefs ended gradually suggesting that there was a gradual evolution to conditions that did not favor oyster survival. Surprisingly, the oyster reefs were growing in slightly deeper water than we anticipated before dying off. The youngest reefs were in only ∼2.5 m of water 1,350 years ago; however, the oldest exposed reef tops we dated would have been active in ∼10 m of water some 2,350 years ago. Our results suggest that oysters may have thrived in deeper waters more abundantly in the past than in modern stressed estuaries.U.S. Development of Offshore Aquaculture: Regulatory, Economic, and Political Factors

Buck, Lisa E.. University of Washington, 2012. 1528916.

Abstract (summary)Many freshwater and coastal aquaculture facilities are currently operating in the United States and contributing seafood products to domestic and global markets. These types of aquaculture have become successful industries, however that success has not yet expanded into United States federal waters. Regulatory, economic, and political factors that might explain the lack of development of an aquaculture industry in the United States Exclusive Economic Zone (EEZ) beyond state waters were examined through available literature, semi-structured interviews, and case examples of offshore aquaculture development projects. Analysis showed that while economic and political factors have a definite influence on the development of offshore aquaculture, the greatest barriers to the growth of the industry in the United States are the lack of a rational and comprehensive federal regulatory framework for offshore aquaculture, and lack of explicit regulatory authority naming NOAA as the lead federal agency. Until these regulatory factors are addressed, development of offshore aquaculture in the United States will continue to be on a project-by-project and permit-by-permit basis. This case-by-case approach, by failing to address systematically important economic, political, jurisdictional, and ethical issues concerning the use of offshore waters for commercial aquaculture, is likely to continue to inhibit development of offshore aquaculture in the future. I conclude with a discussion of possible root causes for the lack of clear federal guidance with regard to offshoreaquaculture, and I make recommendations for addressing the regulatory, economic and political factors that are inhibiting the development of offshore aquaculture in the United States.Genetic Basis for Thermal Tolerance in Two Different Strains of Rainbow Trout (Oncorhynchus mykiss): Case Western and Kamloops

Reale, Paola. West Virginia University, 2012. 1520643.

Abstract (summary)This thesis examines the thermal tolerance based on how expression of Heat Shock Protein (HSP) 70 and HSP90 differ between two different strains of rainbow trout (Oncorhynchus mykiss ), the Case Western strain and the Kamloops strain, and determines if cortisol levels affect HSP expression in red blood cells. The Case Western strain is considered the only warm water trout, only recently was any aspect of its thermal tolerance quantified. Porto (2012) determined critical thermal maxima (CTM) for the Case Western strain and found it to be about 0.15 °C higher than the Kamloops strain. This thesis is comprised of three chapters: (1) an introduction and literature review on the biological history of these two strains of rainbow trout, on studies related to HSPs expression as indicators of thermal tolerance, and studies on the relation between cortisol expression and HSPs expression; (2) an experimental study investigating the differences between HSP70 and HSP90 between the two strains, before and after a heat stress test and between individuals of different sizes; (3) an experimental study investigating the relation between the heat stress protein expression and cortisol levels pre- and post-stress. The results on the HSP70 and HSP90 relative expressions confirm that Case Western strain has higher thermal tolerance, highlighting the importance of this strain as a candidate to be cultured in aquaculturefacilities as an answer to possible impacts of future climate changes. Earlier studies suggested HSP expression varied with age in rainbow trout, but failed to consider strain-specific differences. Our results show that age-specific HSPs expression is not species-specific in rainbow trout as it differs by strain. The results show that the plasma cortisol levels before and after thermal stress do not differ among strains, and that the physiological response to heat stress is species-specific. The variable that has the largest influence on the variance expressed among groups came from the HSP90 gene. We found the stressed Kamloops was the most diverse group, with less thermal tolerance, influenced mostly by the weight of the HSP90 on the total variance.Water Quality Monitoring in a Pilot Marine Integrated Aquaculture System

Kruglick, Alex. University of South Florida, 2012. 1508932.

Abstract (summary)Land based aquaculture systems are growing in popularity, and there is a drive to improve the efficiency of their energy and water systems for both economic and environmental benefit. Recirculating Aquaculture Systems (RAS) generally refer to systems that recycle their wastewater streams to be more or less a zero discharge facility. A more sustainable approach is emerging in the form of Integrated Aquaculture Systems (IAS) where maximum utility is realized from the various components so

that fresh water use is reduced, water quality is improved, energy use is reduced, and new markets are created or fulfilled. Under a grant from the National Oceanic and Atmospheric Administration (NOAA), an interdisciplinary group from MOTE Aquaculture Research Park, Mote Marine Lab, the University of South Florida, and Aquatic Plants of Florida have been working on a pilot IAS in Sarasota, FL starting 10/1/2010 which couples high-value pompano fish production with the production of native FL marine plant species ( Spartina alternaflora (smooth cordgrass),Juncus roemareanus (needlegrass rush), and Rhizophora mangle (red mangrove) for wetlands restoration. This research contributes to the understanding of water quality as a function of space and time in the MOTE IAS system and compared the performance of the plant bed configurations (with and without a sand filter) with a more common geotube membrane used in RAS, for treating effluent sludge from marine fish tank systems.For the same influent concentration from the solids waste tank, the overall average percentage of Total Suspended Solids (TSS) removed was 84%, 84%, and 80% from the south plant bed (SB), north plant bed (NB), and geotube (GT) and the overall average Volatile Suspended Solids (VSS) removed was 85%, 90%, and 87% from the SB, NB, and GT respectively. The plant beds performed as well as the geotube in terms of TSS and VSS removal.Dissolved oxygen concentrations ranged from 0.28 mg/L in the geotube effluent (GTe) to 10.72 mg/L in the moving bed bioreactor influent (MBBRi). Overall averages (n = 5 per sample) of DO between May 2011 and January 2012 varied from 1.97±1.92 mg/L in the solids tank effluent (STe) to 8.20±1.60 mg/L in the MBBRi. pH values ranged from 6.35 STe to 7.74 in the GTe. Overall averages of pH between May 2011 and January 2012 varied from 6.89±0.5 mg/L in the STe to 7.45±0.21 in the MBBRe. Temperature values ranged from 17.3 °C in the GTe in December to 28.8 °C in the SFe during the month of September.The average unfiltered Chemical Oxygen Demand (UCOD) ranged from 105±37 mg/L in the NBe to 231±99 mg/L in the STe. Compared to the STe the percentage of COD removed from the SBe, NBe, GTe, and SFe was 47%, 55%, 53%, and 23% respectively. Average filtered COD (FCOD) ranged from 91±46 mg/L in the NBe to 132±66 mg/L in the STe. Compared to the STe the percentage of FCOD removed from the SBe, NBe, GTe, and SFe was 22%, 31%, 25%, and 2% respectively.The average unfiltered total nitrogen (UTN) concentration ranged from 24±17 mg/L in the SBe to 52±25 mg/L in the MBBRi. The overall average percentage removed was 54%, 46%, 47%, 15% from the SBe, NBe, GTe, and SFe respectively based on the STe concentration. The average filtered total nitrogen (FTN) concentration ranged from 20±13 mg/L in the SBe to 68±37 mg/L in the MBBRi and for the given effluent streams, FTN was either comparable to UTN or higher with the higher values seen prior to and after the moving bed bioreactor (MBBR). The majority of total nitrogen is dissolved. Average filtered N0 3

- -N concentrations ranged from 0.73±0.79 mg/L in the NBe to 29± mg/L in the MBBRe. The overall average percentage removed was 96%, 76%, -2%, 95% from the SBe, NBe, GTe, and SFe based on the STe concentration. Average filtered NH3-N concentrations ranged from 0.2±0.2 mg/L in the MBBRi to 3.9±3.1 in the SFe. The overall average percentage removed was 51%, 80%, 71%, -5% from the SBe, NBe, GTe, and SFe based on the STe concentration.The average unfiltered total phosphorous (UTP) concentration ranged from 30±11 mg/L in the SBe to 37±12 mg/L in the GTe. The average filtered total phosphorous (FTP) concentration ranged from 23±17 mg/L in the MBBRi to 36±29 mg/L in the NBe and for the given effluent streams, FTP was always less than UTP with the NBe being an exception. The average filtered total reactive phosphorus (FOP) concentration ranged from 18±18 mg/L in the MBBRe to 26±15 mg/L in the SBe and for the given effluent streams. Samples taken over an 18 hour period on 2/1/12 showed high variability in terms of concentrations in the solids tank effluent which was not seen in the rest of the system.Metals and trace elements were of similar concentration in all effluents from 5/17/11 to 9/7/11. Accumulation of metals of elements was not observed,but a removal mechanism was not identified. The SBe had the lowest concentrations of Mn, Ni, Se, Fe, and B, however a longer monitoring period is recommended.The IAS is successfully growing pompano in land based low salinity tanks, the fish wastewater is producing wetlands restoration plants and zero discharges of water or solid waste (dead fish an exception) have occurred from the system which began operation in October 2010.Human Perceptions and Attitudes Regarding Geoduck Aquaculture in Puget Sound, Washington: A Q Methodology Approach

Rudell, Paul N.. University of Washington, 2012. 1515983.

Abstract (summary)Geoduck (Panopea generosa ) clam aquaculture on Washington State tidelands is causing disagreement and debate among coastal stakeholders. This study uses Q methodology to investigate the subjective perceptions and attitudes of 36 coastal stakeholders involved in the geoduck aquaculture debate and to identify central issues. A total of 1,338 potential Q statements were generated resulting in a set of 55 Q statements that were chosen to represent the full range of viewpoints. Analysis discovered two social perspectives held by participants, emphasized areas of consensus and disagreement and identified four highly contentious issues. Those following Perspective 1 generally thought favorably about the potential growth of geoduck culture and included participants identified as managers, academic scientists, shellfish growers, tribal members, and students. Those following Perspective 2 were generally against further development of geoduck culture and included waterfront landowners and non-governmental organizations. This study demonstrates the ability of Q methodology to provide framework and structure to the geoduck aquaculturedebate, and highlight promising areas to be addressed by research and outreach.

Red king crab hatchery culture and ecological requirements: Applications for stock enhancementDaly, Benjamin J.. University of Alaska Fairbanks, 2012. 3534200.Abstract (summary)The ecologically and commercially important red king crab (Paralithodes camtschaticus ) is depleted throughout much of the North Pacific and thought to be recruitment limited, making it an appropriate candidate for stock enhancement efforts. This research addresses bottlenecks associated with hatchery production and lays the groundwork for developing release strategies. I investigated effects of diet, stocking density, and size grading on survival, growth, and shell coloration of recently-settled juvenile red king crabs in large-scale hatchery experiments. I also conducted laboratory experiments with fish predators to determine if red king crab predator responses could be enhanced with experience. Finally, I tethered hatchery-cultured red king crabs of two sizes in the field for 24 h trials and used underwater video cameras to identify predators and predation susceptibility. In hatcheryexperiments, dietary astaxanthin supplementation improved survival and shell coloration suggesting that red king crab coloration is plastic and that astaxanthin may provide nutritional or immune system benefits. Size grading strongly influenced survival and growth in the hatchery. Generally, small crabs had higher survival than large and ungraded crabs, but large and ungraded crabs had higher growth, likely from cannibalism. In laboratory experiments, halibut exposure enhanced red king crab crypsis and survival suggesting that cryptic behavior is plastic and may be enhanced with experience. In the field experiment, I identified specific predators of recently-settled red king crabs in a nearshore habitat and showed that survival did not vary with body size or deployment month during the first juvenile instar stages. My research provides an important step for developing a responsible red king crab stock enhancement program by demonstrating that hatchery production can be improved with specific advances in rearing technology, hatchery-cultured red king crabs are morphologically and behaviorally plastic, hatchery-cultured red king crabs tethered in the field show no obvious behavioral deficiencies that may exacerbate predation, and that differences in predation susceptibility during the first juvenile instar stages are subtle and may be ecologically inconsequential for post-release survival. As bottlenecks in hatcheryproduction and survival of released juveniles are overcome, stock enhancement will become increasingly feasible for red king crabs in Alaska.

________Description of spatial and temporal water quality and nitrogen dynamics in a split-pond aquaculture system

McDonnell, Andrew William. Mississippi State University, 2012. 1509317.

Abstract (summary)Production limits have been maximized in earthen pond (EP) aquaculture. Pond design innovations may increase limits of catfish production by enhancing nitrogen processes. The split-pond system (SPS) partitions a pond into fish (20%) and waste treatment/oxygen production compartments (80%). In 2010, an SPS and EP were stocked (March) and harvested (October) with 25,000 catfish ha -1 . Water quality (DO, pH, temp, ORP, CHL-a), nitrogen dynamics (TN, TAN, NO2-, NO3-), nitrogen pathway estimation, and nitrogen budgets were compared. In the waste treatment compartment, maximum DO concentrations exceeded 40 mg L-1 , whereas ORP values provided favorable denitrification conditions. October EP

NO2- concentrations were 3-4 mg L-1 ; 10-fold greater than the SPS. Feed (~90%) and fish (~60%) were the

greatest source and sink of nitrogen, respectively. The SPS may be a promising pond design for the catfish industry through enhanced nitrogen removal and potential opportunity for increased production.Characterization of chondroitin AC lyase in Flavobacterium columnare

Pereira, Michael J. University of Rhode Island, 2012. 1518863.

Abstract (summary)Flavobacterium columnare is a Gram-negative, rod shaped bacterium and is the causative agent of columnaris disease (CD) in many types of freshwater fish. This disease is a significant problem in the aquaculture industry, particularly in the production of channel catfish (Ictularis punctatus ). CD is the second largest cause of economic loss in the catfish industry, following closely behind enteric septicemia (Edwardsiella ictaluri ). F. columnarepossesses a number of putative virulence factors; however, due to the limited number of genetic tools available to manipulate this organism, most of these designations are speculative.Despite this, it is agreed by most that the chondroitin AC lyase must play a role in virulence. Chondroitinases are extracellular enzymes that hydrolyze chondroitin, the molecule responsible for the rigidity of connective tissues. It has been hypothesized that dissolution of chondroitin from connective tissues allows for easier dissemination of the organism throughout its host. In this study, we report the first successful attempt to create an insertional mutation in this gene. We also report the first successful attempt to complement a mutated gene in F. columnare .Mutation of the cslA gene shows a 98% decrease in chondroitinase activity. However, complementation of the cslA mutation only resulted in an activity of 10% in comparison to wild type. Although a significant difference compared to the cslA mutant (p<0.05), the complement failed to restore the wild type phenotype. In an effort to explain this finding, we identified five genes downstream of cslA , arranged in an operon, as confirmed by RT-PCR analysis of wild type total RNA. RT-PCR analysis of cslA mutant revealed a lack of transcription from the downstream genes in the csl operon, demonstrating a polar effect due to the insertion mutation.SDS-PAGE analysis of supernatant proteins revealed two distinct bands that are present in the wild type but absent in the mutant. Although neither band corresponds to the predicted 85kDa size of CslA, we predict that CslA appears as the 67kDa band and undergoes multiple processing steps prior to full activation of the enzyme. Analysis of the complement strain supernatant proteins reveals a 67kDa band at 10% density of the wild type. Restoration of the second distinct band did not occur. Analysis of periplasmic and cytoplasmic fractions did not reveal differences in the protein profiles of the three strains.Finally, the data show that chondroitinase activity was not induced by the addition of chondroitin to liquid culture. However, the addition of chondroitin to an F. columnare culture resulted in the aggregation of previously planktonic cells. This phenomenon may have several implications in the study of this organism, including some possible insight into the regulation of its virulence factors. Further research will be required in order to fully elucidate the role of cslA and chondroitin in the virulence of this very important pathogen of fish.Developing value-added peptide antioxidants from rendering products

Xing, Xiaoting. Clemson University, 2012. 1518335.

Abstract (summary)Synthetic antioxidants, such as butylated hydroxyanisole (BHA), butylated hydroxytoluene (BHT), Vitamin E and ethoxyquin, have been commonly added to formulated animal feeds in order to delay discoloration and deterioration due to oxidation. However, these synthetic antioxidants have been limited in their applications as food additives because of potential health hazards. Specifically, synthetic antioxidants have been considered to be linked to various forms of cancer, most commonly kidney, liver and bladder cancer. In this work, value-added peptide antioxidants from rendering products were developed for use in potential aquaculture and pet food markets as natural antioxidant substitutes for synthetic antioxidants. The antioxidant peptides developed from the rendering protein were studied based on obtaining the hydrolysates fractions, together with evaluation antioxidant properties, ultrafiltration and analysis sequence of identified peptide.In the initial studies, three typical rendering proteins (poultry meal, fish meal and premium pet meal) characteristic compositions of three rendering proteins were investigated, including moisture content, ash

content, fat content, and protein content. Then, the antioxidant capacity of three alkaline rendering proteins hydrolysates, including poultry meal hydrolysates, fish meal hydrolysates and premium pet meal hydrolysates, were examined. The antioxidant activities of alkaline hydrolysates were evaluated using five methods including two based on the free radical scavenging capacity (DPPH, ABTS radical scavenging assay and one oxygen radical absorbance capacity (ORAC) assay). Hydrophobic antioxidant capacities of alkaline hydrolysates were determined by β-Carotene Linoleic Acid System. Oxidation Stability Index (OSI) was used to evaluated the anti-lipid oxidation ability.The antioxidant peptides developed from proteolytic hydrolysis of premium pet meal were the analyzed using Response surface optimization, Ultra-Filtration and LC-MS. The optimum hydrolysis condition on temperature, enzyme to substrate ratio, and the hydrolysis time were obtained by Response Surface Methodology (RSM). Abilities of scavenging ABT*+ free radicals and degree of the hydrolysis were employed as indicators of Response surface methodology. Under the optimum hydrolysis conditions, the proteolytic hydrolysates fractions were separated by the ultrafiltration to obtain different molecular weight proteolytic hydrolysates fractions. During this process, the antioxidant capacity was also evaluated by the ABTS*+ scavenging free radical assay. For the last step, peptides less than 1000Da peptide that were derived from premium pet meal were identified using LC-MS, indicating of the possible amino acid sequences of Leu-Thr-Cys or Iso-Thr-Cys and His-Cys.Potential of great egrets to be vectors for the transmission of a virulent strain of Aeromonas hydrophila between channel catfish culture pond

Jubirt, Madison M.. Mississippi State University, 2012. 1516460.

Abstract (summary)Aeromonas hydrophila is a Gram-negative, rod shaped, facultative anaerobic bacterium that is ubiquitous to freshwater and slightly brackish aquatic environments and can cause infections in fish, humans, reptiles, and avian species. Recent severe outbreaks of disease in catfish aquaculture have been associated with a highly virulent Aeromonas hydrophilastrain (VAH) that is genetically distinct from less virulent strains.Given that A. hydrophila is known to infect birds, we hypothesized that fish eating birds may serve as a reservoir for VAH and spread the pathogen by flying to uninfected ponds. Great Egrets were used in this transmission model because these wading birds frequently predate catfish farms. We found that Great Egrets that were fed VAH infected catfish shed VAH demonstrating their potential to spread VAH. Histologically there were changes found in selected tissue samples.Stress Physiology and Immune Responses of Atlantic Cod ( Gadus morhua) Subjected to Various Challenges

Hori, Tiago Silvestre. Memorial University of Newfoundland (Canada), 2012. NR88101.

Abstract (summary)The Atlantic cod is an economically important species in Canada, as well as in several European countries including Norway, Iceland and Scotland. However, collapse of Atlantic cod stocks has threatened the global Atlantic cod fishing industry. The aquaculture of Atlantic cod could be an alternative source of fish for these markets, but its establishment has been slow, due to the lack of knowledge with regards to certain aspects of this species' biology (e.g health/disease, optimal diet formulation and early maturation). Therefore, the objectives of this thesis were to develop tools to study the stress physiology and immune function of cod, and to apply these to aquaculture relevant questions. In Chapter 2, I: 1) demonstrated that cortisol responsiveness was negatively correlated with growth parameters; and 2) identified differences in the magnitude of the cortisol stress response to handling and potential quantitative trait loci (QTL) associated with this phenotype. In Chapter 3, I investigated the molecular mechanisms that mediate differences in cortisol responsiveness by measuring the mRNA expression of genes involved in cortisol synthesis and tissue responsiveness in Atlantic cod with different magnitudes of cortisol response. In Chapter 4, I report on a stress relevant gene discovery effort conducted as part of the Atlantic C[barbelow]od G[barbelow]enomics and Broodstock Development P[barbelow]roject (CGP), that involved the sequencing and characterization of over 5000 ESTs. Several of the genes identified in this work were validated using quantitative real-time reverse transcription-polymerase chain reaction (QPCR) as heat shock responsive genes, and were subsequently incorporated into the CGP 20K Atlantic cod microarray. Finally, in Chapter 5, I used this microarray platform to study the effect of a gradual temperature increase (from 10 to 16°C over several weeks) on immune-relevant gene transcription, and demonstrated that these

increases in temperature dysregulated the anti-viral transcriptomic response of Atlantic cod; fish held at 16°C responding earlier than Atlantic cod held at 10°C. This research has contributed significantly to the resources available for investigating aquaculture relevant questions in Atlantic cod, and generated novel information that can be used to develop molecular markers for use in Atlantic cod broodstock selection programs.Effects of water temperature, diet, and bivalve size on the ingestion of sea lice (Lepeophtheirus salmonis) larvae by various filter-feeding shellfish

Webb, Janis Louise. University of Victoria (Canada), 2012. MR88414.

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Abstract (summary)The sea louse (Lepeophtheirus salmonis ), whose larvae are planktonic and disseminated in the water column, is an economically important parasite of Atlantic salmon (Salmo Salar ). The effect of temperature (5, 10, 15°C), diet (larvae alone, larvae plus phytoplankton), and bivalve size (small, medium, large) on the amount of L. salmonis larvae ingested by various species of filter-feeding bivalves (Pacific oysters, Pacific scallops, blue/Gallo's mussel hybrids, basket cockles) was examined in a series of laboratory experiments. Four separate temperature/diet experiments were conducted (one for each species) in which large bivalves were individually placed in 2-L containers holding 750 ml of aerated, filtered seawater and fed one of three treatment diets: (1) phytoplankton: ∼7.1 x 10 4 cells ml-1 ofIsochrysis sp. (Tahitian strain, TISO); (2) sea lice larvae: ∼431 larvae (mostly nauplii); and (3) phytoplankton and larvae (at the levels mentioned above). There was also a control treatment of phytoplankton and larvae, but no bivalve. After feeding for 1 h, the bivalve soft tissues were excised and preserved, the digestive system was dissected, and sea lice larvae were removed and counted to provide direct evidence of ingestion. The larvae remaining free swimming in the container were preserved and counted. The proportion missing from the container was used to estimate ingested larvae in statistical analyses. Two additional experiments investigating the effect of bivalve size (small, medium, large) on the ingestion of sea lice larvae were conducted with Pacific oysters and Pacific scallops. The heights for oysters (anterior-posterior axes) were 19.2, 44.2, and 84.0 mm, and scallops (dorsal hinges to ventral margins) were 40.3, 64.1, 102.7 mm. The methodology for the size experiments was as previously described for the temperature/diet experiments with the following changes: (1) the diet of larvae alone was not used; (2) the mean number of larvae in each container was ∼498; (3) the mean concentration of TISO added to each container was ∼7.8 x10 4 cells ml-1 , and (4) the mean water temperature was 10.4°C. The data for the four temperature/diet experiments indicate that all four bivalve species ingested sea lice larvae, whether their diet included phytoplankton or not, and that temperature had no significant effect. The data for the two size experiments indicated that all three sizes of oysters and scallops ingested sea lice larvae and that there was a significant size effect. Large shellfish consumed a significantly greater proportion of the sea lice larvae than the small shellfish. Bivalves grown at salmon net pens as part of an IMTA (Integrated Multi-Trophic Aquaculture) system may be able to reduce the number of sea lice larvae as well as being an additional crop of market value. Future research, conducted at a commercial scale at a salmon farm, is warranted in order to determine if bivalves can serve in this role.An engineered ecosystem for waste management and food production

Amadori, Michael. State University of New York College of Environmental Science and Forestry, 2012. 1514340.

Abstract (summary)This research project investigated an innovative approach to recapture nutrients from post-consumer food waste by converting it into a pelletized fish food for a bench-scale aquaponic system. Two treatments, each with three replicated aquaponic systems, were constructed to determine the effect of using food waste for fish and lettuce production. Food waste pellets had significantly more fat, less mineral content, and similar protein and fiber content compared with commercial fish feed. Nile tilapia ( Oreochromis niloticus ) had significantly greater specific growth rate (SGR) and food consumption rates on the commercial diet than those on the food waste diet. The feed conversion ratio (FCR) between treatments was similar. Lettuce biomass production was significantly reduced in food waste systems. Palatability of post-consumer food waste seemed to be the most significant factor to overcome.

Design of a new generation of breeding pond for the rapid recovery of fish discards

Dionne, France-Line. Ecole Polytechnique, Montreal (Canada), 2012. MR88137.Abstract (summary)It is well know that fresh water aquaculture is an important source of organic pollution. Especially, phosphorus contained in fish farm's discharges contribute to watercourse eutrophication, which is harmful for aquatic life. Thereby, MDDEP estimates that near 65% of watercourses in agricultural area in Quebec are exceeding the threshold concentration of eutrophication of 0.03 mg P/L. With those considerations in mind, Quebec fish farming industry figured out a new strategy in 2004, whose purpose is to reduce the phosphorous discharge to 4.2 kg of phosphorous per produced fish ton by 2014.Fish farming activities require important water inflows. Thus, this project tend to use this resource by opting for fish farm basin design and operation parameters leading to an amelioration of fish discharges removal. The search of favourable parameters has been done using computational fluid dynamics software Fluent .Based on the first generation Gilbert basin, located at Gilbert fish farm in Estrie, a new concept has been developed by modifying the configuration and hydraulic parameters of the existing basin. Water quality and hydraulic measurements have been taken in order to calibrate the model developed in Fluent . Those measurements led to the assessment of starting parameters and were used to validate some of the results.A measured phosphorous removal efficiency between 30 and 46% has been used as a comparison value to validate the simulated first generation Gilbert basin. The simulated values for the removal efficiency ranged from 36.9 to 48.3% for similar flows as those observed on the field. Design and operation parameters were then modified, within realistic ranges, to improve the phosphorous removal efficiency leading to better environmental performance.According to the numerical simulations, a concept with 3 lateral sedimentation traps, a 2.5% bottom slope, a fish-farming zone of 24.4 m by 6.1 m, and a 0.3 m deflector located under the recirculation upstream pipe, has been the most efficient over our range of hydraulic parameters combinations. Efficiency values up to 54% have been obtained for this concept after a first round of simulations.Unfortunately, the basin built on the field of Gilbert fish-farm slightly differs from the proposed concept. Instead of the expected bottom slope of 2.5%, the basin has a bottom slope of 1.85%.First round simulations predicted this would lead to a lower efficiency. Measurements of the removal efficiency on the second generation Gilbert basin, built in autumn 2011, gave an average of 37.9%.Considering this result, new simulations have been performed. Instead of injecting four sizes of particles, a distribution of ten sizes has been used. Again, the simulations show that a bottom slope of 1.85% is clearly less efficient than a bottom slope of 2.5%. The difference in the removal efficiency ranges from 4.3 to 10.2% which strongly favours the initial proposed concept. Results show a potential removal efficiency between 42.2 and 48.1% for the better performing concept. Furthermore, considering that fish activity is known to increase the removal of phosphorous particles, it is reasonable to expect an efficiency exceeding 50%.Studies on the mechanisms of immune evasion in Trypanosoma carassii infections of the goldfish (Carassius auratus L.)

Oladiran, Ayoola. University of Alberta (Canada), 2012. NR89771.

Abstract (summary)Parasites possess variety of mechanisms to modulate or evade host defence systems to maintain chronic infection and ensure their transmission. The protozoan parasiteTrypanosoma carassii is infective to a number of freshwater fish species and can cause significant mortality in aquaculture. T. carassii shares similarities with both T. brucei, the causative agent of sleeping sickness and T. cruzi, which causes Chagas' disease. It is not known how T. carassii escapes host immune responses.My doctoral research focused on the interactions between T. carassii and its fish host with emphasis on the strategies used by the parasite to evade fish immune host defense.. and establish long lasting infections. I identified at the molecular level the key antigens of T. carassii present in excretory/secretory (ES) products and surface protein fractions of the parasite. As a first step toward understanding the importance of select antigens of T. carassii, I produced the recombinant proteins and characterized their roles in immune evasion.Like heat shock protein 70 of other pathogens, I found that T. carassii hsp70 was immunogenic and was present in both ES products and surface protein fraction of the parasite. Recombinant parasite hsp70 significantly increased expression of pro-inflammatory genes and enhanced inflammatory response of

goldfish macrophages. In contrast, another parasite surface molecule, glycoprotein 63 (Gp63) down-regulated both pathogen and cytokine-induced inflammatory responses of goldfish monocytes and macrophages. Parasite gp63 was associated with macrophages and appeared to interfere with signalling mechanisms. Since complement-mediated lysis is one of the main host defence responses against trypanosomes, I cloned and characterized parasite surface molecule called calreticulin. Recombinant T. carassii calreticulin bound to first component of complement, C1q, of not only goldfish but also humans. Further, recombinant T. carassiicalreticulin inhibited C1q-dependent hemolysis.T. carassii infection of goldfish induced increased expression of pro- and anti-inflammatory cytokines. Increased cytokine mRNA levels were observed during the acute phase of infection, and then they returned to normal levels or were down-regulated during the elimination phase of the infection. These findings demonstrate that parasite surface molecules and those found in ES fraction have the capacity to manipulate host inflammatory and antimicrobial responses, thereby ensuring persistence of T. carassii in its host.In vitro Study of the Microsporidian Parasite Loma morhua, Using Cod-derived Cells and Novel Culture Techniques

MacLeod, Michael J.. Wilfrid Laurier University (Canada), 2012. MR91468.

Abstract (summary)The cod populations of the Canadian Atlantic were once highly productive, generating enormous annual harvests and attracting fishing fleets from many nations. However, through the late 1980s improved fishing technology, unprecedented capture rates, and poor fishery management brought wild stocks beyond the point of collapse. Dwindling harvests in the early 1990s resulted in cod fishing moratoriums, and an end to the productivity for which the fishery was once renowned. Atlantic cod remains a popular food worldwide and the collapse of cod fisheries has done little to abate market demands. Consequently, the cod is considered a prime candidate for aquaculture production, providing the impetus for commercial-scale farming operations. As aquaculture efforts continue to grow, disease management challenges have become a prominent concern. Many parasites are prevalent on cod farms, including intracellular pathogens such as viruses and microsporidians. Detailed research into diseases affecting farming operations is imperative if commercial-scale cod aquaculture is to develop.Piscine cell culture techniques represent a valuable tool for studying the intracellular pathogens currently impeding cod aquaculture. To date however, few cell culture models have been made available for the Atlantic cod. This research details the establishment of a larval cod cell line, GML-5, investigations of infective processes in microsporidian parasites, and development of in vitro culture methods for a microsporidian parasite of the Atlantic cod.GML-5 cells have been cultured for two years and survived more than 26 passages in L15 media supplemented with 10% fetal bovine serum and incubated at 18°C. The cells have tested positive for a marker of stem cell-like characteristics, had their origin identified asGadus morhua by DNA barcoding, and been cryopreserved for long-term storage. The cells have been successfully used to support the growth of two microsporidian parasites. Infection-mediating effects of Mg2+ and EDTA have been confirmed in a previously-untested microsporidian species and novel pH treatments were successfully used to stimulate infection and development of Loma morhua in GML-5 cells.The results of this research represent the foundations of an in vitro infection model forLoma morhua , and demonstrate shared responses to specific chemical conditions by microsporidian parasites with highly dissimilar host species.Value chain development for tilapia and catfish products: Opportunities for female participation in Kenya

Ndanga, Leah Z. B.. Purdue University, 2012. 1529720.

Abstract (summary)Fish is an important food source in the diets of many Africans. Fish supply in Kenya is mainly from wild capture fisheries and imported marine fish. There is limited distinction in the marketing of wild caught fish as opposed to farmed fish. Farmed fish is usually sold directly to consumers, or nearby small traders and establishments.Despite government's efforts, access to capital remains a major constraint for fish farming. Article 1 used value chain analysis (VCA) to determine the structure of the Tilapia and Catfish value chains and a cost benefit analysis (CBA) to determine economically viable opportunities for increased female participation in

the value chains. The main opportunities for women are as fish farmers that also act as a hatchery and as fish marketers. Despite the high initial costs, fish farming was noted to have the most benefits to the community. Besides economic development, other benefits identified include improved finances, improved food security, and employment opportunities. Fish marketing has fewer barriers to entry for women.Article 2 identified constraints affecting aquaculture, determined critical success factors, verified how demographic factors influence choice of supply chain participation activity and provided recommendations on opportunities for increased female participation in theaquaculture value chain. The study found that fish production lay in the male domain but relied on the full participation of women and family. Women traditionally have central position in harvesting, post-harvest handling of fish and marketing. Input supply continues to be a major constraint for all value chain actors. Integrated aquaculture and agriculture and pooling resources were noted to be helpful in circumventing some of the input constraints.Article 2 established that despite the constraints, there are definite opportunities for female participation in different aspects of the tilapia and catfish value chain; where to join depends on the woman's characteristics and goals. Female participants seeking flexibility and liquidity should consider fish marketing; those seeking long term financial strength and with strong educational and technical backgrounds should consider input supply; and those looking for long term stability should consider fish farming. Established fish farmers may consider diversifying into input supply and value addition.Use of Polysomic Genetic Markers to Address Critical Uncertainties in White Sturgeon Biology and Management

Schreier, Andrea Marie. University of California, Davis, 2012. 3511869.

Abstract (summary)The application of genetic markers to investigate evolutionary and ecological questions about white sturgeon, Acipenser transmontanus , has been limited due to the species' highly duplicated nuclear genome. Here, polysomic microsatellite markers were used to (1) examine the ancestral level of genome duplication in white sturgeon, (2) examine genetic diversity and patterns of population structure within and among drainages across the species' range, and (3) provide genetic monitoring for a conservation aquaculture program sustaining an endangered white sturgeon population. In the first chapter, we followed the inheritance of eight microsatellite markers in 15 families of white sturgeon from a commercial caviar farm to determine whether white sturgeon (with 250 chromosomes) should be classified as tetraploid or octoploid. The eight microsatellite loci were detected predominantly in four or eight copies, with one locus observed in >8 copies. Numbers of alleles per locus, patterns of allele transmission, and inference of gene copy number in parents suggested that white sturgeon should be considered ancient octoploids. The discovery of dodecaploid parents and their decaploid offspring in the farm population, confirmed by flow cytometry analysis, indicated that some aspect of sturgeon aquaculturewas inducing spontaneous autopolyploidy in white sturgeon.Next, microsatellite markers were applied to examine white sturgeon population structure across the species' range. Population assignment testing was used to determine the origin of white sturgeon sampled in non-natal estuaries, or those not containing a spawning population, to evaluate marine dispersal behavior. The Sacramento-San Joaquin River system was found to contain a single white sturgeon population while the Fraser River exhibited a hierarchical pattern of population structure. Strong levels of genetic divergence were detected above and below a natural barrier, Hells Gate, and fine-scale population substructure was identified above Hells Gate. Population structure in the Columbia River drainage (including the mainstem Columbia and Snake Rivers) was complex and suggested a pattern of isolation by distance. Net downstream gene flow also may have contributed to this pattern, with individuals migrating downstream through impoundments and over barriers with little upstream movement possible. There was no support for the current practice of managing each impounded reach on the Columbia or Snake rivers as a separate population. Lack of population structure within historically continuous river habitat found across the species' range suggested spawning site fidelity in white sturgeon may occur on a regional scale, with local gene flow among geographically proximate spawning sites. Population assignment of samples collected from non-natal estuaries indicated that all populations with ocean access make marine migrations, and individuals did not necessarily originate from the nearest spawning population.Finally, microsatellites were used to conduct genetic monitoring of the Kootenai Tribe of Idaho's conservation aquaculture program (CAP) for the endangered Kootenai River white sturgeon population. Continuous recruitment failure in this population has left it entirely dependent on the CAP for reproduction.

A genetic profile database of wild broodstock used in the CAP was created to monitor hatchery-induced genetic changes in the Kootenai River population. Broodstock genotypes also were used to evaluate the accuracy of parentage assignment in the Kootenai River population, as hatchery managers soon will depend on this analysis to prevent inbreeding when most sexually mature adults available for captive breeding will be derived from hatchery production. Numbers of alleles and numbers of alleles per individual per locus were calculated to monitor the amount of wild type genetic diversity captured in broodstock utilized by the CAP. Parentage analysis with 18 microsatellite markers was validated in known hatchery families from the 2010 year class. Genetic diversity in the Kootenai River population was very low relative to other populations examined, likely due to founder effects and genetic drift after isolation from the mainstem Columbia c. 10,000 YBP. In less than one sturgeon generation, 96% of Kootenai River genetic diversity has been captured in broodstock that contributed offspring that survived to release in the Kootenai River and further propagation will likely preserve additional genetic variation. The 18 microsatellite panel improved parentage assignment accuracy and allowed a greater number of assignments relative to the previous panel used for parentage analysis, suggesting that this technique may become a useful tool in the management of this vulnerable population.Didemnum vexillum: Identity, Origin, and Life History of an Invasive Ascidian

Stefaniak, Lauren Marie. University of Connecticut, 2012. 3520439.

Abstract (summary)

TranslateAbstractOver the past forty years, an increasing number of previously unrecorded populations of a colonial ascidian belonging to the genus Didemnum have been documented in most temperate coastal regions of the world, impacting aquaculture operations, natural rocky habitats, cobble/gravel substrates, and eelgrass beds. Recent morphological analyses identified the populations as Didemnum vexillum Kott, 2002. However, because of incomplete historical records and the numerous mis-identifications of this species, the native range of D. vexillum has not been conclusively known. Also, little is known about the life history cycle, population biology, and native ecology of the species. The goals of this dissertation are four-fold. First, support the morphological identification of D. vexillum using molecular characters. Second, use population genetics to determine the native region of this now cosmopolitan species. Third, describe observations on the distribution and ecology of D. vexillum in Japan, a region where there is a dearth of information on the species. And fourth, quantify aspects of D. vexillum's life history cycle to examine the relative importance of sexual and asexual pathways to reproduction and dispersal of D. vexillum.Temporal Resolution in Time Series and Probabilistic Models of Renewable Power Systems

Hoevenaars, Eric. University of Victoria (Canada), 2012. MR88308.

Abstract (summary)

TranslateAbstractThere are two main types of logistical models used for long-term performance prediction of autonomous power systems: time series and probabilistic. Time series models are more common and are more accurate for sizing storage systems because they are able to track the state of charge. However, the computational time is usually greater than for probabilistic models. It is common for time series models to perform 1-year simulations with a 1-hour time step. This is likely because of the limited availability of high resolution data and the increase in computation time with a shorter time step. Computation time is particularly important because these types of models are often used for component size optimization which requires many model runs.This thesis includes a sensitivity analysis examining the effect of the time step on these simulations. The results show that it can be significant, though it depends on the system configuration and site characteristics. Two probabilistic models are developed to estimate the temporal resolution error of a 1-hour simulation: a time series/probabilistic model and a fully probabilistic model. To demonstrate the application of and evaluate the performance of these models, two case studies are analyzed. One is for a typical residential system and one is for a system designed to provide on-site power at an aquaculture site. The results show that the time series/probabilistic model would be a useful tool if accurate distributions of the sub-hour data can be determined. Additionally, the method of cumulant arithmetic is demonstrated to be a useful technique for incorporating multiple non-Gaussian random variables into a probabilistic model, a

feature other models such as Hybrid2 currently do not have. The results from the fully probabilistic model showed that some form of autocorrelation is required to account for seasonal and diurnal trends.Modifying the fatty acid profile of soybean oil for nutritional and industrial applications

Park, Hyunwoo. The University of Nebraska - Lincoln, 2012. 3510039.

Abstract (summary)The objectives of this study are: 1. To develop of soybean oil low in palmitic acid and elevated in stearic and oleic acids for margarine source. 2. To produce the high omega-3 fatty acid and astaxanthin in soybean seed as a feedstock for aquaculture. Over expression of mangosteen stearoyl-ACP thioesterase gene increased stearic acid content up to 10% to 15%. The identified elevated stearic acid events were crossed with our high oleic acid/low palmitic acid event. Average stearic and oleic acid content ranged 14 to 19% and 68 to 73% respectively. Stearic acid content of elevated stearic acid soybean event and cross line was stable over generation. However, in generation six and seven under field conditions the oleate levels decreased to 30-40%.Decline of marine fish stocks due to over-fishing and the use of wild fish for diets of farmed fish pushed for development of sustainable land based alternative diets for farming fish such as soybean with respect to levels of very long chain omega-3 fatty acids, EPA and DHA. To generate EPA and the high value carotenoid, astaxanthin in soybean, we first created a two gene stack in soybean combining Δ6 and Δ15 desaturase genes, respectively. The resultant event designated 535-9 accumulates stearidonic acid in seed oil up to 35%. We have subsequently generated transgenic events that carry Δ6 elongase and Δ5 desaturase genes. Selected events derived from the latter have been crossed with event 535-9. EPA level in seed oil was up to 4%. In regards to astaxanthin production, we generated transgenic event carrying phytoene synthase, crtZ and crtW genes. Transgenic soybean produced up to 25μg/g astaxanthin. We crossed the four-gene EPA stack with the three gene astaxanthin stack to create a prototype soybean-based feedstock foraquaculture. We identified that the longer chain omega-3 fatty acids ETA and EPA, combined ranged from approximately 3-5% of the oil, along with astaxanthin and β-carotene accumulation from 23 to 44.8 ug/gr and 527 to 1139 ug/gr seed, respectively.Remote sensing of cyanobacteria in turbid productive waters

Mishra, Sachidananda. Mississippi State University, 2012. 3522210.

Abstract (summary)Cyanobacterial algal bloom is a major water quality issue in inland lakes, reservoirs, and estuarine environments because of its scum and bad odor forming and toxin producing abilities. Health risks from cyanobacterial toxin can vary from skin irritations to fever, intestinal problems, and neurological disorders. Terminations of blooms also cause oxygen depletion leading to hypoxia and widespread fish kills. Adding to the problem, many species of cyanobacteria produce odorous compounds such as geosmin and 2-methylisoborneol (MIB) that cause "earthy-muddy" and "musty" odor in drinking water, which is also a serious issue in aquaculture and drinking water industry. Therefore continuous monitoring of cyanobacterial presence in recreational water bodies, surface drinking water sources, and water bodies dedicated for aquaculture is highly required for their early detection and subsequent issuance of a health warning and reducing the economic loss.Remote sensing techniques offers the capability of identifying and monitoring cyanobacterial blooms in a synoptic scale. Over the years, the scientific community has focused on developing methods to quantify cyanobacterial biomass using phycocyanin, an accessory photosynthetic pigment, as a marker pigment. However, because of the confounding influence of chlorophyll- a and other photo pigments, remote retrieval of phycocyanin signal from turbid productive water has been a difficult task. This dissertation analyzes the potential of remote sensing techniques and develops empirical and quasi-analytical algorithms to isolate the phycocyanin signal from the remote sensing reflectance data using a set of radiative transfer equations and retrieves phycocyanin concentration in the water bodies. An extensive dataset, consisting of in situ radiometric measurements, absorption measurements of phytoplankton, colored dissolved organic matter, detritus, and pigment concentration, was used to optimize the algorithms. Validations of all algorithms were also performed using an independent dataset and errors and uncertainties from the algorithms were discussed. Despite the simplicity, an empirical model produced highest accuracy of phycocyanin retrieval, whereas, the newly developed quasi-analytical phycocyanin algorithm performed

better than the existing semi-analytical algorithm. Results show that remote sensing techniques can be used to quantify cyanobacterial phycocyanin abundance in turbid and hypereutrophic waters.The effects of electricity on the survival of fish embryos as a means of controlling invasive cyprinids

Nutile, Samuel A.. Purdue University, 2012. 1530315.

Abstract (summary)Asian carp were first introduced into United States waterways in the 1970's when they escaped from aquaculture facilities, and since then they have become extremely well established and are devastating natural ecosystems in these waterways. A variety of efforts have been investigated to control both the spread and population sizes of these invasive fishes, but none of this research has investigated the potential of using electricity to control these species at early life history stages. The effects of electricity on the early life history stages of fishes has been well documented, and survival of the embryos is related to embryo size, exposure duration, voltage gradient, the developmental stage at the time of exposure, and the current type. Therefore, the objectives of this research were to: 1) use three model cyprinid fish species to determine the voltage type (virtual direct current or pulsed direct current), exposure duration, and voltage gradient necessary to cause significantly increased embryo mortality, and determine the most vulnerable developmental stages of the embryos of these species to estimate the effects of electricity on silver carp embryos; 2) test the effects of multiple exposures on the survival of zebrafish ( Danio rerio) embryos with different resting intervals between shocking events to determine how multiple exposures affects fish embryo survival; and 3) determine the lethal concentration 50 (LC50) of rotenone to zebrafish embryos to test the combined effects of electricity plus rotenone on zebrafish embryos when applied at concentrations at and below the LC50 value during electroshocking to determine if the simultaneous stressors can result in higher mortality than has been previously seen with electrical field exposures alone. The results of this research are consistent with previous research in that embryo survival across all species tested was related to developmental stage and voltage gradient. Zebrafish embryo survival was also affected by differences in current type and exposure duration. Surprisingly, zebrafish embryos were not affected by multiple exposures to electrical fields. Furthermore, when rotenone was added at values 10 and 100X lower than the LC50, no signs of increased mortality were observed. In terms of controlling Asian carp with electricity at early life history stages, the results of this research are discouraging. If the carp respond the same as the species in this study, then the amount of electricity necessary to cause mortality is impractical in a field application. However, since Asian carp embryos are much larger than the embryos used in this study, lower voltage gradients might cause higher mortality compared to the species studied here. Unfortunately, due to complications with obtaining carp embryos, the number of embryos exposed in this research was minimal, and further testing is necessary to explicitly determine the effectiveness of using electricity as a means of controlling these invasive cyprinids.The Effect of Genetic Introgression of Farm-Raised Fish on the Endangered Wild Atlantic Salmon Populations in Maine

Mancini, Chris.Tufts University, 2012. 1506515.

Abstract (summary)This thesis reviews the state of the wild populations of Atlantic salmon in Maine, and in particular their relationship to the farm-raised salmon that escape and interbreed with the wild salmon. This thesis asks whether commercial salmon farms can exist in a common time and place as wild Atlantic salmon, and if so, how?The research revealed that conservation efforts have been so far unsuccessful in restoring a sustainable population of Atlantic salmon to the rivers of Maine and their diminished numbers put the species at a great risk to even a small influx of escaped farm salmon. Farm escapees interbreed with wild salmon, pass on their artificially selected genes, and leave subsequent generations less fit for survival in the wild.Though commercial aquaculture is not wholly responsible for the current fragile state of salmon in Maine, the industry can take a leadership role in aiding the wild salmon's recovery. Recommendations include converting Maine's fish farms to closed-system, land-based operations, and thorough salmon habitat restoration focused on dam removal and watershed conservation.Growth and swimming endurance of juvenile channel catfish in high temperature environments

Arnold, Michael Brigham. Mississippi State University, 2012. 1509069.

Abstract (summary)Channel catfish (Ictalurus punctatus ) are important to aquaculture and natural ecosystems, however little is known regarding effects of high summer temperatures, which are predicted to increase with climate change. Therefore, two studies were conducted to examine physiological effects of high temperatures on juvenile channel catfish. The first examined effects of three cycling thermal regimes (23-27°C, 27-31°C, and 31-35°C) characteristic of culture environments in Mississippi on growth, food consumption, feed conversion ratio, specific growth rate, and activity. The second study measured active and resting metabolic rates and swimming endurance at constant temperatures (27, 31, and 35°C). The best growth and feed conversion occurred at 27-31°C and activity was greatest at 31-35°C. Active metabolism and swimming endurance decreased at 35°C. These results indicate high summer temperatures reduce food consumption, increase activity, impair metabolism and endurance, and therefore present challenges to the culture and management of channel catfish.Malachite Green Adsorption by Activated Carbon from Aquaculture Waste Water

Liu, Jia. University of California, Davis, 2012. 1519681.

Abstract (summary)The delta smelt (Hypomesus transpacificus ) is an endangered species indigenous to the Sacramento River, California. Its life cycle is under study at the Fish Conservation and Culture Laboratory (FCCL) operated by the University of California, Davis. Malachite green (MG) has been used at the laboratory to treat delta smelt eggs and juveniles afflicted with protozoan and fungal infections. Given the potential toxicity of malachite green and of its more persistent degradation products, activated carbon adsorption was evaluated as a possible method to treat wastewater containing malachite green at a maximum concentration of 0.4 mg/L. Activated carbon use for malachite green adsorption has been reported in the past.Adsorption of malachite green from aquaculture wastewater onto activated carbon was investigated with a 2.54 cm diameter column packed with different amounts of carbon. The carbon used (AC412 from Aquatic Eco-systems, Inc.) is a coal based granular activated carbon with a specific surface area of approximately 625 m 2 /g.The process was tested for different contact times, malachite green influent concentrations, and flow rates. In single factor tests, preliminary experiments showed: (i) MG removal efficiency (effluent concentration relative to the initial concentration) increased when contact time rose from 1.39 min to 4.16 min (for the same MG initial concentration of 1.74 mg/L and the same flow rate of 21.9 mL/min in a 2.54 cm diameter column filled with various amounts of activated carbon); (ii) MG removal efficiency decreased when MG initial concentration was raised from 2.65 mg/L to 10.84 mg/L (for the same flow rate of 29.1 mL/min and the same contact time of 1.27 min); (iii) MG removal efficiency decreased when flow rate was increased from 7.0 mL/min to 43.0 mL/min (for the same contact time of 1.27 min and different activated carbon bed lengths and the same MG initial concentration 2.67 mg/L).A two factor factorial experiment confirmed that contact time and influent concentration had statistically significant effects on removal efficiency. Overall, the malachite green removal efficiency increased as contact time increased or as the influent concentration decreased. In addition to the single factor effects, there were significant interactions among them. Temperature was also found to impact malachite green removal efficiency, with higher efficiencies observed at higher temperature. A practical system for use at the FCCL was designed and will be described in detail. The system consists of a column packed with granular activated carbon that will have an estimated life of approximately 8.5 years given the amount of malachite green used at the FCCL.Study of Edwardsiella ictaluri Conserved Genes Towards the Development of an Attenuated Recombinant Vaccine for Fish Host

Santander Morales, Javier Alonso. Arizona State University, 2012. 3505955.

Abstract (summary)Teleosts have the most primitive adaptive immune system. However, in terms of functionality the teleost immune system is similar to birds and mammals. On the other hand, enteric bacterial pathogens of mammals and birds present conserved regulatory mechanisms that control virulence factors. In this context, deletion of conserved genes that control virulence factors have been successfully used as measure to construct live attenuated bacterial vaccines for mammals and birds. Here, I hypothesize that evolutionary conserved genes, which control virulence factors or are essential for bacterial physiology in

Enterobacteriaceae, could be used as universal tools to design live attenuated recombinant bacterial vaccines from fish to mammals. The evolutionary conserved genes that control virulence factors, crp and fur , and the essential gene for the synthesis of the cell wall, asd , were studied in Edwardsiella ictaluri to develop a live recombinant vaccine for fish host. The genus Edwardsiella is one of the most ancient represent of the Enterobacteriaceae family.E. ictaluri , a host restricted pathogen of catfish (Ictalurus punctatus ), is the causative agent of the enteric septicemia and one of the most important pathogens of this fishaquaculture. Although, crp and fur control different virulence factors in Edwardsiella , in comparison to other enterics, individual deletion of these genes triggered protective immune response at the systemic and mucosal level of the fish. Deletion of asdA gene allowed the creation of a balanced-lethal system to syntheses heterologous antigens. I concluded that crp , fur and asd could be universally used to develop live attenuate recombinant Enterobacteriaceae base vaccines for different hosts.Evaluation of Sacred Lotus (Nelumbo nucifera Gaertn.) as an Alternative Crop for Phyto-remediation

Orozco Obando, Warner Steve. Auburn University, 2012. 3520456.

Abstract (summary)Lotus, Nelumbo nucifera , offers a wide diversity of uses as ornamental, edible and medicinal plant. An opportunity for growing lotus as a crop in Alabama also has the potential for phyto-remediation. Lotus was evaluated for remediation of trace elements focusing on manganese (Mn), organic compounds targeting s -metolachlor and filteringaquaculture waste water. Lotus was evaluated for filtering trace elements by establishing a base line for tissue composition and evaluating lotus capacity to grow in solutions with high levels of Mn (0, 5, 10, 15, or 50 mg/L). Increasing Mn concentrations in solution induced a linear increase in lotus Mn leaf concentrations. Hyper-accumulation of Al and Fe was detected in the rhizomes, while Na hyper-accumulated in the petioles, all without visible signs of toxicity. Mn treatments applied to lotus affected chlorophyll content. For example, chlorophyll a content increased linearly over time while chlorophyll b decreased. Radical scavenging activity (DPPH) did not change over time but correlated with total phenols content, showing a linear decrease after 6 weeks of treatment. Ascorbic acid levels increased in response to lower Mn concentrations but at 50 mg/L or higher Mn treatment level, ascorbic acid levels were reduced.Lotus was evaluated for its potential as a phyto-remediator of organic compounds by growing plants in different concentrations of s -metolachlor. In seedlings, biomass accumulation was affected by the treatments. However, membrane integrity, respiration, and photosynthesis were not affected by the treatments. Mature plants did not show symptoms of toxicity but chlorophyll (Chl) changes in content were related to s -metolachlor concentrations (Chl a content increased while Chl b decreased). Potential s -metolachlor metabolites were found in rhizomes from treated seedlings. However, levels detected were too low to be identified. In addition, traces of s -metolachlor applied to seedlings were found in rhizomes, as well as, in leaves from treated mature plants. Lotus proved to be an effective phyto-remediator of nutrient run-off (NH 4

+ , NO3 , P) and suspended solids from waste water from intense aquaculture systems.Investigating vectors for aquatic invasive species of tunicates in the Canadian shellfish aquaculture industry

Ferguson, Louis F.. University of Prince Edward Island (Canada), 2012. MR82261.

Abstract (summary)The potential spread of Didemnum vexillum through aquaculture transfers of Pacific oyster (Crassostrea gigas ) was investigated on the Sunshine Coast and the West Coast of Vancouver Island, BC. Pacific oysters from infested areas are regularly transferred for processing to non-infested areas thereby posing a risk of spreading D. vexillum to new areas. This observational study used concepts of the Hazard Analysis Critical Control Point (HACCP) methodology to identify points (control processes, CPs) where the clusters of oysters received manipulations that could alter the amount of epibiont fouling, notably D. vexillum . Three control processes (CPs) were identified: 1) the harvesting procedure, 2) transportation from the harvesting area to the processing plant, and 3) shucking of the oysters and depositing fouled shells in non-infested waters. The percentage coverage of D. vexillum on oyster clusters was evaluated at each CP for product originating from twoaquaculture sites, Lemmens Inlet and Okeover Inlet. The results from the assessment demonstrated a significant loss of fouling on C. gigas clusters at both sites from Post-Harvesting (CP1) to Post-Shucking (CP3).

A NR viability assay was developed using Botrylloides violaceus , which is an invasive colonial tunicate in PEI, as a proxy to the colonial tunicate D. vexillum as it is not locally found on PEI. B. violaceus was collected from various locations around PEI and mortality could be determined under light microscopy by assessing filtering and reaction to tactile stimuli as clinical markers. A total of 32 B. violaceus segments (3 cm2) were assessed for viability by comparing a treatment (dead - acetic acid immersion) and a control (alive) group by evaluating NR uptake. Determination of viability in B. violaceus was successful in 100 % of experiments. All of the control group were alive, demonstrating a response to tactile stimulus and a noticeable amount of stain inside the zooids. All treatment groups were dead, demonstrated by the lack of staining and non response to tactile stimulus. A total of 27 fouled clusters containing C. gigas and D. vexillum were collected from anaquaculture lease, Lemmens Inlet, BC, for an aerial exposure comprised of 9 equally divided treatments (0 (control), 0.5, 1.5, 3, 6, 12, 24, 48 and 72 hours). Three segments ofD. vexillum were removed from C. gigas and evaluated with the NR stain protocol. Preserved tissues were analyzed and showed no stain uptake for all segments, including the control. This finding demonstrates that D. vexillum has a high tolerance for uncommon situations and may reflect their ability to enter a dormant state during adverse environmental conditions.In the Montague River estuary, PEI, Ciona intestinalis is the dominant tunicate AIS and is now present in adjacent bays. Removal of C. intestinalis from mussels in processing plants can release gametes into effluent water. Two separate trials in this experimental study focused on the effect of turbidity and flow found in effluent water on C. intestinalis egg fertilization. The first trial evaluated the effect of turbidity (0, 300, 600 and 1200 NTU), and the second evaluated the effect of turbidity (0, 300, 600 and 1200 NTU) combined with water flow (0.9583 L/s). These trials illustrate that regardless of turbidity and flow rate a potential propagule pressure still exists when removing tunicates from mussels within processing plants.Tunicates have a detrimental effect on the mussel industry by fouling aquaculture gear, product and by increasing labour time and cost of culture. Management to maintain an economically sustainable aquaculture industry via optimized husbandry practices, from a grower and processor perspective, is required to lessen the impact of current tunicates and to reduce the potential impact from new AIS threats. The continued monitoring, education and communication to minimize, if not stop, the ongoing spread is a necessity, especially for shellfish growers in PEI and BC who are already combating tunicate invaders. (Abstract shortened by UMI.)Cryopreservation spermiation induction and computer assisted analysis of summer flounder (Paralicthys dentatus) spermatozoa

Brown, Ryan T.. University of New Hampshire, 2012. 1521546.

Abstract (summary)The objective of this thesis was to improve the aquaculture practices for summer flounderParalichthys dentatus. The experiments in this thesis examined male reproduction. First a practical method for summer flounder sperm cryopreservation was developed. These experiments examined the various parameters required to successfully freeze and store summer flounder spermatozoa. Success of cryopreservation was measured by examining post thaw viability and fertility.One of the problems facing summer flounder aquaculture is sexually dimorphic growth rates, with females growing larger than males. To overcome this, meiogynogenetic summer flounder were developed, allowing the production of all female stocks. The second set of experiments examined the sperm characteristics and fertility of meiogynogenetic summer flounder sperm. Finally, to overcome small milt volumes in summer flounder the final set of experiments examined the used of exogenous hormones to increase summer flounder sperm production.Consumer preference for farmed fish in Ghana and Kenya: Opportunities for domestic demand-driven aquaculture

Darko, Francis Addeah. Purdue University, 2011. 1501781.

Abstract (summary)Fish production in Ghana and Kenya has been dwindling for a couple of decades now, due primarily to overexploitation of the nations. marine and inland fisheries resources - the main sources of fish in the two countries. There is however potential in aquaculture to revive domestic fish production in both countries. Accordingly, the governments of Ghana and Kenya have undertaken measures to unleash the potential in their respectiveaquaculture industries to boost domestic fish production. The measures undertaken by the

governments and past aquaculture research have mainly focused on production, leaving many consumption questions unanswered. Meanwhile almost all aquaculture output of both countries ends up in the domestic markets. It is therefore pertinent that the preferences of domestic consumers for aquaculture output are analyzed in order to increase the efficiency and competitiveness of the aquaculture industries in Ghana and Kenya.This thesis used choice models to investigate the preferences of consumers in urban Ghana and Kenya for farmed tilapia and catfish, the main aquaculture products in both countries, in order to advise the aquaculture industry on how to promote aquaculture products in the domestic market. The results show that farmed tilapia and catfish are not generally preferred in both Ghana and Kenya due primarily to issues of availability, healthiness and taste. Ghanaian consumers prefer smoked tilapia and catfish while consumers in Kenya prefer fresh and fried forms of tilapia and catfish. The sensory, functional and symbolic attributes of farmed tilapia and catfish, and the socio-demographic features of consumers are important determinants of consumer preference for farmed fish in both countries. The effects of especially the socio-demographic features of consumers differ across the two countries and fish species.

Shrimp Aquaculture and Aguadulce: A Broken Partnership.

Sylvia M. Bolanos, University of Miami

AbstractA socio-economic impact study was conducted in Aguadulce, Panama to analyze the viability of the shrimp aquaculture industry. Two visits in 2004 and 2010 document the changes the industry underwent through the use of a survey and interviews of knowledgeable informants. Interviews were conducted among field and processing plant employees, managers and owners, government officials, and local artisanal fishermen. It was of relevance to understand the viability of this industry at both the town and country level. Changes are evident when comparing the data. The industry has undergone drastic changes resulting from the spread of White Spot Syndrome Virus (WSSV) and the reduced price paid for shrimp in the international market. Job generation will never reach the levels anticipated in the 1980s and 1990s. The industry is no longer viable for small subsistence shrimp farms in Aguadulce and Panama. The survival of this industry for Panama is based on the production of shrimp for a small niche market that desires an organically raised and environmentally sustainable shrimp which consumers are willing to pay a higher price. The survival of this industry will be based on the price consumers are willing to pay for a better product with stringent certification guidelines in comparison to those from Asia.

Shrimp fisheries and aquaculture : Making a living in the coastal frontier of Berau, Indonesia. Bambang Indratno Gunawan. 2012Wageningen University, Netherlands(no abstract; 1st paragraphs)The social sciences are still heavily biased towards the land and development studies on coastal livelihoods are still few (Visser, 2004). The present study aims to help fill the gap by applying methodological tools that provide first hand, field research based data for policies that support people and communities in ways that are meaningful to their daily lives and needs, as opposed to ready-made, generalist interventionist instruments (Appendini, 2001). Over the last quarter of a century the global concern about the sea level rise and marine biodiversity decline have contributed to the call for Integrated Coastal Zone Management (Visser, 2004: 32). Environmental issues such as global warming and climate change have become predominant in the public media. But political and policy interests leading to the call for ICZM primarily serve land-related technical and macro-economic goals. The social-economic resilience of the coastal population, the existing social and environmental differentiation within and between fishers’ communities, and their access to coastal resources are mostly ignored. The acknowledgement, in the early 1990s, of the need to relate sustainable coastal development to poverty alleviation (ibid: 37) also strengthened the call for the integration of social science and (natural) science to understand the effect of human interaction on the marine and coastal environment. For example, the effect of trans-national trade networks on resource exploitation and the competing claims to the marine resources of those who - directly or indirectly - make a living from them, and those who wish to conserve them. While zoning as the administrative boundary marking of marine space is increasingly shown to be

ineffective (Chapter 6; Visser and Adhuri, 2010) there is a need for integrative policies addressing the rapid social transformation of the coastal area. This book aims to provide the necessary knowledge basis for the policy making and implementation of such Integrated Coastal Development in the Berau delta which is a part of the Berau Marine Protected Area (MPA).