Thesis (Ph. D.)--Auburn University. / Abstract. Vita. Includes bibliographical references (p. 66-71).

Thesis (Ph. D.)--Auburn University. / Abstract. Vita. Includes bibliographical references (p. 73-80).

The intestinal microbiome (IM) or the community of commensal and pathogenic microbes that inhabit the intestinal tract of fish has long been of interest in aquaculture because of its hypothesized role in nutrient digestion and fish immunity. Artificial improvement to the IM of fish with pre- and probiotics has been shown to have benefits in some studies; however, the mechanisms behind these supplements are poorly understood because of a lack of knowledge on the basic structure of the IM of fish. The research described here aims to characterize the IM of the highly studied and commercially important Icatlurid catfish, channel catfish Ictalurus punctatus and blue catfish I. furcatus. In this study we evaluated differences between the homeostatic IM, across genotype (Objective 1) and developmental ontogeny (Objective 2), using high-throughput sequencing of 16S rRNA gene amplicons. We compared the IM of four selected strains of blue catfish and three selected strains of channel catfish at 193 days post-hatch (DPH) in Objective 1 (n = 40); while the influence of developmental ontogeny was evaluated by observing the IM of a single family of channel catfish at 3, 65, 125, and 193 DPH Objective 2 (n = 20). The bacterial phyla Fusobacteria, Firmicutes, and Proteobacteria were detected in all fish strains and developmental time points; however, at the genus level the abundances of different bacteria varied among experimental units, as well as being rather variable between individuals. At 3 DPH (n = 5) the IM of channel catfish sac-fry larvae showed the most variation between individuals; with bacteria from the genus Bradyrhizobium dominating the IM of two sac-fry (84% and 88%), and Flavobacterium, Lactobacillus, Comamonadaceae dominating the IM of the remaining three sac-fry analyzed (86%, 99%, and 97% respectively). The dominant bacteria in the gut of all other fish analyzed (n = 55), was Cetobacterium somerae (mean ± SD, 41.4% ± 36%), a commensal microbe that is known to produce vitamin B12. Statistical differences in the abundance of three different bacteria within the order Clostridiales (P ≤ 0.039) were detected in Objective 1, with more of these OTUs inhabiting the gut of channel catfish than that of blue catfish. Statistical differences in the abundance of Edwardsiella, a genus of bacteria known to cause disease in catfish, were detected across the two species of Ictalurid catfish in Objective 1 (P = 0.038), and across developmental ontogeny in Objective 2 (P = 0.021); however, these bacteria were detected at low abundance (0.002% - 0.004%). Comparisons of beta diversity showed significant differences between many strains of Ictalurids, with a highly significant difference between channel catfish and blue catfish (P = 0.001); however, few differences were detected when comparing beta diversity across the four time points over the first 193 DPH in Objective 2, with only 3 DPH and 125 DPH showing significant differences (P = 0.022). Overall these data suggest host-genotype, and to a lesser extent developmental ontogeny, influence the structure of the IM of Ictalurid catfish. As the first study to be conducted on the IM of these fish species, these results have performance implications on the culture of these commercially important catfish, while also enhancing our basic knowledge on the dynamics of the fish microbiome.

A single tube detection kit was designed as a rapid, easy-to use and reliable test to detect Listeria spp.. Various food samples (vegetables and raw catfish fillets) were used in order to validate the performance of the detection kit. L. grayi was detected in one ready-to-eat (RTE) vegetables with the detection kit while no Listeria spp. was detected using the modified FDA-BAM method. In addition, both the detection kit and modified FDA-BAM method indicated that twelve catfish fillets were Listeria positive. The detection kit had 100% sensitivity and specificity in less detection time (24 h) than the modified FDA-BAM method (60% specificity, >72 h). There was no difference (P<0.05) between the kit and the modified FDA-BAM method on MPN for Listeria spp.

Stress during fish culture can impact growth, physiology and fillet quality. Maintenance of high quality seafood is important to ensure the production of a highly marketable product. The present study assessed how sequential stressors affect the physical, physiological, sensory and quality characteristics of channel catfish (Ictalurus punctatus) fillets. Temperature (25°C or 33°C) and dissolved oxygen (DO, ~2 mg/L or >5 mg/L) were maintained for four weeks, followed by socking and transport stress for a total of 12 treatments. After each stage of stress (environment, socking and transport), physical (length, weight and feed consumption), physiological (hematocrit, plasma cortisol, pH, glucose, lactate, total protein, osmolality and ionic composition) and fillet quality (color, texture, sensory and pathogen load) attributes of the fish and fillets were evaluated. Fillet yield decreased with increasing severity of environmental stress. Overall, increasing stress resulted in decreased feed consumption, growth and fillet yields. A cumulative stress response was identified with regard to circulating cortisol and glucose, which increased with each sequential stress event. Under low oxygen conditions there was a suppression of the stress response. Handling imposed a more pronounced physiological response than environmental conditions. The sequential stressors resulted in a less intensely colored fillet that was less red, which suggests the quality changes imposed are beneficial to the marketability of the fillets. However, increased redness in fish reared under high temperatures and oxygen levels suggest that an increased prevalence of red fillets can be expected. Sensory analysis revealed that fillet flavor was acceptable in all treatments with the severe stress treatment preferred due to lower intensity of less favorable flavor attributes. The changes in flavor were presumably due to fasting of the stressed fish and a subsequent purging of fat stores. As fish progressed through the harvest event, cook loss decreased, tenderness increased and pH increased, indicating that stress induced positive textural changes. Proteomic analysis revealed mainly down-regulation of structural and metabolic proteins, which indicates higher proteolytic activity and an adjustment in energy metabolism in response to stress. The overall effects of chronic environmental conditions and handling highlight the importance of managing for stress in cultured channel catfish.

Proteins in catfish by-products were extracted by two methods: Alkaline extraction (AE) and salt extraction (SE). Properties of the fish protein isolate (FPI) were measured by protein yield and content, moisture content, SDS-PAGE protein patterns, color and texture profile, and compared with commercial surimi products. Our results showed that catfish frame had higher protein yield and color similarity with commercial products than the head; AE-FPI had higher yield and gel strength than SE-FPI; SDS-PAGE protein patterns of FPI from catfish frame by SE method was comparable with commercial surimi products. Based on the results, further optimization of the recovery yield of protein extracted by alkaline extraction method, and effect of microbial transglutaminase (MTGase) on gelation properties under various concentration and reaction time was investigated. Results indicate that the protein yield reached up to 60%, and the addition of MTGase in protein isolate effectively improved the gel forming ability.

The overall baseline (as received) moisture, protein and fat content of hybrid catfish (Ictalurus furcatus x Ictalurus punctatus) fillets were 77.8 +/- 1.38%, 16.7 +/- 0.50% and, 5.7 +/- 1.6%, respectively. Small fillets (111 +/- 19 g) had higher (P≤0.05) baseline moisture (78.6 +/- 0.87% vs 76.8 +/- 1.15%) and lower (P≤0.05) fat content (4.7 +/- 0.64% vs 6.8 +/- 1.72%) than large fillets (247 +/- 62 g), whereas protein content was similar (P>0.05) for both sizes. Retained water of the final fresh and frozen fillets was 1.2 +/- 2.03% and 3.1 +/- 1.02%, respectively, irrespective of fillet size. Psychrotrophic (PPC) and total coliform plate counts (TCC) of the baseline fillets were 4 log CFU/g and 1.6 log CFU/g, respectively and were not different between the process steps, except after injection which was higher (P>0.05) than baseline. Moisture-protein ratio and fat content were good (P≤0.05) predictors for retained water in catfish fillets during processing.

This thesis is about implementing an Internet of Things system for measuring water quality in rivers and other aquatic environments with an autonomous water drone, where the data from various components are collected and sent wirelessly to the database in real-time. A Raspberry Pi is connected to the internet through a 4G modem and a wireless satellite communication connection called RockBlock for emergency calls and notifications. In addition, a sonar is also implemented to collect data for the unmanned surface vehicle's (USV) avoidance of collisions. Finally, batteries are connected to solar panels to auto-generate energy and provide the USV with its requested current and voltage. The minimum parameters to measure water quality are four: potential hydrogen, dissolved oxygen, nitrates, and colored dissolved organic matter. As a result, the system in this thesis measures the four parameters mentioned above, plus turbidity and temperature, since the interconnected sensors can also measure those. In addition, optical sensors were chosen because of their exceptional accuracy and precision when measuring water quality. The environment, mainly the aquatic, will benefit from this project and change for the better with time. / Den här vetenskapliga artikeln handlar om att implementera ett Internet of Things system avsett för att mäta vattenkvaliteten i floder och andra vattenmiljöer med en autonom vattendrönare, där datan från diverse komponenter samlas in och skickas trådlöst till databasen i realtid. En Raspberry Pi är ansluten till internet via ett 4G-modem samt en trådlös satellitkommunikationsanslutning som kallas RockBlock för nödmeddelanden och notifikationer. Dessutom implementeras ett ekolod för insamling av data till den autonoma vattendrönaren för undvikande avkollisioner. Slutligen är batterierna anslutna till solcellspaneler för att automatiskt generera energi och förse den autonoma vattendrönaren med tillräcklig ström samt spänning.Det minsta antalet parametrar för att mäta vattenkvalitet är fyra: potentiellt väte, löst syre, nitrat, och färgat löst organiskt material. Som ett resultat mäter systemet i denna avhandling de fyra parametrarna nämnda ovan, plusgrumlighet och temperatur, eftersom de sammankopplade sensorerna ocksåkan mäta dessa. Dessutom valdes optiska sensorer på grund av deras exceptionella noggrannhet och precision vid vattenkvalitetsmätning. Miljön, speciellt vattenmiljön, kommer att gynnas av detta projekt samt förändras till det bättre med tiden.

Catfishes Ictaluridae are important food fish that are harvested from the New River, Virginia by multiple methods, yet standard creel survey approaches do not accurately sample setline effort, a popular fishing gear for catfish. I characterized the New River setline fishery by estimating setline effort and catch rates of catfish and by-catch in 2011, and by investigating the attitudes and opinions of setline users during 2012. Setline effort was highest during June-August, and declined significantly by mid-September. Several dedicated setline users accounted for a significant portion of total setline effort. Experimental setlines baited with live minnows Cyprinidae proved to be an effective method for catching catfish but caught few walleye Sander vitreus, smallmouth bass Micropterus dolomieu, and muskellunge Esox masquinongy. Estimated by-catch of these species by setline fishers is small compared to catch by hook-and-line anglers, though walleye experienced high setline hooking mortality, and catch rates increased in autumn months. Setlines appear to be part of a larger "way of life" for some rural individuals, who may also hunt, trap, and garden as part of activities to supplement their diet or income. New River setline fishers strongly believe that setline fishing has declined significantly in the New River Valley due to improving socioeconomic status of the region, changing recreational values (such as focus on catch-and-release fishing and paddle sports), increasing recreational traffic and law enforcement presence, and decreasing participation in setline fishing by younger generation. / Master of Science

Channel Catfish are broadly distributed in the U.S. and are important commercially and recreationally in many rivers, lakes, reservoirs, and streams. Since they are a popular sportfish, many state-owned lakes are stocked with a variety of sizes to enhance population sizes and provide angling opportunities. The goals of this study were to determine the contributions of stocked fish, determine the fish size at stocking, and to assess the contribution of yearling and catchable sizes to the stocked percentage. Fish samples were obtained from three hatcheries and six lakes within different ecoregions across Arkansas to assess whether chemical signatures were different among locations. Sectioned pectoral spines were analyzed for Sr:Ca and Ba:Ca using laser ablation-ICPMS to determine whether location-specific Sr:Ca and Ba:Ca signatures were reflected in pectoral spine samples, and to assess the accuracy with which fish could be assigned to their collection location using spine Sr:Ca and Ba:Ca. Fin spine core Sr:Ca and Ba:Ca data were also used to identify stocked fish and determine size at stocking for hatchery-origin fish sampled from each of the six lakes. Spine microchemistry represents a non-lethal approach to identify stocked catfish and infer size at stocking, which will better inform allocation of hatchery-produced fish. Differences in pectoral spine Sr:Ca edge signatures among locations were detected, which were primarily driven by differences in geology among ecoregions. Assignment accuracy of fish to collection location using Random Forest Modeling was 88% or greater for all but one of the study lakes. This allowed for application of the random forest model on pectoral spine core Sr:Ca and Ba:Ca to assign individuals sampled from the lakes as hatchery or wild origin. Among all the Channel Catfish sampled from the six lakes, 45% were identified as hatchery origin and 46% of those were stocked as catchable size fish. Contributions of stocked fish varied among study lakes from 0% to 100%. This was the first study to demonstrate that pectoral spine microchemistry can be used for assessing both stocking contribution and inferring fish size at stocking. Overall, this study will aid in the allocation of hatchery-reared catfish by management biologists, and could lead to more projects focused on exploring stocking contribution by microchemistry, such as assessment of how habitat enhancement may influence the contribution of natural reproduction to catfish populations.