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The fishery for Antarctic krill (Euphausia superba) has received considerable attention in recent years, owing largely to the possibility of its significant expansion and the ecological implications of increased extraction of a keystone species. This thesis employed Ecological Footprint (EF) analysis and life cycle assessment (LCA) to measure the resource use, energy use, and emissions associated with three krill-derived products: meal and oil for aquaculture feeds, and omega-3 krill oil capsules for the nutraceutical market. The product supply chains of one krill fishing and processing company, Aker BioMarine, were used as a case study to examine Antarctic krill-derived products. Antarctic krill products were compared to products from similar fisheries targeting other species for reduction into meal and oil, including Peruvian anchovy (Engraulis ringens), Atlantic herring (Clupea harengus), blue whiting (Micromesistius poutassou) and Gulf menhaden (Brevoortia patronus), on the basis of marine footprint, carbon footprint, and fuel use intensity.

The global climate is strongly regulated by the oceans, which store carbon away from the atmosphere for long periods. In an effort to understand the role of the oceans in the carbon cycle, it is necessary to understand the nuances of specific regional and functional marine ecosystems. The continental shelf of the West Antarctic Peninsula (WAP) is one particularly important regional ecosystem that plays a vital role in the Southern Ocean carbon export. Within the seasonally productive marginal ice zone of the WAP, I sought to identify the long-term drivers of particulate organic carbon (POC) flux. The vast majority of exported POC on the WAP was previously found to be made up of krill fecal pellets. I provide evidence that supports the hypothesis that the inherent life cycle of krill drives the observed 5-year oscillation in POC export. At the end of their life cycle, when krill are at their largest body size, the WAP experiences anomalously high POC export events through the production and sinking of large, carbon-rich krill fecal pellets. Conversely, when krill are young and small, POC export is anomalously low. This pattern shows that ecology exerts a first-order control on the the biogeochemical cycles of the WAP. Upon identifying the source and driver of POC export on the WAP, I set out to determine the role heterotrophic bacteria play in POC flux attenuation. I collected krill fecal pellets on the WAP over three years and measured bacterial metabolic activity in terms of bacterial production and respiration, thereby identifying the amount of organic carbon within the sinking fecal pellets that is lost due to bacteria. Overall, fecal pellet POC turnover rate by bacteria is very low. The relationship between bacteria and POC is complex with each having an affect on the other. Despite varied reactions of the free-living bacterial populations to the presence of krill fecal pellets, a consistent pattern emerged in the concentration of nucleic acid within each bacterial cell. Access to fecal pellets increased the metabolic activity of the free-living bacterial population. This finding shows that the egestion of krill fecal pellets metabolically stimulates the surrounding bacterial community, even though bacteria play a minor role in fecal pellet POC flux attenuation. Though bacteria were found to play a minimal role in organic carbon uptake on krill fecal pellets, they are still vital members of the WAP ecosystem and biological pump. I next sought to identify which bacteria in particular were responsible for colonizing and consuming the fecal pellet POC. Krill fecal pellets were genetically sequenced after timed exposure to the free-living water column bacterial community. I found that there is an endemic population of bacteria that are associated with each population of krill and their fecal pellets. This community of fecal pellet-associated bacteria does not change over time, indicating little colonization by free-living bacteria. Krill fecal pellets, aside from being good agents of POC export, seem to be selective environments for certain specialized copiotrophic bacteria. Further, I find that only a small subset of these endemic copiotrophs actively partake in carbon consumption on krill fecal pellets. Overall, these results show that a small endemic, specialized bacterial community play an outsized role in krill fecal pellet POC degradation and flux attenuation, but that krill fecal pellets remain efficient agents of carbon export to the deep ocean.

1. Antarctic krill (Euphausia superba) form aggregations known as swarms that vary greatly in size and density. Six acoustic surveys were conducted as part of multidisciplinary studies at two study sites, the western and eastern core boxes (WCB and ECB), during the 1997, 1998 and 1999 austral summers, at South Georgia. A quantitative, automated, image processing algorithm was used to identify swarms, and calculate swarm descriptors, or metrics. In contrast to acoustic surveys of aggregations of other pelagic species, a strong correlation (r = 0.88, p = 0.02, 95% C.I.= 0.24 to 0.99) between the number of krill swarms and the mean areal krill density [rho.hat] was found. Multivariate analysis was used to partition swarms into three types, based on contrasting morphological and internal krill density parameters. Swarm types were distributed differently between inter-surveys and between on and off-shelf regions. This swarm type variation has implications for krill predators, by causing spatial heterogeneity in swarm detectability, suggesting that for optimal foraging to occur, predators must engage in some sort of adaptive foraging strategy. 2. Krill predator-prey interactions were found to occur at multiple spatial and temporal scales, in a nested, or hierarchical structure. At the largest inter-survey scale, an index of variability, I, was developed to compare variation in survey-scale predator sightings, sea temperature and [rho.hat]. Using I and a two-way ANOVA, core box, rather than year, was found to be a more important factor in determining species distribution. The absence of Blue-petrels (Halobaena caerulea) and the elevated number of Antarctic fur seals (Arctocephalus gazella) suggest that 1998 was a characterised by colder than average water surrounding South Georgia, and a high [rho.hat] in the ECB. At the smaller, intra-survey scales (<80 km, <5 day), the characteristic scale (distances in which predator group size, or krill density were similar, L_s) were determined. For krill and predators L_s varied by survey and the L_s of krill also varied by depth within a survey. Overlap in L_s were stronger between predator species than between a predator species and krill, indicating predators were taking foraging cues from the activity of predators, rather than from the underlying krill distribution. No relationship was found between swarm characteristics and predator activity, suggesting either there is no relationship between krill swarms and predators, or that the predator and acoustic observation techniques may not be appropriate to detect such a relationship. 3. To overcome the 2-D sampling limitations of conventional echosounders, a multibeam echosounder (MBE) observed entire swarms in three-dimensions. Swarms found in the nearshore environment of Livingston Island situated in the South Shetland Islands, exhibited only a narrow range of surface area to volume ratios or roughnesses (R = 3.3, CV = 0.23), suggesting that krill adopt a consistent group behaviour to maintain swarm shape. Generalized additive models (GAM) suggested that the presence of air-breathing predators influenced the shape of a krill swarm (R decreased in the presence of predators: the swarm became more spherical). A 2D distance sampling framework was used to estimate the abundance, N, and associated variance of krill swarms. This technique took into account angular and range detectability (half-normal, [sigma_r.hat] = 365.00 m, CV = 0.16) and determined the vertical distribution of krill swarms to be best approximated by a beta-distribution ([alpha.hat] = 2.62, [CV.hat] = 0.19; [beta.hat] = 2.41, [CV.hat] = 0.15), giving the abundance of swarms in survey region as [N.hat] = 5,062 ([CV.hat] = 0.35). This research represents a substantial contribution to developing estimation of pelagic biomass using MBEs. 4. When using a single- or split-beam missing pings occur when the transmit or receive cycles are interrupted, often by aeration of the water column, under the echosounder transducer during rough weather. A thin-plate regression spline based approach was used to model the missing krill data, with knots chosen using a branch and bound algorithm. This method performs well for acoustic observations of krill swarms where data are tightly clustered and change rapidly. For these data the technique outperformed the standard MGCV GAM, and the technique is applicable for estimating acoustically derived biomass from line transect surveys.

Locomotion is a key characteristic of almost all forms of life and is often accomplished, whether on land, in water, or in the air, by reciprocal motion of two or more appendages. Among the zooplankton, many species propel themselves by rhythmically beating multiple pairs of closely spaced leg-like appendages in a back-to-front (metachronal) pattern. The focus of this study is to understand the mechanical design, kinematic operation, and hydrodynamic result of metachrony in the zooplankton. In the first part of this study, Antarctic krill (Euphausia superba) are investigated as an ecologically important model species that metachronally beats its swimming legs (pleopods) to perform drag-based propulsion. Based on high speed videos of freely swimming Antarctic krill, hovering, fast forward swimming, and upside down swimming are identified as three distinct swimming modes with significantly different stroke amplitudes and beat frequencies. When transitioning between hovering and fast forward swimming, Antarctic krill first increase beat amplitude and secondarily increase beat frequency. In considering the design components that contribute to metachrony being a successful swimming technique, a comparison among many different species shows that the ratio between the appendage separation distance and appendage length is limited to a narrow range of values (i.e. 0.2 - 0.65). In the second part of this study, metachrony is examined at smaller length and time scales by examining the impulsive escape jump of a calanoid copepod (Calanus finmarchicus). The wake generated by the copepod's metachronally beating swimming legs is experimentally measured using a novel (and newly developed) tomographic particle image velocimetry (PIV) system capable of making volumetric 3D velocity measurements with high temporal and spatial resolution using IR illumination. The flow generated by the escaping copepod consisted of a stronger posterior vortex ring generated by the metachronally stroking swimming legs and a weaker one generated anteriorly around the body by the impulsive start of the escape, both of which decayed over time. The experiments also revealed azimuthal asymmetry in the vortices caused by body yawing and the action of the swimming legs, flow features not considered in previous axisymmetric computational and theoretical models of copepod jumps. While not accounting for this asymmetry, an impulsive stresslet is nonetheless useful in modeling the flow created by the escaping copepod and represents the flow more accurately than an impulsive Stokeslet. In the final part of this study, the flow associated with metachronal hovering in Antarctic krill is experimentally and theoretically investigated in regards to the energy requirements of the pelagic lifestyle. Volumetric flow measurements of a hovering Antarctic krill show that each stroking pleopod drags flow behind it such that a downward stream develops medially. The lateral exopodites induce tip vortices which add to the lift force on each appendage. Furthermore, the flow beneath the hovering krill develops into a pulsed jet with a Strouhal number in the 'high-efficiency zone' of 0.2 < St < 0.4. Actuator disk theory is used to make theoretical estimates of the induced power necessary to hover, the results of which match induced power values calculated from measured flow gradients contributing to viscous energy dissipation.

Proteins are a highly diversified group of molecules, andfor their study, advanced analytical tools are required. Inparticular, a need for high-throughput techniques has emergedin order to enable the characterization of large sets ofproteins. In this thesis, improved techniques for proteinseparations as well as new tools for the mass spectrometricanalysis of proteins are described. In the work, presented in the first part of the thesis, arefined extract containing proteases from Antarctic krill (Euphausia superba) was separated and characterized bymeans of capillary electrophoresis (CE) and mass spectrometry(MS). Tailored CE separations of the krill extract revealed thepresence of approximately 50 components. In addition, adetailed CE and MS analysis of fractions, containing individualkrill proteases has been carried out. Trypsin-like proteasesfrom krill exhibited a 12-fold and a 60-fold higher digestionefficiency at 37 °C and 2 °C respectively compared todigests performed with bovine trypsin. Furthermore, thecleavage specificity of the trypsin-like proteases wasstudied. In the last part of the thesis, novel concepts forchip-based nanoelectrospray (nanoESI) and matrix-assisted laserdesorption/ionization (MALDI) mass spectrometry are described.First, a micromachined silicon chip with a two-dimensionalmatrix of out-ofplane nanoESI needles for high-throughputanalysis was fabricated. A two-fold improvement insignal-to-noise reproducibility was obtained. Second, achip-based target for MALDI was developed, which featured pairsof elevated 50×50 µm anchors in close proximity. Theanchors were individually addressable with sample solution. Theminiaturized sample preparations at close distance to eachother allowed a simultaneous ionization of a physicallyseparated sample and standard by one single laser pulse. Thisresulted in a twofold reduction of relative mass errors.Moreover, ion suppression of the analyte was significantlyreduced. The effective utilization of the sample resulted in adetection limit of ca 200 zeptomole of angiotensin I. Key words:Proteins, peptides, proteases, Antarctickrill,Euphausia superba, capillary electrophoresis,fluorosurfactants, mass spectrometry, nanoelectrospray, ESI,MALDI, chip, high-throughput, reproducibility, sensitivity andmass accuracy.

<p>Proteins are a highly diversified group of molecules, andfor their study, advanced analytical tools are required. Inparticular, a need for high-throughput techniques has emergedin order to enable the characterization of large sets ofproteins. In this thesis, improved techniques for proteinseparations as well as new tools for the mass spectrometricanalysis of proteins are described.</p><p>In the work, presented in the first part of the thesis, arefined extract containing proteases from Antarctic krill (<i>Euphausia superba</i>) was separated and characterized bymeans of capillary electrophoresis (CE) and mass spectrometry(MS). Tailored CE separations of the krill extract revealed thepresence of approximately 50 components. In addition, adetailed CE and MS analysis of fractions, containing individualkrill proteases has been carried out. Trypsin-like proteasesfrom krill exhibited a 12-fold and a 60-fold higher digestionefficiency at 37 °C and 2 °C respectively compared todigests performed with bovine trypsin. Furthermore, thecleavage specificity of the trypsin-like proteases wasstudied.</p><p>In the last part of the thesis, novel concepts forchip-based nanoelectrospray (nanoESI) and matrix-assisted laserdesorption/ionization (MALDI) mass spectrometry are described.First, a micromachined silicon chip with a two-dimensionalmatrix of out-ofplane nanoESI needles for high-throughputanalysis was fabricated. A two-fold improvement insignal-to-noise reproducibility was obtained. Second, achip-based target for MALDI was developed, which featured pairsof elevated 50×50 µm anchors in close proximity. Theanchors were individually addressable with sample solution. Theminiaturized sample preparations at close distance to eachother allowed a simultaneous ionization of a physicallyseparated sample and standard by one single laser pulse. Thisresulted in a twofold reduction of relative mass errors.Moreover, ion suppression of the analyte was significantlyreduced. The effective utilization of the sample resulted in adetection limit of ca 200 zeptomole of angiotensin I.</p><p><b>Key words:</b>Proteins, peptides, proteases, Antarctickrill,<i>Euphausia superba</i>, capillary electrophoresis,fluorosurfactants, mass spectrometry, nanoelectrospray, ESI,MALDI, chip, high-throughput, reproducibility, sensitivity andmass accuracy.</p>

Der Antarktische Krill (Euphausia superba) ist eine Schlüsselart des Ökosystems des Südozeans und möglicherwese die biomassereichste Art der Erde. Klimawandelbedingte Lebensraumänderungen, die Expansion der kommerziellen Krillfischerei, sowie sich erholende Bartenwalpopulationen setzen Krillpopulationen jedoch zunehmend unter Druck. Daher besteht ein großer Bedarf, die Auswirkungen dieser verschiedener Stressoren auf Krillpopulationen zu verstehen und vorherzusagen. Dabei helfen Simulationsmodelle, die das Wachstum und die Entwicklung des Krills vorhersagen. Modelle sind vielseitige Instrumente, mit denen sich die Auswirkungen verschiedener Stressoren auf Krill in unterschiedlichen Szenarien bewerten lässt, was sie für Management- und Projektionsstudien besonders nützlich macht. In dieser Arbeit untersuchen wir Möglichkeiten die Robustheit von Modellen zu verbessern, die das Wachstum von Krillindividuen unter verschiedenen Umweltbedingungen vorhersagen. Zunächst haben wir ein bestehendes Wachstumsmodell erweitert, indem wir es um realistischere physiologische Prozesse ergänzt haben, was zu verbesserten Wachstumsvorhersagen führte. Anschließend haben wir in der Vergangenheit publizierte Wachstumsmodelle verglichen, um zu untersuchen, ob die Mechanismen des Krillwachstums verallgemeinerbar sind, da die Modelle für verschiedene Regionen entwickelt und mit unterschiedlichen Daten kalibriert wurden, regelmäßig aber außerhalb dieser Regionen verwendet werden. Diese Information ist wichtig für künftige Simulationsstudien, da eine regionale Spezifität die Modelle in ihrer großskaligen Anwendbarkeit limitieren würde. Die Wachstumsvorhersagen der verschiedenen Modellen bei identischen Inputdaten zeigte dabei, dass die Mechanismen und Wachstumsvorhersagen zwischen den Modellen erheblich variieren. Durch die Identifizierung der Ursachen dieser Modellspezifität, konnten wir das allgemeine Verständnis der Krill-Wachstumsmechanismen verbessern und zu der Entwicklung robusterer Modellen beitragen. Individuenbasierte Modelle ermöglichen die Einbindung vieler Prozesse, wie z. B. Verhalten, was diese Art von Modellen besonders attraktiv macht. Unser mechanistisches Verständnis des Verhaltens von Krill ist jedoch noch begrenzt, und wir haben versucht, dies durch die Analyse eines achtmonatigen Datensatzes über das vertikale Migrationsverhalten des Krills zu verbessern. Die Analysen zeigten, dass das vertikale Migrationsverhalten von Krillschwärmen sehr flexibel ist und wahrscheinlich von mehreren Faktoren wie dem Stadium, der Jahreszeit, den Nahrungsbedingungen und der Anwesenheit von Krillprädatoren bestimmt wird. Diese Studie dient als Grundlage für die Entwicklung von Modellkomponenten, die es erlauben das Krillverhalten in individualbasierte Modelle zu integrieren. Anschließend haben wir das vorhandene Wissen über das Krillverhalten in einem Reviewartikel zusammengefasst und dabei die möglichen Auswirkungen des Klimawandels auf Krillverteilung und das Schwarmverhalten analysiert. Zuletzt haben wir einen Systematic Literature Review durchgeführt, um eine Übersicht von Daten zu erstellen, die für die Modellentwicklung und -parametrisierung genutzt werden können. Auf diese Weise konnten wir Aspekte der Krillökologie identifizieren, für die aktuell besonders wenige Daten existieren, was wertvoll für zukünftige empirische Forschung sein wird. Da die Schließung dieser Datenlücken Zeit brauchen wird, diskutieren wir zudem auch Möglichkeiten zur Modellierung des Krillwachstums trotz bestehender Unsicherheiten. Mit dieser Arbeit leisten wir einen Beitrag zur Entwicklung realistischerer und robusterer individuenbasierter Krill-Wachstumsmodelle.:1. Introduction 2. Article I - The impact of seasonal regulation of metabolism on the life history of Antarctic krill (Euphausia superba) 3. Article II - An intercomparison of models predicting growth of Antarctic krill (Euphausia superba): the importance of recognizing model specificity 4. Article III - An open and lightweight method to analyze the vertical distribution of pelagic organisms using echogram screenshots 5. Article IV - Plasticity and seasonality of the vertical migratory behaviour of Antarctic krill using acoustic data from fishing vessels 6. Article V - Impacts of climate change on krill behaviour and population dynamics 7. Article VI - Mapping the data landscape for developing and parameterizing Antarctic krill models 8. Supervised Research Projects 9. Discussion 10. Literature cited in Introduction and Discussion 11. Appendices