Plankton are generally considered good indicators for ocean climate variability, but plankton data from the Arctic are still comparatively scarce. Due to this scarcity of information, the prevalence of vertical migration behaviour at high latitude is still debated. Atlantic inflow is a key process governing biological diversity in the Arctic Ocean, and the location of the Svalbard archipelago makes it an ideal study area to monitor this inflow. Comparing the zooplankton community within the fjords of Svalbard at various latitudes allowed us to assess the influence of Atlantic inflow and any subsequent changes in zooplankton composition that may have implications for higher trophic levels. Using sediment traps deployed on oceanic moorings, Chapter 3 of this thesis analysed long term observations from sea-ice dominated Rijpfjorden for the first time, and compared the zooplankton to Atlantic Water influenced Kongsfjorden. Chapters 4 and 5 investigated the spatial relevance of our moored observations using shipboard observations, and chapters 6 and 7 present observations of vertical migration across a range of conditions. Kongsfjorden was dominated by Calanus copepods associated with Arctic and Atlantic water, and strongly influenced by Atlantic Water advection. Rijpfjorden was largely influenced by sea-ice formation with higher proportional abundances of macrozooplankton species. Advection brought Atlantic associated species into Rijpfjorden during warmer years. Prevailing hydrology and bathymetry were highlighted as factors forcing zooplankton distribution, while advection was identified as responsible for much of the observed small scale spatial variation amongst weaker swimmers. At an aggregation scale of 0.5 nautical miles, zooplankton distribution was highly patchy and moored observations could only be reliably expanded outwards to a maximum of 1 nautical mile. Low amplitude diel vertical migration (especially by younger copepodids) was identified in surface waters when a food source was available. These observations must be considered within the dynamic framework of advection highlighted by this thesis.

Crustaceans are ubiquitous in the world’s oceans and include species ranged in size from < 1 mm to > 1 m. Information on the natural diet of marine crustaceans, especially the small crustaceans such as copepods, is usually obtained by measuring gut content microscopically or by the use of electronic particle counters, by microscopic examination of gut contents and fecal pellets, and by the use of stable isotopes or taxon-specific pigment markers. Unfortunately, most of these methods involve conducting feeding experiments in artificial laboratory condition, require a high level of taxonomic expertise, and provide only coarse information on food types that are digestion-resistant. Increasingly over the past decade, DNA-based methods have been used to study the natural diet of small marine organisms such as molluscan larva and the lobster larva with high taxonomic resolution. / In this thesis, the diets of two marine crustaceans are investigated. The small calanoid copepod Calanus sinicus (2.5−3.5 mm), one of the animals studied in this thesis, is a dominant member of the marine zooplankton in the continental shelf waters of China and the northwest Pacific Ocean. Copepods of the genus Calanus are generally considered to be herbivorous although information on the natural diet of C. sinicus is scarce. / Another marine crustacean studied in this thesis is the hydrothermal crab Xenograpsus testudinatus. This crab is endemic to the shallow-water hydrothermal vents of Kueishan Island in the northeastern corner of Taiwan. The extreme environment inhabited by X. testudinatus is unsuitable for most marine organisms due to discharge of hot and acidic water with high content of sulphur. Although the diet of X. testudinatus has been studied by several investigations, the taxonomic resolution of the dietary information is poor. / Accurate information of the diet and feeding habit of a species provides the basis for understanding its role in aquatic food webs. In my thesis, the natural diets of the marine copepod C. sinicus from Hong Kong and Taiwan and the hydrothermal vent crab X. testudinatus were investigated using Illumina sequencing of the prey DNA in the gut content. Variable regions of the 18S and 16S rRNA genes in the gut contents are amplified using DNA extracted from gut contents to determine the composition of eukaryotes and prokaryotes in the diet of the marine crustacean. The diet of X. testudinatus are compared to those of the mangrove crabs Perisesarma bidens. / Gelatinous zooplankton including Hydrozoa and unclassified Ctenophora are very common in the gut contents of C. sinicus from both Hong Kong and Taiwan. C. sinicus from Hong Kong contains diatoms and dinoflagellates, while C. sinicus from northern Taiwan also feeds on Anthozoa, Ascidiacea and Malacostraca. Unclassified Proteobacteria and unclassified bacteria are common in C. sinicus from both Hong Kong and Taiwan. Cyanobacteria, mainly Synechococcus, are only found in C. sinicus from Taiwan. My results show that C. sinicus can feed omnivorously on a diverse assemblage of phytoplankton and zooplankton. / The diet of X. testudinatus differs from that of P. bidens. While P. bidens feeds mainly on Magnoliopsida plant, X. testudinatus feeds on a diverse assemblage of organisms including algae, fishes, bivalves, copepods and anthozoans. Although soil bacteria such as Rodobacteraceae and cyanobacteria including Oscillatoriphycidae occur in the gut contents of both crabs, Mycoplasmataceae and Helicobacteraceae, which are suspected to be gut probiotic bacteria, are only found in the vent crabs. My findings suggest that both X. testudinatus and P. bidens are scavengers. / In short, the DNA-based method can provide detailed information on the natural diets of marine crustaceans and provide accurate information on the trophic role of the marine crustaceans in the food webs. / 甲殻類動物在海洋上是很常見的。牠們的體型大小也有很大的差異(由< 1毫米到 > 1米)。有關海洋甲殻類動物食性研究特別是一些細小甲殻類動物例如橈腳類動物通常都是利用電子計量器或以肉眼在顯微鏡下計算，利用電子顯微鏡去鑑定腸及糞便中的食物殘滓及利用穩定同位素或物種獨有的色素去鑑定。不過，這些方法包括實驗室餵食測試需要熟練的鑑定技巧而且這些方法只能夠提供粗略的資訊。例如只限於會經消化後留下硬塊的食物。雖然如此，最近有研究成功利用DNA鑑定的方法去找出一些細小海洋甲殻類動物例如龍蝦及軟體動物的幼體的食性。 / 這篇論文主要研究兩種海洋甲殻類動物的野外食物。其中一種研究對象，細小的橈腳類動物中華哲水蚤 (2.5−3.5毫米)，在中國沿岸海域及西北太平洋是很常見的。雖然有關於中華哲水蚤在食性資料不多，但是哲水蚤類的動物一般被認為是草食性。 / 這篇論文的另一研究對象是烏龜怪方蟹。牠在位於台灣東北部的龜山島的淺水熱噴泉是很常見的。在淺水熱噴泉的生境，由於經常有酸性高溫及含有高濃度硫磺的水噴出，所以那裡是被認為不適合生物居住的。雖然烏龜怪方蟹的食性也有被研究過，但有關牠們的攝食的物種鑑定還是不夠詳細。 / 準確的有關生物的食性的資料可以幫助我們了解該生物在海洋食物網中角色。有見及此，在這篇論文中主要會利用DNA鑑定及Illumina定序技術來研究來自香港及台灣的中華哲水蚤及在淺水熱噴泉的烏龜怪方蟹的食性。在實驗中，腸道中的DNA的18S及16S rRNA基因中DNA序列差異大的區域會被用來鑑定腸道中的有核生物及原生生物。居住在紅樹林的雙齒近相手蟹的攝食也會用來跟烏龜怪方蟹比較。 / 啫哩狀的浮游動物比如水息蟲類動物及櫛水母來自香港及台灣的中華哲水蚤的腸道中是很常見的。在來自香港的中華哲水蚤腸道中找到了硅藻及甲藻，而在來自台灣的中華哲水蚤的腸道中卻找到珊瑚綱動物，海蛸和軟甲綱動物。在來自香港及台灣的中華哲水蚤的腸道中找到的原核生物為不能鑑定的細菌及不能鑑定的變形菌。藍綠藻主要為聚球藻只有在來自台灣的中華哲水蚤的腸道中找到。研究的結果顯示中華哲水蚤是雜食性及攝食很多不同類型的浮游生物。 / 研究結果顯示烏龜怪方蟹所食的食物跟雙齒近相手蟹很不同。雙齒近相手蟹主要攝食雙子葉植物綱植物，而烏龜怪方蟹所吃的食物是高生物多樣性的包括藻類，魚，雙殻綱動物，橈腳類動物及珊瑚綱動物。土壤細菌比如紅桿菌科細菌及藍綠藻都可以烏龜怪方蟹及雙齒近相手蟹的腸道及胃道中找到，而可能是腸道原生細菌的枝原體科細菌及螺旋杆菌科細菌只能夠在烏龜怪方蟹的腸道中找到。研究結果顯示烏龜怪方蟹及雙齒近相手蟹都是拾荒者。 / 總括而言，利用DNA去研究動物食性的方法可以提供更多有關海洋甲殻類動物食性的詳細資料及提供準確的有關海洋甲殻類動物食性層次的資料。 / Ho, Tsz Wai. / Thesis M.Phil. Chinese University of Hong Kong 2015. / Includes bibliographical references (leaves 65-85). / Abstracts also in Chinese. / Title from PDF title page (viewed on 12, October, 2016). / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only.

Les copépodes sont au cœur des flux de matière et d'énergie dans les réseaux trophiques arctiques et subarctiques. La structure et les fonctions des communautés de copépodes dépendent de l'assemblage des espèces dont elles sont constituées, mais on en connait très peu sur les interactions interspécifiques qui peuvent influencer ces propriétés. Les copépodes ont la capacité d'ingérer leurs propres œufs et nauplii (cannibalisme) ainsi que ceux des autres espèces (prédation intraguilde). Il est donc possible que ce type de prédation ait le potentiel de contrôler le recrutement et la dynamique des espèces de copépodes. L'objectif principal des travaux de recherche présentés dans ce mémoire de maîtrise était donc de mieux comprendre la dynamique des interactions interspécifiques au sein des communautés de copépodes arctiques et subarctiques et plus précisément, la prédation intraguilde soupçonnée de façonner ces communautés. Des expériences en laboratoire ont permis de caractériser la prédation intraguilde de l'espèce arctique Metridia longa sur les œufs d'une autre espèce arctique Calanus hyperboreus, ainsi que la prédation intraguilde de cette dernière sur les œufs de l'espèce subarctique Calanus finmarchicus. Différentes conditions de température, concentration d'œufs et nourriture alternative ont été testées. Parmi les conditions d'incubation testées et les différences individuelles dans les traits des prédateurs (par ex. longueur du prosome, stade de développement), seulement la concentration des œufs a eu un effet significatif et positif sur l'ingestion des œufs, et ce pour les deux relations étudiées. Environ un quart des prédateurs incubés ont rempli plus de la moitié de leurs besoins métaboliques avec l'ingestion des œufs seulement. Par la suite, un modèle de distribution verticale des œufs de C. hyperboreus dans le Golfe d'Amundsen a été développé avec l'intégration de la prédation de M. longa afin de vérifier les implications écologiques de cette interaction interspécifique. Nos résultats montrent une relation asymétrique où M. longa a peu d'impact sur le recrutement de C. hyperboreus alors que les œufs interceptés par M. longa peuvent représenter une partie importante de ses besoins métaboliques durant l'hiver. Cependant, l'ingestion des nauplii n'a pas été considérée et devrait être étudiée puisque que ces larves représentent également des proies de choix, susceptibles d'être davantage visées. Ainsi l'impact de la prédation intraguilde aurait pu être sous-estimée.

‘Critical Habitat’ is the habitat required to close the life history of an endangered species and is a fundamental requirement for species recovery for two reasons; the role of habitat in population limitation and viability must be determined, and the habitat must be protected. The North Atlantic right whale is an endangered species that annually migrates to the Grand Manan Basin and Roseway Basin Critical Habitats to feed on diapausing calanoid copepods that are typically aggregated at depths of 100 to 150 m. In this thesis I quantify spatial and temporal variation in the copepod prey field and occupancy of right whales in Roseway Basin, and use this information to identify the location and extent of right whale Critical Habitat. To accomplish this, I measured copepod abundance and energy density (kJ m-3) using optical, acoustic and net collection methods during 2007 to 2009. Oceanographic processes that affect variation in the copepod prey field include slope water intrusions, water mass density, gyre-like circulation and frontal features. Aggregations of diapausing copepods are maintained on the southern slope of Roseway Basin by cross-isobath tidal advection, and are advected along-isobath by the residual flow. Tidal advection at a front, coupled with along-isobath advection and shear in the horizontal currents serve to accumulate copepods along the slope where aggregations are maintained for at least 7 days. The abundance, stage-structure, species composition and aggregation locations of copepods, as well as the hydrography and circulation, were variable among the three years of the study. A 20 year time series of right whales, copepods and hydrography revealed that interannual whale occupancy in the Critical Habitats is variable and can be explained by prey field variation only in Roseway Basin. Factors other than the local prey field affect the number of whales that occupy Grand Manan Basin. Variation in the right whale prey field could not be explained by temperature and phytoplankton-dependent growth in the Scotia - Fundy -Gulf of Maine region. The results of this thesis assisted in establishing the Roseway Basin right whale Critical Habitat in 2008, and the cross-disciplinary nature of the study also provides new insights into the relationships between biology and physics in Scotian Shelf - Gulf of Maine basins.

Graduation date: 1992

Factors affecting energy transfer to higher trophic levels can determine the survival and production of commercially important species and thus the success of fisheries management regimes. Juvenile salmon experience particularly high mortality during their early marine residence, but the root causes of this mortality remain uncertain. One potential contributing factor is the food quality encountered at this critical time. The nutritionally vital essential fatty acids (EFA) docosahexaenoic acid (DHA, 22:6n-3) and eicosapentaenoic acid (EPA, 20:5n-3) are essential to all marine heterotrophs, and their availability has the potential to affect energy transfer through a limitation-driven food quality effect. Assessing variability in DHA and EPA in an ecologically important prey species of juvenile salmon could give insight into the prevalence and severity of food quality effects. On the west coast of Vancouver Island (WCVI), one such species is the calanoid copepod Calanus marshallae. This omnivorous species possesses a high grazing capacity and the ability to store large amounts of lipids. As it is also an important prey item for a diverse array of predators, including juvenile Pacific salmon, C. marshallae plays a key role in energy transfer from phytoplankton to high-trophic iv consumers. This study quantified spatiotemporal variability in the quality of C. marshallae as prey for higher trophic levels using three polyunsaturated fatty acid indicators: DHA:EPA, %EFA and PUFA:SFA (polyunsaturated fatty acids to saturated fatty acids). Samples were collected on the WCVI in May and September of 2010 and May 2011. The environmental parameters included in the analysis were the phase of the Pacific Decadal Oscillation (PDO), sea surface temperature (SST), latitude, station depth, and season (spring versus late summer). Despite a phase shift in the PDO from positive to negative, overall means of the fatty acid indicators did not vary between May 2010 and May 2011. Same-station %EFA values rarely fluctuated more than 5%. DHA:EPA ratios were more variable but without a discernable pattern, while PUFA:SFA ratios decreased in shelf stations and increased offshore. Contrary to expectations, fatty acid indicators showed a weak positive correlation or no relationship with SST, nor was there a relationship with latitude. The narrow temperature range observed across all stations suggests that temperature may not play a significant role in PUFA availability off the WCVI. There were, however, significant relationships between the fatty acid indicators and bottom depth and season. Shelf and slope stations showed significantly higher %EFA and PUFA:SFA than did offshore stations (depth >800 m), with this gradient appearing stronger in May than September. While the food quality represented by C. marshallae was consistent across all shelf stations, the lower food quality observed offshore could potentially affect juvenile salmon growth along the WCVI where the shelf narrows to less than 5 km. / Graduate / dpbevan@uvic.ca

Thesis: Ph. D., Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution), 2015. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Zooplankton, such as copepods, are highly abundant environmental reservoirs of many bacterial pathogens. Although copepods are known to support diverse and productive bacterial communities, little is understood about whether copepods are affected by bacterial attachment and whether they can regulate these associations through mechanisms such as the innate immune response. This thesis investigates the potential role that copepod physiology may play in regulating Vibrio association and the community structure of its microbiome. To this end, the intrinsic ability of oceanic copepod hosts to transcriptionally respond to mild stressors was first investigated. Specifically, the transcriptional regulation of several heat shock proteins (Hsps), a highly conserved superfamily of molecular chaperones, in the copepod Calanusfinmarchicus was examined and demonstrated that Hsps are a conserved element of the copepod's transcriptional response to stressful conditions and diapause regulation. To then investigate whether copepod hosts respond to and regulate their microbiota, the transcriptomic response of an estuarine copepod Eurytemora affinis to two distinct Vibric species, a free-living strain (V. ordalii 12B09) and a zooplankton specialist (V. sp. F10 9ZB36), was examined with RNA-Seq. Our findings provide evidence that the copepod E. affinis does distinctly recognize and respond to colonizing vibrios via transcriptional regulation of innate immune response elements and transcripts involved in maintaining cuticle integrity. Our work also suggests that association with E. affinis can significantly impact the physiology of Vibrio colonists. Finally, the inter-individual variability of the C.finmarchicus microbiome was examined to identify how specifically and predictably bacterial communities assemble on copepods and whether host physiology influences the bacterial community structure. Our findings suggest that copepods have a predictable "core microbiome" that persists throughout the host's entrance into diapause, a dormancy period characterized by dramatic physiological changes in the host. However, diapausing and active populations harbor distinct flexible microbiomes which may be driven by factors such including the copepod's feeding history, body size, and bacterial interactions. This thesis work highlights the role of copepods as dynamic reservoirs of diverse bacterial communities and implicates copepod host physiology as an important contributor to the activity, abundance, and community structure of its microbiome. / by Amalia Aruda Almada. / Ph. D.

The bathypelagic copepods Spinocalanus brevicaudatus, Scaphocalanus brevicornis and Heterorhabdus tanneri have established relatively large, permanent breeding populations in Bute and Jervis Inlet, British Columbia. They are found only rarely in the shallower Strait of Georgia. The preference shown by Spinocalanus brevicaudatus and Scaphocalanus brevicornis was attributed to the deep living habits of breeding adults. The reason for H. tanneri's preference of deep water was not apparent from the distribution study. Two general patterns of vertical distribution were seen among the calanoid capepods in the inlets. The common interzonal species such as Calanus glacialis preferred a definite depth interval near mid-water. The deep-living species such as Spinocalanus brevicaudatus were found throughout the water column below the thermocline, in about equal numbers. Maximum numbers usually occurred in the depth interval immediately below the thermocline. Only females of Metridia pacifica showed a strong diurnal migration pattern in July. This migration became less intense near the head of Bute Inlet. The vertical distribution and migration patterns of Spinocalanus brevicaudatus, Scaphocalanus brevicornis and H. tanneri appeared to increase the chances of secual encounters in these relativelyt rare species. The interzonal and deep-living species showed contrasting life-histories. The interzonal species exhibited a well-defined breeding season, with adults maturing in the winter, and young appearing in the spring. The deep-living species did not show a yearly breeding cycle. Females dominated the population at all times of year, and a relatively small percentage of males and females were always present. A reduction in the male:female sex ratio occurred during or after the last moult in Spinocalanus brevicaudatus and Scaphocalanus brevicornis. In the animals the male has reduced mouth parts and probably dies soon after mating. H. tanneri males do not have reduced mouth parts. This species had a sex ratio close to unity at all times. An increase in total copepod numbers was observed with increasing distance from the head of Bute Inlet. An increase in the percentage of juveniles in the population of most species was also observed with increasing distance from the inlet head. Spinccalanus brevicaudctus, Scaphocalanus brevicornis and H. tanneri are redescribed. Comantenna columbiae is described for the first time. / Graduate

Dt. Titel: Vorhersagemodelle für den Einfluss von Süßwasser Einstrom auf Salzwasser Schichten, Wanderbewegung und Lebenszyklen des Zooplankton im Arktischen Ozean: Szenarien und Trends in der Zukunft