Varved, anoxic sediments in Saanich Inlet, British Columbia, are formed by the annual cycle of summer deposition of diatom frustules and winter inputs of terrigenous material derived from land runoff. The objective of this study was to sample the varve record in order to develop a palaeoceanographic history of the Inlet. Box-cores of varved sediments were collected from Finlayson Arm, Saanich Inlet. The cores were quick, frozen upon recovery, to preserve the laminae, were subsequently sectioned and X-radiographs of the sections prepared. The varves were individually sampled and analysed for their diatom assemblages together with carbon, carbonate, major and minor element concentrations and ²¹⁰Pb activity. The chronology of a representative core determined by ²¹⁰Pb was inconsistent with that determined by varve counting. The geochemical data indicated that the upper 15cm of the core had a distinct elemental composition and a lower porosity that indicated a changed sedimentation rate. It also appeared that around 20 years of sediment had been lost from the core-top. The upper sediment contains a carbonate increase linked to a dust dump from a local cement plant which occurred between 1960-1963. In the lower section of the core, both the diatom and the geochemical data indicate seasonal variation expected from the formation of annual varves. However, a well constrained chronology cannot be obtained for this core because of the non-steady state sedimentation. This makes the interpretation of inter-varve variations in the light of regional climatic records impossible. Nevertheless, a change in production on a cycle of approximately 10-15 years is evident and this study provides conclusions that will be useful to future palaeoceanographic investigations on longer cores from a part of the Inlet where sedimentation is more constant. / Science, Faculty of / Earth, Ocean and Atmospheric Sciences, Department of / Graduate

Comparative ecology and interspecific competition were examined between two sympatric congeners, Sebastes caurinus Richardson 1845 (copper rockfish) and S. maliger (Jordan and Gilbert 1880) (quillback rockfish) in Saanich Inlet, British Columbia, Canada, from 1986-1990. Ecological profiles were constructed through analyses of depth distribution, habitat and species associations, activities, feeding habits, gut allometry, growth, and reproduction. Interspecific competition between copper and quillback rockfish was examined by experimentally manipulating the densities of one or the other species on rocky reefs in Saanich Inlet where they were sympatric. The Pisces IV submersible was used to survey the distribution of rockfish in relatively deep-water (21-140 m) in Saanich Inlet. Copper and quillback rockfish were sympatric in water depths of 21-65 m. They occurred in association with one another the majority of the time (>90%) and their densities were greatest over areas of complex substrate. Size of copper and quillback rockfish was positively correlated with increased depth, primarily due to the absence of small fish in deeper waters. Both species were observed most frequently perched on open substrate or hovering in the water column. Copper rockfish were observed swimming more frequently than quillback rockfish. Copper and quillback rockfish primarily consumed demersal crustaceans throughout the year. Copper rockfish consumed a greater proportion of pelagic fishes than quillback rockfish, whereas quillback rockfish had a greater proportion of pelagic crustaceans in their diet. Levins' (1968) measure of niche breadth of the diet (by mass), as standardized by Hurlbert (1978), was narrow (0.19-0.20) to moderate (0.32-0.51) for quillback and copper rockfish respectively, during spring, summer, and fall. In the winter it was extremely narrow (0.02) for both species due to their feeding predominantly on one prey type, juvenile herring (Clupea harengus) . The Simplified Morisita Index of niche overlap (Horn 1966) in feeding habits (by mass) was relatively high (>0.55) throughout the year, and particularly during the winter (0.99). This high niche overlap in the winter occurred when large schools of juvenile herring were available in the environment and were probably not a limited resource. Extensive niche overlap between copper and quillback rockfish may therefore indicate an abundance of a shared resource rather than competition for the resource. Copper and quillback rockfish consumed the greatest quantity of food during the winter when feeding on juvenile herring, although quillback rockfish consumed significantly less food mass than copper rockfish in the winter. A greater proportion of quillback rockfish were collected with food in their stomachs during the spring and summer, when the numerically dominant food items were pelagic crustaceans. The importance of fish prey in the diets of both copper and quillback rockfish increased with size. Copper rockfish had a shorter intestine and larger stomach relative to similar-sized quillback rockfish. This suggested that the gastrointestinal tract of copper rockfish was better suited to holding and digesting fish and larger crustaceans than quillback rockfish, an observation consistent with differences in their feeding habits. Copper and quillback rockfish had similar growth patterns with no readily identifiable species-specific and sex-specific differences. Both sexes of both species attained asymptotic lengths of 30-31 cm total length and had similar growth coefficients (0.141-0.187). Within each sex, copper rockfish had a smaller increase in mass per unit of body length than quillback rockfish, indicative of a more pelagic lifestyle for copper rockfish. Estimated lengths at first and 100% sexual maturity for female and male copper and quillback rockfish were similar. Male copper rockfish were ripe, and potentially inseminated females, in January and February. Female copper rockfish were found to be carrying fertilized eggs in April and May, and gave birth to their young primarily in June. The reproductive cycle of quillback rockfish preceded that of copper rockfish by approximately one month, with parturition for quillback rockfish occurring mainly in May. The fecundity of copper and quillback rockfish was similar, with a 30-cm fish giving birth to approximately 90,000 young. Visceral fat cycles of mature female copper and quillback rockfish were complementary to their cycles of gonad maturation and increases in gonad size, indicating that they use visceral fat stores as a source of energy for maturation of their eggs and nourishment of their developing young. Visceral fat cycles of mature males were mainly coincident with the maturation and size increase of their gonads, indicating that they did not use visceral fat reserves in the maturation of their gonads. Male rockfish secondarily may have used their fat reserves as an energy source during the period when they were ripe, perhaps for mating activities. Visceral fat accumulation and dissipation in immature males and females appeared to be primarily related to periods of feeding. Interspecific competition between copper and quillback rockfish was asymmetrical, seasonal, and transitory, based on experimental manipulations of the densities of the congeners in natural populations. Copper rockfish did not have a competitive effect on quillback rockfish, but quillback rockfish had a weak competitive effect on copper rockfish. This effect was apparent only during the fall, was strongest in the fall immediately following the density manipulations, and appeared to weaken in the subsequent fall season. The seasonal competitive effect may have been caused by copper rockfish moving onto the study reefs (18-31 m depth) from shallower waters (<20 m) during the fall and winter, creating a short-term 'ecological crunch' in which food or space resources were limited. Overall, comparative ecological profiles of copper and quillback rockfish exhibited a large degree of overlap. Differences observed between them were small but consistently indicated that copper rockfish had a more pelagic lifestyle than quillback rockfish. The otherwise high degree of similarity between the two congeners, however, did not translate into sustained interspecific competition. Ecological theory purporting a major role for interspecific competition in structuring fish communities was therefore not supported by experimental manipulations of population densities of deep-subtidal, temperate zone rockfishes. The asymmetrical, seasonal, and transitory occurrence of weak interspecific competition demonstrated that competition between these rockfish species is dynamic, and cannot account for the pattern of species association. Alternative hypotheses based on the importance of intraspecific competition, predation, or environmental variability must therefore be considered. / Graduate

During some years Neocalanus plumchrus overwinters in Saanich Inlet while in other years they are absent from the fjord (Harrison et al., 1983). The cause of this variation is not known but the annual development of anoxic conditions followed by an intrusion of dense, oxygenated water, was suspected to influence their distribution and abundance. Vertical and horizontal haul samples collected from Saanich Inlet indicated the overwintering population in 1985 (September 1985 to March 1986) was sparse; in September 1986 the population of N. plumchrus was comparably low. In the spring and summer, N. plumchrus is introduced from the Strait of Georgia and Juan de Fuca Strait, and in some years may arise from reproduction within the inlet. So few adults were collected at the three stations in Saanich Inlet in January-March 1986 (<0.20 m⁻³) that their potential contribution to the spring population was considered negligible. Decline in the overwintering population in September 1985 and 1986 appears to be correlated with the occurrence of an extensive deep water renewal. The distribution of N. plumchrus during early stages of their deep water migration (June to August), is influenced by the low oxygen concentrations in the bottom of the inlet (i.e. 0.10-0.30 mL L⁻¹). During the renewal, copepods occurred above the oxygen minimum (75 m) possibly due to their displacement or their avoidance of the low oxygen zone. Subsequently, they were exposed to tidal transport out of the inlet and perhaps to increased predation. On two occasions in which N. plumchrus was present during the winter in Saanich Inlet (1969 & 1974), a high volume of dense water intruded, disrupting the copepod layer during the mixing of the two water masses. Even though a greater volume of water left the inlet some of the copepods could have remained in the water, below sill depth. Neocalanus plumchrus successfully overwinters and reproduces in Sechelt Inlet which is well-oxygenated but has a very shallow sill (15 m) that 'locks' the copepods into the inlet. The fifth copepodite stages also occupy deeper depths in Sechelt Inlet than in Saanich Inlet, even though the bottom depths are comparable. In low oxygen tolerance experiments many factors such as the period of captivity, and the region of origin (i.e. Saanich Inlet versus the Strait of Georgia) caused variable results. Although the minimum oxygen level tolerable during their migration could not be determined, N. plumchrus tolerated levels as low as 0.56 mL L⁻¹ (12% mortality). Sediment trap samples indicate that a massive die off could not account for the loss of N. plumchrus from Saanich Inlet. / Science, Faculty of / Zoology, Department of / Graduate

This thesis presents improvements to a method for measuring the production of biogenic silica (bSiO2) by diatoms, a group of microscopic algae with siliceous cell walls (frustules) that dominate the marine cycling of silicon (Si) and account for a significant proportion of global marine primary productivity. Using the fluorescent dye PDMPO, diatom bSiO2 can be labeled as it is produced and then quantified using fluorometry to determine community-wide bSiO2 production. A distinct advantage of PDMPO over more traditional tracers of bSiO2 production is that the combination of measurements of PDMPO by fluorometry and by fluorescence microscopy allows for the quantification of cell (and thus taxa) specific bSiO2 production within a mixed community. However, the robustness of PDMPO as a quantitative tracer of diatom bSiO2 production has not been sufficiently investigated. To address this, experiments were conducted both in the lab, and at two field locations where diatoms are known to be abundant, namely the continental shelf off the west coast of Vancouver Island, and Saanich Inlet, a highly productive fjord located on southern Vancouver Island. Laboratory culture experiments demonstrated that concentrations of PDMPO >500 nmol L-1 reduced growth rate in the diatom Thalassiosira pseudonana, and affected the Si:PDMPO ratio of incorporation. The relationship between SiO2 and PDMPO incorporation was significantly affected by diatom species, though this effect was small (8%) when cells were lysed. From these experiments, a Si:PDMPO incorporation ratio of 4200 ± 380:1 was determined, which predicted 30% more bSiO2 production for PDMPO incorporation than previous studies, and better agreed with bSiO2 production rates determined using established methods in Saanich Inlet. However, bSiO2 production rates were over-estimated by the PDMPO method when rates were less than 1 µmol L-1 d-1. In a few cases, this occurred when dinoflagellates were numerically dominant, but for the majority of samples, dinoflagellates were low in abundance, and over-estimation by PDMPO may be related to low dissolved Si(OH)4 concentration. Protocols for quantifying PDMPO fluorescence by microscopy were optimized by using a low numerical aperture microscope objective. Additionally, measurements of fluorescence intensity were calibrated using a fluorescent microscope slide as a standard, which served to correct for unevenness of illumination across the field of view. With these protocol modifications, quantification of PDMPO by microscopy agreed with PDMPO measured by fluorometry. When PDMPO was measured by microscopy in the field, the contribution of diatom taxa to PDMPO fluorescence differed from their contribution to cell numbers. In many cases this was due to large diatom taxa producing more bSiO2 per cell than smaller taxa. However, much of the difference between cell numbers and PDMPO fluorescence was not explained by differences in cell size. This suggests that the diatom taxa had different specific bSiO2 production rates, which could be estimated using PDMPO. This thesis highlights the strength of the PDMPO tracer for understanding diatom community dynamics. The use of PDMPO should allow the relationship between diatom community composition, growth and productivity to be better illuminated in the oceans. / Graduate / 0416 / jelong@uvic.ca

The evolution of the sulphur content of humic substances extracted from a near-shore sediment core was investigated. Special attention was taken to avoid S contamination of the humic materials during sample handling and extraction. The S/C ratios increased continuously with depth to values which strongly suggest S addition to the humic matrix during early diagenesis by reactions between organic matter and H₂S or its oxidation products. The light isotopic composition of this organic sulphur supports this view; however, subsequent isotopic exchange has obscured the mechanism initially involved. Since a large fraction of the enrichment occurred above the sulphidic zone, redox boundaries, such as the interface of anoxic microniches within the more oxidized zones, or the sulphidic/suboxic boundary of the sediment column, must have been important sites for S addition. The influence of sulphur enrichment on the complexing capacity of humic materials was also investigated, and it was shown that S-addition increases significantly the number of sites on which Cu is irreversibly bound. Iodine is characteristically enriched at the surface of hemipelagic and nearshore sediments deposited under oxygenated conditions. In such sediments, bulk I/Corg ratios usually decrease with depth to values which are characteristic of anoxic sediments, reflecting a preferential release of iodine during early diagenesis. There is some debate as to whether sedimentary iodine is associated with the iron oxyhydroxide phase or with the organic fraction, and whether the decrease in I/Corg with depth is due to the dissolution of the iron oxyhydroxides or the decomposition of labile organic matter. In this study, it is shown that in a surficial hemipelagic sediment sample and in a nearshore sediment core iodine is mainly associated with the organic fraction and, moreover, that humic substances are involved in the surficial iodine enrichment. Laboratory experiments on the uptake and release of iodine by and from sedimentary humic substances also suggest a mechanism whereby humic materials reduce iodate at the sediment/water interface to an electrophilic iodine species which further reacts with the organic matter to produce iodinated organic molecules. During burial, this excess iodine could be displaced from the organic matrix by nucleophiles such as sulphide ions or thiosulphate, thus providing a possible explanation for the decrease in I/corg ratio with depth observed in many nearshore and hemipelagic sediments. Bulk metal concentrations were measured in the sediments of Saanich Inlet in an attempt to establish the occurrence of trace metal enrichments in the anoxic central basin. Ba, Ni, V, Cr, Zn, Pb, Cu, and Mo were found to be enriched in the anoxic ooze over the possible contributions from lithogenous sources. Spatial and seasonal variations in the chemical composition of the settling particulates collected with interceptor traps gave further indications of the mode of incorporation of these metals. Biogenic Ba and Cr appeared to be associated with opaline silica, although alternative explanations are also possible, particularly for Ba. Zinc seemed to be added to the sediment essentially in association with planktonic materials, while Cu required an additional source directly linked to the anoxic environment. Similarly, Ni, V, and Mo were added to the anoxic sediments by reactions occurring at the sediment-water interface. In the nearshore environment studied here, these metals were not associated to any significant extent with planktonic materials, particularly Ni and Mo. Of all the elements analyzed, Mo showed the largest enrichment in the anoxic sediments of Saanich Inlet. / Science, Faculty of / Earth, Ocean and Atmospheric Sciences, Department of / Graduate

Aspects of the biology of the sepiolid squid Rossia pacifica Berry were studied from specimens obtained by otter trawling at Cape Lazo Gully and Saanich Inlet, British Columbia. Temperature, salinity, and sediment size at Cape Lazo Gully varied from 7.18°C to 11.00°C, 28.01 °/oo to 30.21 °/oo, and from less than l00μd to over 250μd respectively. Living specimens in the laboratory exhibited color changes from dark red-brown to opalescent grey-green. They did not mimic the color of the substrate. Comparisons of the morphometric indices of R. pacifica with other species of this genus showed differences in some indices but not in others. The arm formula is inconsistent, the most common being 3>2>4>1 and 3>2=4>1. The lower beak differs from that of R. maarosoma by having a "tooth" on its shoulder. In an aquarium Rossia spent most of its time resting on the bottom either in a horizontal position or with the anterior end elevated. The squid usually formed a depression in the sandy bottom to rest in. In some instances they threw sand onto their backs. Fish were caught with the tentacles and held with the arms while being eaten. Stomach analysis revealed that crustacea were present in 86.6% of the stomachs that contained food, while fish were present in 16.6%. Shrimp formed the largest portion of the crustacea in the diet. Bivalve molluscs, squid, and ostracods were occasionally found. Proportions of crustacea to fish in the diet were higher in smaller squid and decreased in larger animals. Seasonal variations in the diet were correlated with the biomass of shrimp in the area where the squid were collected; when a low biomass of shrimp was present the squid had a higher proportion of fish in their diet. The female R. pacifica are slightly larger than the males of the same age and grow to a larger size than do the males. The male and female reproductive systems are described. Gonad indices show that the ovaries and nidamental glands begin to mature when the females have a dorsal mantle length of approximately 24.0 mm. Spermatophores were not found in males smaller than 22 mm mantle length. The proportion of males containing spermatophores was 9% at 22 mm and increased through 17% at 24 mm, 50% at 26 mm to 90% at 28 mm. During mating the male attaches to the female from below by means of his second, third, and fourth pairs of arms. Spermatophores are transferred into the dorsal region of the female's pallial cavity by his dorsal, hectocotylized arms. The sex ratio of males to females found at Cape Lazo Gully was 1.2:1.0. Spawning occurs in the fall with the most active period occurring from August through October. This may be correlated with an increase in the water temperature, during this time. The squid have a life span of one year, at the end of which they mate, spawn, and die. / Graduate

A biological front at the mouth of Saanich Inlet results in higher rates of primary productivity at the inlet mouth relative to the head creating a gradient that could influence zooplankton distribution. A shallow sill (75m) at the inlet mouth restricts circulation below sill depth, isolating the deep basin for much of the year. Anoxia develops in the isolated basin and the depth of the anoxic layer changes during the year. During the day, pelagic zooplankton form a deep scattering layer. Between April 2005 and March 2006. I conducted monthly 200kHz acoustic surveys between the mouth and head of Saanich Inlet to test the hypothesis that zooplankton density was greater near the mouth relative to the head. I was also interested in how changing anoxic layer depth affected the distribution of the deep scattering layer. I found that zooplankton density followed a headward gradient in the spring and summer. with the highest densities near the mouth. Zooplankton density was higher near the mouth or the mid-inlet relative to the head in 75% of transects. I did not observe a zooplankton density gradient during the winter. Zooplankton distribution was affected by dissolved oxygen concentration. Deep scattering layer depth was significantly correlated with the depth of the anoxic layer and vertical compression of the deep scattering layer increased as the anoxic layer moved upwards. When the depth of the anoxic layer was less than 90 meters. zooplankton were nearly absent. Vertical migration of the deep scattering layer to surface waters at night has been well documented. but zooplankton migration patterns in the shallow waters of Saanich Inlet have not been described. I used 200kHz acoustic data collected by the VENUS observatory (96m) and an autonomous acoustic system deployed at a shallow site (62m) in Patricia Bay to study zooplankton migration patterns. Horizontal movement of the deep scattering layer over shallow depths following vertical migration was infrequent. Over 41 days of observation at the shallow site. I only observed deep scattering layer zooplankton on 12 days. At the shallow site. night-time volume backscatter was dominated by the emergence of benthic zooplankton. The movement of these scatterers into the water column at night resulted in a 14-fold increase in volume backscatter over daytime values. I observed this emergence pattern at both sites. which represents an important component of benthic-pelagic coupling in Saanich Inlet. In contrast to the deer scattering layer. which migrated to the surface each night, emergent zooplankton remained within 30-40 meters of the seafloor and did not ascend into surface waters.

We investigated oceanic dissolved inorganic nitrogen (N) dynamics, focussing on processes removing bio-available N and ultimately affecting primary productivity, in sulfidic hydrothermal vent fluids discharging from the subsurface on the Juan de Fuca Ridge (northeast Pacific Ocean) and in anoxic bottom waters of Saanich Inlet, a British Columbia fjord, using a combination of geochemical and molecular microbial ecology techniques. During episodes of mixing with oxygenated sea-water, both systems can switch from anoxic to oxic conditions. Strong inter-site variations in the concentrations and δ15N of ammonium (NH4+) in high-T fluids suggested different N sources (deep-sea nitrate (NO3-) versus organic sediments) for hydrothermally discharged NH4+. Increase in the isotopic composition of NO3- (δ15N and δ18O), concomitant with decreased [NO3-], indicated NO3- assimilation or denitrification in the subsurface. NO3- isotope anomalies, i.e. deviations from the 15N:18O isotopic enrichment of 1:1 in marine environments, were observed and confirmed the occurrence of NO3- regeneration in vent fluids. Denitrification was the dominant N-loss pathway, suggesting that bacterial denitrification out-competes anaerobic NH4+ oxidation (anammox) in diffuse hydrothermal vent waters. The diversity of denitrifying bacteria encoding the nirS-form of nitrite reductase was low in vent fluids. Quantitative polymerase chain reaction (qPCR) analysis revealed that denitrifiers accounted for up to 38% (nirk-encoding γ-proteobacteria of the SUP05 cluster) and 8% (nirS-encoding bacteria) of the total bacterial abundance. Furthermore, nirS gene operational taxonomic units from two vent fields clustered into different groups in the phylogenetic tree, suggesting a link between denitrifying bacterial community membership and small-scale geographic isolation and/or fluid physico-chemical properties. Significant correlations existed between fixed N-loss rates and in-situ dissolved inorganic N deficits in the fluids. Based on our rate measurements, and on published data on hydrothermal fluid fluxes and residence times, we estimated that up to ~10 Tg N yr−1 could be removed globally in the subsurface biosphere. In Saanich Inlet, a gradual increase in both the δ15N and δ18O of NO3- associated with a decrease in [NO3-] and an increase in biological excess N2, was observed after bottom water renewal events in fall 2008, following NO3- consumption by denitrifiers in an expanding suboxic zone. N-to-O negative NO3- isotope anomalies were observed in surface and bottom waters, confirming the occurrence of NO3- regeneration and/or external NO3- input. Closed and open-system-model derived NO3- isotope effects in anoxic bottom waters were lower (as low as ~11‰) than the ~25‰ for water column denitrification reported in other studies, suggesting that ~50% of the denitrification could occur, with a highly suppressed isotope effect, in the sediments of the Inlet. / Graduate

Crustaceans, the most abundant group of organisms that make up zooplankton, form a critical link in the food web between primary-producing phytoplankton and planktivorous fish. Examining this link is essential in order to effectively estimate the amount of energy available to higher trophic levels. The most appropriate currency for tracking energy flow through these food webs is to measure production, or the amount of new biomass generated over a given period of time. Although measurements of primary productivity are routinely made in oceanographic studies, estimates of secondary productivity are rare due to their historical reliance on time-consuming methods. The overall objective of this thesis was to determine the factors influencing temporal variations in community-level crustacean productivity. A simplified lab experiment was used to establish a relationship between diet and chitobiase-based estimates of copepod productivity in response to single versus mixed species phytoplankton diets. In addition, the relationships between primary productivity and chitobiase-based productivity for the entire crustacean zooplankton community were examined over two years in Saanich Inlet, British Columbia, Canada. Lastly, this work determined the abiotic and biotic factors most strongly influencing crustacean productivity in the tropical Guanabara Bay, Rio de Janeiro, Brazil, dominated by the microbial loop. Results from this work show that: (i) copepod populations fed a poor food item take longer to develop through early stages, have lower daily growth rates, and exhibit lower productivity than those fed a good quality food item; (ii) important variations in crustacean productivity are missed when biomass estimates, alone, are used to represent food available to higher trophic levels; (iii) relationships between primary productivity and crustacean productivity can vary interannually and are not necessarily controlled by bottom-up processes; (iv) substantial interannual variations in trophic transfer efficiency (TTE) occur even if average TTE is the same across years; and (v) community-level crustacean productivity in tropical regions dominated by the microbial food loop can be as high as, if not higher than, productivity measured in temperate regions. Ultimately, this work provides insight into how accurate productivity estimates can improve our understanding of zooplankton dynamics in both laboratory and field settings in marine ecosystems worldwide. / Graduate

Five profiles of the silver concentration in the subArctic Northeast Pacific Ocean yield a broad correlation between the Ag content and dissolved Si. However, silver is depleted at intermediate depths where the 02 content is low, implying removal from oxygen-deplete waters. An eighteen-month series of measurements of dissolved and particulate Ag from Saanich Inlet, BC indicate that Ag concentrations in near-surface waters are influenced by processes occurring outside the inlet. Dissolved silver was not detected in sulphide-bearing deep waters in the fjord. Ag in sediment-trap particles was associated with both biogenic and mineral phases. The Ag/biogenic Si ratio of the particles is related to the concentration of dissolved Ag in the surface waters suggesting a direct link between availability of the metal and its sequestration by diatoms.