Alkane monooxygenases (encoded by the alkB gene) are a group of microbial enzymes that catalyze the first reaction of alkane degradation. Studies to determine the diversity and prevalence of alkB genotypes in the environment have focused on culturable organisms. The goal of this research was to use culture-independent methods (DGGE, clone library) to identify and characterize alkB genes, and to determine their prevalence in Arctic contaminated soils. General alkB PCR degenerate primers (alkB-Mc) were designed using the conserved nucleotide sequences of the Histidine I Box and Histidine III Box. General alkB-Mc and alkM (Acinetobacter spp. alkane monooxygenase genes) primers were used to screen the soils for the presence of alkane monooxygenase genotypes. A predominance of the Rhodococcus spp. alkB genotypes and the absence of alkM genotypes in these soils was found. alkB PCR fragments amplified from the soils were analyzed by DGGE (Denaturing Gradient Gel Electrophoresis). BlastN and blastX results of the DGGE bands sequences showed that they were similar to Rhodococcus spp. alkB genotypes (~80-90% DNA identity and ~80-90% amino acid homology). An alkB clone library was built using the general alkB-Mc primer set, screened by RFLP (Restriction Fragment Length Polymorphism) and characterized by sequencing of alkB clones. BlastN and blastX results of the alkB clone sequences showed the presence of divergent alkB genotypes (≤ 70% DNA identity and ≤ 67% of amino acid homology to data base sequences). The alignment of the clone-derived amino acid sequences to confirm functional alkane monooxygenase sequences revealed the presence of Histidine Box II and the HYG motif in all of the deduced amino acid clone sequences. These results indicate that the alkB sequences from the clone library represent novel alkB sequences. Both alkB DGGE and clone library techniques were independently able to identify alkB genotypes from High G+C microorganisms as predominant in the 1A03 soil sample. Nevertheless, only the clone library approach identified putative novel alkB sequences. Mineralization of hexadecane and naphthalene was clearly observed at subzero temperatures (-5ºC) in Arctic contaminated soils, proving that the indigenous microbial communities could mineralize these representative hydrocarbons at subzero temperatures in an environment that is predominantly frozen for most of the year.

No description available.

Même les écosystèmes les plus nord du monde ont été affectés par le réchauffement climatique et les lacs de l'Extrême-Arctique ne font pas exception. L'île d'Ellesmere est à la limite nord du Canada et des changements de régime vers des taxons associés à des saisons de croissance plus longues ont déjà été documentés dans les lacs de cette région. La côte nord de l'île d'Ellesmere est dans une région pour laquelle on prévoit le plus grand réchauffement annuel au cours des 80 prochaines années. Il est donc impératif de comprendre le fonctionnement des lacs côtiers sensibles avant que d'autres changements ne se produisent. J'ai étudié une série de quatre lacs de la vallée de Stuckberry (82º54 N, 66º58 W) pour donner un aperçu de leur dynamique phytoplanctonique sous la glace. Mes objectifs étaient 1) identifier et quantifier les communautés photosynthétiques dans les lacs de la vallée de Stuckberry, 2) déterminer les variables physico-chimiques qui ont exercé le contrôle le plus fort sur la variation de la communauté au sein des lacs et entre les lacs, et 3) élargir la compréhension des écosystèmes d'eau douce sous la glace de l'Extrême-Arctique et leur fonction. Les intensités lumineuses et l'oxygène dissous exerçaient un contrôle primordial sur la distribution et l'abondance des organismes photosynthétiques et la conductivité spécifique et l'azote jouaient aussi des rôles importants. Ces variables distinguaient clairement deux lacs oxiques profonds des deux lacs anoxiques peu profonds. Les différences des types de communautés photosynthétiques entre les lacs et les profondeurs étaient liées aux concentrations d'oxygène dissous : la lignée des algues rouges dominait dans les eaux oxiques, tandis que les bactéries sulfureuses pourpres dominaient dans les eaux anoxiques. Les pigments indiquaient aussi que les dinoflagellés, les cryptophytes et les haptophytes étaient abondants partout dans les quatre lacs, alors que les chrysophytes et les chlorophytes étaient présentes en plus faibles concentrations. Ma thèse représente l'une des très rares études de communautés photosynthétiques sous la glace de l'Extrême-Arctique, et elle fait progresser considérablement notre compréhension des processus écologiques dans cette région hautement sensible. / Even the world’s most northern ecosystems have been affected by climate warming and High Arctic lakes are no exception. Ellesmere Island is at the northernmost limit of Canada, and regime shifts have already been documented in its lakes towards taxa associated with longer growing seasons. It has been projected that the northern coast of Ellesmere Island is within a region that will experience the greatest annual warming in the Arctic over the next 80 years, and so understanding the functioning of its sensitive coastal lakes is critical before further changes occur. I studied a series of four lakes in Stuckberry Valley (82º54 N, 66º58 W) to give insight into their under-ice phytoplankton dynamics. My objectives were 1) identify and quantify the photosynthetic communities found in the Stuckberry Valley lakes, 2) determine the physicochemical variables that exerted the strongest control over within- and between-lake community variation, and 3) expand the understanding of under-ice High Arctic freshwater ecosystems and their function. Light intensities and DO concentrations exerted primary control over the distribution and abundance of photosynthetic organisms, in addition to important roles played by specific conductivity and nitrogen. These variables clearly distinguished two deep, oxic lakes from two shallow, anoxic lakes. Differences in photosynthetic community types between lakes and depths was strongly linked to DO concentrations: the red pigment algal line dominated in oxic waters, while purple sulfur bacteria (PSB) were found in anoxic zones. Pigments indicated that dinoflagellates, cryptophytes, and haptophytes were abundant throughout all four lakes, with lower concentrations of chrysophyte and chlorophyte pigments. My thesis represents one of the very few studies of High Arctic under-ice photosynthetic communities, and it significantly advances our understanding of ecological processes in this highly sensitive region.

Thèse ou mémoire avec insertion d'articles. / Les écosystèmes d'eau douce des latitudes extrêmes sont confrontés à une série de menaces liées à des changements climatiques rapides, dépassant les seuils écologiques. Toutefois, l'hétérogénéité des paysages et le manque de données de surveillance à long terme empêchent de prédire avec précision les réactions biotiques au changement climatique. Compte tenu de la diminution prévue de la couverture de glace, la compréhension limitée des réponses biotiques sur de longues périodes dans les lacs de l'Arctique devient évidente. Dans ce contexte, les objectifs de cette thèse comprennent la reconstitution des conditions environnementales de la fin de l'Holocène dans trois lacs situés le long des franges côtières du bras Clements Markham (~82°4ʹ N, ~68°4ʹ W), sur le nord de l'île d'Ellesmere, et l'établissement d'une taxonomie complète des diatomées dans la région étudiée. L'influence présumée de la diminution de la couverture glaciaire a probablement amélioré la disponibilité de la lumière et diversifié les microhabitats récemment dans chaque lac de recherche. Cela se reflète dans la structure des assemblages de diatomées de chaque lac, les diatomées étant manifestement absentes dans la plupart des enregistrements jusqu'aux intervalles les plus élevés. Les premiers assemblages de diatomées de l'Arctique étaient principalement constitués de fragilarioïdes benthiques, qui se sont considérablement diversifiés au cours des 80 dernières années. Ce changement floristique a inclus des espèces planctoniques centrées, représentatives d'une plus grande stabilité thermique résultant de saisons prolongées sans glace. L'émergence et la diversification des diatomées correspondent à des pics notables de la teneur en matière organique et à des hausses de température dans l'Arctique, ce qui corrobore ce nouveau régime écologique. Collectivement, cette recherche élargit la documentation limitée des apparitions récentes de diatomées sur l'île d'Ellesmere, découvrant un changement récent et supplémentaire qui a initié une plus grande diversification des espèces en raison de changements environnementaux récents et rapides. / Freshwater ecosystems at extreme latitudes face a range of threats from rapid climatedriven changes, surpassing ecological thresholds. However, landscape heterogeneity and limited long-term monitoring data hinders accurate predictions of biotic responses to climate change. Given the projected declines in ice cover, the limited understanding of biotic responses over extended timeframes in Arctic lakes becomes evident. Within this context, the objectives of this thesis include reconstructing late-Holocene environmental conditions of three lakes along the coastal fringes of the Clements Markham Inlet (~82°4ʹ N, ~68°4ʹ W), on northern Ellesmere Island and to establish a comprehensive diatom taxonomy in the study region. The presumed influence of declining ice cover likely enhanced light availability and diversified microhabitats recently in each research lake. This was reflected in the diatom assemblage structures, as diatoms were conspicuously absent throughout most of the records until the uppermost intervals. Early Arctic diatom assemblages primarily consisted of benthic fragilarioids, culminating in a substantial diversification over the last ~80 years. This floristic shift included planktonic centric species, representative of greater thermal stability resulting from prolonged ice-free seasons. The emergence and diversification of diatoms corresponded with notable spikes in organic matter content and temperature rises across the Arctic, further corroborating this novel ecological regime. Collectively, this research broadens the limited documentation of recent diatom appearances on Ellesmere Island, uncovering a recent, additional shift that has initiated a wider species diversification due to recent and rapid environmental changes.

La côte nord de l'île d'Ellesmere présente une grande diversité d'écosystèmes aquatiques qui sont façonnés par des conditions environnementales extrêmes. Le réchauffement climatique est plus rapide et plus prononcé dans le haut Arctique que dans la plupart des autres régions du monde, ce qui en fait un endroit stratégique pour l'étude des effects des changements climatiques. De plus, les contaminants, transportés des zones tempérées à l'Arctique par le transport sur de longues distances, représentent un stress additionnel pour ces écosystèmes. L'objectif principal de cette étude était d'évaluer la structure et la dynamique d'écosystèmes aquatiques côtiers du haut Arctique comme indicateurs de changements environnementaux. La glace est très vulnérable au réchauffement climatique et elle peut dépasser des seuils de changement tels que l'intégrité des plates-formes de glace qui bloquent l'embouchure de fjords ainsi que la transition d'un couvert de glace permanent à un couvert de glace saisonnier pour des lacs. Cette thèse doctorale s'articule autour des changements produits en franchissant ces seuils pour la structure verticale de lacs épi-plates-formes et de lacs méromictiques. Un inventaire des fjords de la région délimitée par la plate-forme de glace d'Ellesmere au cours du dernier siècle indique le déclin des lacs épi-plates-formes arctiques, de 17 en 1905 à un seul contenu dans le fjord Milne en 2009. La désintégration des plates-formes de glace associée au réchauffement des dernières décennies soutient leur pertinence comme indicateurs du climat. Des lacs moins profonds, piégés derrière de la glace de mer multi-annuelle au lieu de plate-forme de glace, représentent des systèmes intermédiaires et huit seraient toujours présents dans l'aire d'étude. De la même façon, ces systèmes dépendent de l'intégrité de la glace et peuvent être utilisés comme indicateurs de changements du climat. Le fjord Milne contenait des communautés microbiennes qui étaient distinctes entre le lac épi-plate-forme et la couche d'eau salée. La salinité influence grandement la stratification biologique de ce fjord, en plus des faibles concentrations de nutriments et du peu de lumière qui y limitent la production primaire. Nos résultats indiquent que la transition d'un couvert de glace permanent à un couvert de glace saisonnier pour des lacs méromictiques permet le mélange par le vent de la couche d'eau douce de surface en plus d'y augmenter la disponibilité de la lumière et des nutriments. Des conditions d'eau libre impliqueraient également des différences de concentrations de chlorophylle a et de composition des communautés de phytoplancton. Une variation entre les lacs étudiés pourrait refléter des différences locales dans les bassins versants et le climat. De faibles concentrations de contaminants perfluorés étaient présentes dans les écosystèmes de lacs méromictiques, représentant le site le plus nordique où ces composés ont été détectés. Les changements climatiques pourraient modifier les voies de transfert dans ces écosystèmes en abolissant le courant court-circuit qui y est potentiellement présent, ce qui augmenterait les concentrations et l'exposition pour les organismes aquatiques. Enfin, cette thèse doctorale supporte la pertinence d'utiliser les lacs côtiers du haut Arctique comme indicateurs des changements environnementaux et souligne leur vulnérabilité. Il est essentiel d'assurer le suivi à long terme de ces écosystèmes en tant que sentinelles pour les futurs changements environnementaux à l'échelle planétaire.

Coastal and shallow lakes are often subjected to eutrophication due to nutrients from catchment farming activities. Lake Ellesmere (Te Waihora) is a hyper-eutrophic lake which has gained recent attention because of concerns over its ecological health and fishery status. This study investigated the benthic ecology of the lake by extensive spatial and temporal sampling. Eight littoral sites were sampled on a single occasion, and 20 benthic sites were sampled once per season for one year. Water chemistry conditions, substrate and invertebrate communities varied significantly around the lake. Salinity, pH, DO and seston were primarily affected by freshwater inputs from inflow streams and salt water intrusion due to the lake opening to the sea. On these occasions, salinity reached 32 ‰ at the lake outlet. The lake invertebrate community was depauperate, comprising of only two species of invertebrate predators restricted to the littoral zone and eight benthic invertebrate taxa, dominated by oligochaetes, amphipods and chironomids. Benthic invertebrate abundances also reflect the dominant local substrate, where oligochaetes and chironomids preferred areas of silt substrate, whereas Potamopyrgus preferred harder substrate. Stable isotope and gut analysis determined that the primary food sources within the lake were phytoplankton and algae. Macrophytes provided a minimal contribution to the food web, possibly relating to the change in status from a clear water, macrophyte dominated lake to a turbid, phytoplankton dominated condition since the Wahine Storm in 1968. Isotope analysis also showed that the lake food web was markedly different in its carbon values from food webs of its inflow streams and nearby marine source. However the lake food web did show a marine-derived carbon signature. A mesocosm experiment testing the effect of common lentic predators on the abundance of the lake chironomid Chironomus zealandicus, showed that if invertebrate predators were present in the lake they could markedly reduce the abundance of the pest prey species. This study highlights that the frequent re-suspension of bottom sediments, lake level fluctuation resulting in wetting and drying of littoral zones, and the management of the lake opening to the sea all have an effect on the benthic ecology of Te Waihora.

Lake Ellesmere/Te Waihora is one of New Zealand’s largest coastal, brackish water lakes. It has nationally significant wetland bird populations and is regionally important for iwi. The lake regularly experiences fluctuations in water level, resulting in a continually expanding and contracting littoral zone. This study investigated the impacts of these water level changes on the ecology of the lake. Water chemistry results collected over 12 months, confirm the lake is hypertrophic, due to high nutrient (nitrogen and phosphorus) concentrations resulting in high chlorophyll a levels and low water clarity. Water chemistry conditions were collected at five locations around the lake and showed marked spatial variation, with the eastern most end (Kaituna Lagoon) having generally the best water quality and lowest salinity (mean 4.9 ppt). Mean concentrations of total nitrogen ranged from 1.63 to 2.4 mg/L, chlorophyll a from 50 to 148 ug/L and total suspended solids from 151 – 248 mg/L. Seasonally, highest nutrient concentrations (mean, total nitrogen = 2.625 mg/L, dissolved reactive phosphorus = 0.059 mg/L and total phosphorus = 0.365 mg/L) occurred in late summer months (February – March), slightly decreasing but remaining high throughout winter. The benthic invertebrate community was surprisingly diverse, Crustacea (Paracorophium excavatum), Oligochaeta, Mollusca (Potamopyrgus antipodarum) and Chironomidae (Chironomus zealandicus) were dominant community members in the littoral zone, although 24 other taxa were collected. At high water levels, taxonomic richness increased in the eulittoral zone, while decreasing in the mid-littoral and lower littoral zones. In contrast, density decreased with higher water level in the eulittoral and mid-littoral zones, while increasing in the lower littoral zone. Benthic invertebrate communities appeared to be adapted to periods of intermittent dewatering, and even sustained dewatering under cooler temperatures. Despite the relatively high diversity of benthic invertebrates, invertebrate predators are generally absent from the lake. My results suggest multiple factors and interactions from predation pressure, salinity and lack of macrophytes are likely responsible for the absence of predatory invertebrates such as damselfly (Xanthocnemis zealandica) and dragonfly (Procordulia grayi) larvae. The lack of significant relationships between water quality variables and water level, and the positive relationship between chlorophyll a and salinity, suggests that current lake opening events do not have a positive effective on either water quality or phytoplankton biomass in Lake Ellesmere/Te Waihora. However, the current lake opening regime seems to be favourable to benthic invertebrate survival in the littoral zone, as the lake is predominantly open over winter when temperatures are lower, reducing the risk of desiccation. Anthropogenic activities which modify hydrodynamic and water quality conditions can potentially have a large negative impact on the structure and diversity of the littoral invertebrate community as well as flow on effects through the lake food web. Based on results from this study, I suggest a minimum lake level at Taumutu of 0.6 m during the months from November – April in order to protect benthic invertebrate communities in the eulittoral zone from extensive loss of habitat, extreme temperature and reduced risk of desiccation. Having a minimum set at ~0.6 m would provide sufficient littoral zone habitat for the lakes extensive bird life and fish populations. In addition, immediate efforts are needed into reducing nutrient loads into the lake, through improved farm management (nutrient and stocking budgets) and riparian fencing. Furthermore, physical and chemical water quality properties would benefit from an increased water level over summer months, by reducing water temperatures, diluting readily available nutrient concentrations and potentially reducing phytoplankton (and potentially toxic cyanobacterial) blooms.

The potential impact of sea level rise on Lake Ellesmere - Te Wiahora and the subsequent effect on the efficiency and performance of the L2 Drainage network was investigated in relation to the operation of the L2 Drainage scheme. Lake Ellesmere is currently manually opened for drainage to the sea when the lake levels reach 1.05 m above mean sea level (asl) in summer and 1.13 m asl in winter. With a rise in sea level, the lake opening levels for both summer and winter would have to increase in order to maintain the current hydraulic gradient. Higher lake levels would impact drainage schemes such as the L2 drainage network. An integral research approach was used to study this potential impact, including fieldwork, analysis of data, hydrologic and hydraulic modelling. Both the hydrologic and hydraulic response of the L2 catchment and river were reproduced with reasonable accuracy by the use of computational models. Simulations of 2, 10 and 20 year annual recurrence intervals (ARI) rainstorm events coupled with higher lake levels show increase flooding along the length of the river. An increase in the lake opening levels, coupled with south-easterly wind was shown to have increased the degree of flooding on adjacent farmlands, but only a 3.50 per cent increase of water level (for all conditions simulated) 3.5 km upstream of the L2 River. The study clearly shows that weed growth within the L2 River plays an important part in controlling the water level within the channel. Results show it was responsible for an observed water level rise of 0.30 m from the winter to summer season. The combined use of hydraulic and hydrological models provides an effective tool to study future impacts on the drainage efficiency and performance of the L2 drainage scheme and other similar systems. The potential for both models to be used as a predictive tool for improving the operation of the L2 scheme and Lake Ellesmere was only limited by the difficulty in estimating model parameters especially for the hydrologic model.

Coastal and shallow lakes are often subjected to eutrophication due to nutrients from catchment farming activities. Lake Ellesmere (Te Waihora) is a hyper-eutrophic lake which has gained recent attention because of concerns over its ecological health and fishery status. This study investigated the benthic ecology of the lake by extensive spatial and temporal sampling. Eight littoral sites were sampled on a single occasion, and 20 benthic sites were sampled once per season for one year. Water chemistry conditions, substrate and invertebrate communities varied significantly around the lake. Salinity, pH, DO and seston were primarily affected by freshwater inputs from inflow streams and salt water intrusion due to the lake opening to the sea. On these occasions, salinity reached 32 ‰ at the lake outlet. The lake invertebrate community was depauperate, comprising of only two species of invertebrate predators restricted to the littoral zone and eight benthic invertebrate taxa, dominated by oligochaetes, amphipods and chironomids. Benthic invertebrate abundances also reflect the dominant local substrate, where oligochaetes and chironomids preferred areas of silt substrate, whereas Potamopyrgus preferred harder substrate. Stable isotope and gut analysis determined that the primary food sources within the lake were phytoplankton and algae. Macrophytes provided a minimal contribution to the food web, possibly relating to the change in status from a clear water, macrophyte dominated lake to a turbid, phytoplankton dominated condition since the Wahine Storm in 1968. Isotope analysis also showed that the lake food web was markedly different in its carbon values from food webs of its inflow streams and nearby marine source. However the lake food web did show a marine-derived carbon signature. A mesocosm experiment testing the effect of common lentic predators on the abundance of the lake chironomid Chironomus zealandicus, showed that if invertebrate predators were present in the lake they could markedly reduce the abundance of the pest prey species. This study highlights that the frequent re-suspension of bottom sediments, lake level fluctuation resulting in wetting and drying of littoral zones, and the management of the lake opening to the sea all have an effect on the benthic ecology of Te Waihora.

The Eureka Sound Formation in the eastern Canadian Arctic Archipelago is an Upper Cretaceous to Paleogene pre- and syn-tectonic deposit that records the uplift and segmentation of the Early Carboniferous to Tertiary Sverdrup Basin. Scattered outliers of the Eureka Sound Formation on southern Ellesmere Island rest unconformably on or are faulted against Devonian strata. In the vicinity of Vendom, Stenkul, Baumann and Sor Fiords, the Eureka Sound Formation attains a maximum thickness of 480 m and comprises a sequence of nonmarine and brackish water deposits that ranges in age from mid-Paleocene to Late Eocene. Eureka Sound strata which crop out along the shores of Stenkul Fiord are divided into four lithofacies assemblages. The stratigraphic section is composed mainly of two nonmarine assemblages which alternate throughout the sequence. Lithofacies Assemblage I consists of fining-upward sandstones which attain thicknesses of 20 m and are interpreted as fluvial deposits. Lithofacies Assemblage II comprises interbedded mudstones and coal in seams up to 8 m thick, and are interpreted as floodbasin deposits of an alluvial plain. Two marine lithofacies assemblages (III, IV) are recognized locally and constitute a minor part of the stratigraphic succession. Lithofacies Assemblage III comprises the basal strata in the study area and consists of approximately 90 m of buff-weathering mudstones and interbedded thin coals which were deposit ed in brackish lagoonal, estuarine and salt marsh environments. Lithofacies Assemblage IV occurs locally in the middle of the stratigraphic section and consists of up to 10m of white, well sorted quartz arenites and minor mudstones, which are interpreted as deposits of a barrier island system. To the northeast of Stenkul Fiord at Makinson Inlet, outliers of the Eureka Sound Formation rest unconformably on Paleozoic strata, and are in turn overlain with angular unconformity by as much as 120 m of Early Miocene fanglomerates of the Beaufort Formation. The ages of these sediments, in conjunction with ages reported from the Eureka Sound and Beaufort Formations in other parts of Ellesmere and Axel Heiberg Islands, bracket the timing of the orogenic phase of the Eurekan orogeny in the eastern Arctic as Late Eocene to Miocene. / Science, Faculty of / Earth, Ocean and Atmospheric Sciences, Department of / Graduate