La diversité des protistes marins planctoniques, après avoir été historiquement étudiée sur des critères morphologiques, est depuis récemment sujette à une intense recherche à l’aide d’approches moléculaires. Notamment, les études basées sur l’amplification directe de marqueurs moléculaires à partir d’ADN environnemental ont révélées une exceptionnelle diversité. L’objectif central de ce travail est d’améliorer notre compréhension sur le lien existant entre la connaissance classique des eucaryotes unicellulaires et leur diversité estimée à partir des données moléculaires, en particulier pour une meilleure interprétation des processus évolutifs et écologiques. Pour cela, nous avons utilisé comme système modèle l’ordre des ciliés tintinnidés (Tintinnida) qui constituent un groupe riche en espèces, aisément identifiables au microscope grâce à leur coquille externe (lorica) et communément rencontrés dans l’ensemble des eaux marines et lacustres du monde. Un suivi approfondi sur deux ans des tintinnidés de la Baie de Villefranche-sur-Mer (Mer Méditerrannée, France), couplant des analyses moléculaires de la diversité à partir de cellules individuelles et à partir d’ADN environnemental, a permis de caractériser la composition de ces communautés et leur dynamique temporelle aux échelles macro- et micro-évolutives. La première partie de ce travail a été destinée à la réalisation d’une phylogénie moléculaire de référence pour les tintinnidés en incorporant les séquences de 62 individus de morphologies diverses pour lesquelles des données moléculaires n'étaient pas disponibles. Nous avons amplifié et séquencé les gènes codant pour les ARN ribosomiques (ARNr 18S, 5.8S et 28S) et les espaces intergéniques correspondants (ITS1 et ITS2). La classification taxonomique a été réévaluée d’après les données moléculaires. Dans un deuxième temps, nous avons testé l’efficacité des approches moléculaires conventionnelles (amplification, clonage et séquençage Sanger du gène de l'ARNr 18S) et plus récentes (amplification et pyroséquençage de régions de l'ARNr 18S et de l’ITS), pour décrire la composition des communautés des tintinnidés dans des échantillons environnementaux en les comparant avec des estimations de la diversité par observation morphologique sur les mêmes échantillons. Si il existe de légères incongruences entre les approches et/ou les différents marqueurs employés, les approches cultureindépendantes s’avèrent efficaces pour décrire la diversité morphologique. En revanche, afin de ne pas surévaluer artificiellement le nombre d’espèces estimées à partir des données de pyroséquençage, il faut que des méthodes de débruitage et de regroupement en unités taxonomiques opérationnelles (UTOs) contraignantes soient appliquées. La troisième partie de ce travail a été dédiée au suivi temporel des communautés de tintinnidés à différentes profondeurs dans la baie de Villefranche, basé sur le clonage et le séquençage du gène de l'ARNr 18S et des régions ITS. Il apparaît des différences de distribution au cours de l’année à une même profondeur, en particulier en termes d’abondance de séquences pour une UTO donnée. Malgré un cadre phylogénétique solide et assez enrichi, l’approche moléculaire révèle des séquences éloignées des espèces déjà séquencées. La découverte de ces clades environnementaux souligne potentiellement l’importance écologique d’espèces encore mal connues. Enfin, le séquençage direct du gène de l'ARNr 18S et de l'ITS2 à partir des cellules individuelles de l'espèce <Undella claparedei> a offert l’opportunité d’une étude populationnelle sur une période de deux ans. La diversité intra-spécifique mesurée met à jour des phénomènes d’hybridation entre variantes génétiques. Une structuration génétique temporelle a également été observée pour le gène de l'ARNr 18S. Les implications de ces différentes recherches sont discutées dans le cadre de l’étude de la diversité et de l’écologie des tintinnidés, et plus largement, des protistes marins. / The marine protistan diversity has been historically studied based on morphological characterization but has recently been the object of intense research using molecular approaches. Studies based on the amplification of molecular markers from environmental DNA revealed an outstanding diversity, partly new and uncharacterized. However, the actual extent of this diversity remains poorly known and highly debated. The main goal of this work was to improve our knowledge on protistan diversity to bridge the gap between molecular environmental surveys and classical protistology to better understand the ecology and evolution of unicellular eukaryotes. For this purpose, we used as a model the species-rich order of the tintinnid ciliates (Tintinnida, Ciliophora), which are easily distinguishable because of their secreted shell, the lorica, and commonly found in marine waters all around the globe. A two-year monitoring of the tintinnid populations in the Bay of Villefranche-sur- Mer (Mediterranean Sea, France), combining molecular analyses of the diversity based on single-cells and environmental DNA, gave us the opportunity to describe the tintinnid community composition and its temporal dynamics. In the first part of this work, we constructed a reference molecular phylogeny for the tintinnids including new sequences from 62 specimens of diverse morphologies, for which we amplified and sequenced the ribosomal coding genes (18S, 5.8S and 28S rRNA) and the corresponding intergenic spacers (ITS1 and ITS2). The taxonomic classification of the Tintinnida has been revised based on these molecular data. In the second part, in order to assess the accuracy of molecular-based approaches to describe the natural species assemblages of tintinnids, we compared the morphology-based diversity estimates with those derived from classical (amplification, cloning and Sanger sequencing of the 18S rRNA gene) and more recent (direct pyrosequencing of amplified 18S rRNA genes and ITS regions) molecular approaches. Even if there are still some disagreements between the different methods and/or molecular markers, the culture-independent approaches were efficient to describe the morphological diversity. However, a careful and rigorous analysis of pyrosequencing datasets, including sequence denoising and stringent sequence clustering in Operational Taxonomic Units (OTUs) with well-adjusted parameters, is necessary to avoid overestimating the species number. The third part of the thesis is dedicated to the study of the genetic diversity of tintinnids over a one-year survey in the Bay of Villefranche at five different depths by combining community fingerprinting analysis using denaturing gradient gel electrophoresis (DGGE) with direct PCR amplification and sequencing of 18S, 5.8S, and 28S rRNA genes and ITS regions. These analyses revealed marked seasonal changes, in particular in the sequence abundances of certain OTUs. In addition, despite an enriched phylogenetic reference sequence dataset for the tintinnids, we retrieved two abundant phylotypes without any closely related known species, highlighting the possible ecological relevance of unidentified species. Finally, we studied the intra-specific diversity of populations of the species <Undella claparedei> based on 18S rDNA and ITS direct sequencing of single-cells collected over a period of two years. We detected signals of hybridization and sexual recombination among different genetic variants. We also found genetic structuring of the 18S rRNA gene data differentiating populations collected at different times. The implications of all these results are discussed in the framework of the diversity and ecology of tintinnid ciliates and, more generally, of marine protists

Os ecossistemas aquáticos têm sido afetados pelo uso intensivo de agrotóxicos e pela introdução de espécies exóticas. Para melhor avaliar os efeitos diretos e indiretos dessas atividades sobre as comunidades aquáticas, é essencial a utilização de experimentos em escala mais próxima a real. O objetivo desta pesquisa foi analisar os efeitos do agrotóxico Vertimec® 18 CE, cujo princípio ativo é a abamectina, sobre a comunidade planctônica através de um experimento em mesocosmos com duração de 20 dias. Para reproduzir relações biológicas mais complexas e analisar o impacto da introdução de uma espécie exótica sobre o plâncton, inseriram-se girinos de Lithobates catesbeianus em alguns tratamentos. Foram consideradas duas concentrações do agrotóxico (2 &#956;L L-1 em dose múltipla e 8 &#956;L L-1 em dose única) na ausência e presença de girinos, além de dois tratamentos não contaminados (controle com e sem girinos). Variáveis físicas, químicas e biológicas (clorofila a, aspectos qualitativos e quantitativos do fitoplâncton e do zooplâncton) da água e do sedimento foram monitoradas. A partir dos resultados obtidos, verificou-se que os girinos causaram um aumento na concentração de nutrientes na água e uma diminuição do oxigênio dissolvido e da densidade planctônica. Nos tratamentos contaminados, como um efeito indireto do incremento da concentração de nutrientes e da mortalidade das espécies de Cladocera e Copepoda, a densidade do fitoplâncton e de algumas espécies tolerantes de Rotifera aumentou. No tratamento com a concentração mais elevada do agrotóxico, registrou-se a morte de todos os girinos, proporcionando um aumento na concentração de nutrientes na água e na densidade de algumas espécies fitoplanctônicas, que alcançaram uma densidade total de 96.919 ind mL-1. Estes resultados indicam que a inserção dos girinos e a adição do agrotóxico causaram efeitos diretos e indiretos sobre a comunidade planctônica e a qualidade da água. Conclui-se que os mesocosmos podem contribuir para a compreensão de tais efeitos e oferecer subsídios ao manejo de ecossistemas de água doce impactados por atividades antrópicas. / Aquatic ecosystems have been impacted due to the intensive use of pesticides and the introduction of exotic species. It is essential to use more realistic experiments for assessing direct and indirect effects of these activities on aquatic communities. This thesis aimed to analyze the effects of the pesticide Vertimec® 18 EC, whose active ingredient is abamectin, on plankton community through a mesocosm experiment during 20 days. Tadpoles of the species Lithobates catesbeianus were introduced in some treatments to simulate complex biological relationships and to evaluate the impact of the introduction of such exotic species on plankton. Different treatments were analyzed, including one case of no contamination (control) and two cases of contamination: 2 &#956;L L-1 (multiple dose) and 8 &#956;L L-1 (single dose). Such conditions were considered both with absence and presence of tadpoles. Physical, chemical and biological (chlorophyll a, qualitative and quantitative aspects of phytoplankton and zooplankton) variables of water and sediment were also monitored. The tadpoles caused an increase in the concentration of nutrients and a decrease of dissolved oxygen concentration and plankton density. In the contaminated treatments, as an indirect effect of the nutrient increase and the mortality of species of Cladocera and Copepoda, the density of phytoplankton and some tolerant species of rotifers increased. In the treatment with the highest concentration of the pesticide, all the tadpoles died. As a result of the death of the tadpoles, there was nutrient enrichment in the water, with an associated increase in the density of some phytoplankton species, reaching a total density of 96,919 ind mL-1. These results suggested that direct and indirect effects occurred on plankton community and water quality through the addition of the contaminant and the tadpoles. We conclude that the mesocosms might contribute to the understanding of these effects and provide subsidies for management of freshwater ecosystems impacted by human activities.

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2019 / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 193-220). / Southern Ocean net community productivity plays an out sized role in regulating global biogeochemical cycling and climate dynamics. The structure of spatial-temporal variability in phytoplankton ecosystem dynamics is largely governed by physical processes but a variety of competing pathways complicate our understanding of how exactly they drive net population growth. Here, I leverage two coupled, 3-dimensional, global, numerical simulations in conjunction with remote sensing data and past observations, to improve our mechanistic understanding of how physical processes drive biology in the Southern Ocean. In Chapter 2, I show how different mechanistic pathways can control population dynamics from the bottom-up (via light, nutrients), as well as the top-down (via grazing pressure). In Chapters 3 and 4, I employ a higher resolution, eddy resolving, integration to explicitly track and examine closed eddy structures and address how they modify biomass at the mesoscale. / Chapter 3 considers how simulated eddies drive bottom-up controls on phytoplankton growth and finds that division rates are, on average, amplified in anticyclones and suppressed in cyclones. Anomalous division rates are predominately fueled by an anomalous vertical iron flux driven by eddy-induced Ekman Pumping. Chapter 4 goes on to describe how anomalous division rates combine with anomalous loss rates to drive anomalous net population growth. Biological rate-based mechanisms are then compared to the potential for anomalies to evolve strictly via physical transport (i.e. dilution, stirring, advection). All together, I identify and describe dramatic regional and seasonal variability in when, where, and how different mechanisms drive phytoplankton growth throughout the Southern Ocean. Better understanding this variability has broad implications to our understanding of how oceanic biogeochemisty will respond to, and likely feedback into, a changing climate. / Specifically, the uncertainty associated with this variability should temper recent proposals to artificially stimulate net primary production and the biological pump via iron fertilization. In Chapter 5 I argue that Southern Ocean Iron Fertilization fails to meet the basic tenets required for adoption into any regulatory market based framework. / by Tyler W. Rohr. / Ph. D. / Ph.D. Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution)

Zooplankton samples collected May through August, 1990 to 1996 at site M, 15 m depth in the Indiana waters of Lake Michigan were examined for microcrustaceans, rotifers, and zebra mussel (Dreissena polymorpha) veligers. Abundance numbers per m3 were combined with Coffman's (1995) data to quantify recent trends in the zooplankton.Rotifers dominated the community, with Polyarthra vulgaris, Colurella, Keratella crassa, and K. cochlearis the most prevalent species. Copepods, primarily nauplii and copepodid forms, were the next most abundant taxa. Except for 1994 and 1995, Cladocera abundance was higher than zebra mussel veliger abundance. The cladoceran assemblage was dominated by Bosmina Iongirostris, with very few Daphnia noted. A precipitous decrease in zebra mussels veligers from 1994 to 1996 warrants further investigation to determine the nature and the extent of the population decline.Regression analysis of zebra mussel veliger abundance against abiotic and biotic factors demonstrated veligers varied directly with rotifer abundance and water column temperature and indirectly with cladoceran and yellow perch (Perca flavescens) abundance. A similar regression model of rotifer abundance revealed direct correlation with calanoid, cladoceran, zebra mussel veliger, and yellow perch abundance. / Department of Biology

This research was conducted to provide baseline data on the population dynamics of microcrustacean zooplankton at Prairie Creek Reservoir in Delaware County, Indiana from 24 January 1996 to 30 December 1996. This lake is a shallow lake (average depth <8m) used for recreational fishing and water supply for the local community. No published studies of zooplankton have previously been conducted at this location. I intended to test the hypothesis that Prairie Creek Reservoir has the same microcrustacean populations of shallow lakes in this region. The findings were compared to other studies in several North American lakes and reservoirs. Biotic and abiotic factors were considered as related to the population dynamics of zooplankton. Zooplankton serve as a critical forage base for many fish species, including several of economic importance. Increases and changes in species composition of zooplankton organisms associated with eutrophic conditions may also be an indication of deteriorating water quality (Gannon 1972). The data from this research suggest that Prairie Creek Reservoir has the typical zooplankton populations of a shallow, eutrophic North American lake. The presence of relatively high numbers of organisms generally associated with eutrophic environments, such as Bosmina longirostris, Leptodiaptomus siciloides, Acanthocyclops vernalis, and others supports this idea. The data from this study will be helpful to fisheries and environmental managers and will provide a baseline for future studies. / Department of Biology

Bibliography: leaves 254-267. / Microfiche. / xiii, 267 leaves, bound ill. 29 cm

Thesis (M.A.)--University of Wisconsin, 1949. / eContent provider-neutral record in process. Description based on print version record. Includes bibliographical references (leaves 157-159).

Um dos principais problemas relacionados aos estudos limnológicos realizados manualmente em laboratório consiste no grande esforço, tempo de análise e trabalho especializado necessário. Esses fatores limitam a quantidade de amostras possíveis de serem analisadas em um determinado estudo, já que recursos sejam eles reagentes, recursos financeiros ou tempo são limitados. No presente trabalho foi utilizado um sistema semi-automatizado de medidas de variáveis físicas e químicas da água. O sistema é composto por uma sonda multi-parâmetro (Horiba U-22) e um sistema de posicionamento global (GPS) acoplados a um micro-computador, que realizam medidas georeferenciadas em curtos intervalos de tempo, permitindo um rastreamento horizontal das características da água. Foi ainda desenvolvido um sistema semi-automático para coleta fracionada da comunidade planctônica por meio de bomba de sucção operada por bateria e filtro coletor com rede de plâncton de diferentes aberturas de malha. O material coletado foi fotografado por meio de sistema de aquisição digital de imagens (microscópio Zeiss equipado com câmera AxionCan). Neste trabalho foi produzido um software (Planktonscan) que a partir da análise das imagens capturadas permite produzir dados com estimativas das medidas e dimensões dos organismos, calcular biovolumes e, utilizando fatores de conversão, estimar os valores de biomassa. O software apresenta uma interface para identificação, calcula a densidade dos organismos e produz relatório gráfico com informações sobre os organismos individuais e sobre a comunidade. Os equipamentos e o software foram testados em análises limnológicas e amostragem de plâncton no reservatório do Monjolinho, São Carlos, SP, em dezembro de 2005. Os resultados obtidos foram comparados com os disponíveis na literatura e demonstraram a aplicabilidade do sistema. / A major problem associated with the study of planktonic communities lies on the difficulties of analyzing the collected material, a long time-consuming procedure. Biomass determination is also a step requiring great effort and is subjected to large errors. In the present work a semi-automated system for measuring physical and chemical variables in the water was developed. The system is made up by a flow-pump, a multi-parameter probe and a global positioning system coupled to a microcomputer that performs measurements at short time intervals, allowing a horizontal tracking of the water quality, in much shorter times than traditional methods. Another semi-automated device was developed for collecting separate plankton size fractions. It uses a battery operating suction-pump coupled to a filter with different mesh nets. The collected materials are then submitted to image computer acquisition (Axion Vision Zeiss System). Additionally, in this study a software was produced (Planktonscan), that taking the measures of individuals dimensions (length, width and height) calculates biovolume and using conversion factors calculate the biomass for each zooplankton organism identified in the sample. Both systems were tested, regarding the measurement of limnological variables and plankton sampling, in the Monjolinho Reservoir, SP. The performance was good, resulting in a larger number of points sampled (60) in a shorter sampling time (1 hour) than those usually required. The biomass results provided by Planktonscan software were compared to data from literature, obtained by the traditional gravimetric method for dry weight determination and also with data generated from the use of mathematical models (length dry-weight regressions) available. The results were expressed as species population densities, biomasses and size spectra, evidencing the applicability of the models here developed.

In-situ measurements of surface chlorophyll and zooplankton concentration are compared with in-situ hydrographic measurements and infrared satellite images of the west coast of British Columbia. Their relationships are quantified for a mid-summer and an early winter study period. Winter in-situ hydrographic data showed the shelf to be dominated by Vancouver Island Coastal Current water near-shore, Davidson Current water over the middle shelf, a frontal zone separating these regimes, and North Pacific water over the shelf break. The summer shelf was dominated by topographically induced upwelling in the southern portion of the shelf and stratified regions over the outer shelf and shallow banks further north. Strong northwest winds late in the summer study period induced upwelling along the entire shelf. The surface thermal signature of each of these regimes was identifiable in the satellite imagery. Maximum winter concentrations of chlorophyll and zooplankton were associated with Vancouver Island Coastal Current water and southern portions of the frontal zone. Davidson Current water consistently had the lowest chlorophyll concentrations in the winter study area. Zooplankton concentrations decreased with increasing temperature and distance from shore. The correlation of loge transformed zooplankton concentrations with surface temperature allowed the satellite imagery to explain 49% of the sampled variance. The association of specific chlorophyll concentrations with each hydrographic regime enabled the satellite imagery, in conjunction with an image derived salinity model, to explain 55% of the sampled variance. Image derived plankton models allowed a spatial representation of predicted plankton concentration and the model error. Summer zooplankton concentrations were not consistently related to satellite measured surface temperature but showed a qualitative association with higher chlorophyll concentrations around the outer edge of the upwelling area. Minimum chlorophyll concentrations were found in warm, stratified surface water and intermediate concentrations in the coldest, most recently upwelled water. Maximum concentrations occurred at intermediate temperatures. A least squares fit non-linear equation showed the satellite measured surface temperature patterns explained 72% of the sampled loge transformed chlorophyll variance. Distributions of both zooplankton and chlorophyll concentration retained their association with patterns of sea surface temperature during a wind driven upwelling event. Multivariate cluster analysis of zooplankton taxonomic groups during both winter and summer showed spatial patterns of community composition matched satellite measured patterns of sea surface temperature over the middle and inner shelf. Over the outer shelf, spatial patterns of community structure appeared more closely associated with depth than surface thermal patterns. / Science, Faculty of / Earth, Ocean and Atmospheric Sciences, Department of / Graduate

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2017. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Although over a dozen elements are needed to support phytoplankton growth, only a few are considered to be growth-limiting. As the central atom in vitamin B12, cobalt is crucial for metabolism, but its status as a limiting nutrient is uncertain. This thesis investigates the geochemical controls on oceanic cobalt scarcity and their biological consequences. Analysis of over 1000 samples collected in the Tropical Pacific Ocean reveals a dissolved cobalt distribution that is strongly coupled to dissolved oxygen, with peak concentrations where oxygen is lowest. Large cobalt plumes within anoxic waters are maintained by three processes: 1) a cobalt supply from organic matter remineralization, 2) an amplified sedimentary source from oxygen-depleted coastlines, and 3) low-oxygen inhibition of manganese oxidation, which scavenges cobalt from the water column. Rates of scavenging are calculated from a global synthesis of recent GEOTRACES data and agree with cobalt accumulation rates in pelagic sediments. Because both sources and sinks are tied to the extent of oxygen minimum zones, oceanic cobalt inventories are likely dynamic on the span of decades. Despite extremely low cobalt in the South Pacific gyre, the cyanobacterium Prochlorococcus thrives. Minimum cobalt and iron requirements of a Prochlorococcus strain isolated from the Equatorial Pacific are quantified. Cobalt quotas are related to demand for ribonucleotide reductase and methionine synthase enzymes, which catalyze critical steps in DNA and protein biosynthesis, respectively. Compared to other cyanobacteria, a streamlined metal physiology makes Prochlorococcus susceptible to competitive inhibition of cobalt uptake by low levels of zinc. Although phytoplankton in the Equatorial Pacific are subject to chronic iron-limitation, widespread cobalt scarcity and vulnerability to zinc inhibition observed in culture imply that wild Prochlorococcus are not far from a cobalt-limitation threshold. / by Nicholas James Hawco. / Ph. D.