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Starting from the simplest approximations a hierarchy of numerical models is developed with the intention of improving understanding of how biological and physical mechanisms interact in producing observed structure in plankton patches. Specifically how small scale mixing, strain and growth combine in determining the minimum equilibrium length-scale of phytoplankton filaments. We expand upon a previous study of an exponentially growing tracer in a uniform strain flowto investigate the behaviour of a logistic tracer, a more appropriate approximation of bulk phytoplankton population dynamics. A new equation to describe the minimum expected length-scale is derived. The effect of explicit nutrient representation is also considered. This is not found to affect patch size, although a striking effect on crosssectional profile is observed under certain conditions. We test the derived formula in a more realistic and hence more complex physical environment (a two-dimensional turbulent flow).We investigate inert and logistic growth tracer dispersal and consider the effectiveness of the previously derived formula for predicting minimum length-scales. In addition to inert and logistic growth tracer models we also consider a more sophisticated ecosystem model and assess the propriety of using a logistic tracer for investigations of mesoscale phytoplankton patchiness. An aside is taken to determine the best measure of strain when investigating plankton patch dynamics. A comparison is made of techniques used in comparable previous studies of tracer dynamics and recommendations made for future investigations. Errors resulting from mis-sampling of the tracer field are also considered. These results are intended to provide recommendations when considering oceanic tracer dispersal and calculation of mixing parameters ations. The 'best case' scenario is investigated throughout hence all results provide a robust upper limit of what is possible observationally.

Bio-optical measurements from three of the Atlantic Meridional Transect programme cruises in 2003-2004 were examined to determine spatial variation and correlations between phytoplankton variables. These cruises each crossed approximately 100° of latitude between the UK and the Falkland Islands, covering a range of environments in the Atlantic Ocean. Measurements of primary production were made using a Fast Repetition Rate Fluorometer (FRRF), concentration of phytoplankton pigments using High Performance Liquid Clrromatography (HPLC) and in situ particle absorption using a novel double cast technique with an ac9+ nine wavelength absorption/attenuation meter. Ancillary data in the form of salinity, temperature and chlorophyll concentration profiles were used to determine the spatial distribution of communities and to provide data for calibration. Cluster analysis of pigment data, using multivariate Brae-Curtis statistical analysis, produced effective partitioning of the cruises into functional regions for further work. The study showed that reference blanking was important in oceanic measurements with the FRRF and that separate blanks were required for each chamber. Blanks of unfiltered water from below the euphotic zone coincided best with blanks taken under in situ irradiance in the water column. Positive log linear relationships were shown between FRRF photosynthetic quantum efficiency (Fu/Fm) and, contrary to expectations, between photosystem 11 cross sectional area (σPSII) and measurements of chlorophyll a concentration. Comparisons between FRRF and automated flow cytometry data suggested that the photochemistries of the prokaryotes Synecococcus and Prochlorococcus are significantly different and that the photochemistry of Prochlorococcus is similar to that of eukaryotes. The concentration ratio of chlorophyll α: total pigment was found to follow a positive log linear relationship with chlorophyll a concentration, similar to that of the FRRF variables. A possible causative link between the relative loads of chlorophyll a and total pigment with FRRF variables was suggested. The novel twin filtered and unfiltered casts of the ac9+ produced acceptable particulate absorption spectra. Spectra representing chlorophyll a and total pigment concentrations demonstrated the same positive log linear relationship of the pigment measurements suggesting that this method could be used to determine pigment concentrations and therefore primary production parameters. Direct correlations were found between FRRF primary production parameters and both pigment ratios and absorption ratios, suggesting that absorption measurements could be used to a proxy for primary production parameters.

Le nitrite est un intermédiaire de nombreuses voies du cycle de l’azote, mais est toxique pour la plupart des formes de vies aquatiques. Sa toxicité agit au niveau cellulaire pour les microorganismes, et au niveau de la respiration pour les organismes plus complexes. Il est généralement supposé que ce composé est éliminé rapidement dans l’environnement, et que les microorganismes responsables de son élimination sont efficaces. Cependant les concentrations de nitrite dépassent la norme européenne (1 µM) dans la Seine entre Paris et l’estuaire. Le nitrite est apporté dans la Seine en aval de Paris par les stations d’épuration (STEP), malgré l’ajout de traitements d’élimination de l’azote (nitrification et dénitrification). En plus de leur contenu chimique et organique, les eaux de sorties de STEP contiennent des microorganismes qui peuvent coloniser l’environnement en aval. Dans la colonne d’eau, les mesures de cinétique de nitrification ont montré que les oxydant du nitrite avaient une activité potentielle plus élevée que les oxydant de l’ammonium. De plus, la quantification des microorganismes nitrifiants par qPCR a montré que les oxydants du nitrite (Nitrobacter dans la Seine et Nitrospira dans les rejets de STEP) étaient plus abondants que les oxydants de l’ammonium. Malgré cela, les taux in situ d’oxydation du nitrite étaient similaires aux taux in situ d’oxydation de l’ammonium dans la Seine, bien qu’ils augmentent e tous deux en aval de la STEP. Cet équilibre entre production du nitrite (oxydation de l’ammonium) et élimination du nitrite (oxydation du nitrite) résulte en une très lente élimination du nitrite dans la colonne d’eau. Les hypothèses pouvant expliquer la faible efficacité de l’oxydation du nitrite seraient une inhibition des microorganismes oxydants le nitrite par des polluants présents en Seine, ou le basculement de leur métabolisme vers un comportement mixotrophe de ces oxydants du nitrite. En plus de l’impact significatif sur la concentration du nitrite dans la colonne d’eau, il a été observé un fort impact des STEP sur la composition et la distribution des microorganismes présents dans le sédiment. Les communautés microbiennes du sédiment étaient fortement modifiées par les rejets de STEP, et étaient fortement colonisés par les bactéries du genre Nitrospira. L’étude du sédiment a montré que ce compartiment de la Seine était une source de nitrite pour la colonne d’eau, bien que les taux étaient très faibles par rapport aux concentrations dans la Seine. Le nitrite était produit en conditions anoxiques en amont de la STEP (3-4 cm), mais en surface en aval de la STEP (0-1 cm). En conséquence, le sédiment parait plus sensible à l’influence de la STEP que la colonne d’eau. Dans son ensemble, le cycle de l’azote semble avoir un impact limité sur la dynamique du nitrite dans la Seine, dans la mesure où ses différentes étapes sont équilibrées. Il pourrait donc être supposé que la pollution en nitrite de la Seine est suffisamment peut importante pour ne pas déstabiliser le cycle de l’azote dans la Seine d’une façon mesurable. / Nitrite is an intermediate in many microbial pathways of the nitrogen cycle, but is also toxic for most form of aquatic life. It is toxic at a cellular level for microorganisms, and for the respiration of complex organisms. In general the elimination of this compound is assumed to be fast in the environment, and the microorganisms responsible efficient. In the Seine River however, nitrite concentrations exceed the European norm of 1 µM between Paris and the estuary. The nitrite is released in the Seine River downstream of Paris by the waste water treatment plants (WWTP) despite the addition of nitrogen removal treatments (nitrification and denitrification). In addition to its content chemical compounds and organic matter, the WWTP outlets also contain microorganisms which can colonize the environment downstream. In the water column, measurements of nitrification kinetics showed that nitrite oxidizers had a higher potential activity than ammonia oxidizers. Quantification of nitrifiers by qPCR showed that nitrite oxidizers, Nitrobacter in the environment and Nitrospira in the WWTP outlets were more abundant than ammonia oxidizers. Despite these facts, in situ nitrite oxidation rates were similar to ammonia oxidation rates in the Seine River, even if both were higher downstream of the WWTP. This balance between nitrite production (ammonia oxidation) and elimination (nitrite oxidation) results in a very slow elimination of nitrite in the water column. This led to hypothesize that low nitrite oxidizing’s efficiency was caused by either inhibition by pollutants in the Seine River, or use a mixotrophic metabolism by nitrite oxidizers. In addition to the significant impact on nitrite concentration in the water column, the WWTP were shown to have a significant impact on the composition and distribution of the microorganisms present in the sediment. The microbial communities of the sediment were shown to be highly modified by the WWTP outlets, and were heavily colonized by the Nitrospira genera. The study of the sediment showed that this compartment of the Seine River was a source of nitrite for the water column, even though the rates of production were not significant in relation to the concentrations of nitrite. The nitrite was produced in the anoxic zone upstream of the WWTP (3-4 cm) when it was produced near the surface downstream of the WWTP (0-1 cm). As a consequence, the sediment appears to be more sensitive to the impact of the WWTP than the water column. As a whole the nitrogen cycle in the Seine River was observed to have a very limited impact on the nitrite concentration in the Seine River as its different steps are balanced. This could be viewed as the fact that this nitrite pollution is low enough to not unbalance the nitrogen cycle of the Seine River in a measurable way.