<p>Recent research in microbial ecology has focused on how aquatic bacterial communities are assembled. Only a few of these studies follow a “Gleasonian” approach where the roles of single bacterial populations are in focus. In this thesis, novel molecular tools were used to describe the distribution and evolutionary relationships of microbes in productive aquatic environments. Many new phylogenetic groups of bacteria were identified, likely representing bacterial populations restricted to productive freshwaters. I also addressed the dynamics and functional role of individual bacterial populations in eutrophic lakes and brackish environments with a focus on either biogeochemically significant or potentially pathogenic representatives. <i>Flavobacteria</i> blooms were observed, on occasions characterized by high heterotrophic production. In addition to high temporal dynamics microbial community composition and function differed on the spatial scale, as exemplified by free-living and <i>Cyanobacteria</i>-associated habitats. At the community scale, microbial processes, such as biomass production and substrate uptake could be predicted from the presence and absence of individual bacterial populations. I also studied the niches of potentially pathogenic <i>Vibrio </i>populations in various coastal waters. Using a novel culture-independent method, a <i>V. cholerae</i> population was detected along the entire Swedish coastline. Results from an environmental survey and a laboratory mesocosm experiment reveal that phytoplankton-derived dissolved organic matter enhance the growth of <i>V. cholerae</i> and other <i>Vibrio</i> spp. and hence create a largely overlooked niche for these heterotrophic bacteria. This thesis and future work on the role of individual bacterial populations will facilitate predictions of biogeochemical cycles and the distribution of bacteria in the context of global climate change and local eutrophication.</p>

Physical-biological interactions in the Southern Ocean were investigated using remote sensing data from several different satellite sensors. Satellite sea surface temperature data were used to study the dynamics of the Antarctic Polar Front (PF). Satellite ocean color data were used to estimate surface chlorophyll concentrations and their relation to various physical forcings within the Southern Ocean. A detailed study of phytoplankton blooms at the Antarctic Polar Front revealed that elevated chlorophyll concentrations (phytoplankton blooms) occur most often in areas where the PF interacts with large topographic features within the Southern Ocean. The physical dynamics of the PF are strongly influenced by the topography, and in turn strongly influence phytoplankton bloom dynamics. The analysis of satellite data from the modern Southern Ocean indicates that phytoplankton are limited by the availability of the micronutrient iron in most areas. This iron-limitation implies that the elevated iron inputs during glacial periods would have led to increased phytoplankton primary and export production and a stronger sink for atmospheric CO��� in the Southern Ocean. / Graduation date: 2000

The contribution of phytoplankton productivity to higher trophic levels in salt marshes is not well understood. My study furthers our understanding of possible mechanisms controlling phytoplankton productivity, abundance, and community composition in salt marshes. Across three consecutive springs (2001 to 2003), I sampled the upper Nueces Delta in south Texas, a shallow, turbid, salt marsh system stressed by low freshwater inflow and wide ranging salinity (<15 to >300 ppt). Water column productivity and respiration were estimated using a light-dark bottle technique, and phytoplankton biovolume and community composition were determined using inverted light microscopy. To determine their effect on the phytoplankton community, zooplankton and bacterioplankton abundance and several physical parameters were also assessed. Meaningful relationships among the numerous variables evaluated in this study were identified using principal component analysis (PCA). Despite high turbidity, phytoplankton productivity and biovolume were substantial. Resuspension appeared to play a major role in phytoplankton dynamics, as indicated by a positive relationship between ash weight and biovolume that explained up to 46% of the variation in the PCA. Negative relationships between zooplankton grazers and pennate diatoms of optimal sizes for these grazers suggested a functional grazing food chain in this system. Salinity also may have been important in phytoplankton dynamics, whereas nutrients appeared to play a minor role. Salinity increases may have been responsible for a decoupling observed between phytoplankton and grazers during late spring. Findings suggest hypotheses for future studies focused on the role of phytoplankton in salt marshes, particularly those stressed by reduced freshwater inflow and high salinities.

Degradation of water quality, introduction of dreissenid mussels (notably <i>Dreissena polymorpha</i>) and depletion of oxygen concentrations in the hypolimnion in Lake Simcoe, Ontario prompted a study of phytoplankton primary production to inform efforts to improve the lake conditions. The characterization of algal production is critical since, as primary producers, their biomass is positively correlated with production at higher trophic levels in pelagic food webs and oxygen levels. This study was conducted from August 2010 to August 2011, including the winter season (Dec-Mar). Temporally, the lake displayed a unimodal pattern with late summer to fall production maxima. For all seasons considered, the pelagic daily areal primary production (P_int) was lower in the nearshore than offshore, consistent with the nearshore shunt hypothesis that mussels should be able to deplete phytoplankton more effectively in the nearshore. The sensitivity analysis revealed that chl a and the photosynthetic parameter P^B_max were the most influential variables for explaining such spatial differences. The size distribution of chl a and production varied where both netplankton (>20µm) and nanoplankton (2-20µm) were greatest in fall and picoplankton (<2µm) was highest in summer and early fall. A large chl a peak of nanoplankton was also found in late-winter (Mar) at offshore stations. The seasonal areal primary production (SAPP; May-Oct) and chl a:TP were significantly lower nearshore than offshore, consistent with grazing impacts from the large nearshore dreissenid mussel community. The lake as a whole is quite productive comparable to other large lakes with comparable total P concentrations and dreissenid mussel populations. The latter part of the study showed that the deep chlorophyll layer (DCL) was not as frequent as expected and was detected only 28% of time during late-spring to summer when the lake was thermally stratified (Aug-Sept 2010 and May-Aug 2011). The percent dissolved oxygen (%) did not show any indications of elevated primary production in the DCL although the production estimates suggested that there is a substantial (an average of 55%) amount of primary production occurring below thermocline when a DCL exists. Whether or not the DCL has potential to nourish the benthic filterers (dreissenids) and has ecological significance in the lake remains unclear. Overall, the factors that control phytoplankton primary production in Lake Simcoe seem to operate somewhat differently from other large lakes and further investigation is needed to elucidate them. The analysis of primary production and biomass has improved knowledge of non-summer production and can provide guidance to site-specific P and oxygen remediation.

The structure of phytoplankton communities was examined seasonally across five rivers with a focus on small cells and their relative importance. Picophytoplankton (0.2-2 μm), previously considered insignificant in rivers, reached densities as high as those observed in lakes and oceans (~ 10e4-10e5 cells/mL). Their relative importance was not a function of trophic state with the highest contribution to algal biomass found in the most eutrophic river. Body size distributions were analyzed from both chlorophyll-a size fractions and taxonomic enumerations; no significant effect of river or season was detected, suggesting that phytoplankton size distribution is not a useful metric of change in rivers. Unlike lake ecosystems, the rivers were uniformly dominated by small cells (< 20 μm). Taxonomic analyses of the seasonal succession did not reveal a common periodicity of particular divisions (e.g. diatoms). However, strong dominance was more typical of eutrophic rivers even though taxa richness was similar.

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The Laurentian Great Lakes are the largest system of freshwater on earth containing 22% of the world’s supply. Although part of a single system, each lake shows substantial variation regarding physical, chemical and biological parameters. The main goals of this thesis were to characterize the nutrient status of natural phytoplankton communities while comparing several commonly used measurements of nutrient status and Chlorophyll a (Chl a) fluorescence measurements. The study sites include the western basin (WB), west-central basin (WCB), and central basin (CB) of Lake Erie, the Bay of Quinte in Lake Ontario, and Colpoys Bay in Lake Huron. Independent measures of nutrient status were assessed by measurements of nitrogen (N) debt, phosphorus (P) debt, particulate C:N:P ratios, and alkaline phosphatase activity (APA). Variable fluorescence of chlorophyll a was measured by pulse amplitude modulated (PAM) fluorometry and fast repetition rate (FRR) fluorometry in parallel with the independent measures. In 2005, the phytoplankton communities in Lake Erie were generally N deficient in May, P deficient in June, and neither N nor P deficient in September. The maximum dark adapted quantum yield (Fv/Fm) measured by PAM or FRRF was lower in May and June, and maximal in September, while the functional absorption cross section of photosystem II (σPSII) was maximal in May and June, and minimal in September. Relationships between the variable fluorescence indicators and independent measures of nutrient status showed strong associations with N or P deficient sites having low Fv/Fm and high σPSII. In 2006, the electron transport rate (ETR) and the initial slope (α) derived from the PAM fluorescence rapid light-response curves (RLC) were compared to independent measures and Fv/Fm measurements in Lake Erie. Relationships between ETR, α, independent measures of nutrient status, and Fv/Fm measurements revealed strong associations with nutrient status. Confirming previous reports, N deficiency was highest in the WB during isothermal conditions while P deficiency was highest in the CB during summer stratification. The fluorescence parameters generally decreased as the severity of N and P deficiency increased. N and P enrichment assays also revealed increased values of Fv/Fm, ETR, and α from N and P deficient samples over twenty-four hours. Additionally, spatial variability of P status was evaluated during summer stratification. Colpoys Bay, the most oligotrophic site, had the strongest P deficiency, and evidence for existence of P deficiency was weakest in the Bay of Quinte, the most eutrophic site. Nutrient enrichment assays revealed that all fluorescence parameters showed a positive response to P additions in oligotrophic sites, with no response in eutrophic sites. Community structure was also associated with nutrient status and Chl a fluorescence at all locations. In P deficient sites, nano-flagellates such as chrysophytes and cryptophytes were prevalent; cyanobacteria were dominant at sites that displayed N deficiency.

Variable fluorescence of chlorophyll a (Fv/Fm), measured by pulse amplitude modulated (PAM) fluorometers, is an attractive target for phytoplankton-related water quality management. Lowered Fv/Fm is believed to reflect the magnitude of nutrient sufficiency or deficiency in phytoplankton. This rapid and specific metric is relevant to Lake Erie, which often experiences problematic Cyanobacteria blooms. It is unknown whether PAMs reliably measure phytoplankton nutrient status or if different PAMs provide comparable results. Water samples collected from Lake Erie and two Lake Ontario sites in July and September 2011 were analysed using alkaline phosphatase assay (APA), P-debt, and N-debt to quantify phytoplankton nutrient status and with three different PAM models (PhytoPAM, WaterPAM and DivingPAM) to determine Fv/Fm. The Lake Ontario, Lake Erie East and Central Basin sites were all N- and P-deficient in July, but only the East and Central Basin and one Lake Ontario site were P-deficient in September. The West Basin sites were P-deficient in July and one West Basin site and a river site were N-deficient in September. Between-instrument Fv/Fm comparisons did not show the expected 1:1 relationship. Fv/Fm from the PhytoPAM and WaterPAM were well-correlated with each other but not with nutrient deficiency. DivingPAM Fv/Fm did not correlate with the other PAM models, but correlated with P-deficiency. Spectral PAM fluorometers (PhytoPAM) can potentially resolve Fv/Fm down to phytoplankton group by additionally measuring accessory pigment fluorescence. The nutrient-induced fluorescent transient (NIFT) is the observation that Fv/Fm drops immediately and recovers when the limiting nutrient is reintroduced to nutrient-starved phytoplankton. A controlled laboratory experiment was conducted on a 2x2 factorial mixture design of P-deficient and P-sufficient Asterionella formosa and Microcystis aeruginosa cultures. Patterns consistent with published reports of NIFT were observed for P-deficient M. aeruginosa in mixtures; the pattern for A. formosa was less clear. This thesis showed that Fv/Fm by itself was not a reliable metric of N or P deficiency and care must be taken when interpreting results obtained by different PAM fluorometers. NIFT analysis using spectral PAM fluorometers may be able to discriminate P-deficiency in M. aeruginosa, and possibly other Cyanobacteria, in mixed communities.

The Laurentian Great Lakes are the largest system of freshwater on earth containing 22% of the world’s supply. Although part of a single system, each lake shows substantial variation regarding physical, chemical and biological parameters. The main goals of this thesis were to characterize the nutrient status of natural phytoplankton communities while comparing several commonly used measurements of nutrient status and Chlorophyll a (Chl a) fluorescence measurements. The study sites include the western basin (WB), west-central basin (WCB), and central basin (CB) of Lake Erie, the Bay of Quinte in Lake Ontario, and Colpoys Bay in Lake Huron. Independent measures of nutrient status were assessed by measurements of nitrogen (N) debt, phosphorus (P) debt, particulate C:N:P ratios, and alkaline phosphatase activity (APA). Variable fluorescence of chlorophyll a was measured by pulse amplitude modulated (PAM) fluorometry and fast repetition rate (FRR) fluorometry in parallel with the independent measures. In 2005, the phytoplankton communities in Lake Erie were generally N deficient in May, P deficient in June, and neither N nor P deficient in September. The maximum dark adapted quantum yield (Fv/Fm) measured by PAM or FRRF was lower in May and June, and maximal in September, while the functional absorption cross section of photosystem II (σPSII) was maximal in May and June, and minimal in September. Relationships between the variable fluorescence indicators and independent measures of nutrient status showed strong associations with N or P deficient sites having low Fv/Fm and high σPSII. In 2006, the electron transport rate (ETR) and the initial slope (α) derived from the PAM fluorescence rapid light-response curves (RLC) were compared to independent measures and Fv/Fm measurements in Lake Erie. Relationships between ETR, α, independent measures of nutrient status, and Fv/Fm measurements revealed strong associations with nutrient status. Confirming previous reports, N deficiency was highest in the WB during isothermal conditions while P deficiency was highest in the CB during summer stratification. The fluorescence parameters generally decreased as the severity of N and P deficiency increased. N and P enrichment assays also revealed increased values of Fv/Fm, ETR, and α from N and P deficient samples over twenty-four hours. Additionally, spatial variability of P status was evaluated during summer stratification. Colpoys Bay, the most oligotrophic site, had the strongest P deficiency, and evidence for existence of P deficiency was weakest in the Bay of Quinte, the most eutrophic site. Nutrient enrichment assays revealed that all fluorescence parameters showed a positive response to P additions in oligotrophic sites, with no response in eutrophic sites. Community structure was also associated with nutrient status and Chl a fluorescence at all locations. In P deficient sites, nano-flagellates such as chrysophytes and cryptophytes were prevalent; cyanobacteria were dominant at sites that displayed N deficiency.

This study investigates the tempo-spatial distribution in species composition and abundance of planktonic pteropods in relation to hydrography in the waters around Liu-chiu Yu Island, southwestern Taiwan from February 2006 to October 2007. In total, we recognized 25 pteropod species belonging to 12 genera and six families, with a mean abundance of 7348 ¡Ó 994 ind./ 1000m3. The five most dominant species were Limacina inflata, Creseis virgula var. conica, Creseis acicula, Limacina trochiformis and Creseis clava, together they accounted for 78.7 % of the total pteropods. The surface sea water temperature, salinity, and phytoplankton concen- tration in the waters around Liu-chiu Yu Island were significantly higher in 2006 than in 2007. Pteropod abundance was higher in spring than in other seasons, and higher in deeper waters than in surface waters. Species number of pteropods was significantly higher in 2007 than in 2006, generally higher in summer and lower in autumn, and higher in deeper waters than in surface waters. Species diversity index of pteropods was generally higher in summer and lower in autumn. Cluster analysis of hydrography included 4 clusters (e.g., 2007 summer, summer and autumn, spring and winter, spring), the 2007 summer cluster was different from other seasons. Pteropod assemblage showed apparent difference between seasons, the variation of pteropod assemblages between stations in spring was higher than other seasons. Linear regression showed that the species number (p < 0.01) and diversity index (p < 0.05) were positively correlated with abundance of fish larvae. Abundance of most dominant species of pteropods was significantly and positively correlated with abundance of fish larvae (e.g., Limacina inflata; Creseis virgula var. conica and Limacina trochiformis) and significantly and negatively correlated with phytoplankton abundance (e.g., Limacina inflata, p < 0.001). In addition to the hydrographic factors, the distribution of pteropods might also be affected by predatory fish larvae and phytoplankton supplement.