This research has utilised the Massachusetts Institute of Technology gen- eral circulation model (MITgcm) along with observations taken as part of the River In uences on Shelf Ecosystems (RISE) study to investigate the dynamic processes associated with the Columbia River plume at different temporal and spatial scales. Firstly, a high resolution ( x= y=25 m) investigation of the near-field plume was undertaken using the fully non-hydrostatic mode of the MITgcm. This resulted in the reproduction of a detailed inner plume as well as a series of radiated internal waves. In addition to first mode internal waves, second order waves were radiated from the plume boundary when propagation ve- locity becomes sub-critical. Third mode internal waves were also observed, trapped at the plume head. The fine plume structure produced revealed sec- ondary fronts within the plume that also generated internal waves. These features increase the mixing occurring inside the plume, resulting in greater entrainment of underlying waters into the plume. The use of Lagrangian drifters within the model produced detailed results of the recirculation tak- ing place within the emerging plume and how this recirculation changes with depth. This has implications for the near-field recirculation of biologically important solutes present in the plume waters. A second coarser resolution horizontal grid ( x= y=500 m) was imple- mented to investigate the processes of the large-scale plume with the addi- tion of wind forcing. Experiments with both simplified and realistic wind scenarios were carried out and comparisons with in-situ data were made. This revealed the dominance of wind effects on the outer plume and tidal effects on the inner plume. In the simplified wind cases, the classical the- ory of plume propagation under the action of upwelling and downwelling favourable winds was recreated. For the case of realistic winds, there was some success in reproducing a hindcast of the plume location. Tracer fields were used to represent nutrient concentrations based on observed data. Whilst these results showed variations from observations, they did allow a spatially and temporally complete view to be taken of nutrient distribu- tion in the region.

Entrainment velocity, salt flux and the turbulent diffusivity of salt are estimated in the outflow of a small, radially spreading buoyant outflow, just outside of the Teign Estuary mouth, as a means to compare mixing dynamics between very small and larger-scale estuarine and river plumes, and build on a scant knowledge base regarding the former. The analysis was made using a control volume approach, based on the conservation of momentum, volume and salt, from a Lagrangian perspective. Drifting buoys were used to accomplish this. The analysis was based on that employed by McCabe et al. (2008), with some modifications to fit a small-scale outflow, namely: repeat deployments, shorter drifter tracks, and deployment-specific criteria used for choosing the plume base, a step in the analysis used to calculate vertical entrainment, flux and diffusivity. In addition, temperature was used as a proxy for salinity, and this is evaluated in the results. Overall results were compared to a similar study, which was conducted in the Columbia River plume, a system much larger in scale to the Teign. Drifter experiments were conducted on multiple days, under different conditions (i.e. wind, tides, river flow), and those results are discussed briefly, but the focus is on one specific day, April 3, 2014, where conditions most closely matched those of the comparison study, and those results are compared between the two systems. Entrainment velocity was measured along the drifter tracks, in the near-field plume, where shear-induced mixing dominates. Drifter track subsections were chosen so as to avoid source or frontal dynamics, the plume base was chosen for individual deployments as the plume dynamics could change relatively quickly, and repeat deployments were conducted as a way to look at near-field plume evolution over the course of the ebb (and with a smaller plume, time allowed for this) . On April 3, the mean value for entrainment velocity for the four deployments chosen in the Teign outflow was 4.3 x 10-4 ms-1. The mean cast value was slightly higher at 7.6 x 10-4 ms-1, as casts values were typically measured at the beginning of the drifter tracks. Entrainment values at the cast sites were calculated in the same way as the track values, taking plume thickness from hydrographic casts, as a means to evaluate accuracy of track values, which are based on a modelled plume thickness. A rough estimate for the mean entrainment velocity for one pair of drifters used in the Columbia River was 9 x 10-4 ms-1, approximately double that of the Teign, but within the same order of magnitude. Salt flux values ranged from 0-5 x 10-2 psu ms-1 and from 0-3 x 10-2 psu ms-1 for the Teign and the Columbia, respectively, and diffusivities ranged from 0.5-5.8 x 10-2 m2s-1 and from 0.2-9.6 x 10-3 m2s-1. With a similar range of entrainment and salt flux values, and almost an order of magnitude difference between diffusivity values, it was determined that weaker density gradients in the Teign are responsible for the latter, and that this increased level of mixing results in a larger horizontal horizontal salinity gradient, which balances out the terms in the entrainment equation that are related solely to the physical size of the system (i.e. plume thickness, velocity and the vertical salinity gradient). This higher level of mixing of a smaller physical entity, supports the view that smaller plumes mix more thoroughly over a shorter timescale, resulting in a larger impact to the local environment into which they flow.

This study focuses on deposition processes from sediment laden buoyant river plumes in deltaic regions. The goal is to experimentally examine the effects of various physical phenomena influencing the rate at which sediment is removed from the plume. Previous laboratory and field measurements have suggested that, at times, sedimentation can take place at rates higher than that expected from individual particle settling (i.e., C{W}_{s}). Two potential drivers of enhanced sedimentation are flocculation and interfacial instabilities. We experimentally measured the sediment fluxes from each of these processes using two sets of laboratory experiments that investigate two different modes of instability, one driven by sediment settling and one driven by fluid shear. The settling-driven and shear-driven instability sets of experiments were carried out in a stagnant stratification tank and a stratification flume respectively. In both sets, continuous interface monitoring and concentration measurement were made to observe developments of instabilities and their effects on the removal of sediment. Floc size was measured during the experiments using a separate floc camera setup and image analysis routines. Results from the stratification tank experiments suggest that the settling-driven gravitational instabilities do occur in the presence of flocs, and that they can produce sedimentation rates higher than those predicted from floc settling. A simple cylinder based force balance approach adopting the concept of critical Grashof number was used to develop a model for the effective settling velocity under settling-driven instabilities that is a function of sediment concentration in the plume only. Results from the stratification flume experiments show that under shear instabilities, the effective settling velocity is greater than the floc settling velocity, and increases with plume velocity and interface mixing. The difference between effective and floc settling velocity was denoted as the shear-induced settling velocity. This settling rate was found to be a strong function of the Richardson number, and was attributed to mixing processes at the interface. Conceptual and empirical analysis shows that the shear-induced settling velocity is proportional to U{Ri}^{-2}. Following the experiments, analyses were made among contributions of different mechanisms on the total deposition rate, and the locations that the various mechanisms may be active in the length of a plume. This analysis leads to a conceptual discretization of a plume into three zones of sedimentation behavior and Richardson number. The first zone is the supercritical near-field plume with intense interface mixing. Zone two represents the subcritical region where interface mixing still occurs, and zone three is the high Richardson number zone where mixing at the interface is effectively nonexistent. In zones one and two, individual floc settling and shear-induced settling mechanisms play the major roles in removing sediment from the plume. While, shear-induced settling rate was found to be maximum near the river mouth, its share of the total settling rate increases in the crossshore direction, since sand and large particulates deposit near the inlet and only small particles (with relatively low settling velocity) remain as the plume propagates. The third zone, starts when the interfacial mixing diminishes and leaking commences. / Ph. D.

In the Beaufort Sea, freshwater input from the Mackenzie River creates a relatively warm and turbid plume across the coastal shelf region. To determine the effects of the Mackenzie River plume on marine larval fish abundance, distribution and assemblages; this study sampled larval fish by using 500 μm bongo nets and obtaining oceanographic measurements across the plume gradient during July and August of 2007. Three larval fish assemblages were identified within three water masses: the intense plume assemblage was dominated by Pacific herring (Clupea pallasii pallasii), the diffuse plume assemblage was dominated by the sub-family Lumpeninae and the oceanic assemblage was dominated by Arctic cod (Boreogadus saida). Also, results revealed that there were no significant differences in the total larval fish abundances within these water masses. In conclusion, this study suggests that the Mackenzie River plume might be identified as an Ecologically and Biologically Significant Area (EBSA), based on the uniqueness criteria under Canada’s coastal conservation strategy.

In the Beaufort Sea, freshwater input from the Mackenzie River creates a relatively warm and turbid plume across the coastal shelf region. To determine the effects of the Mackenzie River plume on marine larval fish abundance, distribution and assemblages; this study sampled larval fish by using 500 μm bongo nets and obtaining oceanographic measurements across the plume gradient during July and August of 2007. Three larval fish assemblages were identified within three water masses: the intense plume assemblage was dominated by Pacific herring (Clupea pallasii pallasii), the diffuse plume assemblage was dominated by the sub-family Lumpeninae and the oceanic assemblage was dominated by Arctic cod (Boreogadus saida). Also, results revealed that there were no significant differences in the total larval fish abundances within these water masses. In conclusion, this study suggests that the Mackenzie River plume might be identified as an Ecologically and Biologically Significant Area (EBSA), based on the uniqueness criteria under Canada’s coastal conservation strategy.

The Calvin-Benson-Bassham (CBB) pathway is the primary pathway for the entry of inorganic carbon in the biosphere. Autotrophic organisms use this cycle to ultimately convert CO2 into carbohydrates using a key enzyme known as ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO). The gene that encodes for the large subunit of RubisCO is rbcL and detection of its expression can be used to determine the autotrophic organisms present in the environment. Recently, microarrays have been used to study functional gene expression from environmental samples such as those obtained from sediments and soil. The purpose of this thesis is to combine microarray technology and rbcL expression analysis to investigate phytoplankton populations in the Mississippi River Plume (MRP). Initially, a macroarray was constructed to determine its capabilities of quantifying gene expression in MRP. PCR amplicons were spotted onto a nylon membrane and labeled transcript RNA was hybridized to each array. Due to the large amount of cross hybridization that was observed, a microarray was used. Microarray analysis revealed large amounts of Synechococcus, pelagophyte and prymnesiophyte expression in the surface waters. Furthermore, there was no chlorophte or Prochlorococcus expression observed in the surface waters. Subsurface microarray data showed high levels of pelagophytes and other Form ID organisms. A significant chlorophyte signal was also observed in the subsurface. This study provides a third level of specificity at which phylogenetic diversity has been sampled in the MRP. Although a limited number of samples were analyzed by microarrays, this technology shows promise and this study was viewed as a pilot for their application. The rbcL probes designed were based upon published sequences from 2003 and we now have a much greater understanding of the diversity of rbcL-containing phytoplanktonic phylotypes. Future studies should employ this knowledge for judicious probe selection.

Unraveling the microbiological processes that occur as water travels from a river's mouth into the ocean is critical to understanding the role of river plumes in global biogeochemical cycles. Metranscriptomics, the gene expression of a whole community of organisms, was utilized to examine six stations along the Amazon River Plume (ARP) in 2010 to test thehypothesis that there were measurable differences in gene expression for key biogeochemical genes along the ARP. This body of work focuses on methods developed to identify which genes are biogeochemically important for a particular environment along extreme salinity, nutrient and community gradients in the ARP, and the interpretation of these data. The metatranscriptome of a marine algal bloom of Protoperidinium quinquecorne was collected, as a pilot study, and represented the first published eukaryotic marine algal bloom metatranscriptome. Of the 232 transcripts examined, over 70% were eukaryotic mRNAs, thus demonstrating the successful isolation of eukaryotic transcripts from ribosomal RNAs and prokaryotic RNAs. Transcripts for nutrient and carbon uptake were identified, and reinforced the theory that biogeochemically-relevant genes will be amongst the highly-expressed genes in eukaryotic phytoplankton populations. The final two sections of this dissertation detail two different ways to bioinformatically examine metatranscriptomes from the eukaryotic microbial populations of the ARP. The reproducibility of metatranscriptomes was confirmed with very similar patterns of gene expression between true replicates differing by up to 2 hours and 2.5 km. Similar communities, two diatom-diazatroph association (DDA) stations, also showed stability of expression patterns over 25 days and 238.3 km. A gene database of 31 biogeochemical genes was used to enumerate transcript counts for the six different stations along the ARP. Patterns of gene expression reflected the major physical, chemical and biological influences in those communities. DDA blooms exhibited high silicon transporter expression to acquire silicon for diatoms, and the photosystem II D1 protein replacement was high in these low-turbidity blooms. In a low salinity (salinity 20.7) diatom bloom, nitrate transport genes were highly expressed to account for high growth rates fueled by photosynthesis, and carbonic anhydrase helped counter the low pCO2 waters. The last chapter compares all the sequences to the entire protein family (pfam) library to annotate all possible transcripts for important processes missed with a 31-gene database approach. Pfams for chlorophyll A-B binding protein and bacteriorhodopsin-like proteins ranked among the most-expressed pfams. These two pfams together show evolutionary adaptations to maximize ATP generation in surface community algal blooms. Multidimensional scaling plots illustrated that the patterns of gene expression were unique to each station. This body of work will expand our understanding of river plume eukaryotic phytoplankton communities, and when these data are added to metagenome, prokaryote metatranscriptome and modeling data, modelers will be able to better forecast diversity, transcription and community evolution over broad space and time scales.

River plumes often develop in complex environments, where variable coastal and bottom topography, ambient currents, winds and tides may play important roles in shaping the plume evolution. When all these factors are present, the plume dynamics may become intricate and unclear. The objective of this study is to understand the processes controlling the dynamics of a large river plume that is affected by strong boundary currents, variable winds and complex topography. The Mississippi River (MR) plume is the study case of this dissertation work, and focus is given to the interactions between the plume and the offshore circulation of the Gulf of Mexico (GoM). A series of numerical experiments was designed to investigate the impact of different factors on the development of a large scale river plume in scenarios with variable degrees of complexity. First, a box-like model with an idealized estuary was designed to address the general development of a mid-latitude river plume and assess the variability of the plume with changes in the outflow conditions at the river mouth. The structure and development of the plume in the flat-bottom, receiving basin was highly dependent on the degree of freshwater mixing at the source. Larger freshwater mixing enhanced the estuarine gravitational circulation and modified the dynamical balance at the estuary mouth. Those changes effectively modified the shape of the bulge and length/transport scales of the coastal current. Sloping-bottom conditions further modified the development of the plume. Secondly, a Northern GoM model was designed and numerical experiments were conducted to investigate the specific dynamics of the MR plume, in the presence of both shelf and basin-wide circulation. In particular, buoyancy-driven (due to the MR and all other major Northern GoM rivers) and wind-driven currents were studied on the shelf, while the extension of the Loop Current and associated frontal eddies were considered as major factors in the shelf to offshore interactions; wind-driven, shelfbreak eddies were also considered. Process-oriented experiments demonstrate that westerly and southerly winds promoted the development of a surface Ekman layer that enhances the offshore advection of plume waters. The steep topography in the vicinity of the MR Delta was a favorable condition for that process. When the MR plume was subject to a full-blown scenario (realistically-forced experiment nested within a large-scale model), complex interactions between wind-driven and eddy-driven dynamics determined the fate of the plume waters. Offshore removal is a frequent plume pathway, and the offshore transport can be as large as the wind-driven shelf transport. The offshore pathways depend on the position of the eddies near the shelf edge, their life span and the formation of eddy pairs that generate coherent cross-shelf flows. Strong eddy-plume interactions were observed when the Loop Current (LC) system impinged against the shelfbreak, causing the formation of coherent, narrow low-salinity bands that extended toward the Gulf interior. The offshore transport of MR water is a year-round process, but the interactions between the MR plume and the LC system have large inter-annual variability. Plume to LC interactions are determined by episodic northward intrusions of the LC system in the NGoM. The interactions are dictated by the proximity of the LC system to the MR Delta and by wind effects. On average, plume to LC interactions correspond to ~ 12 % of the year-round, total freshwater transport near the MR Delta, but this percentage can go up to 30 % in individual years. At the time of the plume to LC interactions, an average value of LC freshwater entrainment was estimated to be ~ 4,150 m3 s-1. The findings presented here are a major contribution toward the understanding of the cross-marginal and basin-wide transport of MR waters by a large-scale current system, and the connectivity to remote regions, such as the South Florida region and the Florida Keys.

In the subtropical oligotrophic ocean, nitrogen fixation is an important source of new nitrogen (N) for supporting biological production. Previous studies have found that nitrogen-fixing Diatom-Diazotroph Associations (DDAs) are in high abundance in the intermediate salinity zone of large river plumes such as the Amazon and Mekong rivers, while Trichodesmium spp. becomes more abundant at higher salinities. This recurring pattern in the Amazon River plume suggests that strong salinity and nutrient gradients within the river plumes may lead to a cascade in diazotroph communities. I hypothesized that the Mississippi River, a major source of freshwater, nutrients and sediments to the northern Gulf of Mexico, creates a similar distribution of diazotroph communities. The relationship between large diazotrophs and salinity was examined in samples collected in July 2011 during a flood outflow from the Mississippi River. The dominant DDA, Hemiaulus spp. – Richelia spp., was at greatest abundance (≈31,000 cells L-1) west of the birdfoot delta on the periphery of the plume (≈29 salinity) where bottom water hypoxia was also observed. Trichodesmium spp., a cyanobacterium genus that occurs in both colonial and free trichome morphologies, was abundant at both high (≈35) salinities east of the delta reaching 20+ colonies L-1, as well as in the fresher (≈28) waters of the plume where it reached 3,500 trichomes L-1. Diazotroph distributions were separated east and west of the Mississippi River outflow, with DDAs being most abundant over bottom water hypoxic regions to the west and Trichodesmium spp. in high abundance to the east. The diazotroph – salinity gradient relationships present within the Amazon River plume were not present within the Gulf of Mexico. This study suggests that environmental factors other than salinity, such as nutrients or hypoxia, are influencing the distribution of diazotrophs around the Mississippi River plume. The seasonal hypoxia seen in the Gulf of Mexico with the co-occurring DDA increase could appear in other river systems. / text

Many of the world’s lakes are located at high latitudes in the northern hemisphere where seasonal ice cover is common. The ice restricts lake-atmosphere gas exchange, causing an under-ice accumulation of CO2. However, there are few spatial under-ice CO2 studies of river influence on lakes. Here, I examine the river plume of a river-influenced bay and compare it to a control bay without river influence in lake Örträsk, a humic of 7 km2 lake in boreal Sweden. There was no relationship between CO2 or DIC and distance from the Vargån river outlet in Vargån bay, even though the CO2 and DIC concentration of the river was found lower in Vargån river (median CO2: 53,2 µM; DIC: 178 µM) than in Vargån bay (median CO2: 84,7 µM; DIC: 301 µM). The median values of the control bay were CO2: 92,7 µM and DIC: 345 µM. There was a negative relationship in CO2 concentration with distance in the control bay, but not in DIC. The control bay had a higher concentration of CO2 at 0-60 m distance than Vargån bay, but there was no difference at 70-180 m. The DIC concentration was higher in the control bay than in Vargån bay. I have reported lower CO2 and DIC concentrations in the river than in the lake, which is not in accordance with literature and is probably due to an earlier ice-melt in the river than in the lake. The negative CO2 relationship in the control bay is likely due to sediment respiration.