Columbia River Plume Research Articles

Seasonal and Interannual Salish Sea Inflow Origins Using Lagrangian Tracking

AbstractThe Salish Sea is a semi‐enclosed sea between Vancouver Island and the coast of British Columbia and Washington State, invaluable from both an economic and ecologic perspective. Here we explore the contribution of Pacific water masses to the flow through Juan de Fuca Strait (JdF), the Salish Sea's primary connection to the Pacific Ocean. Quantitative Lagrangian particle tracking within Ariane, an offline Lagrangian tool capable of volume transport calculations, was applied to two numerical ocean models to track the paths and physical properties of water parcels before entering JdF (CIOPS) and within the Salish Sea (SalishSeaCast). During summer upwelling, flow from the north shelf and offshore dominate Pacific inflow, while during winter downwelling, flow from the south shelf and surface flow from the Columbia River plume are the dominant Pacific sources. A weaker and less consistent estuarine flow regime in the winter leads to less Pacific inflow overall and a smaller percentage of said inflow reaching the Salish Sea's inner basins than in the summer. Nevertheless, it was found that winter dynamics are a large driver of interannual variability. This analysis extends the knowledge on the dynamics of Pacific inflow to the Salish Sea and highlights the importance of winter inflow to interannual variability.

Characterizing juvenile salmon predation risk during early marine residence.

Predation mortality can influence the distribution and abundance of fish populations. While predation is often assessed using direct observations of prey consumption, potential predation can be predicted from co-occurring predator and prey densities under varying environmental conditions. Juvenile Pacific salmon Oncorhynchus spp. (i.e., smolts) from the Columbia River Basin experience elevated mortality during the transition from estuarine to ocean habitat, but a thorough understanding of the role of predation remains incomplete. We used a Holling type II functional response to estimate smolt predation risk based on observations of piscivorous seabirds (sooty shearwater [Ardenna griseus] and common murre [Uria aalge]) and local densities of alternative prey fish including northern anchovy (Engraulis mordax) in Oregon and Washington coastal waters during May and June 2010–2012. We evaluated predation risk relative to the availability of alternative prey and physical factors including turbidity and Columbia River plume area, and compared risk to returns of adult salmon. Seabirds and smolts consistently co-occurred at sampling stations throughout most of the study area (mean = 0.79 ± 0.41, SD), indicating that juvenile salmon are regularly exposed to avian predators during early marine residence. Predation risk for juvenile coho (Oncorhynchus kisutch), yearling Chinook salmon (O. tshawytscha), and subyearling Chinook salmon was on average 70% lower when alternative prey were present. Predation risk was greater in turbid waters, and decreased as water clarity increased. Juvenile coho and yearling Chinook salmon predation risk was lower when river plume surface areas were greater than 15,000 km2, while the opposite was estimated for subyearling Chinook salmon. These results suggest that plume area, turbidity, and forage fish abundance near the mouth of the Columbia River, all of which are influenced by river discharge, are useful indicators of potential juvenile salmon mortality that could inform salmonid management.

High-Resolution Carbonate System Dynamics of Netarts Bay, OR From 2014 to 2019

Netarts Bay is a shallow, temperate, tidal lagoon located on the northern coast of Oregon and the site of the Whiskey Creek Shellfish Hatchery (WCSH). Data collected with an autonomous continuous flow-through system installed at WCSH capable of high-resolution (1 Hz) partial pressure of aqueous CO2 (pCO2) and hourly total dissolved inorganic carbon (TCO2) measurements, with combined measurement uncertainties of < 2.0% and 0.5%, respectively, is analyzed over the 2014–2019 interval. Summer upwelling, wintertime downwelling, and in situ bay biogeochemistry represent significant modes of the observed variability in carbonate system dynamics. Summer upwelling is associated with large amplitude diel pCO2 variability, elevated TCO2 and alkalinity, but weak variability in salinity. Wintertime downwelling is associated with bay freshening by both local and remote sources, a strong tidal signature in salinity, TCO2, and alkalinity, with diel pCO2 variability much less amplified when compared to summer. Further, analysis of alkalinity-salinity relationships suggests multiple water masses inhabiting the bay during 1 year: mixing of end-members associated with direct precipitation, coastal rivers, southward displacement of the Columbia River plume, California Current surface and deep upwelled waters. The importance of in-bay processes such as net community metabolism during intervals of high productivity are apparent. These direct measurements of pCO2 and TCO2 have been useful to local hatchery owners who have monitored intake waters following historic seed-production failures related to high-CO2 conditions exacerbated by ocean acidification.

Long-term patterns of mass stranding of the colonial cnidarian Velella velella: influence of environmental forcing

Velella velella is a pleustonic cnidarian noted worldwide for mass stranding of the colonial phase. Utilizing a 20 yr dataset (2000-2019; 23265 surveys) collected by the COASST citizen science program, we examined the spatio-temporal occurrence of mass strandings of V. velella along the Pacific Northwest coast from Washington to northern California, USA. V. velella mass strandings were documented in 14 years, with expansive events in 2003-2006 and 2014-2019. Events predominantly occurred in spring and were synchronous (April) among years, concurrent with shifts to prevailing onshore winds. Autumn mass stranding events occurred infrequently, with no consistent phenology (2005: November; 2014: August). In stranding years, reports of V. velella were mostly synchronous throughout the surveyed area, and events consistently spanned >400 km of coastline, with highest reporting rates in the vicinity of the Columbia River plume, collectively suggesting extensive V. velella blooms throughout the northern California Current system in some years. Annual metrics of spring V. velella reporting rate (proportion of beaches; January-June) were modeled as a function of indices representing sea surface temperature anomaly (SSTa), easterly (onshore) wind speed, and regional upwelling. The best models (based on Akaike’s information criterion corrected for small sample size) indicated that SSTa averaged over the preceding winter (December-February) was positively correlated with spring reporting rate, suggesting that mass strandings of V. velella may be more prevalent in warmer years. As planetary warming continues, and V. velella strandings are easily recorded by citizen science programs globally, we suggest that stranding prevalence may be one relatively easy measure providing evidence for epipelagic ecosystem response.

Ensemble 4DVAR (En4DVar) data assimilation in a coastal ocean circulation model. Part II: Implementation offshore Oregon–Washington, USA

The ensemble four-dimensional variational (En4DVar) data assimilation (DA) system introduced in Part I (Pasmans and Kurapov, 2019) is tested in the coastal waters offshore Oregon and Washington, U.S. West coast, during the spring and summer of 2011. The background error covariance B is derived from the forecast ensemble. Satellite sea-surface temperature (SST), sea-surface height (SSH), and daily-averaged radial surface currents from high-frequency radars (HFRs) are assimilated. The performance of the En4DVar system is compared with a “traditional” 4DVAR system using a static B. It is found that the presence of the Columbia River plume has a profound impact on the ensemble B. Near the plume front the SST–SSS covariance can be up to a factor 20 larger in magnitude than in the static B. This introduces large spatial and temporal variability in the ensemble B. The En4DVar system is more successful than the 4DVAR with the static B preserving the temperature–salinity properties when compared to glider data. The En4DVar system also produces more accurate forecasts and analyses for temperature in the subsurface below 30 m at a buoy location on the continental shelf. In comparisons with other surface and subsurface observations En4DVar shows consistent, albeit not significant, improvement over traditional 4DVAR. Large surface temperature–salinity covariances in combination with the episodic occurrence of large-scale errors in the SST observations lead to erroneous freshening in the centre of the model domain. Adding constraints on the surface salinity corrections based on the prior model reduces this effect.

Spatio-temporal variability and ENSO modulation of turbid freshwater plumes along the Oregon coast

The influence of climate variability on the Northeast Pacific (NEP) ocean is mainly linked to the impact of El Niño Southern Oscillation (ENSO), the Pacific Decadal Oscillation (PDO), and North Pacific Gyre Oscillation (NPGO) on the modulation of coastal circulation, coastal upwelling, and ecosystem response. The impact of climate variability on the interannual variability of freshwater river plumes has been largely unstudied. Here, 14.5 years of ocean color satellite imagery were used to study the interannual variability of turbid freshwater plumes off the Oregon coast. EOF analysis reveals two dominant modes associated with (i) the winter plumes of coastal rivers merged along the entire Oregon shelf (EOF1) in the downstream (northward) direction as coastal-attached buoyancy-driven plumes, and (ii) the offshore Columbia River plume occupying most of the coastal ocean off Oregon (EOF2) as result of its southward and offshore transport during spring-summer upwelling. Large plumes corresponded mainly with certain aspects of ENSO cycles. However, extended ocean time series are needed to better evaluate the influence of PDO and NPGO because of their dominant decadal variability. Anomalously large coastal plumes (EOF1) lagged the canonical El Niño primarily during fall and La Niña during winter. The largest offshore Columbia River plume events occurred after persistent La Niña conditions (e.g. 2008, 2011, 2014).

Discontinuous Galerkin discretization for two-equation turbulence closure model

Accurate representation of vertical turbulent fluxes is crucial for numerical ocean modeling, both in global and coastal applications. The state-of-the-art approach is to use two-equation turbulence closure models which introduces two dynamic equations to the system. Solving these equations numerically, however, is challenging due to the strict requirement of positivity of the turbulent quantities (e.g., turbulence kinetic energy and its dissipation rate), and the non-linear source terms that may render the numerical system unstable. In this paper, we present a Discontinuous Galerkin (DG) finite element discretization of the Generic Length Scale (GLS) equations designed to be incorporated in a DG coastal ocean model, Thetis. To ensure numerical stability, the function space for turbulent quantities must be chosen carefully. In this work, we propose to use zeroth degree elements for the turbulent quantities and linear discontinuous elements for the tracers and velocity. The spatial discretization is completed with a positivity preserving semi-implicit time integration scheme. We validate the implementation with standard turbulence closure model benchmarks and an idealized estuary simulation. Finally, we use the full three-dimensional model to simulate the Columbia River plume. The results confirm that the coupled model generates realistic vertical mixing, and remains stable under strongly stratified conditions and strong tidal forcing. River plume characteristics are well captured.

Changing with the tides: fine-scale larval fish prey availability and predation pressure near a tidally modulated river plume

Tidally controlled river plumes form distinct frontal boundaries that can alter the spatial distributions of larval fishes and their planktonic prey and predators. Variable in nature, they may expose larval fishes to different trophic environments over small spatio-temporal scales, with unknown consequences for survival and recruitment. In the northern California Current, the Columbia River Plume is strongly influenced by twice-daily freshwater injections that create a highly dynamic coastal environment. Using the In situ Ichthyoplankton Imaging System, we examined changes in the fine-scale horizontal and vertical distributions of larval fishes, their prey, and their predators over space and time (ebb/flood tide). In total, 6095 fish larvae and ~1.5 million prey/predator zooplankton were imaged and measured. Plume regions provided substantially higher concentrations of prey and enhanced spatial overlap between larval fishes and their prey relative to oceanic waters. The functionality of river plumes as a refuge from predators was less clear. Predator concentrations were also higher in plume regions, but overlap with larval fishes was taxon-specific and varied with the tide. Notably, regions of high zooplankton concentrations did not necessarily confer high spatial overlap on small scales (meters vertical, kms horizontal) relevant to trophic interactions. Surface salinity and chlorophyll a were the most important factors influencing the spatial overlap of zooplankton with larval fishes. In the vicinity of river plumes, larval fishes experience a diversity of unique prey and predator fields over short spatio-temporal scales, which likely contribute to variable growth and mortality patterns at much finer scales than previously thought.

Applications for marine mammal studies using passive acoustic data from the Coastal Endurance array off Newport, Oregon

The National Science Foundation-funded Ocean Observatories Initiative (OOI) maintains a series of coastal and oceanic monitoring sites that consists of a multitude of physical and biological sensors. As part of this program, OOI has collected continuous, broadband passive acoustic data along the continental shelf and slope off Newport, Oregon since 2016. The Coastal Endurance cabled array consists of two mooring lines that straddle the Columbia River plume, and capture data from this nutrient rich upwelling site along the northeast Pacific coast. In addition to this instrumentation, underwater gliders conduct regular transects to provide better spatial resolution of coastal ocean parameters in the region. Representative data from the continental slope and seamount recording sites of the Coastal Endurance Array were reviewed for vocally active marine mammals. Physical oceanographic variables collected concurrently from the mooring line instrumentation and coastal gliders were used to spatially and temporally characterize the regional marine mammal habitat. This effort demonstrates applications for use of OOI’s accessible, multi-instrument platform for conducting marine mammal ecosystem studies.

Spatial and temporal diving behavior of non-breeding common murres during two summers of contrasting ocean conditions

Successful foraging of marine predators depends on environmental conditions, which also influence prey availability. Neutral or negative El Niño Southern Oscillation and Pacific Decadal Oscillation ocean conditions during the summer of 2013 and strongly positive conditions during the summer of 2015 in the northern California Current System provided a case study to evaluate a marine predator's response to anomalously warm conditions. We used satellite transmitters with saltwater switches to track movements and estimate dive behavior among non-breeding common murres (Uria aalge) off Oregon prior to and during a marine heatwave. We quantified differences in space-use between years, applied linear mixed models to determine environmental influences (e.g. sea surface temperature, surface salinity, chlorophyll a, ocean depth, and calendar date) on dive frequency and dive duration, and contrasted dive activity between time of day, year, and sexes. The majority of birds dispersed away from capture locations, which were situated near the southern range limit of their population. In both years, murres used the Salish Sea and the Columbia River plume; however, murres spent more time foraging in the Columbia River plume and in continental slope habitat during the marine heatwave of 2015. During 2015, dive frequency was reduced, and dive durations were almost twice as long during daytime indicating deeper or more dispersed prey. Increased dive frequency was positively associated with temperature, chlorophyll a, and crepuscular periods. Cluster analysis of dive activity and the top-ranked predictive dive duration model revealed associations between longer-duration dives and decreased dive frequency, marine slope habitat, and cooler ocean temperatures. Murres were relatively inactive throughout the night and we found no sex differences in dive activity. Changes in common murre foraging tactics were associated with ocean warming and revealed selectivity in spatial and temporal use of foraging habitats. Productive marine features including the Columbia River plume provided refuge for murres during apparently poor ocean conditions associated with the marine heatwave. Identifying refuge areas used by highly mobile species experiencing varying ocean conditions is critical for adaptive marine spatial planning that can accommodate a changing ocean climate.

Phosphorus Forms in Sediments of a River-Dominated Estuary

Estuaries are biologically productive transition zones between land and sea that play a vital role in transforming, recycling, and sequestering nutrients and organic matter, thus influencing nutrient loading to coastal systems. Yet, the processes involved in phosphorus (P) transformation and cycling among inorganic and organic P forms are poorly known in estuaries. To better understand the potential for P transformation and sequestration, we identified P forms and estimated their contributions to total P in intertidal wetland sediments of a river-dominated estuary (Columbia River, Oregon, USA) using solution 31P nuclear magnetic resonance spectroscopy (P-NMR). Inorganic P forms dominated sediment P extracts throughout the estuary, with orthophosphate accounting for 71–84% of total extracted P. However, biologically-derived inorganic and organic P forms were also detected. Polyphosphates were found in sediment extracts throughout the estuary, contributing as much as 10% of extracted P. Similar to other wetlands, orthophosphate monoesters and diesters made approximately equal contributions (~ 20%) to total extracted P. However, monoesters (e.g., phytate) were more abundant in sedimentary environments characterized by low organic matter content, while diesters (e.g., DNA) were more abundant in sedimentary environments with high organic matter, regardless of salinity. Collectively, the data show strong evidence for P transformation in sediments of a large, river-dominated estuary, which influences its transport to the coastal Pacific Ocean via the expansive Columbia River plume.

Frontal dynamics at the edge of the Columbia River plume

In the tidal ebb-cycle at the Mouth of the Columbia River, strong density and velocity fronts sometimes form perpendicular to the coast at the edges of the freshwater plume. They are distinct from previously analyzed fronts at the offshore western edge of the plume that evolve as a gravity-wave bore. We present simulation results to demonstrate their occurrence and investigate the mechanisms behind their frontogenesis and evolution. Tidal velocities on average ranged between 1.5 m s−1 in flood and 2.5 m s−1 in ebb during the brief hindcast period. The tidal fronts exhibit strong horizontal velocity and buoyancy gradients on a scale ∼ 100 m in width with normalized relative vorticity (ζz/f) values reaching up to 50. We specifically focus on the front on the northern edge of the plume and examine the evolution in plume characteristics such as its water mass gradients, horizontal and vertical velocity structure, vertical velocity, turbulent vertical mixing, horizontal propagation, cross-front momentum balance, and Lagrangian frontogenetic tendencies in both buoyancy and velocity gradients. Advective frontogenesis leads to a very sharp front where lateral mixing near the grid-resolution limit arrests its further contraction. The negative vorticity within the front is initiated by the positive bottom drag curl on the north side of the Columbia estuary and against the north jetty. Because of the large negative vorticity and horizontal vorticity gradient, centrifugal and lateral shear instability begins to develop along the front, but frontal fragmentation and decay set in only after the turn of the tide because of the briefness of the ebb interval.

Reverse Estuarine Circulation Due to Local and Remote Wind Forcing, Enhanced by the Presence of Along‐Coast Estuaries

AbstractEstuarine exchange flow governs the interaction between oceans and estuaries and thus plays a large role in their biogeochemical processes. This study investigates the variability in estuarine exchange flow due to offshore oceanic conditions including upwelling/downwelling, and the presence of a river plume offshore (from a neighboring estuary). We address these processes via numerical simulations at the mouth of the Salish Sea, a large estuarine system in the Northeast Pacific. An analysis of the Total Exchange Flow indicates that during the upwelling season, the exchange flow is fairly consistent in magnitude and oriented in a positive (into the estuary at depth and out at the surface) direction. However, during periods of downwelling favorable winds, the exchange flow shows significantly more variability including multiple reversals, consistent with observations, and surface intrusions of the Columbia River plume which originates 250 km to the south. Numerical along‐strait momentum budgets show that the exchange flow is forced dominantly by the pressure gradients, particularly the baroclinic. The pressure gradient is modified by Coriolis and sometimes advection, highlighting the importance of geostrophy and local adjustments. In experiments conducted without the offshore river plume, reversals still occur but are weaker, and the baroclinic pressure gradient plays a reduced role. These results suggest that estuaries along strong upwelling coastlines should experience significant modulation in the exchange flow during upwelling versus downwelling conditions. Additionally, they highlight the importance of nearby estuaries impacting one‐another, not only in terms of connectivity, but also altering the exchange flow.

Predator–prey interactions influenced by a dynamic river plume

Marine predator–prey interactions are often influenced by oceanographic processes that aggregate prey. We examined density distributions of seabirds and prey fish associated with the Columbia River plume to determine whether variation in plume size (i.e., volume or surface area) or location influences predator–prey interactions. Common murre (Uria aalge), sooty shearwater (Ardenna grisea), and forage fish, including northern anchovy (Engraulis mordax) and juvenile salmon (Oncorhynchus spp.), occurred disproportionately in plume waters relative to adjacent marine waters. Water clarity, an indicator of plume-influenced waters, was a significant predictor of seabird and prey densities throughout the survey area. Murres occurred within 20 km of the plume center of gravity, whereas shearwaters occurred ∼100 km north of the plume center of gravity, concurrent with the highest densities of prey fish. Global indices of collocation were relatively low between murres and prey compared with the high values between shearwaters and prey. Seabird densities were negatively correlated with plume size, suggesting that seabirds concentrate in the plume to maximize foraging effort. We conclude that variation in Columbia River plume size and location influences predator distributions, which increases predation pressure on prey, including threatened salmonid species.

Controls on Turbulent Mixing in a Strongly Stratified and Sheared Tidal River Plume

AbstractConsiderable effort has been made to parameterize turbulent kinetic energy (TKE) dissipation rate ε and mixing in buoyant plumes and stratified shear flows. Here, a parameterization based on Kunze et al. is examined, which estimates ε as the amount of energy contained in an unstable shear layer (Ri < Ric) that must be dissipated to increase the Richardson number Ri = N2/S2 to a critical value Ric within a turbulent decay time scale. Observations from the tidal Columbia River plume are used to quantitatively assess the relevant parameters controlling ε over a range of tidal and river discharge forcings. Observed ε is found to be characterized by Kunze et al.’s form within a factor of 2, while exhibiting slightly decreased skill near Ri = Ric. Observed dissipation rates are compared to estimates from a constant interfacial drag formulation that neglects the direct effects of stratification. This is found to be appropriate in energetic regimes when the bulk-averaged Richardson number Rib is less than Ric/4. However, when Rib > Ric/4, the effects of stratification must be included. Similarly, ε scaled by the bulk velocity and density differences over the plume displays a clear dependence on Rib, decreasing as Rib approaches Ric. The Kunze et al. ε parameterization is modified to form an expression for the nondimensional dissipation rate that is solely a function of Rib, displaying good agreement with the observations. It is suggested that this formulation is broadly applicable for unstable to marginally unstable stratified shear flows.

Optics of the offshore Columbia River plume from glider observations and satellite imagery

AbstractThe Columbia River (CR) is the largest source of freshwater along the U.S. Pacific coast. The resultant plume is often transported southward and offshore forming a large buoyant feature off Oregon and northern California in spring‐summer—the offshore CR plume. Observations from autonomous underwater gliders and Moderate Resolution Imaging Spectroradiometer (MODIS) satellite imagery are used to characterize the optics of the offshore CR plume off Newport, Oregon. Vertical sections, under contrasting river flow conditions, reveal a low‐salinity and warm surface layer of ∼20–25 m (fresher in spring and warmer in summer), high Colored Dissolved Organic Matter (CDOM) concentration, and backscatter, and associated with the base of the plume high chlorophyll fluorescence. Plume characteristics vary in the offshore direction as the warm and fresh surface layer thickens progressively to an average 30–40 m of depth 270–310 km offshore; CDOM, backscatter, and chlorophyll fluorescence decrease in the upper 20 m and increase at subsurface levels (30–50 m depth). MODIS normalized water‐leaving radiance (nLw(λ)) spectra for CR plume cases show enhanced water‐leaving radiance at green bands (as compared to no‐CR plume cases) up to ∼154 km from shore. Farther offshore, the spectral shapes for both cases are very similar, and consequently, a contrasting color signature of low‐salinity plume water is practically imperceptible from ocean color remote sensing. Empirical algorithms based on multivariate regression analyses of nLw(λ) plus SST data produce more accurate results detecting offshore plume waters than previous studies using single visible bands (e.g., adg(412) or nLw(555)).

Influence of a Coastal Riverine Plume on the Cross-shelf Variability in Hydrography, Zooplankton, and Juvenile Salmon Diets

Riverine plumes in nearshore coastal waters are areas of enhanced production and accumulation of prey and may increase availability of food during a critical period of juvenile salmon survival and hence serve as a nursery area for these juveniles. Physical and biological sampling was conducted along a cross-shelf transect through the Columbia River plume during May 1999. Based on cluster analyses of physical variables, stations considered to be within the core of the plume, at 27.8–46.3 km from shore, were distinct from inshore (7.4–18.5 km) and offshore (55.6–92.7 km) stations. Five variables (temperature at 10 m, salinity at 3 and 10 m, silicate, and chlorophyll) accounted for 92 % of this difference. Both surface neuston and subsurface plankton tows revealed differences in plankton composition at the plume core stations compared to non-plume stations. However, stomach contents of juvenile Chinook salmon were not significantly different inside and outside the plume core. Comparison of similarity indices showed that the stomach composition was more similar to the catch composition in the neuston than the meter net. Fishes, decapod larvae, and hyperiid amphipods occurred in greater proportions and copepods and euphausiids in lesser proportions in the stomachs than in the plankton. There appeared to be a distinctive plume signal, evident in both the physical environment and zooplankton resources sampled inside and outside the plume core, but the plume signature was not as evident in the salmon diets, possibly due to their higher mobility and shorter residence time within the plume.

Anomalous Near-Surface Low-Salinity Pulses off the Central Oregon Coast.

From mid-May to August 2011, extreme runoff in the Columbia River ranged from 14,000 to over 17,000 m3/s, more than two standard deviations above the mean for this period. The extreme runoff was the direct result of both melting of anomalously high snowpack and rainfall associated with the 2010–2011 La Niña. The effects of this increased freshwater discharge were observed off Newport, Oregon, 180 km south of the Columbia River mouth. Salinity values as low as 22, nine standard deviations below the climatological value for this period, were registered at the mid-shelf. Using a network of ocean observing sensors and platforms, it was possible to capture the onshore advection of the Columbia River plume from the mid-shelf, 20 km offshore, to the coast and eventually into Yaquina Bay (Newport) during a sustained wind reversal event. Increased freshwater delivery can influence coastal ocean ecosystems and delivery of offshore, river-influenced water may influence estuarine biogeochemistry.

Microbial Gene Abundance and Expression Patterns across a River to Ocean Salinity Gradient.

Microbial communities mediate the biogeochemical cycles that drive ecosystems, and it is important to understand how these communities are affected by changing environmental conditions, especially in complex coastal zones. As fresh and marine waters mix in estuaries and river plumes, the salinity, temperature, and nutrient gradients that are generated strongly influence bacterioplankton community structure, yet, a parallel change in functional diversity has not been described. Metagenomic and metatranscriptomic analyses were conducted on five water samples spanning the salinity gradient of the Columbia River coastal margin, including river, estuary, plume, and ocean, in August 2010. Samples were pre-filtered through 3 μm filters and collected on 0.2 μm filters, thus results were focused on changes among free-living microbial communities. Results from metagenomic 16S rRNA sequences showed taxonomically distinct bacterial communities in river, estuary, and coastal ocean. Despite the strong salinity gradient observed over sampling locations (0 to 33), the functional gene profiles in the metagenomes were very similar from river to ocean with an average similarity of 82%. The metatranscriptomes, however, had an average similarity of 31%. Although differences were few among the metagenomes, we observed a change from river to ocean in the abundance of genes encoding for catabolic pathways, osmoregulators, and metal transporters. Additionally, genes specifying both bacterial oxygenic and anoxygenic photosynthesis were abundant and expressed in the estuary and plume. Denitrification genes were found throughout the Columbia River coastal margin, and most highly expressed in the estuary. Across a river to ocean gradient, the free-living microbial community followed three different patterns of diversity: 1) the taxonomy of the community changed strongly with salinity, 2) metabolic potential was highly similar across samples, with few differences in functional gene abundance from river to ocean, and 3) gene expression was highly variable and generally was independent of changes in salinity.

Introduction to the Special Issue: Coastal and Marginal Sea Studies

As an important part of the ocean system, the coastal and marginal sea (CMS) is a junction between land and the open ocean where the ocean-land interaction occurs, and also it is the area with substantial marineeconomic activities for many countries. The development of marine economics greatly affects the CMS environment and causes deteriorating environmental problems. The study on the CMS helps to understand how the land and ocean interact, and how the marine environment responses to the land system change resulting from economic developments in coastal regions. Therefore, deeply understanding physical properties of the CMS is of great importance not only in the earth science study, but for marine environmental protection. For past decades, a number of major interdisciplinary research projects have been conducted that were related to the CMS studies and monitoring. The Shelf Edge Exchange Processes (SEEP) experiments took place in the Middle Atlantic Bight (MAB) of the eastern U.S. continental shelf and slope. The experiments included multi-instrumented moorings and oceanographic cruises to address the problem of the fate of continental shelf particulate matter (Walsh et al., 1988; Biscaye et al., 1994). The project of the river influence on shelf ecosystem (RISE) focused on the coastal dynamics and interaction between river and coastal ambient waters supporting primary production in the Columbia River (CR) plume area. The concepts generated by the project improved understanding of the impacts of river plumes worldwide, productivity on eastern boundary systems, and the global carbon cycle (Hickey et al., 2010). The project studies suggested that river-supplied nitrate can help maintain the ecosystem during periods of delayed upwelling (Hickey et al., 2010). In addition to major researches, the observation network is an important issue in CMS studies. The U.S. Integrated Ocean Observing System (IOOS) is a vital system for integrating in-situ data and modeling simulations to provide data sources to support different kinds of applications in the CMS (http://www.ioos.noaa. gov). The system helps coastal hazard mitigation, sustainability of coastal ecosystem, fishery, and water quality, marine operation, etc. (Willis et al., 2008). Satellite imagery provides a new data source to study and monitor coastal marine environments. In the National Oceanic & Atmospheric Administration (NOAA) coastal watch program (CoastWatch, http:// coastwatch.noaa.gov), multi-satellite data of ocean color, sea surface temperature, and sea surface winds are made available to different users to enhance the coastal data accessibility (Hughes et al., 2013). Products available through CoastWatch have expanded beyond the original infrared and visible images to include synthetic aperture radar (SAR) data (Pichel and Clemente-Colon, 2000). Significant progresses in data collection technology and numerical modeling provide abundant data sources, which constitute a major driving force to advance our knowledge in the CMS and promote coastal marine environment management.