Abstracts of CRETM-LMER Publications

Baross, J. A., B. Crump, and C. A. Simenstad. 1994. Elevated 'microbial loop' activities in the Columbia River estuary turbidity maximum. Pp. 459-464 In K. Dyer and R. Orth (ed.), Changing Particle Fluxes in Estuaries: Implications from Science to Management, ECSA22ERF Symposium, Olsen & Olsen Press, Friedensborg.

The abundances of bacteria, protozoa and copepods, as well as bacterial growth rates were measured in both ETM and non-ETM waters from various locations in the Columbia River estuary during 1990, 1991, and 1992 CRETM-LMER cruises. The incidence of protozoa and copepods, and microbial growth rates were strongly correlated with turbidity and salinity. In comparison, the numbers of bacteria showed little variation and generally ranged from 5-20x10⁷·ml^-1. In most cases, flagellates tracked bacterial activities and densities whereas rotifers and copepods tracked ciliates. This high-activity microbial assemblage appeared abruptly with the appearance of the ETM, suggesting that it is entrained with the suspended material. The proportion of bacteria attached to the 20 m m or greater sized suspended material ranged from 17 to 39% in ETM waters and less than 5% in non-ETM waters. This suggests that in addition to dissolved organic material (DOM), particulate organic material (POM) may also be a significant source of nutrients for bacteria.

Bacterial growth rates as estimated by the incorporation of [methyl-3H] thymidine into DNA ranged from less than 4 hr to greater than 60 hr with the fastest rates in flood ETM waters having turbidities exceeding 150 mg·ml^-1 and salinities greater than 3 psu. These growth rates correspond to a carbon demand that ranged from 0.1-1.0 m g C·ml^-1·hr^-1.

At the present time, we interpret that there is a very active 'microbial loop' community of bacteria, protozoa and other secondary producers adapted to the Columbia River ETM. However, since a significant proportion of the actively growing bacteria are attached to particles in the size ranges that could be grazed on by ciliates and copepods, the bacteria could be a major source of nutrients for all size classes of secondary producers.

Cordell, J. R., C. A. Simenstad, and C. A. Morgan. 1992. Establishment of the Asian calanoid copepod Pseudodiaptomus inopinus in the Columbia River estuary. J. Crustacean Biol. 12:260-269.

Five species of introduced planktonic copepods from Asia, including two species of the genus Pseudodiaptomus, have been reported from coastal bays of California. Recently we have found a third species of Pseudodiaptomus endemic to the Indo-Pacific, P. inopinus, to be established in the Columbia River estuary.

Comprehensive studies of both pelagic and epibenthic zooplankton in the Columbia River estuary in 1979 and 1980 did not record P. inopinus (see Simenstad and Cordell, 1985); Jones et al., 1990). In September 1990, we sampled zooplankton at three depths across several tide cycles. These samples contained high densities and all life-history stages of P. inopinus. It now appears that this species has become established and is prominent in the estuarine turbidity maxima (ETM) region. Pseudodiaptomus inopinus cooccurs in the ETM region with extensive populations of the calanoid copepod Eurytemora affinis and the harpacticoid copepod Scottolana canadensis. Preliminary results suggest that the distribution and abundance of these three species vary in response to the physical processes of the ETM. These differences may reduce potential competitive interactions between the preexisting and exotic species. Introduction was probably via ballast water from ships arriving from Asia. However, the establishment of P. inopinus may have been encouraged by a synergism between increased ballast water dumping, decrease in maximum flows due to regulation of the river, and the attenuation of extreme low temperatures in the estuary during the last decade.

Cordell, J. R., C. A. Simenstad, and C. A. Morgan. 1992. The Asian calanoid copepod Pseudodiaptomus inopinus in Pacific Northwest rivers--biology of an invasive zooplankter. N.W. Environ. J. 8:164-165.

(no abstract)

Flinchem, E. P. and D. A. Jay. 2000. An introduction to wavelet transform tidal analysis methods. In Press. Coast. Estuar. Shelf Sci.

Continuous wavelet transforms (CWTs) provide a new approach to understanding nu-merous tidal phenomena that deviate markedly from an
assumed statistical stationarity or exact periodicity inherent in traditional tidal methods. Use of wavelets allows determination of the degree of non-stationarity present in time series, such as estuarine and shelf currents, usually treated as stationary. Wavelets also provide a consistent analysis of tidal and non-tidal variance, a feature often essential for dynamical analyses of non-stationary tides. We summarize basic notions of the wavelet transform, also known as a perfect reconstruction filter bank or a multire-solution analysis, contrast them with those of harmonic analysis and Fourier transforms, con-struct a continuous wavelet transform basis with a scale selection especially adapted to tidal problems, describe possibilities for analysis of scalar and vector quantities, define a criterion for knowledge of independence of process between adjoining scales, and illustrate use of wavelet tools with several examples. In contrast to the nearly periodic barotropic tide typical of coastal stations, this paper analyzes processes that are in part tidally driven but non-stationary, e.g., baroclinic tidal currents, river tides, continental shelf internal tides, and some kinds of biological activity in the coastal ocean. In all cases, wavelet analysis provides a consistent, linear analysis of tidal and non-tidal variance and reveals features that harmonic analysis or a Fourier transform approach could not elucidate.

Crump, B.C. E.V. Armbrust, and J.A. Baross. 1999. Phylogenetic analysis of particle-attached and free-living bacterial communities in the Columbia River, estuary, and adjacent coastal ocean. Applied and Environmental Microbiology 65(7): 3192-3204.

The Columbia River Estuary is a dynamic system in which estuarine turbidity maxima trap and extend the residence time of particles and particle-attached bacteria over those of the water and free-living bacteria. Particle-attached bacteria dominate bacterial activity in the estuary and are an important part of the estuarine food web. PCR-amplified 16S rRNA genes from particle-attached and free-living bacteria in the Columbia River, its estuary, and the adjacent coastal ocean were cloned, and 239 particle sequences were determined. A wide diversity was observed at the species level within at least six different bacterial phyla, including most subphyla of the class Proteobacteria. In the estuary, most particle-attached bacterial clones (75%) were related to members of the genus Cytophaga or of the a, g or d subclass of the class Proteobacteria. These same clones, however, were rare in or absent from either the particle-attached or the free-living bacterial communities of the river and the coastal ocean. In contrast, about half (48%) of the free-living estuarine bacterial clones were similar to clones from the river or the coastal ocean. These free-living bacteria were related to groups of cosmopolitan freshwwater bacteria (b-proteobacteria, gram-positive bacteria, and Verrucomicrobium spp.), and groups of marine organisms (gram-positive bacteria and a-proteobacteria [SAR11 and Rhodobacter spp.]). These results suggest that rapidly growing particle-attached bacteria develop into a uniquely adapted estuarine community and that free-living estuarine bacteria are similar to members of the river and the coastal ocean microbial communities. The high degree of diversity in the estuary is the result of the mixing of bacterial communities from the river, estuary and coastal ocean.

Crump, B., and J. A. Baross. 1996. Particle-attached bacteria and heterotrophic plankton associated with the Columbia River estuarine turbidity maxima. Mar. Ecol. Prog. Ser.138: 265-273.

A significant fraction of the particulate organic matter entering the Columbia River estuary is metabolized or altered before it is carried out to the ocean. Estuarine turbidity maxima are part of the particle-trapping mechanism that lengthens the residence time of river-borne organic material in an estuary, increasing that material's availability to estuarine bacteria and the estuarine food web. In May and June, 1992, water samples in and around the Columbia River estuarine turbidity maxima were analyzed to determine rates of bacterial carbon production, and bacterial and putative bacterivore abundances. Salinity, turbidity, and tidal data were used to interpret bacterial activity patterns, and to identify distributions of bacterial predators. Bacterial carbon production, based on rate of ³H-thymidine uptake, correlated with turbidity, and varied from 0.3 to 0.56 m g l^-1 hr^-1. Sharp peaks in bacterial production were found in the estuarine turbidity maxima, and were determined to be due to particle-attached bacteria by measuring bacterial production directly on particles. Variation in bacterial production outside the estuarine turbidity maxima seemed to be related to tidal cycle, supporting hypotheses on particle cycling in the estuary. Nanoflagellates, small "oligotrich" ciliates and rotifers were the most numerous grazers in the estuary. Correlation analysis between grazer and bacterial abundances and production suggested that rotifers and small ciliates may be the primary consumers of bacteria outside the estuarine turbidity maxima. Rotifers were enhanced in the estuarine turbidity maxima and therefore may be key consumers of particle-attached bacteria.

Cudaback, C. N. and D. A. Jay. Revised. 1996. Formation of the Columbia River plume: hydraulic control in action? In D. G. Aubrey (ed.), Buoyany Effects on Coastal Dynamics, Am. Geophys. Union, Coastal Est. Sci. Monogr. pp.139-154.

The Columbia River plume is a large dynamic feature with a significant effect on circulation along the Northeast Pacific shelf and slope and on local cross-shelf transport of nutrients, pollutants and sediments. Essential characteristics of this plume are determined at its origin in the constricted river entrance, where the meeting of salt and fresh water creates a hightly stratified flow and large vertical shear. The channel is con-stricted laterally by stone jetties in two locations and vertically by a shallow sill. The effect of these constrictions has been examined by analysis of velocity and density data from the Columbia River entrance channel. Along-channel sections and time-series data have been compared with the results of a hydraulic control model incorporating a sinusoidally varying barotropic current (Helfrich, 1995), and show qualitative similarities with the theoretical results. However, significant differences between theoretical and experimental results are due to a complicated time dependence of barotropic forcing, frictional effects and lateral variations in along-channel currents. Barotropic current strength varies with river flow and unequal semidiurnal tides, causing alternate two-layer and unidirectional flows. Turbulent mass transfer between the layers forms a thick interfacial layer, and bottom friction forces peak flood currents into the interfacial layer. Finally lateral variations in current speed cause lateral differences in time-series measurements of internal Froude number. Results of hydraulic control theory can account for some but not all velocity and density observations in the Columbia River entrance channel.

Fain et al. 2000. Particulate Dynamics in a River Estuary.  Submitted to Estuaries.

We have investigated seasonal and tidal-monthly suspended particulate matter (SPM) dynamics in the Columbia River Estuary from May to December 1997 using acoustic backscatter (ABS) and velocity data from four long-term Acoustic Doppler Profiler (ADP) moorings in or near the estuarine turbidity maximum (ETM). The ABS was calibrated and converted to total SPM using vessel data obtained during three seasonal cruises, employing optical backscatter (OBS) as an intermediary. Four characteristic settling velocity (W_s) classes were defined from Owen Tube samples collected during the cruises. An inverse analysis, in the form of a non-negative least squares minimization, was used to determine the contribution of the four W_s-classes to each total SPM profile. The outputs from the inverse analyses were 6-8 month time-series of W_s-specific SPM concentration and transport profiles at each mooring. The profiles extended from the free surface to 2-3 m from the bed, with 0.25-0.50 m resolution. These time series, along with sediment character and composition data, were used to investigate SPM dynamics. Three non-dimensional parameters were defined to investigate how river flow and tidal forcing affect particle trapping: a Rouse number P (balance between vertical mixing and settling), a trapping efficiency E (ratio of maximum SPM concentration in the estuary to fluvial source concentration), and an advection number A (ratio of height of maximum SPM concentration to friction velocity). Results suggest that the most effective particle trapping (maximum values of E) occurs during neap tides with low to moderate river flows. The location of the ETM and the maximal trapping migrated seasonally in a manner consistent with the increase in salinity intrusion length after the spring freshet. Maximal A values occurred during highly stratified neap tides. These results could not have been achieved using either vessel or moored instrumentation alone. Thus, velocity and ABS data from Doppler profiles can, when used in combination with appropriate vessel calibration data, provide an unprecedented level of information regarding estuarine sediment dynamics over a broad range of time scales.

Jay, D.A., P. Orton, D.J. Kay, A. Fain and A.M. Baptista. 1999. Acoustic Determination of Sediment Concentrations, Settling Velocities, Horizontal Transports and Vertical Fluxes in Estuaries. Proceedings of the IEEE Sixth World Conference on Current Measurement. 258-263.

Acoustic Doppler Velocimeter (ADV) and Acoustic Doppler Profiler (ADP) backscatters were calibrated and used to estimate suspended particulate matter (SPM) concentrations, settling velocities, horizontal transports, vertical turbulent fluxes, and parameters related to estuarine particle trapping. Calibration of ADV acoustic backscatter (ABS) was carried out by comparison to material sampled by pump and via an Owen tube, using an optical backscatter (OBS) sensor as an intermediary. The ABS-SPM relationship was variable in time, even within a single tidal cycle. Temporal changer were, however, interpretable in terms of observed SPM characteristics. Estimated upward vertical turbulent SPM fluxes followed a temporal pattern similar to downward settling fluxes, but were much larger. SPM samples for calibration of ABS from a moored ADP (deployment duration ~ 7 mo) were available only during three cruises; an OBS was again used as an intermediary for calibration. As before, variations over time in the ABS-SPM relationship were found, and biofouling altered the ADP backscatter response during part of the deployment. Both profile and continuous wavelet transform time-series analyses were used to test the validity and physical meaning of the SPM data. Because of time variability in the ABS-SPM relationship, parameters were sought that were at least partially independent of this relationship; i.e., those involving ratios of concentrations within a single inferred SPM profile. Despite calibration difficulties, inferred SPM trapping efficiencies (ratio of maximum estuarine SPM to fluvial source SPM), settling velocities and horizontal transports contained valuable information concerning tidal to seasonal SPM processes. These techniques should be widely applicable in systems with SPM concentrations within the dynamic ranges of the ADV and ADP.

Jay, D. A. 1994. Residence time, box models and shear fluxes in tidal channel flows. Pp. 3-12 In K. Dyer and R. Orth (ed.), Changing Particle Fluxes in Estuaries: Implications from Science to Management, ECSA22ERF Symposium, Olsen & Olsen Press, Friedensborg.

Box models and residence time calculations are widely used because they summarize a large amount of information concerning scalar transport and retention in estuaries in a few intuitively understandable numbers. Thus, it is important to understand the physical basis in mass conservation principles of these calculations. The purposes of this paper are: to summarize the physics of horizontal transport of scalars (including particulates and those that are non-conservative) in tidal channel flows, to emphasize the fundamental dynamical relationship between horizontal flux calculations on the one hand and residence times and box models on the other, and to suggest some simple rules for the applicability of these and other vertically integrated models. Horizontal scalar transport in two-dimensional (in the along-channel an vertical directions) systems is related to correlations of velocity shear and scalar stratification at mean and tidal frequencies. These correlations are scalar-specific. Thus, residence times and horizontal exchange coefficients are properties of particular scalars in a reservoir rather than of the reservoir itself. It cannot be assumed that all scalars will behave in the same manner as salt. Because shear transports can be counter-gradient when expressed in terms of time and vertically averaged variables (implying a negative horizontal diffusivity), it is probably better in most circumstances to explicitly include horizontal flux terms in box models than to use a diffusivity formulation.

Jay, D. A., and E. P. Flinchem. 1996. Interaction of fluctuating river flow with a barotrophic tide: a demonstration of wavelet tidal analysis methods. J. Geophys. Res.102:5705-5720.

Wavelet transforms provide a valuable new tool for analysis of tidal processes that deviate markedly from an assumption of exact periodicity inherent in traditional harmonic analysis. A wavelet basis adapted to nonstationary tidal problems is constructed and employed to analyze the modulation of the external tide in a river by variations in streamflow. Interaction of a surface tide with river flow is the best available demonstration of the continuous wavelet transform (CWT) methods developed. It is the simplest and perhaps the only nonstationary tidal process for which both sufficient data and dynamical understanding exist to allow detailed comparisons between CWT analyses and analytical predictions of the response of tides to nontidal forcing. Variations at upriver locations of low-frequency elevation (river stage ZR) and three tidal species are deduced from cross-sectionally integrated equations. For landward propagation in a channel of constant cross section with quadratic friction, the log of the amplitude of the diurnal (D1), semidiurnal (D2) and quarterdiurnal (D4) elevations should vary at far upriver locations with the square root of the river flow (QR), and river stage (ZR) should depend on the square of river flow. Convergent geometry and species-species frictional interactions modify these predictions somewhat. CWT analyses show that the predicted amplitude behavior for the tidal species is approximately correct. Best results are obtained for the dominant, dynamically simplest processes (ZR and D2). In the past, further progress in understanding river tides has been limited by a lack of data analysis tools. Data analysis tools are now clearly better than the available analytical solutions.

Jay, D. A. and J. D. Musiak. 1995. Internal Tidal Asymmetry in Channel Flows: Origins and Consequences. Pp. 219-258 In C. Pattiaratchi (ed.), Mixing Processes in Estuaries and Coastal Seas, Amer. Geophy. Union, Coastal Estuar. Sci. Monogr.

Non-linear, shallow-water processes transfer energy from the surface tide to higher and lower frequencies to create a barotrophic tidal spectrum. Production of higher harmonics or overtides at multitudes of the dominant tidal frequency is termed "barotrophic tidal asymmetry" because it distorts the free surface and causes flood- or ebb-dominant currents, depending on the relative phases of the tide and its overtides. Tidal distortion of the density field drives an analogous transfer of energy to residual and overtide internal modes; i.e., an "internal tidal asymmetry." The actual mechanism responsible for the internal non-linearity is an asymmetry in bed stress that has two primary aspects: (1) differential tidal advection (tidal straining) of a strong horizontal density gradient brings tidal variations in stratification and thus in vertical turbulent mass and momentum exchange; and, (2) baroclinic and barotrophic pressure gradients act in concert on flood but in opposition on ebb. Observations from the Columbia River estuary show that internal tidal asymmetry can cause an entire spectrum of overtide currents. The most prominent of the internal overtides is M₄ (the first overtide in M₂), with maximum current amplitudes of 0.25-0.4 m s^-1 in an environment where the amplitude of the dominant (M₂) current constituent is 0 (1-1.4 m s^-1). These internal M₄ currents are three to 10 times larger than the currents associated with the barotrophic M₄ tide (amplitude 0.01 to 0.03 m), and they exhibit 180° phase changes in the vertical, another factor that distinguishes them from barotrophic tidal currents. Furthermore, the residual surface-to-bed velocity difference of ~ m s^-1 is too large to be accounted for by linear processes (gravitational circulation and mean outflow), and model calculations show that internal tidal asymmetry is also the predominant mechanism causing vertical shear in the residual flow. A literature survey has identified 20 estuaries in addition to the Columbia that exhibit signs of internal tidal asymmetry, and it is likely a common feature of narrow systems with strong tides and river flow. Finally, observations suggest that overtide and residual currents generated by internal tidal asymmetry play a dominant role in maintaining the salt and sediment balances in narrow, stratified estuaries.

Jay, D. A. and J. D. Musiak. 1994. Particle trapping in estuarine tidal flows. J. Geophys. Res. 99: 20,446-461.

Particle trapping in estuarine turbidity maxima (ETM) is caused primarily by convergent mean and/or tidal fluxes of sediment. The result is an approximately bell-shaped along-channel distribution of vertically integrated, tidal cycle mean suspended sediment concentration. Observations from the Columbia River estuary suggest that (1) strong two-layer or internal along-channel residual and overtide flows are generated by time-varying stratification and (2) correlations between the near-bed velocity and the suspended sediment fields at these frequencies are important in landward transport of sediment. A new spatially and temporally integrated form of the sediment conservation equation has been derived to analyze this trapping process. Time changes in tidally averaged sediment concentration between two estuarine cross sections can be shown to be related to the divergence of the seaward, river flow transport; the divergence of velocity shear-sediment stratification correlations for the mean flow and each tidal constituent; and net erosion or deposition at the bed. Vertically integrated variables other than seaward river transport are absent from this integrated balance. Analysis of sediment fluxes using this balance supports the idea that internal residual and overtide circulations are primarily responsible for the landward sediment transport on the seaward side of ETM found near the upstream limits of salinity intrusion. The balance also shows that attempts to represent fluxes causing trapping of sediment in an ETM as a product of a time-mean, vertically integrated, along-channel gradient and a diffusivity inevitably lead to the appearance of countergradient transport and thus a negative diffusivity on the seaward side of the ETM. This result occurs because the trapping process is inherently non-linear and at least two-dimensional and because a one-dimensional representation is physically unrealistic.

Jay, D. A. and others (LMER Scalar Transport Working Group). Recent developments in estuarine scalar flux estimation. Estuaries 20: 262-280.

The purpose of this contribution is to review recent developments in calcula-tion of estuarine scalar fluxes, to suggest avenues for future improvement and to place the idea of flux calculation in a broader physical and biogeochemical context. A scalar flux through an estuarine cross-section is the product of normal velocity and scalar con-centration, sectionally integrated and tidally averaged. These may vary on interannual, seasonal, tidal monthly and event time scales. Formulation of scalar fluxes in terms of an integral scalar conservation expression shows that they may be determined either through "direct" means (measurement of velocity and concentration) or by "indirect" inference (from changes in scalar inventory and source/ sink terms). Direct determina-tion of net flux at a cross-section has a long and generally discouraging history in estuarine oceanography. It has proven difficult to extract statistically significant net (tidally averaged) fluxes from much larger flood and ebb transports, and the best mathematical representation of flux mechanisms is unclear. Observations further suggest that both lateral and vertical variations in scalar transport through estuarine cross-sections are large, while estuarine circulation theory has focused on two-dimensional analyses that treat either vertical or lateral variations but not both. Indirect estimates of net fluxes by determination of the other relevant terms in an integral scalar conservation balance may be the best means of determining scalar import/export in systems with residence times long relative to periods of tidal monthly fluctuations. But this method offers little insight into the interaction of circulation modes and scalar fluxes, little help in verifying predic-tive models and may also be difficult to apply in some circumstances. Thus, the need to understand, measure and predict anthropogenic influences on transport of carbon, nu-trients, suspended matter, trace metals and other substances across the land-margin brings a renewed urgency to the issue of how to best carry out estuarine scalar flux de-termination. An interdisciplinary experiment is suggested to test present understanding, available instruments and numerical models.

Jay, D. A. and C. A. Simenstad. 1996. Downstream Effects of Water Withdrawal in a Small, High-Gradient Basin: Erosion and Deposition on the Skokomish River Delta. Estuaries 19: 501-517.

The purpose of this paper is to analyze downstream effects of freshwater flow diversion from a small, active-continental-margin river basin. The Skokomish River delta is a tributary estuary to Hood Canal in Washington State that receives drainage from the southeastern side of the Olympic Mountains. Its drainage basin is steep, and rainfall is high. Approximately 40% of the annual average runoff of the entire system has been diverted from the North Fork Skokomish River for power production since completion of two dams in 1930; this water does not pass through the lower river or over the delta. Extensive logging has occurred in the remainder of the basin. Comparison of pre-diversion (1885) and post-diversion (1972) bathymetric surveys shows that deposition (about 0.03 to 0.022 m yr-1) has occurred on the inner delta and erosion (up to 0.033 m yr-1) on the outer delta. This steepening of the delta surface has apparently been caused by a loss of sediment transport capacity in the lower river and estuary combined with an increased sediment supply due to logging. Although the total area of unvegetated tidal flats has decreased by only about 6%, there has been a more than 40% loss of highly productive low intertidal surface area. A conservative estimate of loss of eelgrass (Zostera marina) beds is 18%; a reduction in the size of mesohaline mixing zone has also occurred. These habitat losses are similar to those observed elsewhere in the world in larger river basins that have suffered water withdrawals of the same magnitude, but their impacts cannot either be evaluated or understood casually through consideration of simple measures like changes in total estuarine deltaic area. Evaluation of estuarine effects of anthropogenic modification must, therefore, include consideration of both changes in habitat function and in the physical processes. These must be evaluated within the totality of the riverbasin-estuary system that causes these changes. In this case, sediment transport constitutes the critical link between fluvial alterations and the remote downstream, estuarine consequences thereof.

Jay, D.A. and E.P. Flinchem. 1999. A comparison of methods for analysis of tidal records containing multi-scale non-tidal background energy. Continental Shelf Research.

Many tidal phenomena, including river tides, estuarine currents, and shelf and fjord internal tides, are non-stationary. These tidal processes are poorly understood and largely beyond the realm of practical prediction, even when the perturbing phenomenon causing the non-stationary behavior is itself fairly predictable. Our inadequate understanding of these phenomena has been exacerbated by an absence of a self-consistent procedure for analysis of the entire spectrum of non-stationary motions, tidal and non-tidal. The most difficult methodological situation occurs when the disturbing non-tidal signal is stronger than the tidal one and has an event-like character. Such sharp changes in forcing are multi-scale, containing energy at tidal frequencies, as well as at larger scales. Because of the distinct response of different parts of the tidal spectrum to non-tidal perturbations, multi-scale forcing events have the potential to provide a valuable new generation of tests of tidal dynamics models. This paper compares three techniques for the analysis of such signals, using artificial tidal records of known frequency content to ascertain which method most accurately represents evolving frequency content. The methods are: a) conventional least-squares, short-term harmonic analysis (STHA); b) a modified STHA (or mSTHA) that uses a smoothing window and augments the frequency structure of the analysis wave; and c) linear convolution analysis in the form of continuous wavelet transforms (CWT). Results show that STHA and mSTHA lack a definable frequency response and mix energy between tidal and non-tidal signals in an unpredictable manner. STHA also effectively imposes a boxcar window on the data, the effects of which can be severe for short records. In general, STHA and mSTHA results using short windows will be least reliable in the circumstances where short windows are most desired -- when the signal is highly non-stationary. There is, moreover, no simple way to set a minimum window length for STHA/mSTHA that will produce stable results, except to make the window too long to capture the fluctuating variance being sought. In contrast, CWT correctly recovers both tidal and non-tidal variance, as long as resolution limits set by the Heisenberg uncertainty principle are respected. Whatever method is chosen, use of window lengths less than ~4-6 days requires great care, unless diurnal and subtidal energy are insignificant.

Jay, D. A., W. R. Geyer and D. R. Montgomery. 1999. An ecological perspective on estuarine classification. In press. Estuarine Science, A Synthetic Approach to Research and Practice, J. E. Hobbie (ed.), Island Press.

Estuaries are more diverse than any other marine environment. Scientists and managers presently face a range of issues associated with
global alteration of estuarine systems without a thorough understanding of how such changes affect either estuaries or the larger coastal and
global oceans to which they are connected. To allow study of representative systems characteristic of the spectrum of estuarine types, there is an urgent need to develop an estuarine classification system that connects physical proc-esses (circulation and sediment transport) to biogeochemistry and ecology. Traditional classification systems focused almost exclusively on the influences of tidal forcing and buoyancy on circulation in narrow estuaries. We argue that a predictive, process-based geomorphic classification system should include other types of physical forcing; i.e., the effects of wind, wind waves and sea ice. Fluid mechanics and geomorphology can be connected through description of forcing variables for sediment movement in estuaries in terms of hydrodynamic parameters. One important parameter is residence time (TR), which strongly influences biogeochemical and ecological processes vital to the lower levels of the estuarine food chain. We argue, moreover, that not just mean TR, but its temporal variability and spatial heterogeneity should be considered. Finally, we suggest a hypothesis concerning estuarine particle retention processes that, if correct, should allow prediction of residence time and trapping efficiency for at least some estuarine types within the next few years.

Kay, D. J., D. A. Jay, and J. D. Musiak. Salt transport through an estuarine cross-section calculated from moving vessel ADCP and CTD data. In D. G. Aubrey (ed.), Buoyany Effects in Estuaries, Am. Geophys. Union, Coastal Est. Sci. Monogr. (submitted)

Definition of the mechanisms for scalar transport is important in understanding of biological, chemical, and geological processes in estuaries. The purposes of this study are to 1) understand the meaning of two distinct salt balance expressions based on a tidally varying estuarine volume and a non-varying mean volume, 2) test various simplifications to the salt balance expression based on wave theory, and 3) test the method of using a 1.2 Mhz acoustic Doppler current profiler (ADCP) and a conductivity-temperature-depth profiles (CTD) for studying the important transport processes. Velocity measurements made with a 1.2 Mhz ADCP and salinity measurements made with a CTD profiler at a cross-section in the Columbia River estuary were used to examine the flux of salt in the estuary. Two forms of the salt balance are examined. The 'full balance' results from a) direct integration of the temporal correlations of velocity and salinity over the time varying cross-sectional area, and b) averaging of this product over a tidal cycle. The 'mean balance' results from spatial integration of the mean salt conservation equation over the mean cross-sectional area. This removes the necessity of calculating numerous terms involving correlations that are, at least for micro and mesotidal estuaries, in sum small. This expression represents the change in the time-mean salinity in the time-mean upstream estuarine volume. Possible simplifications to these salt balances based on results from wave theory are also examined and tested. Decomposition of the salt flux expression into lateral and vertical "shear terms" was employed with both balances to examine the effects of lateral and vertical variations in the velocity and salinity fields of the net salt flux. Vertical shear terms were found to be significant while lateral shear terms were small. The salt flux was dominated by a balance between landward tidal advection of the tidal salinity field and the seaward mean advection of the mean salinity field. Results suggest that ADCP technology, especially the higher resolution broad-band ADCP, can be used in combination with scalar measurements to make high quality flux measurements in estuaries.

Keil R.G., E. Tsamakis, C. B. Fuh, J. C. Giddings and J. I. Hedges J.I. 1994. Mineralogical and textural controls on the organic composition of coastal marine sediments: hydrodynamic separations using SPLITT-fractionation. Geochim. Cosmochim. Acta 58: 879-893.

SPLITT-fractionation was used to sort hydrodynamically surficial sediments from the Washington margin, USA, into sand- (>250, 63-250 m m), silt- (35-63, 17-35, 8-17, 3-8 m m), and clay-sized (1-3, 0.5-1, <0.5 m m) fractions. Two types of organic matter were discerned: distinct organic debris and organic matter associated with inorganic sedimentary particles. Discrete organic detritus was a minor component (<10%) of the organic carbon in all the sediment fractions except in sand-sized fractions (>64 m m) from the shelf, where terrestrially-derived vascular plant debris accounted for >95% of the organic matter. Organic matter that could not be separated from the inorganic sediment accounted for >90% of the total organic matter in most fractions, and loadings of organic carbon increased as the surface area of the inorganic particles increased. For the sand- and silt-sized fractions, the observed relationship of 0.8 1 ± 0.04 mg C m^-2 (r = 0.97) was consistent with the hypothesis that a monolayer of organic matter is sorbed to the mineral surfaces. Clay-sized particles had lower organic loadings (0.37 ± 0.07 mg C m^-2 , r = 0.85), probably because the large interlamellar area of expandable clays was inaccessible to most organic molecules. After correcting for interlamellar area, clay-sized particles have the same organic carbon:surface area relationship as sands and silts (0.78 ± 0.08 mg C m^-2 , r = 0.96). While total organic matter concentrations were largely controlled by sediment surface area, the elemental composition of the organic matter appears to be partially affected by sediment mineralogy, and shifted from carbon-rich material (atomic C:N ~ 18.0) in larger, quartz-dominated fractions to N-rich material (C:N~9) in the smaller, clay mineral-dominated fractions. Nitrogen enrichment relative to carbon (atomic N:C) was correlated with the amount of total clay (r = 0.80), smectite (r = 0.79), and the iron content (r = 0.74) of the sediments. Measurements of stable carbon isotopes indicate that clay-sized particles preferentially transport sorbed soil organic matter to deep sites while sand-sized fractions contain terrestrial plant debris (discrete and sediment-associated) that is transported along the shelf. The concentrations of terrestrially-derived organic matter in organic matter from shelf and slope sediments was estimated to be 60-85% and 10-15%, respectively. The quantity, bulk chemical composition, and distribution of marine and terrestrially derived organic matter to Washington margin sediments are influenced by (1) the surface area of the sediment minerals, (2) the mineralogical composition of the sedimentary matrix, and (3) the natural hydrodynamic sorting of sedimentary minerals along the continental margin. The major fraction of organic material in these sediments is sorbed to mineral grains. Interactions between organic material and mineral surfaces strongly influence the distribution and elemental composition of the organic material present in marine sediments.

LTER Coordinating Committee (Boynton, W., J. T. Hollibaugh, D. Jay, M. Kemp, J. Kremer, C. Simenstad, S. V. Smith, and I. Valiela). 1992. Understanding changes in coastal environments: the Land Margin Ecosystems Research Program. EOS 73: 481-485.

(no abstract)

Morgan, C. A. 1993. Sink or swim? Copepod population maintenance in the Columbia River estuarine turbidity maxima region. M.S. thesis, Univ. Washington, Seattle, WA. 85 pp.

Extensive sampling during three different hydrological seasons between 1990-1992 in the Columbia River estuary of Oregon and Washington focused on zooplankton populations in the estuarine turbidity maxima (ETM). The ETM is a region of particle trapping that occurs near the upstream extent of salinity intrusion and is characterized by high turbidity and high concentrations of inorganic and organic particles, microbes, and zooplankton. The sampling design involved measuring zooplankton composition and densities in relation to ETM circulation by collecting water samples from near-bottom to the surface with concurrent measurements of physical characteristics (salinity, temperature, turbidity, particle characterization, and current direction/velocity).

Copepods were numerically dominant, comprising 88 to 95% of the total zooplankton assemblage. In addition, the epibenthic calanoid copepod Eurytemora affinis and the harpacticoid copepod Coullana canadensis were found to predominate in the ETM with densities of £ 1.6 x 10⁵ m^-3 and 5.1 x 10⁶ m^-3, respectively. C. canadensis was most abundant during the summer and comprised 21 to 59% of the total copepods. E. affinis was most abundant during the spring and comprised 17 to 58% of the total copepods. These estuarine copepods were rarely found at upriver and downriver sampling stations, suggesting that their populations are effectively maintained in the estuary. The concurrent measurement of physical variables and zooplankton samples permitted direct comparisons between copepod densities and physical characteristics.

Statistical analysis revealed a high correlation of near-bottom C. canadensis densities with the ETM occurring at the beginning of the flood tide and near the end of the ebb tide. Analysis of variance by tide stage and depth indicated that densities of C. canadensis were higher during all tide stages at near-bottom depths and at all depths during flood tides. Harmonic analysis of the time series revealed that peak near-bottom densities of this species were occurring at tidal frequencies of 1/23.9 (K₁) and 1/12.4 (M₂) hours. All of these results suggest that C. canadensis is maintained in the estuary through the same near-bottom circulation features that are trapping and concentrating particles in the ETM region.

Conversely, the more motile E. affinis reached peak densities only once during the tidal cycle, near the ebb ETM. E. affinis near-bottom densities were highly correlated with negative (ebb) velocities. The analysis of variance by tide stage and depth revealed that during the ebb tide densities were higher near-bottom, while during the flood and transition tide stages, densities were more distributed into the upper water column. Harmonic analysis of the time series for this species indicated that near-bottom densities had a periodicity that corresponded to the M₂ tidal component.

Both species appear to maintain viable populations in this food rich region through behavioral adaptations to circulation. The patterns in density distribution seen in C. canadensis and E. affinis imply differences in population position in the water column. This may be due to a combination of life history characteristics and tidal migration rhythms. These findings suggest that these two copepod species are able to maintain populations in this dynamic system through slightly different, but highly effective mechanisms.

Morgan, S. R. 1992. Seasonal and tidal influence of the estuarine turbidity maximum on primary biomass and production in the Columbia River estuary. M.S. thesis, Ore. State Univ., Corvallis, OR. 87 pp.

The Columbia River estuary was sampled during high (May-June), intermediate (July), and low (September-October) river flow seasons to further define the role of the ETM with respect to its effect on primary biomass and production, and to discover how this effect changes in space and time.

Strong ETMs were determined to be largely near-bottom phenomenon resulting in decreased values of % chlorophyll a (Chl a) and potential production per unit of chlorophyll a. Moderate ETMs also resulted in decreased values of % Chl a but increases were seen in values of overall concentration of pigment and potential productivity per unit of chlorophyll a, indicating the moderate ETMs retained some photosynthetically active cells and pigments.

Seasonal differences were noted as values of the Chl a per unit of particulate organic carbon (Chl a/POC) and % Chl a were highest during May-June, suggesting a spring bloom pattern with the onset of longer, sunnier days. Potential production, however, was highest during mid-summer (intermediate river flow) coinciding with the emission of maximum solar radiation. Increases in salinity had a deleterious effect on values of % Chl a during the low and intermediate river flow seasons, but had no effect on these values during the high-flow season.

Spring- and neap-tide temporal patterns indicate periods of maximum salinity gradients were commensurate with near-uniform particle properties throughout the water column, while periods of weakened salinity gradient were commensurate with a distinction between bottom and surface particle properties. These results may be attributed to various physical properties of the water column other than changes in salinity alone.

Prahl F. G. and Coble P. G. 1994. Input and behavior of dissolved organic carbon in the Columbia River Estuary. Pp. 451-457 In K. Dyer and R. Orth (ed.), Changing Particle Fluxes in Estuaries: Implications from Science to Management, ECSA22ERF Symposium, Olsen & Olsen Press, Friedensborg.

Dissolved organic carbon (DOC) was monitored at three water depths in various time series at a fixed location in the main channel of the Columbia River Estuary. The series represented periods of low (October 1990) and intermediate (July 1991) river flow. Most DOC data for each series plot along a conservative mixing line for river water (» 1.8-2.3 mg C^.l^-1 at 0 psu salinity) with sea water (» 0.75-1 mg C^.l^-1 at 32 psu salinity). DOC elevated ³ 2-fold above the river concentration for a particular time series occurred occasionally during flooding and ebbing periods characterized by enhanced estuarine turbidity. Unlike the case for turbidity, however, the highest DOC did not always occur in bottom waters implying that DOC does not have an immediate link with suspended particulate concentration. The episodic DOC pulses are attributed to tidal drainage of water from biologically productive peripheral bays adjoining the estuary.

An effort was initiated to better characterize the nature of the DOC pulses. DOC and its spectroscopic properties were monitored in waters ebbing at surface and bottom depths from a peripheral bay near the river mouth. Three distinct maxima were identified in a three-dimensional map of fluorescence intensity versus excitation-emission wavelength. The intensity for each maximum diminished with salinity, implying the dominant source of fluorescence is dissolved organic matter in river water. Water samples characterized by DOC levels violating simple conservative mixing of river water with sea water did not display corresponding high fluorescence intensity. The DOC pulses injected tidally to the main estuary from adjacent peripheral bays are comprised of non-fluorescent forms of otherwise yet chemically uncharacterized organic material.

Prahl, F. G., J. R. Ertel, M. A. Goni, M. A. Sparrow and B. Eversmeyer. 1994. Terrestrial organic carbon contributions to sediments on the Washington margin. Geochim. Cosmochim. Acta 58: 3035-3048.

Elemental and stable carbon isotopic compositions and biomarker concentrations were determined in sediments from the Columbia River basin and the Washington margin in order to evaluate geochemical approaches for quantifying terrestrial organic matter in marine sediments. The biomarkers include: an homologous series of long-chain n-alkanes derived from the surface waxes of higher plants; phenolic and hydroxyalkanoic compounds produced by CuO oxidation of two major vascular plant biopolymers, lignin and cutin. All marine sediments, including samples collected from the most remote sites in Cascadia Basin, showed organic geochemical evidence for the presence of terrestrial organic carbon. Using endmember values for the various biomarkers determined empirically by two independent means, we estimate that the terrestrial contribution to the Washington margin is ~60% for shelf sediments, ~30% for slope sediments, and decreases further to £ 15% in basin sediments. Results from the same geochemical measurements made with depth in gravity core 6705-7 from Cascadia Seachannel suggest that our approach to assess terrestrial organic carbon contributions to contemporary deposits on the Washington margin can be applied to the study of sediments depositing in this region since the last glacial period.

Prahl F. G., Hayes J. M. and Xie T. -M. 1992. Diploptene, an indicator of soil organic matter in Washington coastal sediments. Limnol. Oceanogr. 37: 1290-1300.

The pentacyclic triterpene 17b (H),21b (H)-hop-22(29)-ene (diploptene) occurs in sediments throughout the Columbia River drainage basin and off the southern coast of Washington state in concentrations comparable to long-chain plantwax n-alkanes. The same relationship is evident for diploptene and long-chain n-alkanes in soils from the Willamette Valley. Microorganisms indigenous to soils and soil erosion are indicated as the biological source and physical process, respectively, for diploptene in coastal sediments. Similarity between the stable carbon isotopic composition (d ¹³C_PDB) of diploptene isolated from soil in the Willamette Valley (-31.2± 0.3‰) and from sediments deposited throughout the Washington coastal environment (-31.2± 0.5‰) supports this argument. Values for d for diploptene in river sediments are variable and 8-17‰ lighter, indicating that an additional biological source such a methane-oxidizing bacterial makes a significant contribution to the diploptene record in river sediments. Selective biodegradation resulting from a difference in the physicochemical association within eroded particles can explain the absence of the more ¹³C-depleted form of diploptene in Washington coastal sediments, but this mechanism remains unproven.

Reed, D. J. and J. Donovan. 1994. The character and composition of the Columbia River estuarine turbidity maximum. Pp. 445-450 In K. Dyer and R. Orth (ed.), Changing Particle Fluxes in Estuaries: Implications from Science to Management, ECSA22ERF Symposium, Olsen & Olsen Press, Friedensborg.

Eularian sampling of suspended sediment concentration and salinity in the Columbia River Estuary during both low and intermediate river flow conditions has allowed detailed description of the character of estuarine turbidity maxima (ETM). Our sampling and CTD profiling have confirmed that during moderate river flow conditions (July 1991) ETM were more pronounced on spring- and neap-tides compared to low flow conditions (September/October 1990). The position of the ETM in the estuary is associated with the upstream limit of salinity intrusion, confirming our theoretical understanding of ETM phenomena in the Columbia. Typically, there is a difference in character between ETM occurring on flood- and ebb-tides. In addition to differences in magnitude of ETM, sampling of suspended sediments indicates that significant particle aggregation is associated with the passage of ETM.

Simenstad, C. A., C. A. Morgan, J. R. Cordell, and J. A. Baross. 1994b. Flux, passive retention, and active residence of zooplankton in Columbia River estuarine turbidity maxima. Pp. 473-482 In K. Dyer and R. Orth (ed.), Changing Particle Fluxes in Estuaries: Implications from Science to Management, ECSA22ERF Symposium, Olsen & Olsen Press, Friedensborg.

Particle trapping processes in estuarine turbidity maxima (ETM) in the Columbia River Estuary, Oregon-Washington, USA, may significantly affect both the community and population structure and production of estuarine zooplankton. One of the fundamental questions being addressed in the Columbia River Estuary Turbidity Maxima (CRETM) studies is how near-bottom (i.e. epibenthic) zooplankton associated with the ETM are able to maintain reproductively viable populations through evolutionary or behavioral adaptations to ETM circulation. Estuarine populations are up to an order of magnitude more abundant (£ » 1 x 10^6.m^-3) than either fluvial (£ » 1 x 10^4.m^-3) or oceanic zooplankters (£ » 3 x 10^6.m^-3) transported into the estuary, and are estimated to account for >75% of the primary consumption by metazoans in the estuary. The estuarine zooplankton assemblage is overwhelmingly dominated by the harpacticoid copepod Coullana (formerly Scottolana) canadensis and Pseudobradya sp., the calanoid copepod Eurytemora affinis, and the recently introduced exotic calanoid, Pseudodiaptomus inopinus. Results from the initial (1990; low river flow) CRETM cruise imply a relationship between the physical processes of ETM trapping and zooplankton densities. Densities of the less-motile harpacticoid copepod Coullana canadensis are highly correlated with the concentration of suspended sediment above the bed, most likely because these copepods are (passively) resuspended with the fine particles that rest on the surface of the bed. More motile Eurytemora affinis reach their highest densities at the end of ebb ETM events but are considerably (one fourth) less dense just prior or early in the flood ETM. Pseudodiaptomus inopinus appeared predominantly during slack after ebb-tide. Thus, both passive entrapment and active behavior (e.g. vertical migration in the case of Eurytemora affinis) may allow these consumers to maintain their population centers in this region of high food particle quantity and quality.

Consistently high densities of reproducing copepod populations associated with ETM imply a correspondingly high food particle field within ETM to maintain production. Pilot copepod grazing rate experiments, coupled with ¹⁴C-leucine measurements of heterotrophic activity, initially infer relatively low grazing rates. However, consideration of bacteria/protozoan carbon respired by the copepods and the effect of copepod grazing to suppress microbe activity implies a tighter linkage between the ETM microbial loop and zooplankton. These early CRETM-LMER studies indicate that the populations structure and production of estuarine zooplankton may be due principally to complex physical, geochemical and microbial processes within estuarine turbidity maxima. These processes likely promote both passive and active mechanisms of estuarine retention by the zooplankters and high production and availability of their food resources.

Simenstad, C. A., D. A. Jay and C. R. Sherwood. 1992. Impacts of watershed management on land-margin ecosystems: The Columbia River estuary as a case study. Pp. 266-306 In R. J. Naiman (ed.), New Perspective in Watershed Management, Springer-Verlag, New York. 543 pp.

Patterns of land use development that have arisen in the Columbia River basin over the last century are occurring in large river basins worldwide. The consequent modifications of river flow, physical properties, and discharge of sediment and other constituents appear as cumulative effects in land-margin ecosystems, where estuarine processes intercept, entrap, and transform both riverine and oceanic material. These watershed changes alter both the input to the estuary and the fundamental estuarine processes. Our studies of the Columbia River estuary indicate that these human alterations to watersheds can affect the interaction between river flow and the tides, modifying circulation patterns important to estuarine food webs. Mean river flow has decreased approximately 20% since the 19th century; probably 6 to 8% is due to irrigation withdrawal, the remaining 12 to 14% to climate variability. Regulation of river flow has reduced spring freshet flows to about 50% of the natural level, and has increased fall minimum flows by 10 to 50%. The reduction in spring freshets has lowered modern-day sediment input to the estuary to ~25% of that recorded in the latter part of the 19th century. Navigation structures and filling and diking in the lower river and estuary have decreased the tidal prism by about 15%, increasing sediment residence time and shoaling, simplified the channel network, and concentrated flow in the navigation channel. In addition to sediment, temperature, organic matter, nutrients, pollutants, and biotic influxes at the estuarine interface, changes in the river discharge regime have modified estuarine stratification, mixing, and residence time. Such modifications have profound effects on sensitive estuarine processes such as those that occur in the estuarine turbidity maximum (ETM), where trapping of suspended material occurs, organic matter is incorporated in a dynamic microbial loop, and important food web linkages to higher level consumers occur. A landscape perspective on the impacts of watershed alterations needs to be included in our emerging regional and global approaches to ecosystem management if land-margin impacts are to be predicted and mediated.

Simenstad, C. A., Reed, D. A. Jay, J. A. Baross, F. G. Prahl and L. F. Small. 1994a. Land-margin ecosystem research in the Columbia River estuary: investigations of the couplings between physical and ecological processes within estuarine turbidity maxima. Pp. 437-444 In K. Dyer and R. Orth (ed.), Changing Particle Fluxes in Estuaries: Implications from Science to Management, ECSA22ERF Symposium, Olsen & Olsen Press, Friedensborg.

Extensive development of the Columbia River basin over the past century and the consequent alteration of its river flow and transport of material are symptomatic of large watersheds worldwide. Such changes are ultimately manifested in cumulative effects at the land margin, where estuarine circulation processes are strongly affected by changes in river flow and inorganic and organic matter are intercepted, trapped and often transformed. Such geochemical and biological transformations are concentrated in the physically-controlled structure of an estuarine turbidity maxima (ETM), where linkages to the estuary's food web are accentuated through active microbial loops and primary consumer metazoan populations. Our land-margin ecosystem research in the Columbia River is investigating physical, chemical, and biological processes occurring in ETM-controlled food webs of river-dominated estuaries and seeks to determine the nature and quantity of organic matter and biota exported to the nearshore ocean. This paper introduces our conceptual and technical approaches to the study of ETM processes, emphasizing the strong interdisciplinary integration of physical and ecological disciplines that is regard to understand such complex systems.

Small, L. F., and S. R. Morgan. 1994. Phytoplankton attributes in the turbidity maximum of the Columbia River Estuary, USA. Pp. 465-472 In K. Dyer and R. Orth (ed.), Changing Particle Fluxes in Estuaries: Implications from Science to Management, ECSA22ERF Symposium, Olsen & Olsen Press, Friedensborg.

During spring-tides, strong and very strong Estuarine Turbidity Maxima (ETMs) in the Columbia River Estuary were associated with decreased chlorophyll-a/POC (Particulate Organic Carbon) ratios, and with decreased percentages of chlorophyll-a (% Chl-a) in total chlorophyllous-type pigment (chlorophyll-a plus phaeopigments), in the estuarine water column. Strong ETMs (100-200 mg ^. l^-1 of dry suspended particles) had little effect on the DCMU-enhanced fluorescence index during spring-tides, but the few very strong ETMS (>200 mg ^. l^-1) probably did. Moderate (50-100 mg ^. l^-1) and weak (<50 mg ^. l^-1) ETMs during spring-tides had little effect on Chl-a/POC, % Chl-a and the DCMU index, even near the estuary bottom. Salinity largely controlled changes in the three indices during spring-tides, with surface and near-bottom values converging on the flood-tide, diverging on the ebb. Differences among seasons were mainly a matter of scale, not pattern. During neap-tides ETMs were usually weak, but during one very strong neap-ETM the Chl-a/POC, % Chl-a and DCMU indices were not depressed, suggesting resuspension of photosynthetically-active, just-settled phytoplankton. As during spring-tides, salinity mainly controlled top-bottom and flood-ebb changes in the three indices during neaps.

Suspended particulate matter (SPM) was about 5% particulate organic carbon (POC) and about 0.63% particulate organic nitrogen (PON), whether SPM concentrations were high (in ETMs) or low (non-ETM). POC/PON averaged 9.3 by atoms, and a single POC-to-PON relationship applied, with high correlation, through all seasons, depths and ETM strengths. % Chl-a was always low in strong ETMs and in high-salinity water, indicating a large phaeopigment component therein, but it varied substantially by season (lowest values in autumn, highest in spring). The DCMU-enhanced fluorescence index was a function of % Chl-a, with the relationship in spring different from a combined summer-autumn relationship. The DCMU index apparently was related to ¹⁴C productivity through the effect of % Chl-a, but when this effect was removed the relationship disappeared.

Baptista, A. M., M. Wilken, P. Pearson, C. McCandlish, D. Jay, B. Beck, S. Das, J. Hunt, P. Barrett. Towards a Nowcast-Forecast System for the Columbia River Estuary. Proceedings of the 5th International Conference on Estuarine and Coastal Modeling, Alexandria, VA (in press)

We envision that detailed nowcast-forecast systems (NFS) will become essential supporting tools for management, engineering, and research in coastal and estuarine systems. To both assess and push current limits of NFS, we have since mid-1996 been developing CORIE, a demonstration nowcast-forecast system for the Columbia River estuary. The Columbia River extends over 7 US states and one Canadian province, and its discharge is the second largest among U.S. rivers. The estuary has a very complex density-driven circulation, occurring over a shallow natural topography carved by two deep channels of markedly different characteristics and uses. The Columbia system is the focus of several environmental and management controversies that may measurably reshape the culture and economy of the US Pacific Northwest states.

includes three main components: a real-time data acquisition system, a set of highly resolved numerical models of circulation and transport, and a data management system. Our real-time data acquisition system includes a base moored instrumentation network for tides, currents, water and air temperature, salinity, turbidity, and wind, consisting currently of 11 multi-sensor stations. Spread-spectrum radio technology is used for remote acquisition. Episodic vessel-based cruises complement the information from the base network.

unstructured grid numerical models are being used to progressively enhance the description of circulation and transport in the estuary. Early focus has been on regional tidal propagation over the complex topography of the estuary, but will progressively shift towards the vertical structure of the circulation (short term) and to residual transport and to water quality and ecosystem dynamics (long-term).

Data management is a critical part of CORIE, responsible to ensure that "data packets" flow reliably into a central database, from where they are subject, with as large a degree of automation as possible, to multi-level stages of processing and visualization. These stages include "fast" quality control, process-oriented scientific processing, assimilation into numerical models, World Wide Web access to multiple technical and non-technical audiences, etc.  

The present paper will describe the various components of CORIE, both conceptually and relative to their current implementation stage.  

This research is partially funded by the Office of Naval Research and the National Science Foundation. Thanks are due to the Marine Science Program and Integrated Technologies Program of the Clatsop Community College for extensive vessel, staging facilities, and machine shop support of the field operations. Thanks are also due to the REINAS Project for providing key supporting data acquisition and management software, and to the U.S. Coast Guard, Oregon Department and Transportation, U.S. Army Corps of Engineers, and Community Information Center for various logistical supports.

Fortunato, A. B., and A. M. Baptista. 1996. Evaluation of horizontal gradients in sigma-coordinate shallow water model. Atmosphere-Ocean 34: 489-514.

horizontal gradients in three-dimensional shallow water models that use bottom-following sigma coordinate can lead to large errors near steep bathymetry. A technique that has been proposed to minimize this problem involves computing horizontal gradients in cartesian coordinates, while treating all other terms in a sigma-coordinate framework. We study this technique through both truncation error analysis and numerical experimentation, and compare it to the direct application of sigma coordinates. While the cartesian coordinate method can be more attractive when horizontal gradients are zero, the sigma coordinate method can be more accurate in other physically relevant situations. Also, the cartesian coordinate method introduces significant numerical diffusion of variable sign near the bottom (where physical diffusion is particularly small), thus potentially leading to instabilities. Overall, we consider the sigma coordinates to be the best approach.

Fortunato, A. B., and A. M. Baptista. 1996. Vertical discretization in tidal flow simulations. Internat. J. Numerical Methods Fluids 22:815-834.

We propose an empirical law for vertical nodal placement in tidal simulations that depends on a single parameter, p. The influence of dimensionless numbers on the optimal value of p is analysed through a series of numerical experiments for an individual vertical, and a single value of p is found to be adequate for all cases. The proposed law can lead to gains in accuracy of over two orders of magnitude relative to a uniform grid, and compares favorably with non-uniform grids previously used in the literature. In practical applications, the most effective use of this law may require each vertical to have a different number of nodes. Criteria for the distribution of the total number of nodes among different verticals are also proposed, based on the concept of equalizing errors across the domain. The usefulness of the overall approach is demonstrated through a two-dimensional laterally-averaged application to a synthetic estuary.

Crump, B.C., J.A. Baross, and C.A. Simenstad. 1997. Dominance of particle-attached bacteria in the Columbia River estuary, USA. Aquat. Microb. Ecol. 14:7-18.

Particle-attached bacteria are a central component of the detrital food web of many turbid coastal and estuarine ecosystems. The Columbia River estuary, at the terminus of a 660,000 km² watershed in northwestern North America, is a turbid, partially-mixed system that has a flushing time of 1-3 days. Several large, well-defined estuarine turbidity maxima (ETM) extend the residence time of both mineral and organic particles transported through the estuary. Water samples collected in the North Channel of the estuary every 2 h for 148 h (6 tidal cycles) in May, 1995 were analyzed to determine the concentration and production of particle-attached and free-living bacteria, extracellular enzyme activity, turbidity, salinity, and particulate organic carbon concentration (POC). The concentration of particle-attached bacteria, defined as those caught by a 3 mm filter, averaged 1.02x106 (sd=1.00x106) cells ml^-1, and correlated with turbidity and POC, and thus to some extent with the tidal cycle that maintains the ETM. The concentration of free-living bacteria was more constant, averaging 1.25x106 (sd=0.4x106) cells ml^-1. Particle-attached bacterial carbon production, calculated from the rate of incorporation of ³H-thymidine, averaged 1.61 (sd=1.10) mg l^-1 h^-1, accounted for 90% (sd=9%) of total bacterial carbon production, and correlated with turbidity and POC. Extracellular enzyme activity, measured as the rate of hydrolysis of fluorescently-labeled compounds, increased with turbidity and was predominantly associated with particles. Particle-attached bacteria probably account for most of the bacterial degradation of particulate organic material in the estuary, and the transfer of that material into the detrital food web. The hydrodynamics of estuary contribute to the dominance of particle-attached bacteria by extending the residence time of particles in the ETM, and by quickly flushing free-living cells through the estuary, perhaps preventing the development of an estuarine population of free-living bacteria.

Morgan, C. A., J. R. Cordell, and C. A. Simenstad. 1997. Sink or swim? Copepod population maintenance in the Columbia River estuarine turbidity maxima region. Mar. Biol. 129:309-317.

Maintenance of estuarine zooplankton populations in large river-dominated estuaries with short residence times has been an intriguing subject of investigation. During three different hydrologic seasons, autumn 1990, summer 1991, and spring 1992, we intensively sampled zooplankton populations in the estuarine turbidity maximum (ETM) region of the Columbia River estuary of Oregon and Washington, USA. One of the principle objectives was to investigate retention mechanisms of the predominant zooplankton species, the harpacticoid copepod Coullana canadensis and the epibenthic calanoid copepod Eurytemora affinis. In the ETM, C. canadensis densities mirrored those of turbidity gradients and were almost always greater at the river bed, while E. affinis densities were greater higher in the water column during the ebb. Cross-correlationa nd time-series analysis determined that C. canadensis densities were positively correlated with turbidity and that most of the variability was explained by the lunisolar diurnal (K1)and principle lunar (M2) tidal components occurring once every 23.93 h and once every 12.42 h, respectively. This indicates that C. canadensis populations are most probably maintained in the estuary throught the same near-bottom circulation features that trap and concentrate particles in the ETM> In contrast, densities of the more motile species E. affinis were highly correlated with negative velocities, or ebb tide, and most of the variaibility in population densities could be explained by the principle lunar tidal component; therefore, we hypothesize that this species is probably vertically migrating on a tidal cycle into different flow layers to avoid population losses out of the estuaries.

Cordell, J. R., and S. M. Morrison. 1996. The invasive Asian copepod Pseudodiaptomus inopinus in Oregon, Washington, and British Columbia estuaries. Estuaries 19: 629-638.

At least six species of Asian copepods have been recently introduced to the west coast of North America. Among them is Pseudodiaptomus inopinus, which became established and abundant in the Columbia River estuary between 1980 and 1990. Subsequently, the tidal regions of 18 smaller rivers in the Pacific Northwest were sampled, using near-bottom pumps and vertical plankton net hauls. These samples indicate that P. inopinus has not only invaded at least seven other estuaries in the region, but that it is sometimes the dominant zooplankter in these systems. P. inopinus occurred in estuaries of both large and small rivers and in rivers with and without international shipping. Two factors may be important in the establishment of this copepod: temperature and extent of salinity intrusion. In our samples, average autumn temperature of rivers with established P. inopinus populations was 19.3 C, whereas those without P. inopinus had an average temperature of 12.4 C. rivers with P. inopinus had salinity intrusions zones of more than 1 km length abd those without P. inopinus usually had intrusion zones of less than 1 km.

Prahl, F.G., L.F. Small, and B. Eversmeyer. in press. Biogeochemical characterization of suspended particulate matter in the Columbia River estuary. Mar. Ecol. Prog. Ser.

In order to understand what controls the composition of suspended particulate material (SPM) in estuarine turbidity maxima (ETM), a set of SPM samples collected in the Columbia River and estuary (northwestern USA) during 3 seasons (fall 1990, summer 1991, spring 1992) was analyzed for detrital mineral (Min), total organic matter [OM, as 2 x particulate organic carbon (POC)], biogenic silica (BSi), chlorophyll a, d¹³C, and lignin. In most samples, Min, OM, and BSi collectively accounted for 100% of total SPM mass, although their relative importance changed seasonally. The ETM was a trap for organic matter during all 3 seasons, which can explain the intense microbial activity and microcrustacean grazing observed previously. The organic matter was particularly enriched in chlorophyll a in late spring to early summer. The source of this seasonal enrichment was mainly riverine phytoplankton. The organic matter contribution to ETM from the ocean was minor compared to the river, but apparently not negligible. Despite large seasonal variations in chlorophyll content, the d¹³C of POC concentrated in ETM remained nearly constant between -26 and -25.5 ‰. Vascular plant debris, as depicted by lignin phenol content, always comprised a minor fraction of the organic matter in ETM, although ETM had higher lignin levels than the OM of surrounding waters. Intertidal mudflats are if not an additional source of organic matter at least an important site for transforming riverine organic matter that is ultimately concentrated in ETM.

Prahl, F. G., L. F. Small, B. A. Sullivan, J. Cordell, C. A. Simenstad, B. C. Crump and J. A. Baross. 1998. Biogeochemical gradients in the lower Columbia River. Hydrobiologia 361:37-52.

Water, suspended particulate materials (SPM), and biota were sampled between June 14 and 22, 1992 at forty-five mid-channel sites along a downstream gradient in the lower 350 km of the Columbia River drainage, at four mid-channel sites in the lower 27 km of the Willamette drainage and at the mouths of nine smaller tributaries to the Columbia. Water samples were analyzed for nutrient (ammonium, nitrate, phosphate, silicate), dissolved organic carbon DOC) and SPM concentration, bacterial cell density and activity, and zooplankton composition and density. The SPM samples were analyzed for particulate organic carbon (POC), plant pigment (chlorophyll and phaeopigment) and major metal (Al, Mn, Ti, V) content as well as stable isotopic (d¹³C) composition of the POC. Willamette waters displayed significantly higher nutrient and DOC concentrations than those in the mainstem Columbia or any of the smaller tributaries. Elevated nutrient and DOC concentrations are attributed to runoff from the extensive agricultural lands found throughout the Willamette Valley. Regardless of collection site, total Al content of all riverborne particles was high (5.8±0.5% by weight), indicating total SPM mass was predominantly (~70%) detrital mineral. Nonetheless, the majority of riverborne organic matter was not allochthonous but rather derived from healthy phytoplankton as indicated by high chlorophyll a to POC (Chl:POC) values. Chlorophyll a concentration increased by almost 100% downstream in the mainstem Columbia between Bonneville Dam and the estuary. This apparent increase in phytoplankton biomass was not accompanied by a parallel decrease in any nutrient concentration probably because non-point source additions occurred all along the drainage and compensated for nutrient loss due to phytoplankton growth. Despite nutrient concentrations near eutrophic levels, phytoplankton biomass in the Willamette was significantly lower than that in the mainstem Columbia. This particular contrast between the Willamette and the mainstem Columbia is likely due to light limitation imposed on the phytoplankton by specific differences in the mixing dynamics of the two flow regimes. POC in Willamette waters displayed a 50% reduced chlorophyll content and 2-2.5‰ ¹³C-depletion relative to that present in waters from the mainstem Columbia. These compositional dissimilarities may simply reflect physiological differences between the diatom communities that comprised the bulk of phytoplankton in these two systems at the time of sampling. Alternatively, they may be caused by greater contribution of POC from non-phytoplankton sources in the Willamette. An argument is advanced suggesting that methanotrophy has contributed up to 5% of the POC that was measured in the Willamette River at the time of our study.

Oliveira, A., and A. M. Baptista. 1997. Diagnostic modeling of residence times in estuaries. Wat. Resources Res. 33:1935-1946.

The variability of estuarine residence times is elucidated through accurate, diagnostic numerical tracking of a large number of particles, complemented with statistical analysis. Residence times are shown to have strong spatial and temporal variability, which is accentuated by exchanges between the estuary and the coastal ocean due to chaotic stirring at the mouth. The concept of a single residence time per estuary, while convenient from both ecological and engineering viewpoints, is therefore shown to be an oversimplification. Maps of residence times and cumulative histograms are examined as alternatives. The former are attractive only for once-through tracers, while the latter appear useful over a broader range of tracer characteristics.

Cudaback, C. N., 1998. The effect of vertical mixing on along-channel transport in a layered flow. Ph.D. dissertation, University of Washington, Seattle, WA

The Columbia River has a large, biologically productive estuary whose ecosystem depends on the balance of salt and fresh water. Outflow from the river also forms a vast buoyant plume which affects circulation for hundreds of miles along the coast. Both the estuarine salt balance and the initial state of the plume are determined by flow through the narrow entrance channel. I have made a three-part study of the effects of interfacial turbulence and bottom friction on along-channel transport through the Columbia River entrance channel.

My observations in the Columbia River entrance channel show that both interfacial mixing and bottom friction significantly affect circulation. The pycnocline is thinned by lateral advection on flood and thickened by vertical mixing on ebb and . On late flood, the pycnocline is close to the surface and quite thin; on late ebb, its center is below mid-depth and it fills 3/4 of the water column. Bottom friction retards the near-bottom currents, so early flood currents are strongest at mid-depth, and peak flood currents are strongest at the surface. At peak ebb and peak flood, salinity transport is strongest at mid-depth.

A two-layer time-dependent model [Helfrich, 1995] simulates along-channel currents and layer thicknesses. By assuming a near-critical bulk Richardson number, I estimated the pycnocline thickness from the two-layer model results. Bottom friction raises the pycnocline and causes tidal variations in vertical shear, which drive the changes in pycnocline thickness. This model replicates the observed pycnocline quite well, but cannot simulate mid-depth currents.

I created a new three-layer time-dependent model, in which the middle layer represents the pycnocline. Mixing of salt and fresh water creates water of intermediate density, which is modeled as entrainment from the top and bottom layers into the middle layer. This model simulates along-channel circulation at all stages of the tide, including the mid-depth maximum at early flood. It also simulates the vertical distribution and tidal average of salinity transport. For the best fit to observations, the three-layer model requires significantly more bottom friction than the two-layer model; this is consistent with the formulation of the bottom roughness coefficient.