X2 Workshop Notes

sponsored a day-long workshop on X2. Held at the Contra Costa Water District (CCWD) building in Concord, the workshop was attended by approximately 100 people from the IEP and related agencies, consulting firms, and stakeholders

Observing larval transport processes affecting population connectivity : progress and challenges

Author Posting. © Oceanography Society, 2007. This article is posted here by permission of Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 20, 3 (2007): 40-53.Population connectivity is inherently bio-physical: it is determined by physical transport and dispersion, as well as biological processes such as timing of spawning, larval behavior, and mortality. Knowledge of connectivity is essential for understanding ecosystem responses to changing environmental conditions. It establishes the spatial scales over which a population is connected, and in turn the primary spatial scale of population interactions and ecosystem dynamics. Concepts in population connectivity were initially developed in terrestrial ecology, where dispersal may occur at different life stages. In the simplest form, a one-dimensional dispersal curve describes the distribution of settlers away from a source region as a function of distance. As this spatial distribution varies in time, the “dispersal kernel” defines a spatial probability density function of settlers aggregated over time (see, e.g., Okubo and Levin, 2002). This dispersal kernel may be three dimensional, but is often reduced to two dimensions (e.g., animals on a plain) or one dimension (e.g., animals living along the land-water interface).GG received support from the Director of Research at WHOI. SGM is grateful to NSF Ocean Sciences for their support through grants OCE0425312, OCE 0452800, and OCE 0622967. JLL thanks NSF Ocean Sciences for support through grants OCE-9907884, OCE-0326110, and OCE-0528575 and the State of California for support through the Coastal Ocean Current Mapping Program (State Coastal Conservancy)—a component of CeNCOOS, the Central and Northern California Ocean Observing System

Coupled effects of vertical mixing and benthic grazing on phytoplankton populations in shallow, turbid estuaries

Coastal ocean waters tend to have very different patterns of phytoplankton biomass variability from the open ocean, and the connections between physical variability and phytoplankton bloom dynamics are less well established for these shallow systems. Predictions of biological responses to physical variability in these environments is inherently difficult because the recurrent seasonal patterns of mixing are complicated by aperiodic fluctuations in river discharge and the high-frequency components of tidal variability. We might expect, then, less predictable and more complex bloom dynamics in these shallow coastal systems compared with the open ocean. Given this complex and dynamic physical environment, can we develop a quantitative framework to define the physical regimes necessary for bloom inception, and can we identify the important mechanisms of physical-biological coupling that lead to the initiation and termination of blooms in estuaries and shallow coastal waters? Numerical modeling provides one approach to address these questions. Here we present results of simulation experiments with a refined version of Cloern\u27s (1991) model in which mixing processes are treated more realistically to reflect the dynamic nature of turbulence generation in estuaries. We investigated several simple models for the turbulent mixing coefficient. We found that the addition of diurnal tidal variation to Cloern\u27s model greatly reduces biomass growth indicating that variations of mixing on the time scale of hours are crucial. Furthermore, we found that for conditions representative of South San Francisco Bay, numerical simulations only allowed for bloom development when the water column was stratified and when minimal mixing was prescribed in the upper layer. Stratification, however, itself is not sufficient to ensure that a bloom will develop: minimal wind stirring is a further prerequisite to bloom development in shallow turbid estuaries with abundant populations of benthic suspension feeders

Connecting wind-driven upwelling and offshore stratification to nearshore internal bores and oxygen variability

This study utilizes field observations in southern Monterey Bay, CA, to examine how regional-scale upwelling and changing offshore (shelf) conditions influence nearshore internal bores. We show that the low-frequency wind forcing (e.g., upwelling/relaxation time scales) modifies the offshore stratification and thermocline depth. This in turn alters the strength and structure of observed internal bores in the near-shore. An internal bore strength index is defined using the high-pass filtered potential energy density anomaly in the nearshore. During weak upwelling favorable conditions and wind relaxations, the offshore thermocline deepens. In this case, both the amplitude of the offshore internal tide and the strength of the nearshore internal bores increase. In contrast, during strong upwelling conditions, the offshore thermocline shoals toward the surface, resulting in a decrease in the offshore internal tide amplitude. As a result, cold water accumulates in the nearshore (nearshore pooling), and the internal bore strength index decreases. Empirical orthogonal functions are utilized to support the claim that the bore events contribute to the majority of the variance in cross-shelf exchange and transport in the nearshore. Observed individual bores can drive shock-like drops in dissolved oxygen (DO) with rapid onset times, while extended upwelling periods with reduced bore activity produce longer duration, low DO events

Does the Sverdrup critical depth model explain bloom dynamics in estuaries?

In this paper we use numerical models of coupled biological-hydrodynamic processes to search for general principles of bloom regulation in estuarine waters. We address three questions: What are the dynamics of stratification in coastal systems as influenced by variable freshwater input and tidal stirring? How does phytoplankton growth respond to these dynamics? Can the classical Sverdrup Critical Depth Model (SCDM) be used to predict the timing of bloom events in shallow coastal domains such as estuaries? We present results of simulation experiments which assume that vertical transport and net phytoplankton growth rates are horizontally homogeneous. In the present approach the temporally and spatially varying turbulent diffusivities for various stratification scenarios are calculated using a hydrodynamic code that includes the Mellor-Yamada 2.5 turbulence closure model. These diffusivities are then used in a time- and depth-dependent advection-diffusion equation, incorporating sources and sinks, for the phytoplankton biomass. Our modeling results show that, whereas persistent stratification greatly increases the probability of a bloom, semidiurnal periodic stratification does not increase the likelihood of a phytoplankton bloom over that of a constantly unstratified water column. Thus, for phytoplankton blooms, the physical regime of periodic stratification is closer to complete mixing than to persistent stratification. Furthermore, the details of persistent stratification are important: surface layer depth, thickness of the pycnocline, vertical density difference, and tidal current speed all weigh heavily in producing conditions which promote the onset of phytoplankton blooms. Our model results for shallow tidal systems do not conform to the classical concepts of stratification and blooms in deep pelagic systems. First, earlier studies (Riley, 1942, for example) suggest a monotonic increase in surface layer production as the surface layer shallows. Our model results suggest, however, a nonmonotonic relationship between phytoplankton population growth and surface layer depth, which results from a balance between several \u27\u27competing\u27\u27 processes, including the interaction of sinking with turbulent mixing and average net growth occurring within the surface layer. Second, we show that the traditional SCDM must be refined for application to energetic shallow systems or for systems in which surface layer mixing is not strong enough to counteract the sinking loss of phytoplankton. This need for refinement arises because of the leakage of phytoplankton from the surface layer by turbulent diffusion and sinking, processes not considered in the classical SCDM. Our model shows that, even for low sinking rates and small turbulent diffusivities, a significant percentage of the phytoplankton biomass produced in the surface layer can be lost by these processes

Nearshore internal bores and turbulent mixing in southern Monterey Bay

We observed transient stratification and mixing events associated with nearshore internal bores in southern Monterey Bay using an array of instruments with high spatial and temporal resolution. The arrival of the bores is characterized by surging masses of dense (cold) water that tend to stratify the water column. The bore is followed by a gradual drop in the temperature throughout the water column over several hours (defined here as the bore period) until a sharp warm-front relaxation, followed by high frequency temperature fluctuations, returns the column back to nearly its original state (defined here as the mixing period). Mixing periods revealed increased temperature variance at high frequencies (ω \u3e ), as well as a greater percentage of events where dynamic instabilities may be present (Ri\u3c 0.25), suggesting active mixing of the stratified water column. Turbulent dissipation rates in the stratified interior during the mixing period, estimated using the technique of isopycnal slope spectra, revealed mean values the same order of magnitude as near-bed bottom-generated turbulence. Observations indicate that local shear-produced turbulent kinetic energy by the warm front relaxations dominates mixing in the stratified interior. The non-canonical nature of these bore and relaxation events is also investigated with a numerical model, and the dynamics are shown to depend on the internal Iribarren number. Our results suggest that nearshore internal bores interacting with local bathymetry dramatically alter local dynamics and mixing in the nearshore with important ecological implications

Transport Between Palau and the Eastern Coral Triangle: Larval Connectivity or Near Misses

Physical connectivity by transport of larvae between different habitats plays a fundamental role in marine population dynamics and is often assessed using circulation models assuming that computed large-scale connectivity describes the actual connectivity. This paper presents observations of drifters released into the Philippine Sea offshore of the western lagoon of Palau that were tracked as were first carried by the Mindanao Eddy toward Mindanao and other parts of the Celebes and Sulu Seas, where they were removed from the water. While following expected transport pathways for this region, our drifters remained at least several kilometers offshore of the various islands they passed by, suggesting that larvae moving similarly would have been too far offshore to recruit to nearshore reefs. Thus, estimates of connectivity made using large-scale models must be taken as upper bounds to connectivity across ocean basins. Plain Language Summary A major consideration in marine conservation is the connectivity between different habitats or regions of the ocean, that is, the degree to which populations in those places are linked to each through the movement of eggs, larvae, eggs, or adults between them. One area of particular interest is the Western Pacific and its connections with the Coral Triangle. In this study, we deployed a set of satellite-tracked surface drifters offshore of the west side of Palau that moved in the local ocean circulation toward and then past Mindanao, in some cases completing multiple circuits around the Philippine Sea. These drifter tracks demonstrate an important aspect of connectivity in the ocean: In the absence of strong and directed swimming, local flow processes on ocean shelves that can act to transport materials toward shore may control the real extent of connectivity across ocean basins. Thus, the degree of connectivity inferred from large-scale flows (either modeled or observed remotely) is an upper bound on the actual degree of connectivity. Importantly, these results demonstrate that marine conservation efforts for coral reefs based on ocean-basin scale connectivity need to include consideration of flow behavior at ocean boundaries where reefs are located

Morphologically driven sedimentation patterns on a coral reef

Sedimentation on coral reefs has often been analyzed with a focus on coral ecology and limited description of sedimentation dynamics, or with a focus on hydrodynamics and reef platform development, without connections to the benthic assemblages. Research on interactions between reef morphology, hydrodynamics, and sedimentation, and how they shape coral populations deserves further attention. Here we investigate the role of the spur and groove (SAG) morphology in driving water flow and sediment movement. Our study was undertaken in SAGs characterized by a well-developed coral community, and results were compared to an adjacent low coral cover area without SAGs. Mean flow and wave velocities were measured in SAG and non-SAG areas and coupled with the analysis of sediment size and sorting to calculate thresholds for sediment movement. Wave orbital velocities were an important driver of sediment suspension. The suspension threshold due to mean flow was reached 80-100% of the time on spurs. In grooves, it was reached 60% of the time during off-shore flows, but only 33% of the time during on-shore flows, suggesting that net seaward sediment transport occurs within grooves. The steeper bathymetry in grooves (8% slope) relative to the non-SAG area (4%) could have also promoted gravity-driven seaward sediment and rubble accumulation, favoring substrate stabilization at the SAG slope base. The hydrodynamics and sedimentation patterns within the SAGs likely offer a more favorable condition for coral growth. In the non-SAG area, different flow patterns are expected to promote the formation of sediment deposits, preventing a similar benthic colonization

Similarity scaling of turbulence spectra and cospectra in a shallow tidal flow

Author Posting. © American Geophysical Union, 2011. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 116 (2011): C10019, doi:10.1029/2011JC007144.Measured turbulence power spectra, cospectra, and ogive curves from a shallow tidal flow were scaled using Monin-Obukhov similarity theory to test the applicability to a generic tidal flow of universal curves found from a uniform, neutrally stable atmospheric boundary layer (ABL). While curves from individual 10 min data bursts deviate significantly from similarity theory, averages over large numbers of sufficiently energetic bursts follow the general shape. However, there are several differences: (1) Variance in the measured curves was shifted toward higher frequencies, (2) at low frequencies, velocity spectra were significantly more energetic than theory while cospectra were weaker, and (3) spectral ratios of momentum flux normalized by turbulent kinetic energy (TKE) indicate decreased fluxes and/or elevated TKE levels. Several features of the turbulence structure may explain these differences. First, turbulent dissipation exceeded production, indicating nonequilibrium turbulence, possibly from advection of TKE. Indeed, using the production rate rather than dissipation markedly improves agreement in the inertial subrange. Second, spectral lag of the largest eddies due to inhomogeneous boundary conditions and decaying turbulence could explain spectral deviations from theory at low frequencies. Finally, since the largest eddies dominate momentum transfer, the consequence of the cospectra difference is that calculated ogive curves produced smaller total momentum fluxes compared to theory, partly because of countergradient fluxes. While ABL similarity scaling applied to marine bottom boundary layers (MBBLs) will produce curves with the general shape of the universal curves, care should be taken in determining details of turbulent energy and stress estimates, particularly in shallow and inhomogeneous MBBLs.The data were collected with support from NSF grant ECCS‐0308070 to SGM as part of the LOBO program (Ken Johnson, P.I.). The analysis presented here was supported by the Department of Defense (DoD) through the National Defense Science and Engineering Graduate Fellowship (NDSEG) Program and through ONR grant N00014‐ 10‐1‐0236 (Scientific officers: Thomas Drake, C. Linwood Vincent, and Terri Paluszkiewicz). Additional support was provided by the Stanford Graduate Fellowship (SGF)