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McDonald, K.L., 2020. Differences in the morphology of restored and invaded foredunes on the North Spit of Humboldt Bay, California, U.S.A. Journal of Coastal Research, 36(5), 973–980. Coconut Creek (Florida), ISSN 0749-0208. Invasive plants have altered wide-ranging coastal dune vegetation communities worldwide, and the effects of nonnative vegetation and invasive plant management on dune geomorphology are of interest to many coastal land managers, researchers, and coastal communities. This study compared the slopes, elevations, and profiles of invaded and restored foredunes on the North Spit of Humboldt Bay, California, using data from a high-resolution 2010 digital elevation model. Restoration of foredunes by removing invasive European beachgrass (Ammophila arenaria [L.] Link) took place over the last three decades in approximately half of the study area, and the restored areas now primarily support American dunegrass (Elymus mollis Trin.) and other native dune species. Despite recently voiced public concerns that restoration might be permanently lowering the foredune, restored and invaded areas showed no significant difference in height. However, invaded foredunes were significantly steeper with a flatter, plateau-like top, while restored areas were more gently sloping with rounded peaks. Foredune heights increased from the southern end of the study area to the north, regardless of restoration status, suggesting that other factors control foredune height. [ABSTRACT FROM AUTHOR]

A large-scale monitoring program associated with the establishment of a marine protected area network in southern California provided an opportunity to observe and document unique or rare species across the region. Scientists and students from several educational and research institutions surveyed 145 subtidal reefs, 39 intertidal reefs, and five sandy beaches from 2011–2017, a period of time where oceanographic and climatic conditions changed serially and dramatically. In conjunction with an increase in monitoring frequency and locations, dramatic shifts in oceanographic climate during this same time period likely caused shifts in tolerable habitat conditions for many nearshore species. Here we describe range extensions, both to the north and south, of 14 marine fish, invertebrate, and algae species as observed during the 2011–2012 South Coast MPA Baseline Program and subsequent monitoring efforts. [ABSTRACT FROM AUTHOR]

The stimulation and dominance of potentially harmful phytoplankton taxa at a given locale and time are determined by local environmental conditions as well as by transport to or from neighboring regions. The present study investigated the occurrence of common harmful algal bloom (HAB) taxa within the Southern California Bight, using cross-correlation functions to determine potential dependencies between HAB taxa and environmental factors, and potential links to algal transport via local hydrography and currents. A simulation study, in which Lagrangian particles were released, was used to assess travel times due to advection by prevailing ocean currents in the bight. Our results indicate that transport of some taxa may be an important mechanism for the expansion of their distributions into other regions, which was supported by mean travel times derived from our simulation study and other literature on ocean currents in the Southern California Bight. In other cases, however, phytoplankton dynamics were rather linked to local environmental conditions, including coastal upwelling events. Overall, our study shows that complex current patterns in the Southern California Bight may contribute significantly to the formation and expansion of HABs in addition to local environmental factors determining the spatiotemporal dynamics of phytoplankton blooms. [ABSTRACT FROM AUTHOR]

Montes, J.M.; Lavín, M.F., and Parés-Sierra, A.F., 2016. Seasonal heat and salt balance in the Upper Gulf of California. The salinity and heat balance, as well as the seasonal variation of the average absolute salinity (〈 SA〉) and conservative temperature (〈 Θ〉), were described by using data from 24 cruises within four domains in the Upper Gulf of California (UGC). Monthly values of SA and Θ, and surface fluxes obtained from ERA-Interim reanalysis data sets were fitted to a seasonal signal, and the horizontal fluxes of salinity and heat content were calculated by using balance equations. The UGC exports salt and heat to the Northern Gulf of California (NGC) almost all year, with an annual mean of 1.6 g/kg per year for the salinity flux and 0.16 terawatts (TW) for the heat flux. The results suggest that the net excess of evaporation (∼0.8 m/y) and heat gain by the surface (∼70 W/m2) are the main factors controlling the exchange of salinity and heat between the UGC and the NGC. To help identify the relevant dynamic factor involved in the heat and salinity balances, a high-resolution numerical model, the regional ocean modeling system (ROMS), was implemented for the region. The main feature of the UGC circulation consists of a cyclonic surface flow that extends downward as a laterally sheared flow pattern, with inflow at the Sonora coast side and outflow at the Baja California coast side. Although the cyclonic circulation pattern remains most of the year, the maximum velocities (∼0.20 m/s) are reached in June. The results indicate that the major exchange between the UGC and the NGC occurs in June and July when the net volume transport (∼0.9 Sverdrups) is dominated by the horizontal overturning transport. [ABSTRACT FROM AUTHOR]

To better understand suspended-sediment transport in a tidal slough adjacent to a large wetland restoration project, we deployed continuously measuring temperature, salinity, depth, turbidity, and velocity sensors in 2010 at a near-bottom location in Alviso Slough (Alviso, California, USA). Alviso Slough is the downstream reach of the Guadalupe River and flows into the far southern end of San Francisco Bay. River flow is influenced by the Mediterranean climate, with high flows (∼90 m s) correlated to episodic winter storms and low base flow (∼0.85 m s) during the summer. Storms and associated runoff have a large influence on sediment flux for brief periods, but the annual peak sediment concentrations in the slough, which occur in April and May, are similar to the rest of this part of the bay and are not directly related to peak discharge events. Strong spring tides promote a large upstream sediment flux as a front associated with the passage of a salt wedge during flood tide. Neap tides do not have flood-directed fronts, but a front seen sometimes during ebb tide appears to be associated with the breakdown of stratification in the slough. During neap tides, stratification likely suppresses sediment transport during weaker flood and ebb tides. The slough is flood dominant during spring tides, and ebb dominant during neap tides. Extreme events in landward (salt wedge) and bayward (rainfall events) suspended-sediment flux account for 5.0 % of the total sediment flux in the slough and only 0.55 % of the samples. The remaining 95 % of the total sediment flux is due to tidal transport, with an imbalance in the daily tidal transport producing net landward flux. Overall, net sediment transport during this study was landward indicating that sediment in the sloughs may not be flushed to the bay and are available for sedimentation in the adjacent marshes and ponds. [ABSTRACT FROM AUTHOR]

Abstract: The dispersal and dilution of urban wastewater effluents from offshore, subsurface outfalls is simulated with a comprehensive circulation model with downscaling in nested grid configurations for San Pedro and Santa Monica Bays in Southern California during Fall of 2006. The circulation is comprised of mean persistent currents, mesoscale and submesoscale eddies, and tides. Effluent volume inflow rates at Huntington Beach and Hyperion are specified, and both their present outfall locations and alternative nearshore diversion sites are assessed. The effluent tracer concentration fields are highly intermittent mainly due to eddy currents, and their probability distribution functions have long tails of high concentration. The dilution rate is controlled by submesoscale stirring and straining in tracer filaments. The dominant dispersal pattern is alongshore in both directions, approximately along isobaths, over distances of more than 10km before dilution takes over. The current outfall locations mostly keep the effluent below the surface and away from the shore, as intended, but the nearshore diversions do not. [Copyright &y& Elsevier]

Typical spring and summer conditions offshore of California consist of strong northerly low-level wind contained within the cool, well-mixed marine boundary layer (MBL) that is separated from the warm and dry free troposphere by a sharp temperature inversion. This system is often represented by two layers constrained by a lateral boundary. Aircraft measurements near Point Conception, California, on 3 June 2012 during the Precision Atmospheric MBL Experiment (PreAMBLE) captured small-scale features associated with northerly flow approaching the point with the added complexity of encountering opposing wind in the Santa Barbara Channel. An extremely sharp cloud edge extends south-southwest of Point Conception and the flight strategy consisted of a spoke pattern to map the features across the cloud edge. Lidar and in situ measurements reveal a nearly vertical jump in the MBL from 500 to 100 m close to the coast and a sharp edge at least 70 km away from the coast. In this case, it is hypothesized that it is not solely hydraulic features responsible for the jump, but the opposing flow in the Santa Barbara Channel is a major factor modifying the flow. Just southeast of Point Conception are three distinct layers: a shallow, cold layer near the surface with northwesterly winds associated with an abrupt decrease in MBL height from the north that thins eastward into the Santa Barbara Channel; a cool middle layer with easterly wind whose top slopes upward to the east; and the warm and dry free troposphere above. [ABSTRACT FROM AUTHOR]

Toxicity tests are often used in sediment assessment programs. However, the choice of methods has been largely limited to acute tests. Where sublethal methods have been used, there has been little consistency among programs in the types of the sublethal tests used. The goal of this study was to develop a method for choosing a suite of acute and sublethal tests for use in a California statewide assessment program, and to develop a set of method-specific thresholds for classifying the degree of toxicity within a multiple line of evidence framework consisting of sediment chemistry, benthic community structure, and sediment toxicity. A group of candidate methods was evaluated using feasibility and performance criteria. Toxicity thresholds were calculated based on test variability and sensitivity. As a result of the evaluation, 3 acute toxicity methods using amphipods ( Eohaustorius estuarius, Rhepoxynius abronius, and Leptocheirus plumulosus), and 2 sublethal methods using a polychaete and mussel embryos ( Neanthes arenaceodentata growth and Mytilus galloprovincialis embryo development at the sediment-water interface) were selected for recommendation. Thresholds for toxicity categories corresponding to Nontoxic, Low Toxicity, Moderate Toxicity, and High Toxicity were developed for each test method. Although these toxicity categories and thresholds provide a consistent framework for the interpretation of test results among different methods, additional research is needed to determine their effectiveness for predicting impacts to benthic communities. Integr Environ Assess Manag 2012; 8: 625-637. © 2011 SETAC [ABSTRACT FROM AUTHOR]

Integration of multiple lines of evidence (MLOE) data in a sediment quality triad assessment can be accomplished by means of numerous approaches, with most relying on some form of expert best professional judgment. Best professional judgment (BPJ) can be problematic in application to large data sets or in a regulatory setting where the assessment protocol needs to be transparent and consistently reproducible. We present a quantitative, objective framework for integrating the results of triad-based assessments and test its efficacy by applying it to 25 California sites and comparing the resulting classifications with those of 6 experts who were provided the same data. The framework is based on integrating the answers to 2 questions: 1) is there biological degradation, and 2) is chemical exposure high enough to potentially result in a biological response? The framework produced results that matched the median classifications of the experts better than did 5 of the 6 experts. Moreover, the framework was unbiased, with samples that differed from the median expert response evenly divided between those classified as more or less impacted. The framework was also evaluated by application to a set of sites from known degraded and reference areas, which the framework distinguished well. Although any framework needs to be flexible to supplemental data when they are available, the framework presented provides an objective means for using a triad-based approach in large-scale assessments for which relying on expert input for every sample is impractical. Integr Environ Assess Manag 2012; 8: 589-596. © 2010 SETAC [ABSTRACT FROM AUTHOR]

Benthic macrofauna are used extensively for environmental assessment, but the area sampled and sieve sizes used to capture animals often differ among studies. Here, we sampled 80 sites using 3 different sized sampling areas (0.1, 0.05, 0.0071 m2) and sieved those sediments through each of 2 screen sizes (0.5, 1 mm) to evaluate their effect on number of individuals, number of species, dominance, nonmetric multidimensional scaling (MDS) ordination, and benthic community condition indices that are used to assess sediment quality in California. Sample area had little effect on abundance but substantially affected numbers of species, which are not easily scaled to a standard area. Sieve size had a substantial effect on both measures, with the 1-mm screen capturing only 74% of the species and 68% of the individuals collected in the 0.5-mm screen. These differences, though, had little effect on the ability to differentiate samples along gradients in ordination space. Benthic indices generally ranked sample condition in the same order regardless of gear, although the absolute scoring of condition was affected by gear type. The largest differences in condition assessment were observed for the 0.0071-m2 gear. Benthic indices based on numbers of species were more affected than those based on relative abundance, primarily because we were unable to scale species number to a common area as we did for abundance. Integr Environ Assess Manag 2012; 8: 649-658. © 2010 SETAC [ABSTRACT FROM AUTHOR]

Submarine groundwater discharge (SGD) was quantified at select sites in San Francisco Bay (SFB) from radium (Ra and Ra) and radon (Rn) activities measured in groundwater and surface water using simple mass balance box models. Based on these models, discharge rates in South and Central Bays were 0.3-7.4 m day m. Although SGD fluxes at the two regions (Central and South Bays) of SFB were of the same order of magnitude, the dissolved inorganic nitrogen (DIN) species associated with SGD were different. In the South Bay, ammonium (NH) concentrations in groundwater were three-fold higher than in open bay waters, and NH was the primary DIN form discharged by SGD. At the Central Bay site, the primary DIN form in groundwater and associated discharge was nitrate (NO). The stable isotope signatures (δN and δO) of NO in the South Bay groundwater and surface waters were both consistent with NO derived from NH that was isotopically enriched in N by NH volatilization. Based on the calculated SGD fluxes and groundwater nutrient concentrations, nutrient fluxes associated with SGD can account for up to 16 % of DIN and 22 % of DIP in South and Central Bays. The form of DIN contributed to surface waters from SGD may impact the ratio of NO to NH available to phytoplankton with implications to bay productivity, phytoplankton species distribution, and nutrient uptake rates. This assessment of nutrient delivery via groundwater discharge in SFB may provide vital information for future bay ecological wellbeing and sensitivity to future environmental stressors. [ABSTRACT FROM AUTHOR]

A multichannel seismic (MCS) experiment spanning 600 km across the Alarcón Rise and its conjugate rifted margins in the southern Gulf of California (western North America) provides insight into the spatial and temporal evolution of extension between Baja California and the mainland (Mexico). Stratigraphic analysis of multiple rift basins within the Alarcón spreading corridor indicates an initial stage of oblique extension starting ca. 14-12 Ma. This initial phase of extension was characterized by the formation of several large basins in the center of the gulf and on the southeast margin with negligible synrift sedimentation. A second phase of oblique extension, likely synchronous with large-scale basin opening in the central and northern Gulf of California, began ca. 8-5 Ma and was characterized by the formation of smaller half-grabens distributed across the conjugate margins that contain both synrift and postrift deposits. A key feature imaged within the MCS data is a highly refl ective, ropey layer at the top of basement, interpreted to be either volcanic rocks from the 25-12 Ma Comondú Group, and/or early rifting volcanic rocks that are between 11 and 9 Ma, or younger. This volcanic layer is extensively faulted, suggesting that it predates the episode of early extension. Upper crustal extension appears to be equally distributed across conjugate margins, forming a symmetrical continental rift. Two styles of rifted basin are observed; older basins (estimated as 14-11 Ma using sedimentation rates) show distributed extension with extensive basement faulting. In contrast, the younger basins (likely post-6 Ma) are asymmetrical with synrift deposits thickening into the basin-bounding faults. The northeastsouthwest geomorphic expression of the Tamayo bank and trough and other features provides additional evidence that northwestsoutheast oblique extension began ca. 12 Ma. These new spatial and temporal constraints, when combined with a crustal thickness profi le obtained across the entire Alarcón corridor, suggest that signifi cant northwestsoutheast oblique extension within the Gulf of California started well before 6 Ma, in contrast to earlier models. [ABSTRACT FROM AUTHOR]

Abstract: Benthic indices are useful indicators of sediment condition, but many indices are difficult to employ because they require large calibration datasets. The AZTI''s Marine Biotic Index (AMBI) requires minimal local calibration, but it was developed in Europe and the validity of its extension to distant regions is unclear. Here we compare its performance in Southern California''s marine bays with that of the Benthic Response Index (BRI), a locally derived data-intensive index. AMBI was calibrated in four ways: (1) using the original AMBI species’ classifications developed in Europe; (2) augmenting the original classifications with closely related taxa, following AMBI guidelines; (3) using local expertise to independently classify taxa; and (4) revision of the local expert classifications by European developers of the index. These approaches were applied to a 685 sample data set and assessed relative to the BRI by comparing samples’ classification from best to worst and by evaluating the level of agreement in assigning samples into four condition categories. The AMBI was validated against environmental proxies of disturbance and expert judgement, using consensus agreement about sample condition developed by nine benthic ecologists. The first AMBI approach did not work well, as only 24% of the 928 taxa were on the original AMBI species list, resulting in only 11% of the samples meeting the required 20% of classified individuals for AMBI application. The other approaches classified substantially more taxa, allowing application to 75–98% of the samples. Both of these approaches were significantly correlated with the BRI, though the correlations were lower than between the AMBI runs. None of the AMBI approaches, though, compared well with either the BRI or the validation data when placing samples into perturbation categories, with the AMBI having a greater central tendency. AMBI categorized less than 5% of the samples as reference compared to almost one-third of the samples by the experts or BRI, and substantially underestimating the number of severely affected samples. Species most responsible for disagreements between BRI and AMBI approaches were identified. Four modifications to enhance AMBI performance were identified: (1) incorporate local expertise in assigning ecological classifications, (2) use transformed abundance weighting to reduce the effect of dominant species, (3) calibrate the categorization scaling using expert judgement, and (4) use the AMBI in combination with other measures, such as the M-AMBI. The success of these modifications is specific to this study, but they are likely to enhance AMBI''s performance worldwide. [Copyright &y& Elsevier]

The article presents a study that deals with fatty acid and alcohol profiles of lipids in Rhincalanus rostrifrons or R. cornutus. It determines lipid profiles for wax ester, triacylglycerol, phospolipid, free fatty acid, sterol, and free fatty alcohol fractions for these three species which came from the eastern tropical north Pacific, Gulf of California, and Gulf of Mexico. It reveals storage lipids as the dominant component of total lipid in all three Rhincanalus species. It cites the role of genetic predisposition in governing lipid profiles.

Abstract: The formation of beach megacusps along the shoreline of southern Monterey Bay, CA, is investigated using time-averaged video and simulated with XBeach, a recently developed coastal sediment transport model. Investigations focus on the hydrodynamic role played by the bay''s ever-present rip channels. A review of four years of video and wave data from Sand City, CA, indicates that megacusps most often form shoreward of rip channels under larger waves (significant wave height (H s )=1.5–2.0m). However, they also occasionally appear shoreward of shoals when waves are smaller (H s ~1m) and the mean water level is higher on the beach. After calibration to the Sand City site, XBeach is shown to hindcast measured shoreline change moderately well (skill=0.41) but to overpredict the erosion of the swash region and beach face. Simulations with small to moderate waves (H s =0.5–1.2m) suggest, similar to field data, that megacusps will form shoreward of either rip channels or shoals, depending on mean daily water level and pre-existing beach shape. A frequency-based analysis of sediment transport forcing is performed, decomposing transport processes to the mean, infragravity, and very-low-frequency (VLF) contributions for two highlighted cases. Results indicate that the mean flow plays the dominant role in both types of megacusp formation, but that VLF oscillations in sediment concentration and advective flow are also significant. [Copyright &y& Elsevier]

The article presents a study on how the design of marine protected areas (MPAs) is affected by the movement of small adult black rockfish known as Sebastes melanops. The movements of the rockfish were analyzed by implanting them with acoustic transmitters in Carmel Bay, California. The tagged fish were monitored from August 2006 to January 2008 and their vertical movements were correlated with various environmental variables. Based from the result of the study, the researchers concluded that the understanding of the differences in fish movements among age classes is needed in designing MPAs that are intended for the protection of all life stages of a species.

The coastal Pacific Ocean off northern and central California encompasses the strongest seasonal upwelling zone in the California Current ecosystem. Headlands and bays here generate complex circulation features and confer unusual oceanographic complexity. We sampled the coastal epipelagic fish community of this region with a surface trawl in the summer and fall of 2000-05 to assess patterns of spatial and temporal community structure. Fifty-three species of fish were captured in 218 hauls at 34 fixed stations, with clupeiform species dominating. To examine spatial patterns, samples were grouped by location relative to a prominent headland at Point Reyes and the resulting two regions, north coast and Gulf of the Farallones, were plotted by using nonmetric multidimensional scaling. Seasonal and interannual patterns were also examined, and representative species were identified for each distinct community. Seven oceanographic variables measured concurrently with trawling were plotted by principal components analysis and tested for correlation with biotic patterns. We found significant differences in community structure by region, year, and season, but no interaction among main effects. Significant differences in oceanographic conditions mirrored the biotic patterns, and a match between biotic and hydrographic structure was detected. Dissimilarity between assemblages was mostly the result of differences in abundance and frequency of occurrence of about twelve common species. Community patterns were best described by a subset of hydrographic variables, including water depth, distance from shore, and any one of several correlated variables associated with upwelling intensity. Rather than discrete communities with clear borders and distinct member species, we found gradients in community structure and identified stations with similar fish communities by region and by proximity to features such as the San Francisco Bay. [ABSTRACT FROM AUTHOR]

Shoreline concentrations of fecal indicator bacteria (FIB) and fecal indicator viruses (FIV) in Avalon Bay (Catalina Island, California) display a marked diurnal pattern (higher at night and lower during the day) previously attributed to the tidal flux of sewage-contaminated groundwater and the tidal washing of contaminated sediments, coupled with light and dark die-off of FIB and FIV (Boehm, et al, Environ. Sci Technol 2009, 43, 8046-8052). In this paper we document the existence of strong (peak velocities between 20 to 40 cm/s) transient currents in die nearshore waters of Avalon Bay that occur between 07:00 and 20:00 each day. These currents, which have a significant onshore component, are generated by andiropogenic activities in the Bay, including prop wash from local boat traffic and the docking practices of large passenger ferries. A budget analysis carried out on simultaneous measurements of FIB at two cross-shore locations indicates that anthropogenic currents contribute to the diurnal cycling of FIB concentrations along the shoreline, by transporting relatively unpolluted water from offshore toward the beach. The data and analysis presented in this paper support the idea that anthropogenic currents represent a significant, and previously overlooked, source of variability in shoreline water quality. [ABSTRACT FROM AUTHOR]

California's Bay Delta, where freshwater from the Sacramento and San Joaquin rivers meets the saltwater from San Francisco Bay, has been mired in litigation and political controversy for decades. In the 2009 Delta Reform Act, the California State Water Board was ordered to conduct hearings to establish flow criteria to protect public trust resources in the Bay Delta. This article examines how the statutory deployment of the public trust in the 2009 Delta Reform Act built on the California Supreme Court's 1983 National Audubon decision, and details the California State Water Board proceedings leading up to the public trust Delta flow criteria adopted in August 2010. [ABSTRACT FROM AUTHOR]

Fossil foraminifers (Elphidium excavatum forma selseyensis) recovered from a sediment core from the San Francisco Bay are analyzed for their oxygen isotopic composition. About 8 m of core believed to represent the first 600 years of the current (Holocene) bay's existence at the sample site (from approximately 7650-7050 cal YBP) are highlighted here. This record, deposited at a high, uniform accumulation rate, shows pronounced variation in measured carbonate δ18O, including some of the highest values in the entire Holocene record at the site. It is proposed that this interval records a period during which the fundamental mixing dynamics of the modern estuary became established. We interpret the extremely high δ18O values at about 7400 cal YBP as being indicative of a strongly stratified estuary sampled below its halocline and argue that subsequent details of the isotope record suggest a gradual decrease in water column stratification until conditions qualitatively characteristic of the modern estuary are established about 7300 cal YBP. [ABSTRACT FROM AUTHOR]

The relationship between alongshore rip channel migration and sediment transport is investigated using time-averaged video images to identify the positions of rip channels at three sites along southern Monterey Bay, California, over 1–3year periods. Daily migration rates are calculated for each site. The basic Coastal Engineering Research Center (CERC) formula for bulk alongshore sediment transport is used to estimate alongshore transport rates at each site, based on hourly input of directional wave spectra measured at an offshore buoy and shoaled and refracted to the nearshore. The wave transformation model is validated by comparison with measured nearshore directional wave spectra in 13m water depth. An expanded CERC formulation that accounts for the additional forcing of alongshore wave height gradients is also tested but rejected. Correlation coefficients between daily rates of calculated alongshore transport and rip channel migration are low: 0.01, 0.44, and 0.38 at the Sand City, Stilwell, and Marina sites, respectively. The problem of digitization noise, associated with video-based rip channel identification, is discussed and several filtering methods are used to increase the signal to noise ratio and obtain improved correlations. Results indicate that higher frequency migration events (on time scales shorter than 8days) will likely be obscured below the digitization “noise floor”, but that longer period oscillations (such as tidal and seasonal cycles) show up clearly in both rip migration and sediment transport datasets. Daily rates are cumulatively summed to generate time series of representative overall rip migration distance and net alongshore transport, and the cumulative summing procedure is shown to be similar to applying a low-pass filter. Mean migration is demonstrated to lag behind net transport in the summertime, suggesting that a minimum level of alongshore forcing is required to generate detectable rip migration. Rip channel migration and net alongshore transport have correlation coefficients that range from 0.76 to 0.94 at the three sites. [Copyright &y& Elsevier]

Abstract: To assess benthic macrofaunal community condition in Southern California, 838 sites were sampled using spatially random designs in 1994, 1998, or 2003. Benthic community condition was assessed on a four-category scale and the area in each category estimated. Overall, benthic macrofauna in Southern California were in good condition during 2003, with 98% of the area in reference condition or deviating only marginally. There was no evidence of disturbance near Channel Islands or small wastewater discharges, and virtually none on the mainland shelf. In contrast, bay and estuary macrofaunal communities were more frequently disturbed with nearly 13% of the area supporting disturbed benthos. The condition of the mainland shelf did not change substantially over the 9-year period, with 1.6–2.8% of the area in poor benthic condition. Southern California benthic condition evaluations may be improved by extending the depth and salinity ranges of assessment tools, and improving trend detection methods. [Copyright &y& Elsevier]

Abstract: This paper presents MEPBAY and SMC software tools that allow comprehending and solving problems in headland-bay beach through a parabolic model. These tools can be employed as coastal engineering design tools (including nourishment designs) and also for academic purposes. They are oriented to different end-users, including coastal technicians, scientists and undergraduates and as coastal engineering design tools, they can be applied to different operational levels (pre-design and design). The aim of the paper is to present design guidelines, the capabilities of the tools, their potential use and applications. Both tools were applied to analyze San Lorenzo Beach and demonstrate their ability at different project levels. [Copyright &y& Elsevier]

Abstract: In the summer of 2001, a coastal ocean measurement program in the southeastern portion of San Pedro Bay, CA, was designed and carried out. One aim of the program was to determine the strength and effectiveness of local cross-shelf transport processes. A particular objective was to assess the ability of semidiurnal internal tidal currents to move suspended material a net distance across the shelf. Hence, a dense array of moorings was deployed across the shelf to monitor the transport patterns associated with fluctuations in currents, temperature and salinity. An associated hydrographic program periodically monitored synoptic changes in the spatial patterns of temperature, salinity, nutrients and bacteria. This set of measurements show that a series of energetic internal tides can, but do not always, transport subthermocline water, dissolved and suspended material from the middle of the shelf into the surfzone. Effective cross-shelf transport occurs only when (1) internal tides at the shelf break are strong and (2) subtidal currents flow strongly downcoast. The subtidal downcoast flow causes isotherms to tilt upward toward the coast, which allows energetic, nonlinear internal tidal currents to carry subthermocline waters into the surfzone. During these events, which may last for several days, the transported water remains in the surfzone until the internal tidal current pulses and/or the downcoast subtidal currents disappear. This nonlinear internal tide cross-shelf transport process was capable of carrying water and the associated suspended or dissolved material from the mid-shelf into the surfzone, but there were no observation of transport from the shelf break into the surfzone. Dissolved nutrients and suspended particulates (such as phytoplankton) transported from the mid-shelf into the nearshore region by nonlinear internal tides may contribute to nearshore algal blooms, including harmful algal blooms that occur off local beaches. [Copyright &y& Elsevier]

Many types of indices have been developed to assess benthic invertebrate community condition, but there have been few studies evaluating the relative performance of different index approaches. Here we calibrate and compare the performance of five indices: the Benthic Response Index (BRI), Benthic Quality Index (BQI), Relative Benthic Index (RBI), River Invertebrate Prediction and Classification System (RIVPACS), and the Index of Biotic Integrity (IBI). We also examine whether index performance improves when the different indices, which rely on measurement of different properties, are used in combination. The five indices were calibrated for two geographies using 238 samples from southern California marine bays and 125 samples from polyhaline San Francisco Bay. Index performance was evaluated by comparing index assessments of 35 sites to the best professional judgment of nine benthic experts. None of the individual indices performed as well as the average expert in ranking sample condition or evaluating whether benthic assemblages exhibited evidence of disturbance. However, several index combinations outperformed the average expert. When results from both habitats were combined, two four-index combinations and a three-index combination performed best. However, performance differences among several combinations were small enough that factors such as logistics can also become a consideration in index selection. [Copyright &y& Elsevier]

The Bay-Delta, the largest estuary in the western United States, is home to more than 750 plant and animal species and is home to California's greatest source of water. For more than a decade however, the Bay-Delta has also been home to a battle between agriculturalists, environmentalists, and urban water users. The Bay-Delta's ecosystem health, levee stability, and water supply and quantity is in a state of continual decline, and these interest groups have become entangled in disputes over how to address these problems. In 1994, CALFED, a group of state and federal agencies, was created in an effort to address the daunting problems facing the Bay-Delta. CALFED prepared a Program Environmental Impact Statement/Report (PEIS/R), detailing its proposed program to address what it defined as the four main problems facing the Bay-Delta: water supply instability, poor water quality, declining ecosystem health, and levee instability. Believing that all problem areas needed to be addressed concurrently, CALFED did not consider any alternatives to the program that did not satisfy all four areas. In 2000, before CALFED's program was implemented, a group of interested parties brought suit in district court, claiming that CALFED's PEIS/R was deficient and did not satisfy the requirements of the California Environmental Quality Act (CEQA). The plaintiffs asserted that under CEQA, not every goal or problem must be addressed in a single PEIS/R. Therefore, plaintiffs claimed that CALFED should have included alternatives to the program that did not address every problem. Specifically, the plaintiffs asserted that CALFED should have considered reducing water exported from the Bay-Delta, as although it would not solve the water supply instability problem, it would reduce environmental impact. Ultimately, the California Supreme Court decided that CALFED's PEIS/R met CEQA's requirements and that the agency was correct when it decided that it did not need to consider alternatives that did not meet each of the four goals. This Note argues that the California Supreme Court was correct in its decision, despite the fact that the decision seemingly goes against CEQA's purpose and rules. The Note will also explain why CEQA's procedural requirements are crucial and must be followed of the statute has a chance to effect substantive change. CEQA's requirement that an agency consider program alternatives that are less environmentally harmful is one way to reach major substantive change, but this Note will explain that this alternatives analysis is dependent on two other procedural requirements. First, the preparation of an EIR and its labeling as a program or project EIR affects the alternatives analysis in that programs and projects require different levels of detail in their discussion of alternatives. Second, how the goal of the EIR is narrowed will similarly affect the alternatives considered. [ABSTRACT FROM AUTHOR]

The article presents a study regarding the movements of leopard sharks in Elkhorn Slough, California. It notes that bays and estuaries are impacted by human activity as they play important roles in the life history of the leopard sharks. Leopard sharks were used in the study to understand its habitat use, spatial associations and their ecological roles. Acoustic transmitters were tagged on 21 female leopard sharks from August 2003 to February 2005. The seasonal change in tagged sharks are associated with changes in temperature, salinity and dissolved oxygen. The study suggests for a focus in preserving and restoring intertidal mudflats as part of the efforts in protecting leopard shark habitats in bays and estuaries.

Between 1995 and 2006, manned submersible fish surveys were conducted on the sea floor throughout the Southern California Bight. A total of 401 dives (comprising 1,015 transects and 14,373 habitat patches) were made in waters between 19 and 365 m deep. All natural habitat types were included, although both soft sea floors and rocky reefs were surveyed more than any other type. A total of 717,526 fishes, representing a minimum of 137 species and 47 families, were observed. Rockfishes (genus Sebastes), with a minimum of 50 species and 647,495 individuals (90.2% of all fishes observed), dominated most of the habitats. The most abundant species, squarespot ( Sebastes hopkinsi), halfbanded ( Sebastes semicinctus), shortbelly ( Sebastes jordani), and pygmy rockfishes ( Sebastes wilsoni), are dwarf taxa that either school or aggregate. The most abundant non-rockfish species was the benthic and territorial blackeye goby ( Rhinogobiops nicholsii). Both species richness and overall fish densities were highest in the shallowest sites. Most of the fishes in all habitats were small (≤20 cm TL long) and economically important species were generally uncommon. Forty-four species were found to be characteristic of the study area (occurring in at least 5% of the transects) and these species formed three faunal associations centered around depths of 62, 105, and 168 m. Based on size frequency distributions, at least 18 of the characteristic species exhibited ontogenetic movements, with young-of-the-year and older juveniles living in relatively shallow waters and larger individuals generally in deeper depths. In this study, the abundance of juvenile widow rockfish ( Sebastes entomelas), and the virtual absence of adults, in southern California waters may demonstrate an ontogenetic northward movement of this species. This research implies that substantial harvesting of larger species by commercial and recreational fishers has helped alter some fish assemblages, allowing small and “weedy” species to thrive. [ABSTRACT FROM AUTHOR]

Systematic consideration of uncertainty in data, model structure, and other factors is generally unaddressed in most Total Maximum Daily Load (TMDL) calculations. Our previous studies developed the Management Objectives Constrained Analysis of Uncertainty (MOCAU) approach as an uncertainty analysis technique specifically for watershed water quality models, based on a synthetic case. In this study, we applied MOCAU to analyze diazinon loading in the Newport Bay watershed (Southern California). The study objectives included (1) demonstrating the value of performing stochastic simulation and uncertainty analysis for TMDL development, using MOCAU as the technique and (2) evaluating the existing diazinon TMDL and generating insights for the development of scientifically sound TMDLs, considering uncertainty. The Watershed Analysis Risk Management Framework model was used as an example of a complex watershed model. The study revealed the importance and feasibility of conducting stochastic watershed water quality simulation for TMDL development. The critical role of management objectives in a systematic uncertainty assessment was well demonstrated. The results of this study are intuitive to TMDL calculation, model structure improvement and sampling strategy design. [ABSTRACT FROM AUTHOR]

Ammonia oxidation in marine and estuarine sediments plays a pivotal role in the cycling and removal of nitrogen. Recent reports have shown that the newly discovered ammonia-oxidizing archaea can be both abundant and diverse in aquatic and terrestrial ecosystems. In this study, we examined the abundance and diversity of ammonia-oxidizing archaea (AOA) and betaproteobacteria (β-AOB) across physicochemical gradients in San Francisco Bay – the largest estuary on the west coast of the USA. In contrast to reports that AOA are far more abundant than β-AOB in both terrestrial and marine systems, our quantitative PCR estimates indicated that β-AOB amoA (encoding ammonia monooxygenase subunit A) copy numbers were greater than AOA amoA in most of the estuary. Ammonia-oxidizing archaea were only more pervasive than β-AOB in the low-salinity region of the estuary. Both AOA and β-AOB communities exhibited distinct spatial structure within the estuary. AOA amoA sequences from the north part of the estuary formed a large and distinct low-salinity phylogenetic group. The majority of the β-AOB sequences were closely related to other marine/estuarine Nitrosomonas-like and Nitrosospira-like sequences. Both ammonia-oxidizer community composition and abundance were strongly correlated with salinity. Ammonia-oxidizing enrichment cultures contained AOA and β-AOB amoA sequences with high similarity to environmental sequences. Overall, this study significantly enhances our understanding of estuarine ammonia-oxidizing microbial communities and highlights the environmental conditions and niches under which different AOA and β-AOB phylotypes may thrive. [ABSTRACT FROM AUTHOR]

Aim The influence of landscape structure on the distribution patterns of bats remains poorly understood for many species. This study investigates the relationship between area and isolation of islands and the probability of occurrence of six bat species to determine whether persistence and immigration abilities vary among bat species and foraging guilds. Location Thirty-two islands in the Gulf of California near the Baja California peninsula in north-west Mexico. Methods Using logistic regression and Akaike information criterion (AIC) model selection, we compared five a priori models for each of six bat species to explain patterns of island occupancy, including random patterns, minimum area effects, maximum isolation effects, additive area and isolation effects and compensatory area and isolation effects. Results Five species of insectivorous bats ( Pipistrellus hesperus, Myotis californicus, Macrotus californicus, Antrozous pallidus and Mormoops megalophylla) displayed minimum area thresholds on incidence. The probability of occurrence tended to decrease at moderate distances of isolation ( c. 10–15 km) for these species (excepting A. pallidus). The distributions of two non-insectivorous species ( Leptonycteris curasoae and Myotis vivesi) were not influenced by island size and isolation. Main conclusions Minimum area thresholds on incidence suggest that island occupancy by insectivorous bats may be limited by resource requirements. Islands smaller than 100 ha typically did not support occupancy or use by insectivorous bats, except at minimal isolation distances. Insectivorous bat species may also be more sensitive to moderate levels of habitat isolation in some landscape contexts than previously expected. Our results suggest that differences in foraging habits may have important implications for understanding the distribution patterns of bats. [ABSTRACT FROM AUTHOR]

Abstract: In order to determine wave transformations in an elongated bay, a numerical solution was used to interpret yearlong records of bottom pressure and wind velocity obtained at the mouth and head of Concepción Bay, on the Gulf of California side of the Baja California peninsula. Observed wind waves were predominantly produced by southeastward winds in the winter and north–northwestward winds in the summer. Typical mean wave periods at the bay entrance were between 3 and 5s. In contrast, the waves at the head of the bay had predominant periods <3s. The energetic long-period swell waves were dissipated somewhere in the bay as they were not observed at the head of the bay. This study centered in identifying the effects that caused swell waves to attenuate in the bay. The ‘Simulating WAves Nearshore (SWAN)’ model was used to determine the cause for such wave attenuation. Model results showed that swell waves were attenuated because of the combined effects of bottom friction, wave breaking, whitecapping, refraction and wave blocking by the coastline. Most of the attenuation (close to 90%), however, was caused by wave blocking owing to the change of coastline orientation of the bay. This wave blocking mechanism should therefore be explored further in embayments of complex coastline morphology. [Copyright &y& Elsevier]

The vertical distribution of the turbulent kinetic energy dissipation rate was measured using an array of four acoustic Doppler velocimeters in the shallow embayment of Grizzly Bay, San Francisco Bay, California. Owing to the combination of wind and tide forcing in this shallow system, the surface and bottom boundary layers overlapped. Whitecapping waves were generated for a significant spectral peak steepness greater than 0.05 or above a wind speed of 3 m s-1. Under conditions of whitecapping waves, the turbulent kinetic energy dissipation rate in the upper portion of the water column was greatly enhanced, relative to the predictions of wind stress wall-layer theory. Instead, the dissipation followed a modified deep-water breaking-wave scaling. Near the bed (bottom 10% of the water column), the dissipation measurements were either equal to or less than that predicted by wall-layer theory. Stratification due to concentration gradients in suspended sediment was identified as the likely cause for these periods of production–dissipation imbalance close to the bed. During 50% of the well-mixed conditions experienced in the month-long experiment, whitecapping waves provided the dominant source of turbulent kinetic energy over 90% or more of the water column. [ABSTRACT FROM AUTHOR]

To describe the hydrographical variability at the North Mouth of La Paz Bay, its main point of communication with the Gulf of California, CTD data were analyzed from four sampling surveys conducted during an annual cycle (May, July and October 2001, and February 2002). The results showed an absence of the mixed layer and intense temperature and salinity stratification in spring and summer. In autumn a 30-m mixed layer was registered, with a temperature of 28.5°C, while in winter an unusual 100-m mixed layer was detected, with a temperature of 17.9°C. Particular noteworthy is the similarity of the structure between the surface and subsurface layers of the bay and gulf. The most significant difference was the presence of Pacific Intermediate Water (PIW) in the gulf, which does not intrude into the bay due to the barrier created by the sill at the mouth. The T-S diagrams revealed the presence of Gulf of California Water (GCW), Subtropical Subsurface Water (SSW) and PIW in May. In July, however, four water masses were identified: GCW, Equatorial Surface Water (ESW), SSW and PIW. In October, a significant amount of ESW and a considerable decrease in GCW were detected, but in February only GCW and SSW were found. This study shows important hydrographic seasonal variability in the area of the North Mouth, with marked differences between the bay and the gulf, contributing to the understanding of the regional oceanography. [ABSTRACT FROM AUTHOR]

The green sturgeon, Acipenser medirostris, is a long-lived, iteroparous, anadromous acipenserid that is native to the San Francisco Bay Estuary, California. Sub-adult and adult fish are oceanic, but enter the estuary during the spring and remain through autumn. Little is known about green sturgeon distribution within the estuary or what, if any, physical parameters influence their movements. We report the results of a telemetry study conducted between September 2001 and November 2002. Five sub-adult and one adult green sturgeon were captured by trammel net in the San Pablo Bay region of the estuary. We implanted depth-sensing, ultrasonic transmitters within the peritoneum of individuals and tracked them from a boat for 1 – 15 h per day over periods ranging from 1 to 12 days. Salinity, temperature, and dissolved oxygen profiles of the water column were measured hourly. Observed movements were categorized as either non-directional or directional. Non-directional movements, accounting for 63.4% of observations, were closely associated with the bottom, with individuals moving slowly while making frequent changes in direction and swim speed, or not moving at all. Directional movements consisted of continuous swimming in the top 20% of the water column while holding a steady course for extended periods. Four of the five sub-adult fish remained within the confines of San Pablo Bay for the duration of their tracking period. The remaining sub-adult moved over 45 km up-river into Suisun Bay before contact was lost. The adult fish exited the bay and entered the ocean 6 h after release near Tiburon, CA, a movement of approximately 10 km. The sub-adult fish typically remained at the shallower depths (<10 m) of the estuary, but there were no apparent preferences for temperature, salinity, or dissolved oxygen, with the fish moving widely and rapidly across the range of these physical parameters. Activity is believed to be independent of light level with no discernable crepuscular, nocturnal, or diurnal peaks in activity. [ABSTRACT FROM AUTHOR]

The article investigates billfish reproduction at the entrance of the Gulf of California. 8361 billfish samples were examined from January 1990 to December 2004 to determine reproductive state. Ripe striped marlin were found from May through December while mature sailfish were found from July through November.

Collaborative approaches to environmental and natural resource management are on the rise in the United States. This article examines collaborative governance in four high-profile and large-scale ecosystems: the Northwest Power and Conservation Council's Fish and Wildlife Program in the Columbia River Basin, the Chesapeake Bay Program, the CALFED Bay-Delta Program in California's San Francisco Bay/Sacramento-San Joaquin River Delta, and the Florida Everglades Restoration Program. We compare the governance structures of these four institutional arrangements by examining how collaboration occurs or is organized at three different levels of decision making: constitutional, collective choice (or policymaking), and operational (or implementation). This includes an examination of governance and advisory bodies as well as coordinating and monitoring structures. [ABSTRACT FROM AUTHOR]

San Francisco Bay has been considered an HNLC or HNLG (high nutrient low chlorophyll or low growth) region with nonlimiting concentrations of inorganic nutrients yet low standing stocks of phytoplankton. Most of the studies leading to this conclusion come from the South Bay and little is known about nutrient processes and phytoplankton productivity in the northern and central parts of the estuary. Data collected over 3 yr (1999-2003) in Suisun, San Pablo, and Central Bays describe the availability of dissolved inorganic nitrogen (DIN), silicate, and phosphate and the seasonal variability in phytoplankton abundance. Rate measurements of fractionated nitrogen productivity provide the relative contributions of different forms of DIN (ammonium and nitrate) and different sized phytoplankton to the development of seasonal phytoplankton blooms. Regional differences in bloom dynamics are observed with Suisun Bay, the least saline, highest nutrient, most turbid region having less phytoplankton biomass and productivity than San Pablo and Central Bays, except in the abnormally wet spring of 2000. Spring blooms in San Francisco Bay are driven primarily by high rates of nitrate uptake by larger phytoplankton cells following a period of increased ammonium uptake that depletes the ambient ammonium. The smaller occasional fall blooms are apparently fueled mostly by ammonium uptake by small sized phytoplankton. The data suggest that the HNLC condition in the northern and central parts of San Francisco Bay is due primarily to light availability modulated by the interaction between ammonium and nitrate, and the relative amounts of the two forms of the DIN pool available to the phytoplankton. [ABSTRACT FROM AUTHOR]

Abstract: Hydrographic and current measurements in the Northern Gulf of California from December 1994 through March 1995 show conditions that are markedly different from those accepted as typical for winter. A rapid subsurface warm water intrusion (∼0.5°C warmer) was observed, which reduced the stratification and stopped, and eventually reversed the typical anticyclonic winter circulation. An empirical orthogonal function analysis of the mean vertical structure of temperature and salinity of historical hydrographic data reveals that similar conditions occurred during March 1973 (warm water intrusion and weakening of stratification). In this study, it is proposed that these anomalous conditions are due to a combination of local and remote forcings: extensive water-mass formation in the Upper Gulf of California and the arrival of an intraseasonal downwelling coastally trapped wave to the Northern Gulf of California. [Copyright &y& Elsevier]

Abstract: Data from seven oceanographic cruises in the southern Gulf of California from 1997 to 2002 are used to describe the thermohaline variability and the geostrophic circulation. Baroclinic patterns exhibited spatial and temporal variability. A deepening of isotherms at the center of the section was evident in February 1999, suggesting anticyclonic flow. In May 1998 and November 1997, cyclonic flow was suggested by shoaling of isotherms at the center of the section. Other cruises showed alternating cores of flow into and out of the Gulf (August 1998, September 1997 and October 2002). Neither a seasonal nor a spatial pattern in geostrophic flows was apparent, suggesting that the exchange of waters between the cyclonic flow of Pescadero basin and the interior of the Gulf is complex. Relatively high salinities were recorded during most of the cruises indicating that Gulf of California Water (GCW) was present most of the year. Higher salinities were observed during winter and spring, although during summer, relatively high and low salinities were both observed as surface and subsurface cores. Temperature and salinity characteristics of California Current waters were observed only in August 1995 when they reached as far north as Cerralvo Island at ∼50dbar. During El Niño conditions in November 1997, a mixed layer (∼70dbar) and deepening of the thermocline (∼50dbar) characterized anomalous conditions; during this cruise an asymmetric salinity pattern was observed with low salinities characteristic of Tropical Surface waters at the center and east of the section, while maximum salinities (34.9

Because of its presence in antifouling coatings, stormwater, and industrial and municipal discharges, copper is a ubiquitous contaminant in estuarine and coastal environments. We integrated a system-wide field program with a one-dimensional model to evaluate the overall mass balance of copper in a representative coastal harbor, San Diego Bay, California. Field results from four surveys over 1 yr showed remarkably similar distributions of total copper, with a general increase from the ocean into the Bay followed by a slight decrease in the inner Bay. Total copper concentrations ranged from 5 nmol L-1 to nearly 60 nmol L-1. Highest levels for both total and dissolved copper were observed during the winter. Results from a one-dimensional model accounting for the balance of sources, flushing, and losses to the sediment illustrated the importance of accounting for losses of copper to the sediment, without which water column concentrations are overestimated by as much as a factor of five. The time scale for the loss term is on the order of 8-10 d. The model reproduced the field measurements quite well with a loss term controlled by partitioning and settling parameters. The overall balance of total copper in the Bay appears to be split between losses to the ocean via tidal flushing and losses to the sediments via settling. Settling plays an important role in the fate of copper in the Bay, and the sediments are a key endpoint for copper. [ABSTRACT FROM AUTHOR]

Respiration and calcium carbonate production by the invasive Asian clam, Potamocorbula amurensis, were calculated to assess their importance as CO[sub2] sources in northern San Francisco Bay. Production, calculated using monthly population density and size structure measured at three sites over 7 yr and a shell length/CaCO[sub3] conversion factor, averaged 221 (± 184) g CaCO[sub3] m[sup-2] yr[sup-1]. Net calcium carbonate production by this exotic bivalve releases CO[sub2] at a mean rate of 18 (± 17) g C m[sup-2] yr[sup-1]. Respiration by P. amurensis, estimated from secondary production, releases additional CO[sub2] at a mean rate of 37 (± 34) g C m[sup-2] yr[sup-1]. Therefore, total net CO[sub2] production by P. amurensis averages 55 (± 51) g C m[sup-2] yr[sup-1] in an estuarine domain where net primary production consumes only 20 g inorganic C m[sup-2] yr[sup-1]. CO[sub2] production by P. amurensis in northern San Francisco Bay is an underestimate of the total CO[sub2] supply from the calcified zoobenthic communities of San Francisco Bay, and results from other studies have suggested that this rate is not unusual for temperate estuaries. Global extrapolation yields a gross CO[sub2] production rate in the world's estuaries of 1 x 10[sup14] g C yr[sup-1], which suggests that calcified benthic organisms in estuaries generate CO[sub2] equal in magnitude to the CO[sub2] emissions from the world's lakes or from planetary volcanism (the net source is determined by the highly variable rate of CO[sub2] consumption by carbonate dissolution). This biogenic CO[sub2] source is increasing because of the continuing global translocation of mollusks and their successful colonization of new habitats. [ABSTRACT FROM AUTHOR]

The archaic, deep-sea cephalopod Vampyroteuthis infernalis occurs in dark, oxygen-poor waters below 600 m off Monterey Bay, California. Living specimens, collected gently with a remotely operated vehicle (ROV) and quickly transported to a laboratory ashore, have revealed two hitherto undescribed means of bioluminescent expression for the species. In the first, light is produced by a new type of organ located at the tips of all eight arms. In the second, a viscous fluid containing microscopic luminous particles is released from the arm tips to form a glowing cloud around the animal. Both modes of light production are apparently linked to anti-predation strategies. Use of the tip-lights is readily educed by contact stimuli, while fluid expulsion has a much higher triggering threshold. Coelenterazine and luciferase are the chemical precursors of light production. This paper presents observations on the structure and operation of the arm-tip light organs, the character of the luminous cloud, and how the light they produce is incorporated into behavioral patterns. [ABSTRACT FROM AUTHOR]

Presents a study which determined the phase speciation and estuarine behavior of monomethyl mercury (MeHg) in surface waters of the San Francisco Bay estuary. Background of studies on MeHg; Materials and methods used; Measurement of the concentration of MeHg; Relationship between MeHg and suspended particulate matter; Correlation between unfiltered and filter-passing MeHg concentrations.

We tested the hypothesis that temperature, salinity, and dissolved oxygen affect elasmobranch distribution and abundance in Tomales Bay, California, with monthly longline samples over a 20 month period. We used a Poisson regression under generalized least squares and found that temperature and salinity were the most important factors determining the distribution and abundance of the three most common elasmobranch species, bat ray, Myliobatis californica, leopard shark, Triakis semifasciata, and brown smoothhound shark, Mustelis henlei. Females of all three species were more abundant than males throughout the Bay, and were most abundant in the warmer, more saline inner bay. All three species apparently left Tomales Bay in late fall as water temperatures in the bay decreased to <10–12° C, and returned in early spring after temperatures increased to > 10° C. Three of 257 bat rays tagged in Tomales Bay were recaptured, all within 1 km of their tagging location despite having been free for up to 583 d. [ABSTRACT FROM AUTHOR]

Stormwater discharges from Chollas Creek, a tributary of San Diego Bay, have been shown to be toxic to aquatic life. The primary objective of this study was to provide the linkage between in-channel measurements and potential impairments in the receiving waters of San Diego Bay. This study addressed this objective within the context of four questions: (1) How much area in San Diego Bay is affected by the discharge plume from Chollas Creek during wet-weather conditions?; (2) How much of the wet-weather discharge plume is toxic to marine aquatic life?; (3) How toxic is this area within the wet-weather discharge plume?; and (4) What are the constituent(s) responsible for the observed toxicity in the wet-weather plume? The stormwater plume emanating from Chollas Creek was dynamic, covering areas up to 2.25 km2. Approximately half of the plume was estimated to be toxic to marine life, based upon the results of purple sea urchin (Strongylocentrotus purpuratus) fertilization tests. The area nearest the creek mouth was the most toxic (NOEC = 3 to 12% plume sample), and the toxicity decreased with distance from the creek mouth. The toxicity of plume samples was directly proportional to the magnitude of plume mixing and dilution until, once outside the plume margin, no toxicity was observed. Trace metals, most likely zinc, were responsible for the observed plume toxicity based upon toxicity identification evaluations (TIEs). Zinc was also the constituent identified from in-channel samples of Chollas Creek stormwater using TIEs on the storms sampled in this study, and in storms sampled during the previous storm season. [ABSTRACT FROM AUTHOR]

The San Francisco Bay Area hosts a diverse insect fauna and a dense cluster of urban areas. The high diversity of insects in the Bay Area arises for three primary reasons: its location in the California biotic province, the diverse local environment and the entomologist-area effect. The juxtaposition of high insect diversity and an area intensively used by humans led to the first recorded extinction as well as the first efforts to conserve insects in the United States. Habitat loss due to urbanization, agriculture, and invasive species is largely responsible for local extinctions and reduction in abundance of the remaining species. Invasive species such as the Argentine ant and pathogens causing mortality of oaks and pines are poised to have substantial impacts on the insect fauna of the Bay Area in the near future. Understanding which taxa can or cannot persist in remnant habitat patches within an urban or agricultural matrix, and what management practices would encourage persistence should be a focus of future research. Assessments of population status should be focused on insects at risk of extinction because of their restricted geographic ranges, low vagility, interactions with invasive species, or known reduction in their habitat. Assessments that combine examinations of museum collections, literature, and field surveys might enable determination of the status of many species within the Bay Area. Such an approach might better define the scope and magnitude of the problem of conserving insects in an increasingly urbanized region. [ABSTRACT FROM AUTHOR]