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Planning for future ocean conditions requires historical data to establish more informed ecological baselines. To date, this process has been largely limited to instrument records and observations that begin around 1950. Here, we show how marine macroalgae specimens from herbaria repositories may document long-term ecosystem processes and extend historical information records into the nineteenth century. We tested the effect of drying and pressing six macroalgae species on amino acid, heavy metal and bulk stable isotope values over 1 year using modern and archived paper. We found historical paper composition did not consistently affect values. Certain species, however, had higher variability in particular metrics while others were more consistent. Multiple herbaria provided Gelidium (Rhodophyta) samples collected in southern Monterey Bay from 1878 to 2018. We examined environmental relationships and found δ15N correlated with the Bakun upwelling index, the productivity regime of this ecosystem, from 1946 to 2018. Then, we hindcasted the Bakun index using its derived relationship with Gelidium δ15N from 1878 to 1945. This hindcast provided new information, observing an upwelling decrease mid-century leading up to the well-known sardine fishery crash. Our case study suggests marine macroalgae from herbaria are an underused resource of the marine environment that precedes modern scientific data streams. [ABSTRACT FROM AUTHOR]

From February 2019 through January 2021, data were collected by an acoustic vector sensor moored on the seafloor at a depth of approximately 900 m just outside of Monterey Bay, California, near a major shipping lane off the California coast. Analysis of the vector sensor data has shown the ability to accurately determine bearings to merchant vessels at ranges up to 60 km. This paper examines the features of the low-frequency soundscape using spectral probability densities and evaluates directional features through vector intensity processing as well as coherent linear and adaptive processing of the vector sensor channels. Merchant vessel acoustic data were analyzed using the 1/3 octave band centered at 63 Hz. Over the period analyzed, a reduction in merchant vessel noise was observed between February and June 2020 relative to the same period in 2019, consistent with a reduction in vessel traffic due to the worldwide response to COVID-19. The directional features of the data evaluated through adaptive processing methods also suggest this reduction can be most clearly distinguished towards the south, where the shipping lane is limited to transiting vessels, rather to the north-northwest, where merchant vessels tend to congregate on approach into the San Francisco Bay area. [ABSTRACT FROM AUTHOR]

This study evaluates the feasibility of applying the Estimating the Circulation and Climate of the Ocean (ECCO) data assimilation (DA) framework to a submesoscale-resolving model [Massachusetts Institute of Technology General Circulation Model (MITgcm), at 1-km grid resolution]. This is in preparation for future studies to understand and assimilate the novel swath measurements of sea surface height from the Surface Water and Ocean Topography (SWOT) satellite mission. The model domain is centered at the SWOT calibration/validation (CalVal) site, located 300 km offshore of Monterey Bay, California. We assimilate vertical profiles of temperature and salinity from a linear array of three SWOT prelaunch CalVal moorings, between September and December 2019. Two model solutions are analyzed: 1) a nonassimilating forward simulation termed "first-guess" and 2) an optimized solution that assimilates the in situ observations. Both runs are nested within the global 1/12° Hybrid Coordinate Ocean Model that uses Navy Coupled Ocean Data Assimilation (HYCOM/NCODA) analysis. We evaluate the performance by comparing the two model solutions against assimilated and withheld in situ observations. We show that by assimilating hydrographic data, the model performance over the first-guess solution is improved with an error-to-observation reduction of 30%–45% for temperature, 14%–41% for salinity, and 44%–56% for steric height. Over the study period, the average steric height error at the three assimilated moorings was 1.27 cm for the optimized solution versus 2.6 cm for the first-guess solution. A comparison to withheld glider observations shows that the optimized solution outperforms the first-guess solution with an error-to-observation reduction of approximately 38% in steric height (1.5 versus 2.4 cm). This study indicates, for the first time, that the MITgcm–ECCO framework can be successfully applied to the reconstruction of submesoscale ocean variability, via the nesting of a high-resolution regional domain into a global outer domain. [ABSTRACT FROM AUTHOR]

Animal culture evolves alongside genomes, and the two modes of inheritance—culture and genes—interact in myriad ways. For example, stable geographic variation in culture can act as a reproductive barrier, thereby facilitating genetic divergence between "cultural populations." White-crowned sparrows (Zonotrichia leucophrys) are a well-established model species for bird song learning and cultural evolution, as they have distinct, geographically discrete, and culturally transmitted song types (i.e., song dialects). In this study, we tested the hypothesis that divergence between culturally transmitted songs drives genetic divergence within Nuttall's white-crowned sparrows (Z. l. nuttalli). In accordance with sexual selection theory, we hypothesized that cultural divergence between mating signals both preceded and generated genetic divergence. We characterized the population structure and song variation in the subspecies and found two genetically differentiated populations whose boundary coincides with a major song boundary at Monterey Bay, California. We then conducted a song playback experiment that demonstrated males discriminate between songs based on their degree of divergence from their local dialect. These results support the idea that discrimination against non-local songs is driving genetic divergence between the northern and southern populations. Altogether, this study provides evidence that culturally transmitted bird songs can act as the foundation for speciation by sexual selection. [ABSTRACT FROM AUTHOR]

Editorial. Highlights the 11th IEEE International Requirements Engineering Conference held in Monterey Bay, California. Increase in interest in requirements engineering (RE) for commercial-off-the-shelf systems; Growing interest in the skill set of the requirements engineer; Aim to learn and to share experiences on effective ways to implement RE in an organization.

Striped Bass (Morone saxatilis), a non-native, anadromous fish introduced to California in 1879, is a popular sport fish and piscivorous predator in the San Francisco Bay/Delta ecosystem, but comparatively little is known about its distribution and ecology in estuaries and rivers of the California coast. Here we review recent scientific papers, consultant reports, and correspondence to evaluate its distribution in coastal estuaries and rivers, evidence for local reproduction, and scope for impacts on native fishes, especially salmonids. Striped Bass is extremely rare in the ocean along the north coast, and has not turned up in extensive surveys of Humboldt Bay, the Eel River estuary, or the Russian River estuary. It is, however, a perennial feature of seining surveys in estuaries south of the Golden Gate and along Monterey Bay, usually sporadically and as a very small proportion of total catch. It has become quite common in the Carmel River estuary, and is occasionally caught in the ocean further south. Small upstream migrations, possibly for spawning, have been observed in the Salinas River and Carmel River, but no evidence of eggs or larvae has been found--perhaps due to a lack of ichthyplankton surveys anywhere except in Elkhorn Slough. However, the species' reproductive ecology is not a good match to the hydrologic structure of most coastal stream systems, requiring a large long river where adults can spawn, in combination with an extensive, ramifying estuarine system where larvae can accumulate. One potential good match is the Salinas River system, especially in its historic form as the Salinas River/Old Salinas River Channel/Elkhorn Slough complex of the 19th century. Despite the modest presence of the species on the coast between the Golden Gate and Carmel, it still has scope for large impacts on emigrating salmonids, due to its extreme piscivory at larger size-classes and its ability to exploit migration bottlenecks as feeding grounds. Most likely the individuals observed in coastal estuaries originated in the San Francisco Bay/Delta system and use local systems opportunistically for foraging, but the hypothesis of local reproduction cannot be ruled out without further study. [ABSTRACT FROM AUTHOR]

Thin layers of phytoplankton have an important impact on coastal ocean ecology. The high spatial and temporal variability of such layers makes autonomous underwater vehicles (AUVs) ideal for their study. At the Monterey Bay Aquarium Research Institute (MBARI, Moss Landing, CA), the authors have used an AUV for obtaining repeated high-resolution surveys of thin layers in Monterey Bay, CA. The AUV is equipped with ten “gulpers” that can capture water samples when some feature is detected. In this paper, the authors present an adaptive triggering method for an AUV to capture water samples at chlorophyll fluorescence peaks in a thin layer. The algorithm keeps track of the fluorescence background level and the peaks' baseline in real time to ensure that detection is tuned to the ambient conditions. The algorithm crosschecks for concurrent high values of optical backscattering to ensure that sampling targets true particle peaks and not simply physiologically controlled fluorescence peaks. To let the AUV capture the thin layer's peak without delay, the algorithm takes advantage of the vehicle's sawtooth (i.e., yo-yo) trajectory: in one yo-yo cycle, the vehicle makes two crossings of the thin layer. On the first crossing, the vehicle detects the layer's fluorescence peak and saves the peak height; on the second crossing, as the fluorescence measurement reaches the saved peak height (plus meeting additional timing and depth conditions), a sampling is triggered. Based on the thin layer's vertical position in the vehicle's yo-yo profiles, the algorithm selects the pair of detection and triggering crossings so as to minimize the spacing between them. We use the algorithm to postprocess a data set of 20 AUV missions in the 2005 Layered Organization in the Coastal Ocean (LOCO) Experiment in Monterey Bay, CA, and compare its performance with that of a threshold triggering method. In October 2009, the presented method was field tested in an AUV mission in northern Monterey Bay, CA. [ABSTRACT FROM AUTHOR]

For estimating lateral flux in the ocean using fixed or mobile platforms, the authors present a method of analyzing the estimation error and designing the sampling strategy. When an array of moorings is used, spatial aliasing leads to an error in flux estimation. When an autonomous underwater vehicle (AUV) is run, measurements along its course are made at different times. Such nonsynopticity in the measurements leads to an error in flux estimation. It is assumed that the temporal–spatial autocovariance function of the flux variable can be estimated from historical data or ocean models (as in this paper). Using the temporal–spatial autocovariance function of the flux variable, the mean-square error of the flux estimate by fixed or mobile platforms is derived. The method is used to understand the relative strengths of moorings and AUVs (assumed here to be able to maintain constant speed) under different scenarios of temporal and spatial variabilities. The flux estimate by moorings through trapezoidal approximation generally carries a bias that drops quadratically with the number of moorings. The authors also show that a larger number of slower AUVs may achieve a more accurate flux estimate than a smaller number of faster AUVs under the same cumulative speed, but the performance margin shrinks with the increase of the cumulative speed. Using the error analysis results, one can choose the type of platforms and optimize the sampling strategy under resource constraints. To verify the theoretical analysis, the authors run simulated surveys in synthesized ocean fields. The flux estimation errors agree very well with the analytical predictions. Using an ocean model dataset, the authors estimate the lateral heat flux across a section in Monterey Bay, California, and also compare the flux estimation errors with the analytical predictions. [ABSTRACT FROM AUTHOR]

Harmful algal blooms (HABs) are common in Monterey Bay, CA, and have resulted in repeated closures of shellfish fisheries and the poisoning and death of marine mammals. In the majority of instances, HAB events in this region are first detected by the presence of sick or dying animals. The phrase "cryptic blooms" was adopted to denote the appearance of poisoning at higher trophic levels with no prior evidence of a large phytoplankton bloom. We hypothesize that the onset of many HAB events goes undetected because the bloom is initially concentrated in discrete thin subsurface layers in the water column that are easily missed by conventional sampling and monitoring methods. In this paper, we report on the detection and monitoring of a subsurface layer of phytoplankton in northern Monterey Bay, CA, using a high-resolution, autonomous profiler. This 'thin layer,' which measured from 10 cm to 3 m in thickness (85%<2 m; 54%<1 m), persisted over a 7-day period near the base of the pycnocline. The phytoplankton assemblage in the layer was primarily composed of a multi-species assemblage of Pseudo-nitzschia including the toxin-producing species Pseudo-nitzschia australis. Concentrations of toxic phytoplankton (P australis), cyanobacteria, and bacteria in the layer were significantly higher than outside the layer (P< 0.05). Counts of total Pseudo-nitzschia spp. showed similar levels of enrichment in the layer compared to outside the layer. Our findings indicate that, when monitoring for HABs, it is critical to sample at scales appropriate to resolve thin layers. Thin layers have been identified as a common recurrent feature in a variety of coastal systems, suggesting that the use of autonomous high-resolution vertical profilers coupled with targeted sampling, could allow more timely detection of HABs in many coastal environments. [ABSTRACT FROM AUTHOR]

A high resolution, data assimilating ocean model of the Monterey Bay area (ICON model) is under development within the framework of the project “An Innovative Coastal-Ocean Observing Network” (ICON) sponsored by the National Oceanographic Partnership Program. The main objective of the ICON model development is demonstration of the capability of a high resolution model to track the major mesoscale ocean features in the Monterey Bay area when constrained by the measurements and nested within a regional larger-scale model.This paper focuses on the development of the major ICON model components, including grid generation and open boundary conditions, coupling with a larger scale, Pacific West Coast (PWC) model, atmospheric forcing etc. Impact of these components on the Model''s predictive skills in reproducing major hydrographic conditions in the Monterey Bay area are analyzed.Comparisons between observations and the ICON model predictions with and without coupling to the PWC model, show that coupling with the regional model improves significantly both the correlation between the ICON model and observed ADCP currents, and the ICON model''s skill in predicting the location and intensity of observed upwelling events.Analysis of the ICON model mixed layer depth predictions show that the ICON model tends to develop a thicker than observed mixed layer during the summer time, and while assimilation of sea surface temperature data is enough for development of observed thin mixed layer in the regional larger-scale model, the fine-resolution ICON model needs variable heat fluxes as surface boundary conditions for the accurate prediction of the vertical thermal structure.The paper targets researchers involved in high-resolution numerical modeling of coastal areas in which the dynamics are determined by the complex geometry of a coastline, variable bathymetry and by the influence of complex water masses from a complicated hydrographic system (such as the California Current system). [Copyright &y& Elsevier]

Managing for the effects of climate change on species whose populations are currently imperiled requires detailed knowledge of the relationship between their demographic rates and climate variables. We sought this information for the West Coast breeding population of snowy plover (Charadrius nivosus), which was federally listed as threatened in 1993 due to substantial declines in the numbers of plovers breeding along the coast and in the number of sites occupied for breeding. Snowy plovers employ a serially polygamous breeding system in which the male typically tends chicks to independence. This unusual breeding system is favored by male‐biased sex ratios in local populations. As part of a multispecies study of the effect of climate change on population growth, we used mark–capture models to examine climate drivers of adult survival for 1219 snowy plovers banded at Monterey Bay over 38 years and known to overwinter on the surrounding north‐central California outer coast. Nonclimate variables, including sex and unmeasured annual mortality risks (e.g., predator abundance), were the primary factors affecting adult survival. However, there is evidence that cold weather, particularly extended cold snaps with daily low temperatures below 2°C and daily high temperatures below 10°C, decreases overwinter survival. Exceptionally cold winters had a particularly strong effect on adult female plovers, contributing to the male‐biased adult sex ratios. Future winter climate on the north‐central California coast is projected to be generally warmer with fewer and shorter cold snaps. Reduced mortality from cold winter weather may mitigate other threats faced by plovers, such as anthropogenically enhanced predator populations, habitat loss, and accelerated sea level rise, while altering the adult sex ratio and potentially shifting the evolutionary landscape maintaining the plover's unusual breeding system. [ABSTRACT FROM AUTHOR]

Spinosyn insecticides are widely used in conventional berry production, and spinosad is regarded as the most effective insecticide for managing Drosophila suzukii (Matsumura) (Diptera: Drosophilidae), spotted-wing drosophila, in organic berry crops. Following the 2017 identification of spinosad resistance in caneberry fields in the Watsonville area, Santa Cruz Co., California, we conducted a study to examine the seasonal and annual susceptibility of D. suzukii over a three-year period. Adult flies were collected from two conventional and two organic caneberry fields in the Monterey Bay region, California, at 'early', 'middle', and 'late' time points during the 2018–2020 growing seasons, and their susceptibility to spinosad was assessed. Results demonstrated that spinosad susceptibility in the D. suzukii field populations generally decreased during the fruit production season (from June through November), and over consecutive seasons. LC50 values of adults from the conventional sites were determined to be as high as 228.7 mg l–1 in 2018, 665.6 mg l–1 in 2019, and 2700.8 mg l–1 in 2020. For the organically managed fields, LC50s of adults were as great as 300.0 mg l–1 in 2018, 1291.5 mg l–1 in 2019, and 2547.1 mg l–1 in 2020. Resistance ratios based on the LC50 values were as high as 10.7-, 13.2-, and 16.9-fold in 2018, 2019, and 2020, respectively. These results should serve as a caution for growers in other production areas, facilitate informed choice of insecticides used in D. suzukii management, and emphasize the need to develop effective insecticide resistance management strategies for this insect. [ABSTRACT FROM AUTHOR]

In this paper, a novel finite volume model with unstructured mesh and implicit dual time stepping is proposed for simulating unsaturated infiltration flows based on Richards's equation (RE), which is one of the most challenging problems in earth science. In time, a matrix-free fully implicit dual time stepping algorithm is developed to discrete the equation, and in space, the equation is discretized by the finite volume model with unstructured grid. The new method is assessed and evaluated by benchmark and engineering water infiltration cases. Both numerical solutions in the literature and solutions of a commercial package called GEO-Studio are used to verify the accuracy of the proposed algorithm. An unsteady water infiltration simulation case is carried out as the application of the current model by using the topographic dataset of the Monterey Bay in California. The results demonstrate that the new algorithm is robust and practical, with fast convergence and high accuracy. [ABSTRACT FROM AUTHOR]

Abstract: Glider observations were essential components of the observational program in the Autonomous Ocean Sampling Network (AOSN-II) experiment in the Monterey Bay area during summer of 2003. This paper is focused on the impact of the assimilation of glider temperature and salinity observations on the Navy Coastal Ocean Model (NCOM) predictions of surface and subsurface properties. The modeling system consists of an implementation of the NCOM model using a curvilinear, orthogonal grid with 1–4km resolution, with finest resolution around the bay. The model receives open boundary conditions from a regional (9km resolution) NCOM implementation for the California Current System, and surface fluxes from the Coupled Ocean–Atmosphere Mesoscale Prediction System (COAMPS) atmospheric model at 3km resolution. The data assimilation component of the system is a version of the Navy Coupled Ocean Data Assimilation (NCODA) system, which is used for assimilation of the glider data into the NCOM model of the Monterey Bay area. The NCODA is a fully 3D multivariate optimum interpolation system that produces simultaneous analyses of temperature, salinity, geopotential, and vector velocity. Assimilation of glider data improves the surface temperature at the mooring locations for the NCOM model hindcast and nowcasts, and for the short-range (1–1.5 days) forecasts. It is shown that it is critical to have accurate atmospheric forcing for more extended forecasts. Assimilation of glider data provided better agreement with independent observations (for example, with aircraft measured SSTs) of the model-predicted and observed spatial distributions of surface temperature and salinity. Mooring observations of subsurface temperature and salinity show sharp changes in the thermocline and halocline depths during transitions from upwelling to relaxation and vice versa. The non-assimilative run also shows these transitions in subsurface temperature; but they are not as well defined. For salinity, the non-assimilative run significantly differs from the observations. However, the glider data assimilating run is able to show comparable results with observations of thermocline as well as halocline depths during upwelling and relaxation events in the Monterey Bay area. It is also shown that during the relaxation of wind, the data assimilative run has higher value of subsurface velocity complex correlation with observations than the non-assimilative run. [Copyright &y& Elsevier]

Abstract: This paper investigates the transport structure of surface currents around the Monterey Bay, CA region. Currents measured by radar stations around Monterey Bay indicate the presence of strong, spatial and temporal, nonlinear patterns. To understand the geometry of the flow in the bay, Lagrangian coherent structures (LCS) are computed. These structures are mobile separatrices that divide the flow into regions of qualitatively different dynamics. They provide direct information about the flow structure but are geometrically simpler than particle trajectories themselves. The LCS patterns were used to reveal the mesoscale flow conditions observed during the 2003 Autonomous Ocean Sampling Network (AOSN-II) experiment. Drifter paths from the AOSN experiment were compared to the patterns induced by the LCS computed from high-frequency radar data. We verify that the fate of the drifters can be better characterized based on the LCS than direct interpretation of the current data. This property can be exploited to optimize drifter deployment. [Copyright &y& Elsevier]

High-frequency (HF) radar technology produces detailed velocity maps near the surface of estuaries and bays. The use of velocity data in environmental prediction, nonetheless, remains unexplored. In this paper, we uncover a striking flow structure in coastal radar observations of Monterey Bay, along the California coastline. This complex structure governs the spread of organic contaminants, such as agricultural runoff which is a typical source of pollution in the bay. We show that a HF radar-based pollution release scheme using this flow structure reduces the impact of pollution on the coastal environment in the bay. We predict the motion of the Lagrangian flow structures from finite-time Lyapunov exponents of the coastal HF velocity data. From this prediction, we obtain optimal release times, at which pollution leaves the bay most efficiently. [ABSTRACT FROM AUTHOR]

Common ravens (Corvus corax; ravens) are known nest predators that have the ability to negatively impact nesting birds, including imperiled species of seabirds and shorebirds. We conducted systematic necropsies of ravens that were lethally controlled in Monterey Bay, California, USA during 2013-2015, in or near western snowy plover (Charadrius nivosus nivosus) nesting areas, in an effort to better understand body condition, overall health, and diet of individual ravens. Raven predation of snowy plover nests has increased over the years in the Monterey Bay study area, and lethal removal of ravens has been employed to reduce predation. Most ravens examined in this study were in moderate to excellent body condition and also exhibited good organ health. There were statistically significant differences between male and female morphometrics (mass, culmen length, and wing length; P < 0.05). Stomach content analysis indicated a varied diet with consumption of animal remains and eggshell fragments, and anthropogenic sources of food (e.g., human food items and human-produced nonfood items). Our study provides evidence that lethal control of ravens targeted some individual ravens that were responsible for depredating snowy plover nests. [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]

A marine sanctuary is an environment where the interests of science and society meet. Land and marine managers need access to the best scientific data available that describe the environment and environmental processes in sanctuaries. The sidescan sonar imagery, bathymetry, sample analyses and other data discussed in the papers in this volume have been made available as a U.S. Geological Survey CDROM publication. [Copyright &y& Elsevier]

Harbor porpoises, Phocoena phocoena, off California, comprise four recognized population stocks: Morro Bay (MOR), Monterey Bay (MRY), San Francisco‐Russian River (SFRR), and Northern California‐Southern Oregon (NCSO). The three southernmost stocks experienced substantial bycatch in gill net fisheries during the 1970s and 1980s. While the SFRR stock received full protection from gill nets in 1989, the MOR and MRY stocks continued to experience at least some bycatch through 2001–2002. We examined long‐term population trends for these four harbor porpoise stocks, based on two sets of systematic, aerial line‐transect surveys conducted off California during summer/fall of 1986–2017. We applied a Bayesian hierarchical framework to specify a process model of population density and an observation model of porpoise counts during line‐transect surveys. Growth rates were estimated for periods with and without bycatch. Posterior distributions indicate the MOR, MRY, and SFRR stocks, respectively, grew at 9.6%, 5.8%, and 6.1% per year after gill nets were largely or fully eliminated for each stock. Abundance off northern California appears stable or slightly increasing. This study provides a first empirical estimate of maximum net reproductive rate for harbor porpoise (at least 9.6%), and demonstrates that porpoise populations can recover from substantial gill net impacts if bycatch is eliminated. [ABSTRACT FROM AUTHOR]

The California Current System is thought to be particularly vulnerable to ocean acidification, yet pH remains chronically undersampled along this coast, limiting our ability to assess the impacts of ocean acidification. To address this observational gap, we integrated the Deep-Sea-DuraFET, a solid-state pH sensor, onto a Spray underwater glider. Over the course of a year starting in April 2019, we conducted seven missions in central California that spanned 161 glider days and >1600 dives to a maximum depth of 1000 m. The sensor accuracy was estimated to be ± 0.01 based on comparisons to discrete samples taken alongside the glider (n = 105), and the precision was ± 0.0016. CO2 partial pressure, dissolved inorganic carbon, and aragonite saturation state could be estimated from the pH data with uncertainty better than ± 2.5%, ± 8 μmol kg-1, and ± 2%, respectively. The sensor was stable to ± 0.01 for the first 9 months but exhibited a drift of 0.015 during the last mission. The drift was correctable using a piecewise linear regression based on a reference pH field at 450 m estimated from published global empirical algorithms. These algorithms require accurate O2 as inputs; thus, protocols for a simple predeployment air calibration that achieved accuracy of better than 1% were implemented. The glider observations revealed upwelling of undersaturated waters with respect to aragonite to within 5 m below the surface near Monterey Bay. These observations highlight the importance of persistent observations through autonomous platforms in highly dynamic coastal environments. [ABSTRACT FROM AUTHOR]

Environmental DNA (eDNA) analysis allows the simultaneous examination of organisms across multiple trophic levels and domains of life, providing critical information about the complex biotic interactions related to ecosystem change. Here we used multilocus amplicon sequencing of eDNA to survey biodiversity from an eighteen-month (2015–2016) time-series of seawater samples from Monterey Bay, California. The resulting dataset encompasses 663 taxonomic groups (at Family or higher taxonomic rank) ranging from microorganisms to mammals. We inferred changes in the composition of communities, revealing putative interactions among taxa and identifying correlations between these communities and environmental properties over time. Community network analysis provided evidence of expected predator-prey relationships, trophic linkages, and seasonal shifts across all domains of life. We conclude that eDNA-based analyses can provide detailed information about marine ecosystem dynamics and identify sensitive biological indicators that can suggest ecosystem changes and inform conservation strategies. Increasingly, eDNA is being used to infer ecological interactions. Here the authors sample eDNA over 18 months in a marine environment and use co-occurrence network analyses to infer potential interactions among organisms from microbes to mammals, testing how they change over time in response to oceanographic factors. [ABSTRACT FROM AUTHOR]

Finding high-value locations for in situ data collection is of substantial importance in ocean science, where diverse bio-physical processes interact to create dynamically evolving phenomena. These cover a variable spatial extent, and are sparse and difficult to predict. Autonomous robotic platforms can sustain themselves in harsh conditions with persistent presence, but require deployment at the correct place and time. To that end, we consider the use of remote sensing data for building compact models that can improve skill in predicting sub-mesoscale features and inform onboard sampling. The model enables prediction of regional patterns based on sparse in situ data, a capability that is essential in regions where use of satellite remote sensing in real time is often limited by cloud cover. Our model is based on classification of sea-surface temperature (SST) images, but the technique is general across any remotely sensed parameter. Images having similar magnitude and spatial patterns are grouped into a compact set of conditional means representing the dominant states. The classification is unsupervised and uses a combination of dictionary learning and hierarchical clustering. The method is demonstrated using SST images from Monterey Bay, California. The consistency of the classification result is verified and compared with oceanographic forcing using historical wind measurements. The established model is then shown to work in a real application using measurements from an autonomous surface vehicle (ASV), together with forecast and sampling strategies. Finally an analysis of the model prediction error is presented and compared across different paths and survey duration. [ABSTRACT FROM AUTHOR]

This study examines the occurrence of humpback whale (Megaptera novaeangliae) song in the northeast Pacific from three years of continuous recordings off central California (36.713°N, 122.186°W). Song is prevalent in this feeding and migratory habitat, spanning nine months of the year (September–May), peaking in winter (November–January), and reaching a maximum of 86% temporal coverage (during November 2017). From the rise of song in fall through the end of peak occurrence in winter, song length increases significantly from month to month. The seasonal peak in song coincides with the seasonal trough in day length and sighting-based evidence of whales leaving Monterey Bay, consistent with seasonal migration. During the seasonal song peak, diel variation shows maximum occurrence at night (69% of the time), decreasing during dawn and dusk (52%), and further decreasing with increasing solar elevation during the day, reaching a minimum near solar noon (30%). Song occurrence increased 44% and 55% between successive years. Sighting data within the acoustic detection range of the hydrophone indicate that variation in local population density was an unlikely cause of this large interannual variation. Hydrographic data and modeling of acoustic transmission indicate that changes in neither habitat occupancy nor acoustic transmission were probable causes. Conversely, the positive interannual trend in song paralleled major ecosystem variations, including similarly large positive trends in wind-driven upwelling, primary productivity, and krill abundance. Further, the lowest song occurrence during the first year coincided with anomalously warm ocean temperatures and an extremely toxic harmful algal bloom that affected whales and other marine mammals in the region. These major ecosystem variations may have influenced the health and behavior of humpback whales during the study period. [ABSTRACT FROM AUTHOR]

The approach for modeling bioluminescence (BL) potential is proposed. The approach consists of (1) estimation of the adjoint (by backward in time integration of the adjoint model), (2) generation of ensembles of BL potential initial conditions and source minus sink term, and (3) estimation of two integrals: the integration of the adjoint with the BL potential initial conditions and the integration of the adjoint with the BL potential source minus sink term. In this case, the impact of physical processes on BL potential dynamics is introduced through the one backward integration of the adjoint. The proposed approach has been applied to modeling of the BL potential changes in the area of the submesoscale filament, which developed during the upwelling event in the Monterey Bay area, California. Comparisons of modeled histograms with those observed show that predicted changes in mean BL potential values in the area of filament very closely resemble the observed ones: increase over 5 days in mean BL potential values in the top 15 m and decrease in mean BL potential values between 30 and 45 m depth in the area of the filament. There is a similar good qualitative and quantitative agreement between observed and model-predicted differences in histograms when BL potential values in 30–45 m depth are compared to the BL potential values in the top 15 m. [ABSTRACT FROM AUTHOR]

Greatly enhanced atmospheric carbon dioxide (CO2) levels relative to well-mixed marine air are observed during periods of offshore winds at coastal sensor platforms in Monterey Bay, California, USA. The highest concentrations originate from urban and agricultural areas, are driven by diurnal winds, and peak in the early morning. These enhanced atmospheric levels can be detected across a ~100km wide nearshore area and represent a significant addition to total oceanic CO2 uptake. A global estimate puts the added sea-air flux of CO2 from these greatly enhanced atmospheric CO2 levels at 25 million tonnes, roughly 1% of the ocean’s annual CO2 uptake. The increased uptake over the 100 km coastal swath is of order 20%, indicating a potentially large impact on ocean acidification in productive coastal waters. [ABSTRACT FROM AUTHOR]

Cross-shelf exchange resulting from wind- and wave-driven flows across the inner shelf has been the focus of a considerable body of work. This contribution extends recent analyses to the central California coastline using 5-yr of moored current observations. Acoustic Doppler Current Profiler (ADCP) data from stations across the Monterey Bay (two in the northern bay and one in the southern bay), in water depths of ~20 m, showed net offshore transport throughout the year. For the northern bay sites, cross-shelf exchange was dominated by Ekman transport driven by along-shelf diurnal sea breezes during the upwelling season. Intense stratification in the northern bay leads to very shallow observed Ekman layers (~5-8 m), and consequently no overlap between bottom and surface Ekman layers within a few hundred meters of the coast. The total transport is less than predicted by theory consistent with models of shallow-water Ekman transport. The observed transport (~42% of full Ekman transport) is shown to be caused by the influence of a positive vorticity that effectively increases the Coriolis parameter. Wave-driven return flow estimated from an offshore buoy was strongly correlated with observed transport during nonupwelling conditions for the northern, outer bay site, but not for the two inner bay sites (northern and southern). In the southern bay, winds and waves have a significantly reduced effect on the cross-shelf exchange. Internal tidal bores are believed to contribute most of the observed cross-shelf exchange in this region. [ABSTRACT FROM AUTHOR]

Coastal upwelling is a wind-driven ocean process. It brings cooler, saltier, and usually nutrient-rich deep water upward to replace surface water displaced offshore due to Ekman transport. The nutrients carried up by upwelling are important for primary production and fisheries. Ocean life can aggregate at the boundary between stratified water and upwelling water—the upwelling front. In an upwelling water column, temperature, salinity, and other water properties are much more homogeneous over depth than in stratified water. Drawing on this difference, we set up a key measure for differentiating upwelling and stratified water columns—the vertical temperature difference between shallow and deep depths. The vertical temperature difference is large in stratified water but small in upwelling water. Based on this classifier, we developed a method for an autonomous underwater vehicle (AUV) to autonomously detect and track an upwelling front. During the Controlled, Agile, and Novel Observing Network (CANON) Experiment in April 2011, the Tethys long-range AUV ran the algorithm to autonomously track an upwelling front in a dynamic coastal upwelling region in Monterey Bay, CA. The AUV transected the upwelling front 14 times over two days, providing a very high-resolution depiction of the front. [ABSTRACT FROM AUTHOR]

Cabled ocean observatories enabling large amounts of power and two-way com-munication bandwidth for underwater experiments are a future approach for study-ing the oceans. On April 21,2011, at Monterey Bay, California, USA, a network node composed of a junction box (JBox) and three scientific instruments was deployed at the Monterey Accelerated Research System (MARS) site for a 6-month uninter-rupted sea trial. The JBox is a facility that can provide multiple wet-mateable con-nections for various instruments. Each connection can draw 500 W of power and has 10/100 Mbit/s network communication. The current study presents the design and construction of the JBox with focus on the following aspects: a power distribution system with high reliability; a flexible springloaded mechanical structure for heat dissipation; communication that incorporates various data protocols; and self-protection against faults like over-current, short fault, ground fault, and flooding. The deployment and operation of the JBox is described. The sea trial results show that the technologies and methods applied on the JBox and the deploying approach are applicable and worthy of consideration for long-term cabled ocean observatories. [ABSTRACT FROM AUTHOR]

Urmy, S. S., Horne, J. K., and Barbee, D. H. 2012. Measuring the vertical distributional variability of pelagic fauna in Monterey Bay. – ICES Journal of Marine Science, 69: 184–196.Temporal variability is an important feature of aquatic ecosystems that can be difficult to measure. A stationary, upward-facing scientific echosounder was used to record the vertical distribution of pelagic fauna in Monterey Bay, CA, for 18 months. To characterize the distributions, a suite of metrics, including measures of density, abundance, location, dispersion, occupancy, evenness, and aggregation, was developed and tested. An algorithm to detect and count the number of acoustic backscatter layers was developed using image-analysis techniques. The metrics recorded a strong seasonal cycle, with total backscatter reaching a minimum during the spring upwelling season and peaking in autumn and winter. Variability in the vertical distribution of animals was greatest at long time-scales and decreased as a power (−1.050 to −1.585) of signal frequency. There were significant peaks in the power spectrum at 12- and 24-h periods, corresponding to the semi-diurnal tide and diel vertical migration. The diel signal was strongest in late winter and weakest during the spring upwelling season. Active acoustics are a useful addition to ocean observatories, and the metrics presented provide a useful set of tools to quantify the distribution and temporal variability of pelagic fauna. [ABSTRACT FROM PUBLISHER]

A detailed energy analysis of the barotropic and baroclinic M2 tides in the Monterey Bay area is performed. The authors first derive a theoretical framework for analyzing internal tide energetics based on the complete form of the barotropic and baroclinic energy equations, which include the full nonlinear and nonhydrostatic energy flux contributions as well as an improved evaluation of the available potential energy. This approach is implemented in the Stanford Unstructured Nonhydrostatic Terrain-Following Adaptive Navier-Stokes Simulator (SUNTANS). Results from three-dimensional, high-resolution SUNTANS simulations are analyzed to estimate the tidal energy partitioning among generation, radiation, and dissipation. A 200 km × 230 km domain including all typical topographic features in this region is used to represent the Monterey Bay area. Of the 152-MW energy lost from the barotropic tide, approximately 133 MW (88%%) is converted into baroclinic energy through internal tide generation, and 42%% (56 MW) of this baroclinic energy radiates away into the open ocean. The tidal energy partitioning depends greatly on the topographic features. The Davidson Seamount is most efficient at baroclinic energy generation and radiation, whereas the Monterey Submarine Canyon acts as an energy sink. Energy flux contributions from nonlinear and nonhydrostatic effects are also examined. In the Monterey Bay area, the nonlinear and nonhydrostatic contributions are quite small. Moreover, the authors investigate the character of internal tide generation and find that in the Monterey Bay area the generated baroclinic tides are mainly linear and in the form of internal tidal beams. Comparison of the modeled tidal conversion to previous theoretical estimates shows that they are consistent with one another. [ABSTRACT FROM AUTHOR]

Between 2007 and 2009, we witnessed three aggressive interactions between harbor porpoises and bottlenose dolphins in Monterey Bay, California. This is the first time such aggression has been documented in the Pacific, and the first time a harbor porpoise was collected immediately after witnessing its death, inflicted by bottlenose dolphins. Of the bottlenose dolphins present, 92% were males either confirmed (61%) or putative (31%). Since 2005, 44 harbor porpoise deaths inflicted by bottlenose dolphins were documented in California. Aberrant behavior was rejected as a cause of aggression, based on widespread documentation of similar behaviors in other populations of free-ranging bottlenose dolphins. The evidence for interspecies territoriality as a form of competition for prey was weak: there is little dietary overlap and there are differences in bottlenose dolphin and harbor porpoise distribution patterns in California. Object-oriented play was plausible as a form of practice to maintain intraspecific infanticidal skills or a form of play to maintain fighting skills between male associates. Contributing factors could be high-testosterone levels, as attacks occurred at the height of the breeding season, and/or a skewed operational sex ratio. Ultimately, we need more information about bottlenose dolphin social structure at the time of the aggression. [ABSTRACT FROM AUTHOR]

The Environmental Sample Processor (ESP) is a device that allows for the underwater, autonomous application of DNA and protein probe array technologies as a means to remotely identify and quantify, in situ, marine microorganisms and substances they produce. Here, we added functionality to the ESP through the development and incorporation of a module capable of solid-phase nucleic acid extraction and quantitative PCR (qPCR). Samples collected by the instrument were homogenized in a chaotropic buffer compatible with direct detection of ribosomal RNA (rRNA) and nucleic acid purification. From a single sample, both an rRNA community profile and select gene abundances were ascertained. To illustrate this functionality, we focused on bacterioplankton commonly found along the central coast of California and that are known to vary in accordance with different oceanic conditions. DNA probe arrays targeting rRNA revealed the presence of 16S rRNA indicative of marine crenarchaea, SAR11 and marine cyanobacteria; in parallel, qPCR was used to detect 16S rRNA genes from the former two groups and the large subunit RuBisCo gene (rbcL) from Synecchococcus. The PCR-enabled ESP was deployed on a coastal mooring in Monterey Bay for 28 days during the spring-summer upwelling season. The distributions of the targeted bacterioplankon groups were as expected, with the exception of an increase in abundance of marine crenarchaea in anomalous nitrate-rich, low-salinity waters. The unexpected co-occurrence demonstrated the utility of the ESP in detecting novel events relative to previously described distributions of particular bacterioplankton groups. The ESP can easily be configured to detect and enumerate genes and gene products from a wide range of organisms. This study demonstrated for the first time that gene abundances could be assessed autonomously, underwater in near real-time and referenced against prevailing chemical, physical and bulk biological conditions. [ABSTRACT FROM AUTHOR]

A hybrid background error covariance (BEC) model for three-dimensional variational data assimilation of glider data into the Navy Coastal Ocean Model (NCOM) is introduced. Similar to existing atmospheric hybrid BEC models, the proposed model combines low-rank ensemble covariances with the heuristic Gaussian-shaped covariances to estimate forecast error statistics. The distinctive features of the proposed BEC model are the following: (i) formulation in terms of inverse error covariances, (ii) adaptive determination of the rank m of with information criterion based on the innovation error statistics, (iii) restriction of the heuristic covariance operator to the null space of , and (iv) definition of the BEC magnitudes through separate analyses of the innovation error statistics in the state space and the null space of . The BEC model is validated by assimilation experiments with simulated and real data obtained during a glider survey of the Monterey Bay in August 2003. It is shown that the proposed hybrid scheme substantially improves the forecast skill of the heuristic covariance model. [ABSTRACT FROM AUTHOR]

Aircraft measurements obtained during the 2003--04 Autonomous Ocean Sampling Network (AOSN-II) project were used to study the effect of small-scale variations of near-surface wind stress on coastal upwelling in the area of Monterey Bay. Using 5-km-long measurement segments at 35 m above the sea surface, wind stress and its curl were calculated with estimated accuracy of 0.02--0.03 N m−−2 and 0.1--0.2 N m−−2 per 100 kilometers, respectively. The spatial distribution of wind speed, wind stress, stress curl, and sea surface temperature were analyzed for four general wind conditions: northerly or southerly wind along the coastline, onshore flow, and offshore flow. Wind stress and speed maxima frequently were found to be noncollocated as bulk parameterizations imply owing to significant stability and nonhomogeneity effects at cold SST pools. The analyses revealed that complicated processes with different time scales (wind stress field variation, ocean response and upwelling, sea surface currents, and heating by solar radiation) affect the coastal sea surface temperature. It was found that the stress-curl-induced coastal upwelling only dominates in events during which positive curl extended systematically over a significant area (scales larger than 20 km). These events included cases with a northerly wind, which resulted in an expansion fan downstream from Point Añño Nuevo (wind speed peaks greater than about 8--10 m s−−1), and cases with an offshore/onshore flow, which are characterized by weak background upwelling due to Ekman transport. However, in general, observations show that cold pools of sea surface temperature in the central area of Monterey Bay were advected by ocean surface currents from strong upwelling regions. Aircraft vertical soundings taken in the bay area showed that dominant effects of the lee wave sheltering of coastal mountains resulted in weak atmospheric turbulence and affected the development of the atmospheric boundary layer. This effect causes low wind stress that limits upwelling, especially at the northern part of Monterey Bay. The sea surface temperature is generally warm in this part of the bay because of the shallow oceanic surface layer and solar heating of the upper ocean. [ABSTRACT FROM AUTHOR]

Sex differences in adult mortality may be responsible for male-skewed adult sex ratios and male-skewed parental care in some birds. Because a surplus of breeding males has been reported in serially polyandrous populations of Snowy Plover Charadrius alexandrinus, we examined sex ratio, early-season nesting opportunities, adult survival and annual reproductive success of a Snowy Plover population at Monterey Bay, California. We tested the hypotheses that male adult survival was greater than female survival and that a sex difference in adult survival led to a skewed adult sex ratio, different mating opportunities and different annual productivity between the sexes. Virtually all females left chicks from their first broods to the care of the male and re-nested with a new mate. As a result, females had time to parent three successful nesting attempts during the lengthy breeding season, whereas males had time for only two successful attempts. Among years, the median population of nesting Plovers was 96 males and 84 females (median difference = 9), resulting in one extra male per eight pairs. The number of potential breeders without mates during the early nesting period each year was higher in males than in females. Adult male survival (0.734 ± 0.028 se) was higher than female survival (0.693 ± 0.030 se) in top-ranked models. Annually, females parented more successful clutches and fledged more chicks than their first mates of the season. Our results suggest that in C. alexandrinus a sex difference in adult survival results in a male-skewed sex ratio, which creates more nesting opportunities and greater annual productivity for females than for males. [ABSTRACT FROM AUTHOR]

Abstract: An In Situ Ultraviolet Spectrophotometer (ISUS) was coupled to a benthic chamber to characterize the bisulfide flux emanating from a warm spring at the Extrovert Cliff locality within Monterey Bay, California. The chamber was periodically flushed with bottom seawater to reset chemical concentrations, which enabled deployments over multiple days. Data from several deployments, each lasting at least 10 days, were used to calculate flow rates, fluid concentrations, and fluxes over time. The bisulfide concentration of the fluid entering the chamber varied from 75 to 4500μmoll−1. Positive temperature anomalies up to 3.5° were associated with these elevated concentrations. Linear flow rates ranged from 2 to >17mday−1, while the bisulfide fluxes varied from 0.2 to 80molm−2 day−1. The bisulfide originated at depth and was not produced in the surface sediments via an anaerobic oxidation of methane coupled to sulfate reduction. Tides modulated the flow as well as the composition of the fluid entering the chamber. It appeared that a deep sourced fluid, which supplied the bisulfide, was mixed with a second, ambient seawater-like fluid before entering the flux chamber. At low tides, flow rates were at their highest and the contribution of the deep sourced fluid to the fluid entering the chamber was at a maximum. [ABSTRACT FROM AUTHOR]

A full-scale adaptive ocean sampling network was deployed throughout the month-long 2006 Adaptive Sampling and Prediction (ASAP) field experiment in Monterey Bay, California. One of the central goals of the field experiment was to test and demonstrate newly developed techniques for coordinated motion control of autonomous vehicles carrying environmental sensors to efficiently sample the ocean. We describe the field results for the heterogeneous fleet of autonomous underwater gliders that collected data continuously throughout the month-long experiment. Six of these gliders were coordinated autonomously for 24 days straight using feedback laws that scale with the number of vehicles. These feedback laws were systematically computed using recently developed methodology to produce desired collective motion patterns, tuned to the spatial and temporal scales in the sampled fields for the purpose of reducing statistical uncertainty in field estimates. The implementation was designed to allow for adaptation of coordinated sampling patterns using human-in-the-loop decision making, guided by optimization and prediction tools. The results demonstrate an innovative tool for ocean sampling and provide a proof of concept for an important field robotics endeavor that integrates coordinated motion control with adaptive sampling. [ABSTRACT FROM AUTHOR]

Coupled biological and physical oceanographic models are powerful tools for studying connectivity among marine populations because they simulate the movement of larvae based on ocean currents and larval characteristics. However, while the models themselves have been parameterized and verified with physical empirical data, the simulated patterns of connectivity have rarely been compared to field observations. We demonstrate a framework for testing biological-physical oceanographic models by using them to generate simulated spatial genetic patterns through a simple population genetic model, and then testing these predictions with empirical genetic data. Both agreement and mismatches between predicted and observed genetic patterns can provide insights into mechanisms influencing larval connectivity in the coastal ocean. We use a high-resolution ROMS-CoSINE biological-physical model for Monterey Bay, California specifically modified to simulate dispersal of the acorn barnacle, Balanus glandula. Predicted spatial genetic patterns generated from both seasonal and annual connectivity matrices did not match an observed genetic cline in this species at either a mitochondrial or nuclear gene. However, information from this mismatch generated hypotheses testable with our modelling framework that including natural selection, larval input from a southern direction and/or increased nearshore larval retention might provide a better fit between predicted and observed patterns. Indeed, moderate selection and a range of combined larval retention and southern input values dramatically improve the fit between simulated and observed spatial genetic patterns. Our results suggest that integrating population genetic models with coupled biological-physical oceanographic models can provide new insights and a new means of verifying model predictions. [ABSTRACT FROM AUTHOR]

A high-resolution (250 m) primitive equation model is used to simulate the depth-averaged and baroclinic M2 tides in the Monterey Bay region. The model shows a high level of skill in comparisons with sea level observations. ADCP current observations within the submarine canyon are reasonably well reproduced. The modeled depth-averaged currents have a complex spatial pattern with magnitudes in excess of 0.1 m s−1 near Moss Landing. During the second half of flood (ebb) tide, the flow is into (out of) the bay through the canyon but out of (into) the bay over the shelf regions. This depth-averaged flow pattern is not evident in a diagnostic run, implying a feedback between the internal tides and the pressure gradient in the bay. The depth-integrated baroclinic (total minus depth-averaged) energy fluxes show a complex beamlike pattern due to the interaction of energy from multiple sources. The beams have magnitudes up to 1 kW m−1 interspersed with regions of near-zero depth-integrated flux. Energy entering the bay propagates northward from generation regions along the continental margins to the south of the bay (notably on the flanks of Sur Platform) and is steered into the canyon. A localized increase in depth-integrated baroclinic flux magnitude (up to 5 times the values elsewhere in the domain) closely follows the canyon axis near the mouth of the bay, presumably due to topographic focusing. Upper ocean velocities from a long-term surface mooring (MBARI M1) are used to assess the temporal variability of the M2 tide outside the canyon. [ABSTRACT FROM AUTHOR]

The black surfperch Embiotoca jacksoni and the striped surfperch E. lateralis (Embiotocidae, Perciformes) are livebearing temperate reef fishes that live sympatrically over a large portion of their distribution range, where they exhibit strong ecological competition. In order to assess whether mating strategies reflect competition, we investigated multiple paternity in these two species in an area of sympatry. We sampled 24 pregnant females (12 for each species) in Monterey Bay, California, used microsatellite analysis and assessed paternity with the COLONY software. While broods are relatively small (12 to 36 offspring), they were always sired by multiple fathers (2 to 9), with no correlation between the size of a brood and the number of fathers. The number of sires for each brood was not significantly different between the two species (approximately 3.5 sires per brood). We tested the deviation from stochasticity of fathered offspring for each father in one brood. Results showed a significant deviation for both E. jacksoni and E. lateralis. However, this deviation was not found to be significant between species. The striking similarity in the dynamics of multiple paternity in these species, when sampled in sympatry, may result from several alternative scenarios, including phylogenetic inertia, reproductive behaviour, and ecological competition. [ABSTRACT FROM AUTHOR]

In November-December 2007 a widespread seabird mortality event occurred in Monterey Bay, California, USA, coincident with a massive red tide caused by the dinoflagellate Akashiwo sanguinea. Affected birds had a slimy yellow-green material on their feathers, which were saturated with water, and they were severely hypothermic. We determined that foam containing surfactant-like proteins, derived from organic matter of the red tide, coated their feathers and neutralized natural water repellency and insulation. No evidence of exposure to petroleum or other oils or biotoxins were found. This is the first documented case of its kind, but previous similar events may have gone undetected. The frequency and amplitude of red tides have increased in Monterey Bay since 2004, suggesting that impacts on wintering marine birds may continue or increase. [ABSTRACT FROM AUTHOR]

The nonlinear multiscale dynamics of the Monterey Bay circulation during the Second Autonomous Ocean Sampling Network (AOSN-II) Experiment (August 2003) is investigated in an attempt to understand the complex processes underlying the highly variable ocean environment of the California coastal region. Using a recently developed methodology, the localized multiscale energy and vorticity analysis (MS-EVA) and the MS-EVA-based finite-amplitude hydrodynamic instability theory, the processes are reconstructed on three mutually exclusive time subspaces: a large-scale window, a mesoscale window, and a submesoscale window. The ocean is found to be most energetic in the upper layers, and the temporal mesoscale structures are mainly trapped above 200m. Through exploring the nonlinear window–window interactions, it is found that the dynamics underlying the complex surface circulation is characterized by a well-organized, self-sustained bi-modal instability structure: a Bay mode and a Point Sur mode, which are located nearMonterey Bay and west of Point Sur, respectively. Both modes are of mixed types, but they are distinctly different in dynamics. The former is established when the wind relaxes, while the latter is directly driven by the wind. Either way, the wind instills energy into the ocean, which is stored within the large-scale window and then released to fuel temporal mesoscale processes. Upon wind relaxation, the generated mesoscale structures propagate northward along the coastline, in a form with dispersion properties similar to that of a free thermocline-trapped coastal-trapped wave. Between these two modes, a secondary instability is identified in the surface layer during 15–21 August, transferring energy to the temporal submesoscale window. Also studied is the deep-layer flow, which is unstable all the time throughout the experiment within the Bay and north of the deep canyon. It is observed that the deep temporal mesoscale flow within the Bay may derive its energy from the submesoscale window as well as from the large-scale window. This study provides a real ocean example of how secondary upwelling can be driven by winds through nonlinear instability and how winds may excite the ocean via an avenue distinctly different from the classical paradigms. [ABSTRACT FROM AUTHOR]

The central California coast is a highly productive, biodiverse region that is frequently affected by the toxin-producing dinoflagellate Alexandrium catenella. Despite the consistent presence of A. catenella along our coast, very little is known about the movement of its toxins through local marine food webs. In the present study, we investigated 13 species of commercial finfish and rock crabs harvested in Monterey Bay, California for the presence of paralytic shellfish toxins (PSTs) and compared them to the presence of A. catenella and PSTs in sentinel shellfish over a 3-year period. Between 2003 and 2005, A. catenella was noted in 55% of surface water samples ( n = 307) and reached a maximum concentration of 17,387 cells L−1 at our nearshore site in Monterey Bay. Peak cell densities occurred in the month of July and were associated with elevated shellfish toxicity in the summers of 2004 and 2005. When A. catenella was present, particulate PSTs were detected 71% of the time and reached a maximum concentration of 962 ng STXeq L−1. Of the 13 species tested, we frequently detected PSTs in Pacific sardines ( Sardinops sagax; maximum 250 μg STXeq 100 g−1), northern anchovies ( Engraulis mordax; maximum 23.2 μg STXeq 100 g−1), brown rock crabs ( Cancer antennarius; maximum 49.3 μg STXeq 100 g−1) and red rock crabs ( C. productus; 23.8 μg STXeq 100 g−1). PSTs were also present in one sample of Pacific herring ( Clupea pallas; 13.3 μg STXeq 100 g−1) and one sample of English sole ( Pleuronectes vetulus; 4.5 μg STXeq 100 g−1), and not detected in seven other species of flatfish tested. The presence of PSTs in several of these organisms reveals that toxins produced by A. catenella are more prevalent in California food webs than previously thought and also indicates potential routes of toxin transfer to higher trophic levels. [ABSTRACT FROM AUTHOR]

Extreme male dwarfism occurs in Osedax (Annelida: Siboglinidae), marine worms with sessile females that bore into submerged bones. Osedax are hypothesized to use environmental sex determination, in which undifferentiated larvae that settle on bones develop as females, and subsequent larvae that settle on females transform into dwarf males. This study addresses several hypotheses regarding possible recruitment sources for the males: (i) common larval pool— males and females are sampled from a common pool of larvae; (ii) neighbourhood— males are supplied by a limited number of neighbouring females; and (iii) arrhenotoky— males are primarily the sons of host females. Osedax rubiplumus were sampled from submerged whalebones located at 1820-m and 2893-m depths in Monterey Bay, California. Immature females typically did not host males, but mature females maintained male ‘harems’ that grew exponentially in the number of males as female size increased. Allozyme analysis of the females revealed binomial proportions of nuclear genotypes, an indication of random sexual mating. Analysis of mitochondrial DNA sequences from the male harems and their host females allowed us to reject the arrhenotoky and neighbourhood hypotheses for male recruitment. No significant partitioning of mitochondrial diversity existed between the male and female sexes, or between subsamples of worms collected at different depths or during different years (2002–2007). Mitochondrial sequence diversity was very high in these worms, suggesting that as many as 106 females contributed to a common larval pool from which the two sexes were randomly drawn. [ABSTRACT FROM AUTHOR]

Elkhorn Slough is a shallow, tidally forced estuary that is directly connected to Monterey Bay. It is ebb-dominated and, due to continued erosion, the tidal prism has tripled over the past 40 years. Water level measurements at four locations are used to examine tidal and nontidal oscillations in Elkhorn Slough. The tidal response of Elkhom Slough differs from that of Monterey Bay primarily due to the generation of a relatively large number of shallow-water tidal constituents that are due to tidal distortion caused by friction along the bottom and lateral boundaries, intertidal storage, and nonlinear advection. The shallow-water constituents range from 3 to almost 15 cycles per day (cpd) and include a rich variety of overtides and compound tides, whose amplitudes generally increase toward the head of the slough. The tidal harmonics are seasonally dependent, with lower amplitudes during the fall and winter and higher amplitudes in summer. The tidal constituents were examined using two types of spectral decomposition, the conventional power spectrum and the more recent Hilbert spectrum. Unlike the power spectrum, the Hubert spectrum does not reveal any harmonic structure in the data. Energy associated with tidal distortion in this case appears to be broadly distributed across the spectral continuum. At least four nontidal oscillations occur in Elkhorn Slough with frequencies of 26.0, 39.7, 52.7, and 66.9 cpd. The Hilbert spectrum reveals maxima at 26, 39.7, and 66.9 cpd, but not at 52.7 cpd, suggesting that it is harmonically related to the oscillation at 26.0 cpd. The nontidal oscillations fall' into the range of frequencies associated with the natural oscillations of Monterey Bay. However, evolutionary power spectra indicate that they appear to be permanent features of the system and thus are not necessarily consistent with seiche-like oscillations that are often transient and subject to damping. These oscillations could be caused by several factors including edge waves along the coast of Monterey Bay, long-period surface waves of atmospheric origin that enter the bay from offshore, or breaking internal waves in and around the Monterey Submarine Canyon. In conclusion, detailed hydrodynamic models are needed to provide a better understanding of how tidal harmonics are generated and preserved in Elkhorn Slough, and to determine the origin of the natural oscillations in Monterey Bay. [ABSTRACT FROM AUTHOR]

Remotely operated vehicle dive video recordings of deep-sea squid ink release were examined to determine species, ink release type, release depth, and accompanying behavior/s. Ink release was commonly observed between the surface and 1,842.1 m in Monterey Bay, CA, and surrounding waters. Six ink release types were observed: pseudomorphs, pseudomorph series, ink ropes, clouds/smokescreens, diffuse puffs and mantle fills. Each species released ink throughout all or most of its depth range; inking was not limited to shallow, sunlit waters. Individuals of each species produced one ink release type more commonly than other types, however, multiple ink types could be released by individuals of all species. Common behaviors preceded and/or followed each release type; pseudomorphs and pseudomorph series were generally associated with escape behaviors, while ink ropes, clouds, and puffs normally involved the animal remaining adjacent to or amid the ink. Deep-sea squids may use ink for defensive purposes similar to those of shallow-dwelling species when they release pseudomorphs, pseudomorph series, or large clouds, and may use ink puffs in intra-specific communication. The function of ink ropes and mantle fills is unknown. [ABSTRACT FROM AUTHOR]

Abstract: In the mesopelagic zone, at depths of 200–1000m in the Monterey Submarine Canyon, CA, medusae in three genera of scyphozoa, Atolla, Periphylla and Poralia, were observed, videotaped and collected over a 9-year period (1990–1998). Environmental data were obtained simultaneously using a remotely operated vehicle (ROV) with sensors for depth, temperature, salinity and dissolved oxygen. Shipboard measurements of these same properties at two reference stations in the region defined the local water masses and helped identify species niches using the metric of spiciness and oxygen levels of the waters in which medusae were visually “captured”. The most abundant genus of mesopelagic scyphomedusae was Atolla, found associated most strongly with the spicy (warm, salty) waters of the California Undercurrent, usually above the core of the oxygen minimum zone (OMZ; O2>0.5ml/l). The least abundant mesopelagic scyphomedusa was Periphylla, which occurred in more variable waters, including those with a greater contribution of fresher, colder (less spicy), subarctic water and, hence, most like those at the offshore California Current station in the most depleted oxygen zone (averaging O2 <0.3ml/l). Poralia was mostly confined to the densest, coldest water, with peak abundance at the lower boundary of the OMZ (i.e., 0.3< O2<0.5ml/l). These spiciness measures on local isopycnal surfaces within the mesopelagic zone, supported by data on dissolved oxygen concentrations, indicate highly significant but fine-scale habitat differences in species habitats in Central California waters. This in situ investigation appears to be one of only a few studies to document fine-scale, water mass affinities of mesopelagic zooplankton. [Copyright &y& Elsevier]

Since the well-known failures of many experimental colleges and programs in the 1960s and 1970s, policymakers and scholars are often cynical about the possibilities for organisational innovation, particularly within public universities. Public university innovation is possible, however, when organisational actors seek to institutionalise reform and use the legitimacy of reform to obtain adequate human and financial resources. An illustrative case study of California State University at Monterey Bay is used to describe how institutionalisation processes can be used to establish, support and expand public university innovation, which may be increasingly crucial to meet political and competitive demands for university adaptation. [ABSTRACT FROM AUTHOR]

The vesicomyid Calyptogena kilmeri is one of the most abundant bivalves inhabiting chemosynthetic environments shallower than c. 1500 m along central California. We estimated the population size structure, biomass, rates of individual growth, somatic production, and mortality for C. kilmeri, based on sampling of seep habitats and tag–recapture studies at chemosynthetic communities in Monterey Bay, California. The composite growth rate of C. kilmeri over all sites was relatively high (K = 0.25), reaching c. 80% of asymptotic length (104.7 mm) in 6.6 years. The density of C. kilmeri was estimated as 938.5 ind. m−2 and biomass density varied from 704 to 2059 g ash free dry mass (AFDM) m−2. Somatic production was also high (294–297 g·AFDM·m−2 year−1), and production/biomass ratios for C. kilmeri varied from 0.14 to 0.42 among sites, related to variation in size–frequency distributions among sites. Instantaneous mortality rates estimated from size distributions ranged from 0.17 to 0.24 year−1. Growth and somatic production by C. kilmeri are in the range reported for chemosynthetic bivalves from hydrothermal vent and seep habitats, as well as photosynthetic-based assemblages of inshore or intertidal bivalves, and greatly exceed rates reported for heterotrophic deep-sea benthos. [ABSTRACT FROM AUTHOR]