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Prior to burning down in 1906 CE, Point Alones in the Monterey Bay region of Central California was home to one of the largest Chinese fishing communities in the United States of America. Both historical records and the recovery of numerous cartilaginous fish (Chondrichthyes) vertebrae during archaeological excavations of the village indicate sharks were among the taxonomic groups being regularly harvested by its inhabitants. However, as shark vertebrae are difficult to identify past the family-level using conventional morphology-based approaches, our understanding of the Point Alones shark fishery remains incomplete. In this study, we address this issue by using ancient DNA analysis to assign species-level identifications to a sample of 54 shark vertebrae from the site. We successfully amplified a 173 bp fragment of the mitochondrial cytochrome c oxidase I gene from 47 of the 54 analyzed specimens (87.03%). Our results indicate that Tope Shark (Galeorhinus galeus; n = 39) was the primary focus of the site's shark fishery, with Brown Smooth-Hound (Mustelus henlei; n = 7) and Leopard Shark (Triakis semifasciata; n = 1) also harvested to a lesser extent. All three of these species are found locally in the waters overlying the continental shelf, suggesting Chinese fishers were harvesting sharks from these coastal environments. While some of the sharks caught by fishers from Point Alones were likely being consumed at the village, historical records suggest a significant number of fins from harvested Tope Sharks were also likely being exported to China and other diaspora communities. [ABSTRACT FROM AUTHOR]

Recent work using compound-specific stable isotopes of amino acids (CSI-AA) in proteinaceous deep-sea corals opens a new realm of high-fidelity reconstruction for biogeochemical and ecological changes in the ocean. However, underlying these CSI-AA paleoceanographic applications are a series of fundamental assumptions, which hold first that baseline-proxy AA isotope values fixed at the base of food webs represent integrated δ13C and δ15N values of primary production, and second they are unaltered during subsequent export and incorporation from particles into corals. We explored long-term δ13C and δ15N CSI-AA data on a sediment trap time series together with contemporaneous, geographically close deep-sea bamboo corals (Isidella sp.) in the California margin, directly testing these assumptions for the first time. Our data show that isotope values of essential (δ13C EAA) and source AAs (δ15N Phe) in sinking particles quantitatively track bulk δ13C and δ15N values of export production. These CSI-AA baseline proxies varied independently of carbon flux, trophic position (TP CSI-AA) and microbial alteration, suggesting that they were well preserved in the sinking particles consumed by corals. Paired comparisons between sinking particles and corals revealed minor elevations of δ13C EAA (by ∼2‰) and δ15N Phe (by ∼1‰) in available coral specimens. We hypothesize that the difference in δ13C EAA is due to the geographic offset in δ13C values of primary production expected between the (more offshore) sediment trap site and (more onshore) coral specimens, whereas the δ15N Phe offset is likely related to expected minor trophic fractionation. Using empirical models derived from the sediment trap time series, we demonstrate for the first time that CSI-AA in proteinaceous deep-sea corals can reconstruct known bulk δ15N values of export production, source nitrogen δ15N values, and exported TP CSI-AA values with very good fidelity. Together, these findings represent a major advance in our understanding of AA isotope behavior in modern and paleoarchives, and can be used to underpin the rapidly evolving use of CSI-AA-based tools in multiple paleoceanographic studies and archives. [ABSTRACT FROM AUTHOR]

The organic sulfur compound dimethylsulfoniopropionate (DMSP) is synthesized by numerous species of marine phytoplankton, and its volatile degradation products are a major source of biogenic sulfur to the atmosphere. A massive bloom of the dinoflagellate Akashiwo sanguinea occurred in Monterey Bay, CA, USA, in the fall of 2016 and led to exceptionally high seawater DMSP concentrations that peaked at 4,240 nM. Bacterial consumption rates showed that only a small fraction of the DMSP standing stock flowed through the dissolved DMSP pool per day, contributing to the high DMSP concentrations and creating conditions conducive to production of dimethylsulfide (DMS). Conservative calculations of DMS yield from this persistent A. sanguinea bloom suggest substantial regional‐scale inputs of DMS‐sulfur to the atmosphere. Other recently reported major coastal blooms of A. sanguinea, along with indications that this species may benefit from climate change conditions, reveal a mechanism that could alter oceanic contributions to atmospheric sulfur pools. Plain Language Summary: Marine phytoplankton produce the organic sulfur compound dimethylsulfoniopropionate (DMSP), which is used for osmotic balance and serves as a carbon and sulfur source to marine bacteria. A massive bloom of a dinoflagellate in Monterey Bay, CA, USA, in 2016 resulted in extremely high concentrations of DMSP over a 6‐week period, the highest DMSP concentrations yet recorded. This extended bloom established ideal conditions for the release of volatile sulfur from the ocean. More frequent and extensive blooms of DMSP‐producing phytoplankton have been observed and may affect ocean contributions to the atmospheric sulfur pool and the formation of cloud condensation nuclei. Key Points: A dinoflagellate bloom of exceptional proportions occurred in Monterey Bay and offshore regions of the Pacific Ocean in fall 2016DMSP concentrations during 46 days of the Akashiwo sanguinea bloom were the highest ever recordedOnly a small fraction of the DMSP standing stock flowed through the dissolved pool each day, creating conditions conducive to high DMS flux [ABSTRACT FROM AUTHOR]

Natural resource sustainability depends on adaptive capacity: the latent ability of a social-ecological system to rely on or implement effective strategies to cope with disturbances. We propose and implement a new three-step framework for studying a social-ecological system's adaptive capacity that consists of assessment, strategy identification, and activation. We apply this framework to analyze the adaptive capacity of the Monterey Bay wetfish fisheries community in response to a significant stressor in the system: El Niño Southern Oscillation (ENSO). We conducted 49 semi-structured interviews with participants engaged in these fisheries and/or providing ENSO information. Of the 67 social-ecological strategies identified through a literature review, we found 42 contribute to high adaptive capacity to ENSO. The most influential strategies were matching formal and informal rules to system dynamics, diversifying livelihoods, enhancing economic safety nets, social learning, and accessing early warning systems. Our findings suggest approaches for enhancing adaptive capacity in other resource systems. [ABSTRACT FROM AUTHOR]

Highlights • An integrated deployment of multiple in situ platforms uncovered detailed aspects of population and toxicity dynamics of Pseudo-nitzschia across divergent bloom years in Monterey Bay. • Shifts in Pseudo-nitzschia species composition and abundance leading into the 2015 bloom in Monterey Bay were consistent with observations made further north off Oregon and Washington coasts during the northeast Pacific warm anomaly. Abstract Monterey Bay, California experiences near-annual blooms of Pseudo-nitzschia that can affect marine animal health and the economy, including impacts to tourism and commercial/recreational fisheries. One species in particular, P. australis , has been implicated in the most toxic of events, however other species within the genus can contribute to widespread variability in community structure and associated toxicity across years. Current monitoring methods are limited in their spatial coverage as well as their ability to capture the full suite of species present, thereby hindering understanding of HAB events and limiting predictive accuracy. An integrated deployment of multiple in situ platforms, some with autonomous adaptive sampling capabilities, occurred during two divergent bloom years in the bay, and uncovered detailed aspects of population and toxicity dynamics. A bloom in 2013 was characterized by spatial differences in Pseudo-nitzschia populations, with the low-toxin producer P. fraudulenta dominating the inshore community and toxic P. australis dominating the offshore community. An exceptionally toxic bloom in 2015 developed as a diverse Pseudo-nitzschia community abruptly transitioned into a bloom of highly toxic P. australis within the time frame of a week. Increases in cell density and proliferation coincided with strong upwelling of nutrients. High toxicity was driven by silicate limitation of the dense bloom. This temporal shift in species composition mirrored the shift observed further north in the California Current System off Oregon and Washington. The broad scope of sampling and unique platform capabilities employed during these studies revealed important patterns in bloom formation and persistence for Pseudo-nitzschia. Results underscore the benefit of expanded biological observing capabilities and targeted sampling methods to capture more comprehensive spatial and temporal scales for studying and predicting future events. [ABSTRACT FROM AUTHOR]

Abstract Anthropogenic input of carbon dioxide (CO 2) into the atmosphere and its uptake by the ocean with associated changes in ocean chemistry have created an urgent need to expand coverage of sea surface and atmospheric carbon dioxide observations. Conventional sampling platforms (e.g. ships and moorings) do not provide the spatial and temporal resolution needed to assess the effects of rapidly changing carbon dioxide conditions and are expensive to operate. Through a series of deployments beginning in March 2012, two versions of the Wave Glider autonomous surface vehicles from Liquid Robotics, Inc. have been instrumented with sensors to measure pH, partial pressure of CO 2 (p CO 2) of the atmosphere and sea surface, and wind speed and direction, from which instantaneous sea-air fluxes of CO 2 can be calculated. These deployments, most near Monterey Bay, California, were highly correlated with Δ p CO 2 measurements obtained from the Monterey Bay Aquarium Research Institute's (MBARI) long-term mooring station M1, as well as from shipboard observations. In the central California upwelling system with highly variable p CO 2 levels, the gliders captured large spatial gradients associated with upwelling fronts. Differences in sea surface p CO 2 as large as 470 μ atm over < 0.5 km were observed. Unlike traditional ship sampling methods, however, this new generation of sampling platforms is capable of continuous long-term (months) deployments at a fraction of the cost. The vehicles thus have the potential of filling important gaps in present understanding of the effects of global change on ocean chemistry. [ABSTRACT FROM AUTHOR]

Abstract Sediment traps were deployed at two depths (300 m and 1200 m) off Monterey Bay (36°40′N and 122°25′W, Central California) for 7.3 years (1998–2005). The sediment trap data provided information about the quantity and quality of settling material, and allowed exploration of the relationship of the sinking material with the environmental conditions in this coastal upwelling region. The magnitude and composition of the settling material were highly variable over time. Organic carbon (C org) fluxes ranged between 4–296 mg C m−2 day−1 and 0.1–142 mg C m−2 day−1 for shallow and deep sediment traps, respectively. The time series of C org vertical flux was characterized by pulses of intense fluxes that were associated with peaks of primary production, generally during upwelling periods. Despite considerable variability, fluxes varied seasonally with highest values during the upwelling season and the lowest in winter. Attenuation of C org vertical fluxes with depth (300 m vs. 1200 m) varied between 31% and 24% except for the late upwelling period, when there was an increase with depth likely due to resuspension of material from Monterey Canyon. Calculation of a seasonal vertical budget of organic carbon off Monterey Bay resulted in a transfer between 4.0% and 4.9% of the primary production to the deep ocean, suggesting that coastal upwelling efficiently sequestered CO 2. [ABSTRACT FROM AUTHOR]

Fluvial sediment deposits can provide useful records of integrated watershed expressions including flood event magnitudes. However, floodplain and estuarine sediment deposits evolve through the interaction of watershed/marine sediment supply and transport characteristics with the local depositional environment. Thus extraction of watershed scale signals depends upon accounting for local scale effects on sediment deposition rates and character. This study presents an examination of the balance of fluvial sediment dynamics and local scale hydro-geomorphic controls on alluviation of an abandoned channel in the Salinas River Lagoon, CA. A set of three sediment cores contained discrete flood deposits that corresponded to the largest flood events over the period of accretion from 1969 to 2007. Sedimentation rates scaled with peak flood discharge and event scale sediment flux, but were not influenced by longer scale hydro-meteorological activities such as annual precipitation and water yield. Furthermore, the particle size distributions of flood deposits showed no relationship to event magnitudes. Both the responsiveness of sedimentation and unresponsiveness of particle size distributions to hydro-sedimentological event magnitudes appear to be controlled by aspects of local geomorphology that influence the connectivity of the abandoned channel to the Salinas River mainstem. Well-developed upstream plug bar formation precluded the entrainment of coarser bedload into the abandoned channel, while Salinas River mouth conditions (open/closed) in conjunction with tidal and storm surge conditions may play a role in influencing the delivery of coarser suspended load fractions. Channel adjacent sediment deposition can be valuable records of hydro-meteorological and sedimentological regimes, but local depositional settings may dominate the character of short term (interdecadal) signatures. [ABSTRACT FROM AUTHOR]

The Brandt's Cormorant of the California Current is a “boom-or-bust” species like its congeners in other eastern boundary, upwelling driven ecosystems, and like many of the prey upon which they depend. These birds produce many recruits when fish availability is high, leading to rapidly increasing populations, but few recruits, and may even exhibit die-offs, when the opposite is true. Unlike cormorants in the Peru and Benguela currents, however, Brandt's Cormorant population changes have yet to be correlated with those of its prey. Herein, using multi-decadal time series of cormorant colony size, diet, prey availability and mortality, in the context of changes in breeding site and fishery management, we provide insight into why central California colonies near San Francisco — a major portion of this species' global population — expanded from principally one offshore island in the 1960–70s to include a large mainland component by the 1990s. Involved were increases and decreases, respectively, of northern anchovy, a coastal forage species, and young-of-the year rockfish, more prevalent offshore. With protection of breeding sites and a shift towards ecosystem-based fisheries management by the 1990s, variations of the central California Brandt's Cormorant population are now driven naturally by forage fish availability, and perhaps inter- and intraspecific competition for prey and space when population sizes are high. This species, owing to its “boom-or-bust” natural history and the relative ease of assessing breeding population size and diet, may be ideal for monitoring the state of the central California Current food web. [ABSTRACT FROM AUTHOR]

Often in calculating a sediment budget there is an unknown contribution, which is ascribed to the residual of the balance, and the budget cannot be fulfilled. The temporal and spatial variations and sediment size within a littoral cell provide additional information to define sediment budgets. The approach here is to consider only medium to coarse sand (grain size > 0.25 mm) over a long time period during significant changes of natural and anthropogenic inputs and losses that allow calculating several budgets to isolate the unknown inputs and outputs to close the system. Considering only medium to coarse sand eliminates including the cross-shore transport of fine sand by waves, which is poorly quantified. To demonstrate these concepts, shoreline recession rates measured over a 101-year time period are used to calculate sediment budgets for southern Monterey Bay, California, littoral cells. The coarse sandy shoreline is backed by extensive bluffs and dunes that reach 44 m in elevation. Intensive sand mining of coarse sand derived directly from the beach and surfzone started in 1927 and continues today. A contribution of about 100 k m 3 /year of medium to coarse sand from the Salinas River is calculated from measured shoreline accretion for the period 1910–1945 starting when the river first flowed into the littoral cell, prior to damming of the river and significant losses owing to sand mining. Sediment budgets are calculated for 1940–1989 and 1989–2011 to spatially identify the loss of about 200 k m 3 /year attributed to different mining operations that captured the littoral transport. The primary contributions of medium to coarse sand to the littoral system is approximately 180 k m 3 /year from the eroding dunes and beaches. Only a quarter of the dune sand is found to be compatible with the coarser beach sand with the finer fraction carried offshore. A conclusion is that sand mining is the cause of the observed high recession rates. [ABSTRACT FROM AUTHOR]

Background: Larvaceans in the genus Bathochordaeus are large, often abundant filter feeders found throughout much of the world ocean. The first described species, Bathochordaeus charon, was reported over 100 years ago by Chun. However in the time since, few specimens have matched Chun's original description, resulting in ambiguity on the validity of B. charon as a species. Methods: Specimens of Bathochordaeus charon were identified based on morphological traits, molecular data and observations made on high definition video. Results: The first records of Bathochordaeus charon from the northeast Pacific Ocean off central California and Oregon, USA are reported. Morphology and molecular data clearly distinguish B. charon from its congener, B. stygius. Conclusions: This paper establishes the first review of Bathochordaeus charon since its original description, extends the range of this species to the northeast Pacific Ocean, and provides the first molecular evidence for two species of Bathochordaeus. [ABSTRACT FROM AUTHOR]

A 6-month deployment of instrumentation from April to October 2012 in 90 m water depth near the outer edge of the mid-shelf mud belt in southern Monterey Bay, California, reveals the importance regional upwelling on water column density structure, potentially accounting for the majority of the variability in internal tidal energy flux across the shelf. Observations consisted of time-series measurements of water-column currents, temperature and salinity, and near-bed currents and suspended matter. The internal tide accounted for 15–25% of the water-column current variance and the barotropic tide accounted for up to 35%. The subtidal flow showed remarkably little shear and was dominated by the 7–14 day band, which is associated with relaxations in the dominant equatorward winds typical of coastal California in the spring and summer. Upwelling and relaxation events resulted in strong near-bed flows and accounted for almost half of the current stress on the seafloor (not accounting for wave orbital velocities), and may have driven along-shelf geostrophic flow during steady state conditions. Several elevated suspended particulate matter (SPM) events occurred within 3 m of the bed and were generally associated with higher, long-period surface waves. However, these peaks in SPM did not coincide with the predicted resuspension events from the modeled combined wave–current shear stress, indicating that the observed SPM at our site was most likely resuspended elsewhere and advected along-isobath. Sediment flux was almost equal in magnitude in the alongshore and cross-shore directions. Instances of wave–current shear stress that exceeded the threshold of resuspension for the silty-clays common at these water depths only occurred when near-bed orbital velocities due to long-period surface waves coincided with vigorous near-bed currents associated with the internal tide or upwelling/relaxation events. Thus upwelling/relaxation dynamics are primarily responsible for variability in the internal tide, as well as transport of near-bottom sediment in the mid-self mud belt during the relatively quiescent summer months. [ABSTRACT FROM AUTHOR]

This paper describes the use of machine learning methods to build a decision support system for predicting the distribution of coastal ocean algal blooms based on remote sensing data in Monterey Bay. This system can help scientists obtain prior information in a large ocean region and formulate strategies for deploying robots in the coastal ocean for more detailed in situ exploration. The difficulty is that there are insufficient in situ data to create a direct statistical machine learning model with satellite data inputs. To solve this problem, we built a Random Forest model using MODIS and MERIS satellite data and applied a threshold filter to balance the training inputs and labels. To build this model, several features of remote sensing satellites were tested to obtain the most suitable features for the system. After building the model, we compared our random forest model with previous trials based on a Support Vector Machine (SVM) using satellite data from 221 days, and our approach performed significantly better. Finally, we used the latest in situ data from a September 2014 field experiment to validate our model. [ABSTRACT FROM AUTHOR]

Faecal indicator bacteria ( FIB) and harmful algal blooms ( HABs) threaten the health and the economy of coastal communities worldwide. Emerging automated sampling technologies combined with molecular analytical techniques could enable rapid detection of micro-organisms in-situ, thereby improving resource management and public health decision-making. We evaluated this concept using a robotic device, the Environmental Sample Processor ( ESP). The ESP automates in-situ sample collection, nucleic acid extraction and molecular analyses. Here, the ESP measured and reported concentrations of FIB ( Enterococcus spp.), a microbial source-tracking marker (human-specific Bacteriodales) and a HAB species ( Psuedo-nitzschia spp.) over a 45-day deployment on the Santa Cruz Municipal Wharf (Santa Cruz, CA, USA). Both FIB and HABs were enumerated from single in-situ collected water samples. The in-situ qPCR efficiencies ranged from 86% to 105%, while the limit of quantifications during the deployment was 10 copies reaction−1. No differences were observed in the concentrations of enterococci, the human-specific marker in Bacteroidales spp., and P. australis between in-situ collected sample and traditional hand sampling methods ( P > 0·05). Analytical results were Internet-accessible within hours of sample collection, demonstrating the feasibility of same-day public notification of current water quality conditions. Significance and Impact of the Study This study presents the first report of in-situ qPCR enumeration of both faecal indicators and harmful algal species in coastal marine waters. We utilize a robotic device for in-situ quantification of enterococci, the human-specific marker in Bacteriodales and Pseudo-nitzschia spp. from the same water samples collected and processed in-situ. The results demonstrate that rapid, in-situ monitoring can be utilized to identify and quantify multiple health-relevant micro-organisms important in water quality monitoring and that this monitoring can be used to inform same-day notifications. [ABSTRACT FROM AUTHOR]

Blooms of toxin-producing Microcystis aeruginosa occur regularly in freshwater systems throughout California, but until recently potential impacts in the coastal ocean have been largely ignored. Twenty-one sites in and around Monterey Bay were surveyed for evidence of microcystin toxin (2010–2011) at the land–sea interface. Following this initial survey four major watersheds in the Monterey Bay area were surveyed (2011–2013) for microcystin concentration, nutrients, alkalinity and water temperature to identify potential environmental factors correlated with the abundance of microcystin at the land–sea interface. During the first year microcystin was detected in 15 of 21 sites. Data from years two and three were analyzed by principal components analysis and mixed effects model. Results indicated that coastal nutrient loading (nitrate, phosphate silicate, ammonium, urea), were statistically significant predictors of the microcystin concentrations in the watersheds with clear evidence for seasonality at some sites. Microcystin was frequently at highest concentration in the autumn; however, at some locations high levels of toxin were measured during spring. Because this toxin has the ability to biomagnify and persist within food webs, elevated levels within the watershed may decrease potential for health and survival of wildlife and humans exposed to freshwater and marine waters. The widespread occurrence of microcystin at low to moderate levels throughout the year and throughout the sampled watersheds demonstrates the potential difficulty for management. [ABSTRACT FROM AUTHOR]

This article describes an oral history immersion trip and service learning project in the Monterey Bay region of Central California designed to develop the ecoliteracy of high school students and involve them in community building. Through their oral history interviews, students learned that the seafood industry faces numerous challenges to sustainability and through their advocacy project they sought to heighten consumer awareness toward the goal of a sustainable fishing industry in the region. Along with developing ecoliteracy, the project achieved many core outcomes, including critical thinking skills, compassion, interdisciplinary communication, and community building. [ABSTRACT FROM PUBLISHER]

This article describes an oral history immersion trip and service learning project in the Monterey Bay region of Central California designed to develop the ecoliteracy of high school students and involve them in community building. Through their oral history interviews, students learned that the seafood industry faces numerous challenges to sustainability and through their advocacy project they sought to heighten consumer awareness toward the goal of a sustainable fishing industry in the region. Along with developing ecoliteracy, the project achieved many core outcomes, including critical thinking skills, compassion, interdisciplinary communication, and community building. [ABSTRACT FROM AUTHOR]

Abstract: Monterey Submarine Canyon is a large, sinuous canyon off the coast of California, the upper reaches of which were the subject of an internal tide observational program using moored profilers and upward-looking moored ADCPs. The mooring observations measured a near-surface stratification change in the upper canyon, likely caused by a seasonal shift in the prevailing wind that favoured coastal upwelling. This change in near-surface stratification caused a transition in the behaviour of the internal tide in the upper canyon from a partly standing wave during pre-upwelling conditions to a progressive wave during upwelling conditions. Using a numerical model, we present evidence that either a partly standing or a progressive internal tide can be simulated in the canyon, simply by changing the initial stratification conditions in accordance with the observations. The mechanism driving the transition is a dependence of down-canyon (supercritical) internal tide reflection from the canyon floor and walls on the depth of maximum stratification. During pre-upwelling conditions, the main pycnocline extends down to 200m (below the canyon rim) resulting in increased supercritical reflection of the up-canyon propagating internal tide back down the canyon. The large up-canyon and smaller down-canyon progressive waves are the two components of the partly standing wave. During upwelling conditions, the pycnocline shallows to the upper 50m of the watercolumn (above the canyon rim) resulting in decreased supercritical reflection and allowing the up-canyon progressive wave to dominate. [Copyright &y& Elsevier]

Background OMEGA is an integrated aquatic system to produce biofuels, treat and recycle wastewater, capture CO2, and expand aquaculture production. This system includes floating photobioreactors (PBRs) that will cover hundreds of hectares in marine bays. To assess the interactions of marine mammals and birds with PBRs, 9 × 1.3 m flat panel and 9.5 × 0.2 m tubular PBRs were deployed in a harbor and monitored day and night from October 10, 2011 to Janurary 22, 2012 using infrared video. To observe interactions with pinnipeds, two trained sea lions (Zalophus californianus) and one trained harbor seal (Phoca vitulina richardii) were observed and directed to interact with PBRs in tanks. To determine the forces required to puncture PBR plastic and the effects of weathering, Instron measurements were made with a sea otter (Enhydra lutris) tooth and bird beaks. Results A total of 1,445 interactions of marine mammals and birds with PBRs were observed in the 2,424 hours of video recorded. The 95 marine mammal interactions, 94 by sea otters and one by a sea lion had average durations of three minutes (max 44 min) and represented about 1% of total recording time. The 1,350 bird interactions, primarily coots (Fulica americana) and gulls (Larus occidentalis and L. californicus) had average durations of seven minutes (max. 170) and represented 5% of recording time. Interactive behaviors were characterized as passive (feeding, walking, resting, grooming, and social activity) or proactive (biting, pecking, investigating, and unspecified manipulating). Mammal interactions were predominantly proactive, whereas birds were passive. All interactions occurred primarily during the day. Ninety-six percent of otter interactions occurred in Winter, whereas 73% of bird interactions in Fall, correlating to their abundance in the harbor. Trained pinnipeds followed most commands to bite, drag, and haul-out onto PBRs, made no overt undirected interactions with the PBRs, but showed avoidance behavior to PBR tethers. Instron measurements indicated that sea-otter teeth and gull beaks can penetrate weathered plastic more easily than new plastic. Published data suggest that otter bites may penetrate plastics, but pecking forces are not sufficient to do so. Conclusions Otter and bird interactions with experimental PBRs were benign. Large-scale OMEGA systems are predicted to have both positive and negative environmental consequences. [ABSTRACT FROM AUTHOR]

Background: OMEGA is an integrated aquatic system to produce biofuels, treat and recycle wastewater, capture CO2, and expand aquaculture production. This system includes floating photobioreactors (PBRs) that will cover hundreds of hectares in marine bays. To assess the interactions of marine mammals and birds with PBRs, 9 × 1.3 m flat panel and 9.5 × 0.2 m tubular PBRs were deployed in a harbor and monitored day and night from October 10, 2011 to Janurary 22, 2012 using infrared video. To observe interactions with pinnipeds, two trained sea lions (Zalophus californianus) and one trained harbor seal (Phoca vitulina richardii) were observed and directed to interact with PBRs in tanks. To determine the forces required to puncture PBR plastic and the effects of weathering, Instron measurements were made with a sea otter (Enhydra lutris) tooth and bird beaks. Results: A total of 1,445 interactions of marine mammals and birds with PBRs were observed in the 2,424 hours of video recorded. The 95 marine mammal interactions, 94 by sea otters and one by a sea lion had average durations of three minutes (max 44 min) and represented about 1% of total recording time. The 1,350 bird interactions, primarily coots (Fulica americana) and gulls (Larus occidentalis and L. californicus) had average durations of six minutes (max. 170) and represented 5% of recording time. Interactive behaviors were characterized as passive (feeding, walking, resting, grooming, and social activity) or proactive (biting, pecking, investigating, and unspecified manipulating). Mammal interactions were predominantly proactive, whereas birds were passive. All interactions occurred primarily during the day. Ninety-six percent of otter interactions occurred in winter, whereas 73% of bird interactions in fall, correlating to their abundance in the harbor. Trained pinnipeds followed most commands to bite, drag, and haul-out onto PBRs, made no overt undirected interactions with the PBRs, but showed avoidance behavior to PBR tethers. Instron measurements indicated that sea-otter teeth and gull beaks can penetrate weathered plastic more easily than new plastic. Conclusions: Otter and bird interactions with experimental PBRs were benign. Large-scale OMEGA systems are predicted to have both positive and negative environmental consequences. [ABSTRACT FROM AUTHOR]

Abstract: Harmful algal blooms (HABs) can threaten animal and human health through the production of toxins such as domoic acid. These blooms have become more frequent and toxic over the last few decades. In this study, we investigate the role that nutrients play in a toxic, subsurface bloom of Pseudo-nitzschia in northeastern Monterey Bay, California. Profilers and towed instruments were deployed and laboratory analyses of discrete water samples were conducted to describe the physical and biogeochemical conditions of the sampling site and to characterize the bloom. The subsurface Pseudo-nitzschia bloom occurred within a well-defined layer, containing high levels of domoic acid. In situ images taken within the layer revealed diatom flocs—indicators of nutrient stress. Nutrient ratios and alkaline phosphatase activity, commonly used to determine the nutritional status of phytoplankton, suggest that the Pseudo-nitzschia cells were phosphate stressed, and we speculate that this physiological stress led to increased toxicity of the bloom. Understanding how frequently blooms such as these are characterized by nutrient stress could improve our ability to predict the occurrence of HABs. With increased anthropogenic input of nutrients, such blooms could occur more often and with greater degrees of toxicity in the future. [Copyright &y& Elsevier]

As a demonstrator for technologies for the next generation of ocean color sensors, the Hyperspectral Imager for the Coastal Ocean (HICO) provides enhanced spatial and spectral resolution that is required to understand optically complex aquatic environments. In this study we apply HICO, along with satellite remote sensing and in situ observations, to studies of phytoplankton ecology in a dynamic coastal upwelling environment-Monterey Bay, CA, USA. From a spring 2011 study, we examine HICO-detected spatial patterns in phytoplankton optical properties along an environmental gradient defined by upwelling flow patterns and along a temporal gradient of upwelling intensification. From a fall 2011 study, we use HICO's enhanced spatial and spectral resolution to distinguish a small-scale "red tide" bloom, and we examine bloom expansion and its supporting processes using other remote sensing and in situ data. From a spectacular HICO image of the Monterey Bay region acquired during fall of 2012, we present a suite of algorithm results for characterization of phytoplankton, and we examine the strengths, limitations, and distinctions of each algorithm in the context of the enhanced spatial and spectral resolution. [ABSTRACT FROM AUTHOR]

Owing to the paucity of data on the red muscle of deep-sea fishes, the goal of this study was to determine the proportions of red muscle in demersal fishes and its enzymatic activities to characterize how routine swimming abilities change with depths of occurrence. Cross sectional analysis of the trunk musculature was used to evaluate the proportion of red muscle in 38 species of Californian demersal fishes living at depths between 100 and 3000 m. The activity of metabolic enzymes was also assayed in a sub-set of 18 species. Benthic fishes had lower proportions of red muscle and lower metabolic enzyme activities than benthopelagic species. Mean proportion of red muscle declined significantly with depth with the greatest range of values in shallow waters and species with low proportions found at all depths. This suggested that while sedentary species occur at all depths, the most active species occur in shallow waters. Citrate synthase activity declined significantly with depth across all species, indicating that the mass-specific metabolic capacity of red muscle is lower in deep-sea species. These patterns may be explained by coupling of red and white muscle physiologies, a decrease in physical energy of the environment with depth or by the prevalence of anguilliform body forms and swimming modes in deep-living species. [ABSTRACT FROM AUTHOR]

Abstract: Amoebophrya is a marine parasite recently found to infect and kill bloom-forming dinoflagellates in the California Current System (CCS). However, it is unknown whether parasitism by Amoebophrya can control dinoflagellate blooms in major eastern boundary upwelling systems, such as the CCS. We quantified the abundance of a common bloom-forming species Akashiwo sanguinea and prevalence of its parasite (i.e., % infected cells) in surface water samples collected weekly from August 2005 to December 2008 at the Santa Cruz Wharf (SCW), Monterey Bay, CA. Additionally, we measured physical and chemical properties at the SCW and examined regional patterns of wind forcing and sea surface temperature. Relative abundance of the net phytoplankton species was also analyzed to discern whether or not parasitism influences net phytoplankton community composition. Epidemic infection outbreaks (>20% parasite prevalence in the host species) may have contributed to the end or prevented the occurrence of A. sanguinea blooms, whereas low parasite prevalence was associated with short-term (≤2 weeks) A. sanguinea blooms. The complete absence of parasitism in 2007 was associated with an extreme A. sanguinea bloom. Anomalously strong upwelling conditions were detected in 2007, suggesting that A. sanguinea was able to outgrow Amoebophrya and ‘escape’ parasitism. We conclude that parasitism can strongly influence dinoflagellate bloom dynamics in upwelling systems. Moreover, Amoebophrya may indirectly influence net phytoplankton species composition, as species that dominated the net phytoplankton and developed algal blooms never appeared to be infected. [Copyright &y& Elsevier]

To a tsunami wave, bays and harbors represent oscillatory systems, whose resonance (normal) modes determine the response to tsunami and consequently the potential hazard. The direct way to obtain the resonance modes of a water reservoir is by solving the boundary problem for the eigenfunctions of the linearized shallow-water wave equation. The principal difficulty of posing such a problem for a basin coupled to an ocean is specifying the boundary between the two. The technique developed in this work allows the normal modes of a semi-enclosed water body to be obtained without a-priori restricting the resonator area. The technique utilizes complex Empirical Orthogonal Function analysis of modeled tsunami wave fields. On the examples of Poverty Bay in New Zealand and Monterey Bay in California (United States), we demonstrate that the normal modes can be identified and isolated using the EOFs of a data set comprised of the concatenated time-series collected from different tsunami scenarios in a basin. The analysis of the modeled tsunami wave fields for the normal modes can also answer the question of how likely and under which conditions the different modes are exited, due to feasible natural events. [ABSTRACT FROM AUTHOR]

Abstract: Thin phytoplankton layers are common features in the coastal environment; however sampling these fine-scale optical features across broad horizontal scales remains a challenge. To investigate the horizontal spatial structure of thin phytoplankton layers, we performed an overnight survey in northern Monterey Bay, CA, USA using a SeaSciences Acrobat towed-vehicle. Physical and optical measurements were collected between the surface and near-bottom-depths along four parallel, across-shore transects. Three coherent chlorophyll features were observed: (1) a broad, sub-surface patch at the offshore end, (2) a near-surface patch at the nearshore end, and (3) a deep patch located between the nearshore and offshore patches. The offshore and nearshore patch were separated by a change in seafloor slope and a region of compressed, shoaling isopycnals. Both the offshore and nearshore features were located at the pycnocline, had similar optical properties, and were co-located with a low-salinity intrusion. The deep chlorophyll patch had associated physical and optical properties that were distinct from the patches at the pycnocline. The results from this study further underscore the heterogeneous horizontal spatial structure of thin layers and also add to the growing evidence suggesting that low-salinity intrusions may be strongly linked to the formation of thin phytoplankton layers over the northern shelf of Monterey Bay. [Copyright &y& Elsevier]

Abstract: Fine-structure (centimeters to meters) in vertical profiles of acoustic volume scattering strength is a common and ecologically significant characteristic of the coastal marine water column. The processes that create these structures modify the availability of food and exposure to predation for secondary producers at and below spatial and temporal scales that characterize their daily ambits. Thin acoustic scattering layers may persist for weeks at a particular coastal location, but they may also appear and disappear in only a few hours. These layers are usually evidence of mesozooplankton and micronekton having aggregated at peaks, gradients, or boundaries in the vertical distribution of various water column properties that characterize a marine ecosystem. The behaviors of both predators and prey are implicated in the generation of complex, time-dependent patterns of fine-structure. Specifically, diel vertical migration to layers of prey, isolumes, isotherms, isopycnals, or chemoclines can be responsible for the nighttime formation of thin acoustic layers. Physical processes such as horizontal shear, internal waves, water mass intrusions, tidal forcing, wind mixing of the upper water column, and horizontal advection modify acoustic scattering patterns by changing the vertical distributions of organisms that scatter sound. [Copyright &y& Elsevier]

Sequestration of carbon dioxide (CO2) in the ocean is being considered as a feasible mechanism to mitigate the alarming rate in its atmospheric rise. Little is known, however, about how the resulting hypercapnia and ocean acidification may affect marine fauna. In an effort to understand better the protistan reaction to such an environmental perturbation, the survivorship of benthic foraminifera, which is a prevalent group of protists, was studied in response to deep-sea CO2 release. The survival response of calcareous, agglutinated, and thecate foraminifera was determined in two experiments at ∼3.1 and 3.3 km water depth in Monterey Bay (California, USA). Approximately 5 weeks after initial seafloor CO2 release, in situ incubations of the live–dead indicator CellTracker Green were executed within seafloor-emplaced pushcores. Experimental treatments included direct exposure to CO2 hydrate, two levels of lesser exposure adjacent to CO2 hydrate, and controls, which were far removed from the CO2 hydrate release. Results indicate that survivorship rates of agglutinated and thecate foraminifera were not significantly impacted by direct exposure but the survivorship of calcareous foraminifera was significantly lower in direct exposure treatments compared with controls. Observations suggest that, if large scale CO2 sequestration is enacted on the deep-sea floor, survival of two major groups of this prevalent protistan taxon will likely not be severely impacted, while calcareous foraminifera will face considerable challenges to maintain their benthic populations in areas directly exposed to CO2 hydrate. [ABSTRACT FROM AUTHOR]

Abstract: On two cruises in August and September 2003 (hereafter cruises 2 and 3) during wind relaxations and transitions to upwelling conditions, thin layers of phytoplankton were observed in or a few meters below the stratified transition layer at the mixed layer base and in regions of sheared flow on the flanks of eddies, filaments, and fronts near Monterey Bay, California. On an earlier cruise in August (cruise 1), no thin layers were found after a prolonged wind relaxation. Chlorophyll concentrations and shear were both an order of magnitude less than on cruises 2 and 3. Our vertical profiles were made using a fluorometer mounted on a conductivity–temperature–depth package, which was lowered from the ship as slowly as every 10km on five cross-shore transects. Remotely sensed sea-surface temperature, chlorophyll, and currents are required to understand the temporal and spatial evolution of the circulation and to interpret the quasi-synoptic in situ data. Decorrelation scales are from lagged temperature and salinity covariances. Objectively mapped sections of the in situ data indicate the waters containing thin layers were recently upwelled at either the Point Sur or Point Año Nuevo upwelling centers. Spatially limited distributions of phytoplankton at the coastal upwelling centers ( alongshore, 20km cross-shore, and 30m thick) were transformed into thin layers by current shear and isolated from wind-driven vertical mixing by the stratification maximum of the transition layer. Vertically sheared horizontal currents on the flanks of the eddies, filaments, and fronts horizontally stretched and vertically thinned phytoplankton distributions. These thin, elongated structures were then observed as thin layers of phytoplankton in vertical fluorescence profiles at four stations on cruise 2 and eight stations on cruise 3. Light winds during relaxations did not mix away these thin layers. On cruise 2, thin layers were found at eddies at the inshore and offshore ends of a 100-km-long filament, while broader subsurface chlorophyll maxima were found along the filament. This result suggests that higher-resolution sampling along and across a filament may find thin layers forming and dissipating along its length. On cruise 3, thin layers were found at three adjacent stations across an upwelling front and may have extended continuously for , but neither species composition nor bio-optical data are available to confirm this conjecture. The thin layers were 1–5m thick in the vertical at full width half maximum and had peak fluorescence values from . (Bottle chlorophyll samples showed fluorometer chlorophyll readings may have been large, but the scatter in this relation was considerable especially at the larger fluorescence values detected in thin layers.) While sheared currents thinned an initially thick subsurface chlorophyll maximum into thin layers, the peak values in these thin layers exceeded concentrations in the upwelled source waters and were unexplained by our data. [Copyright &y& Elsevier]

Abstract: In the process of developing a tide-permitting coastal ocean forecasting system, tidal signals are added to an oceanic general circulation model for Monterey Bay, California. The model, which is configured from the regional ocean modeling system (ROMS), has three one-way nested domains with the finest resolution of 1.6km in the horizontal direction and 32 levels in the vertical direction. In present research, the tidal simulation of the system is validated against tide gauges, ADCP current observations, high-frequency radar surface-current observations, and compared with the output from two barotropic tidal models. The results indicate that the barotropic tides from the model compare well with observations in terms of sea-surface height, with discrepancies in amplitude of less than 10% of the amplitude of the most energetic constituent. However, the discrepancy for the barotropic tidal currents can reach 30% among models with similar accuracy in sea-surface height. The generation and propagation of baroclinic tides associated with the Monterey Submarine Canyon are qualitatively reproduced by the model with weaker strength. The surface tidal current simulation is improved, especially in terms of magnitude, when the model has a more realistic stratification through changes in both barotropic and baroclinic tidal currents. [Copyright &y& Elsevier]

Abstract: The linear systems approach is used to forecast offshore near-surface and subsurface temperatures in Monterey Bay and further offshore based on coastal sea surface temperatures (SSTs) at Pacific Grove. SST from Pacific Grove provided the input to the system and the forecast parameters or outputs were temperature at 1m and 100m at the M1 buoy located 20km from Pacific Grove near the center of Monterey Bay, and temperature at 1m at the M2 buoy located 55km from Pacific Grove. To forecast temperatures at the M1 and M2 buoys, Box-Jenkins, State-Space, ARX, and ARMAX models were employed. Model formulation, implementation, forecasting procedures, and methods of evaluation are presented. Seven and 30-day forecasts were routinely made for the daily observations although other forecast horizons were employed. For all models and variables, RMS differences between the forecasts and the observations increased rapidly between 1 and 15 days. Beyond about 30 days, RMS differences tended to remain almost constant with increasing forecast horizon. Overall, model forecasts were best for temperature at 100m at the M1 buoy, due to the fact that temperature is well conserved at depth. Differences in performance between the models were small but the ARMAX model often produced forecasts that were slightly better than the rest, a result that we attribute to a more complete specification of the noise. Although the Box-Jenkins and State-Space models have the potential to produce better forecasts, because more terms must be specified to implement them, the opportunity to produce less-than-optimal results is also greater. Finally, because of seasonal changes in the circulation of Monterey Bay, it is possible that causality was violated, upon occasion, placing certain constraints on the results. Models based on the linear systems approach, where they can be implemented, could serve as a useful adjunct to hydrodynamic ocean circulation models by providing additional information for model initialization, evaluation, and data assimilation. Using the same approach, operational forecasts of the coastal circulation could be made by including forecast winds and the predicted tides as inputs, and CODAR-observed surface currents as the output. In a less glamorous but still useful role, they could be used to fill significant gaps in offshore records where data continuity and quality are important. [Copyright &y& Elsevier]

• Isotope analysis and DA measurements are a novel method to study DA transfer. • Foraging characteristics contribute to a population's capacity to accumulate toxins. • Anchovies are better sentinel species for coastal-pelagic regions than mussels. • Prey size selectivity explains the capacity for anchovies to accumulate DA. • DA accumulation and δ13C gradients reflect spatial mismatches. • Baseline isotope values of C and N differ among habitats. Given the effects of harmful algal blooms (HABs) on human and wildlife health, understanding how domoic acid (DA) is accumulated and transferred through food webs is critical for recognizing the most affected marine communities and predicting ecosystem effects. This study combines stable isotopes of carbon (δ13C) and nitrogen (δ15N) from bulk muscle tissue with DA measurements from viscera to identify the foraging strategies of important DA vectors and predators in Monterey Bay, CA. Tissue samples were collected from 27 species across three habitats in the summer of 2018 and 2019 (time periods without prominent HABs). Our results highlight an inshore-offshore variation in krill δ13C values and DA concentrations ([DA]; ppm) in anchovies indicating differences in coastal productivity and DA accumulation. The narrow overlapping isotopic niches between anchovies and sardines suggest similar diets and trophic positions, but striking differences in [DA] indicate a degree of specialization, thus, resource partitioning. In contrast, krill, market squid, and juvenile rockfish accumulated minimal DA and had comparatively broad isotopic niches, suggesting a lower capacity to serve as vectors because of potential differences in diet or feeding in isotopically distinct locations. Low [DA] in the liver of stranded sea lions and their generalist foraging tendencies limits our ability to use them as sentinels for DA outbreaks in a specific geographic area. Collectively, our results show that DA was produced a few kilometers from the coastline, and anchovies were the most powerful DA vector in coastal-pelagic zones (their DA loads exceeded the 20 ppm FDA regulatory limits for human consumption), while mussels did not contain detectable DA and only reflect in situ DA, δ13C, and δ15N values. Our study demonstrates the efficacy of combining multiple biogeochemical tracers to improve HAB monitoring efforts and identify the main routes of DA transfer across habitats and trophic levels. [ABSTRACT FROM AUTHOR]

Abstract: A sudden and nearly synchronous emergence of the red tide forming dinoflagellate Cochlodinium along more than 800km of California coastline was initially observed in late summer 2004. Thereafter high cell concentrations have been detected on an annual basis. Here, we present quantitative and semi-quantitative data indicating that Cochlodinium was uncommon in the phytoplankton community in California prior to 2004 and is now persisting as a more regular component and one that seasonally can cause red tides. The quantitative portion of this study was primarily conducted in Monterey Bay, where cell densities reached at least 6×104 cellsL−1 during the initial outbreak. A semi-quantitative comparison of California coastal counties by the California Department of Health Services (CDHS) was also made: of the 15 counties surveyed (most with multiple sites per county), cells were detected only from Los Angeles County in the south to San Mateo County in the central region (seven counties), but not in the northern part of the state (six counties). Two counties in the central region of the state, San Luis Obispo and Santa Cruz, displayed intense and frequent periods of elevated Cochlodinium cell abundances. Although not observed in the state-wide CDHS survey, we occasionally found cells in San Diego County with densities up to 2.7×104 cellsL−1. Though these colonial dinoflagellates have been recognized in California for over 80 years, with several “blooms” recorded prior to 2004, the species’ geographic range and abundance in recent years suggest significant shifts in the nearshore phytoplankton community of this region of the eastern Pacific. [Copyright &y& Elsevier]

Sediment samples were collected to delineate the distribution of contaminants along the central California coast. Sampling included a variety of Canyons and shelf/slope areas to evaluate contaminant transport patterns and potential delivery to Canyons and the continental slope to a depth of 1200m. Sediments were collected and analyzed for organic contaminants using standard techniques of the NOAA National Status and Trends Program (NS&T). DDT is distributed on the shelf within a zone of fine-grained sediments between Half Moon and Monterey Bays. DDT was found at higher concentrations in Ascension, Año Nuevo, and Monterey/Soquel Canyons than in Pioneer and Carmel Canyons, the Gulf of the Farallones, or the continental slope. The Monterey Bay watershed appears to be the primary source of DDT. In contrast, PAHs and PCBs on the shelf appear to be derived primarily from San Francisco Bay. DDT appears to be delivered to the deep ocean via the Canyons more than from cross-shelf sediment transport. Sediment budget estimates for the continental shelf north of Monterey Bay need further refinement and more data to account for the movement of material from Monterey Bay onto the shelf. [Copyright &y& Elsevier]

Abstract: Patchiness or spatial variability is ubiquitous in marine systems. With increasing anthropogenic impacts to coastal resources and coastal systems being disproportionately large contributors to ocean productivity, identifying the spatial scales of this patchiness, particularly in coastal waters, is of critical importance to understand coastal ecosystem dynamics. The current work focuses on fine scale structure in three coastal regions. More specifically, we utilize variogram analyses to identify sub-kilometer scales of variability in biological and physical parameters measured by an autonomous underwater vehicle (AUV) in the Mid-Atlantic Bight, Monterey Bay, and in San Luis Obispo Bay between 2001 and 2004. Critical scales of variability in density, turbidity, fluorescence, and bioluminescence are examined as a function of depth and distance offshore. Furthermore, the effects of undersampling are assessed using predictive error analysis. Results indicate the presence of scales of variability ranging from 10s to 100s of meters and provide valuable insight for sampling design and resource allocation for future studies. [Copyright &y& Elsevier]

Diel vertical migration (DVM) is a common zooplankton behavior in which organisms reside in surface or near-surface waters at night and at deeper depths during the day. In many upwelling regions, DVM reduces the transport of organisms away from the region. It is unclear, however, what role DVM plays in recruitment (the arrival of larvae or juveniles to locations where they will become reproducing adults) to upwelling regions. In this study, we estimate the influence of DVM on zooplankton transport, the level of recruitment of locally produced propagules (self-recruitment), and sources of recruits in the upwelling region near Monterey Bay, California, by simulating the trajectories of fixed-depth and vertically migrating organisms with a drifter-tracking algorithm driven by climatological velocity fields from a three-dimensional hydrodynamic model. Our simulations suggest that DVM into subsurface poleward and onshore currents during the day does not fully compensate for equatorward and offshore transport in the surface Ekman layer at night and does not retain zooplankton in the Monterey Bay region. Our simulations also suggest that DVM decreases the ability of zooplankton to return to the region after being transported away and shifts source regions for recruits closer to the bay. While DVM does not appear to substantially increase the potential for self-recruitment to the region, this study indicates that other mechanisms, such as transport during non-upwelling periods, continuous transport below the surface, increases in mean transport depth over time, or seasonal changes in hydrography, may still enable relatively high levels of self-recruitment to this highly advective region. [ABSTRACT FROM AUTHOR]

Abstract: The discovery in 2002 of a natural whale-fall at 2893m depth in Monterey Bay, California, led to the description of Osedax, a novel genus of bone-eating worms (Annelida: Siboglinidae). Osedax obtain their nutrition via ramifying roots that host symbiotic bacteria and consume whale bones. To assess the bathymetric range of these unusual worms and their role in whale-fall community succession, we sank beached whale carcasses at three additional depths (1820, 1018, and 385m) in the Monterey Submarine Canyon. The four sunken carcasses experienced different temperature, oxygen, and disturbance regimes and hosted megafaunal communities that differed in both species diversity and composition. However, Osedax were found at all four sites, and molecular analyses allowed us to assign them to six distinct species, four of which are new to science. The previously known species, O. rubiplumus (1820–2893m) and O. frankpressi (2893m), were found below the oxygen minimum zone. One of the new species appears to be a late successional species that attacks sediment-covered bone fragments at the 2893-m whale-fall. The other new species occur at the shallower whale-falls, which are in oxygen-poor water. One is an early colonizer at the 1018-m whale-fall, and two occur at the 385-m whale-fall. Dense Osedax populations at the 1018-m whale-fall led to rapid degradation of whale bones, whereas sparse Osedax populations were associated with slow degradation at the 385-m whale-fall. Thus, we hypothesize that Osedax may be a foundation species in Monterey whale-fall communities, regulating the longevity of whale bones and thereby affecting the succession of associated megafauna. [Copyright &y& Elsevier]

Abstract: This work presents a procedure for developing a high-resolution, regional climatology estimate, named RClimo, off the coast of central California. This high-resolution climatology may provide an alternative way to initialize numerical nowcast/forecast exercises in coastal regions. The methodology includes two primary steps: (1) averaging available data on a high-resolution grid and (2) objective interpolating the resulting average profiles onto a regular grid. The first step involves the computation of averages over density layers in the vertical and allowing for data gaps in the horizontal if data are unavailable at a high resolution. The OA in the second step uses anisotropic correlation length scales derived from the data themselves and an averaging radius to preserve the scales and variability of the synoptic fields. The dataset used to compute this climatology includes the archived CalCOFI dataset, the Autonomous Ocean Sampling Network (AOSN) 2003 experiments near Monterey Bay, and many other previously undocumented profiles from various sources. As part of the climatology product, associated uncertainty is also generated through density averaging and employing the Gauss–Markov minimum error variance during Objective Analysis. The final climatology estimate is hence subject to greater error for larger mapping-grid size or lower data density, suggesting uncertainties that vary in space. The maximum value of the resulting error distribution for the RClimo estimate from the 50-km bins is less than 11% of the temperature estimate and 1% of the salinity estimate, whereas those for the 20-km-bin RClimo are 11% and 0.9%, respectively. We have conducted comparisons between the RClimo and 1/4° Levitus climatology fields via numerical simulations initialized with each field. Simulations were performed using Regional Ocean Modeling System (ROMS) and for the month of August, a peak period of upwelling-favorable wind, with and without the atmospheric forcing. The RClimo simulations produced reasonably realistic features like filaments, fronts, meanders, eddies, alongshore currents (∼50cms−1) and inshore undercurrents (∼15cms−1) under typical upwelling-favorable winds. In contrast, the Levitus simulations showed insignificant evolution over most of the domain, with or without winds. In the future, one could apply this methodology for other months and seasons in Monterey Bay, as well as develop similar high-resolution climatology for other coastal regions. [Copyright &y& Elsevier]

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]

Abstract: Time serial multibeam bathymetry is used to evaluate geomorphic trends and submarine processes in the upper 4 km of Monterey Canyon, California. Seven high-resolution bathymetric surveys conducted between September 2002 to February 2005 show that the upper canyon axis and head grew in volume 1000000 m3 ±700000 m3, at an average annual rate of 400000 m3/a±300000 m3/a through lateral erosion and vertical incision. This net loss of substrate during the 29-month period is parsed between local erosion of 1400000 m3 and local deposition of 350000 m3. A submarine landslide with a scar void volume of 70000 m3 and debris pile of 52000 m3 occurred between March 2003 and September 2004. During the subsequent months until February 2005, the slide scar grew 40% in volume while the debris pile shrank by 80%. The canyon-head rim adjacent to Moss Landing Harbor prograded seaward and retreated shoreward significantly (up to 50 m) during the study suggesting frequent episodes of sediment build up and subsequent down-canyon failure. A large field of sand waves located in the channel axis was completely reworked in each time series except for a 24 h period where no wave crest movement was noted, and a 32 day period where up-canyon migration of approximately 7 m was recorded in the northern tributary. [Copyright &y& Elsevier]

Drifting Macrocystis pyrifera (L.) C. Agardh sporophytes have long been viewed as the primary long-distance dispersal vector; yet, few data exist that support the ability of reproductive viable sporophytes to actually travel the presumed hundreds to thousands of kilometers. This study addressed the reproductive longevity of experimental and naturally occurring M. pyrifera drifters. Temporal variability in sporophyte size and reproduction was estimated for experimental drifting sporophytes that were tethered to surface buoys and compared with attached plants (controls). Reproductive viability was also studied for beach-cast drifters (BCD), and naturally drifting sporophytes observed during field surveys in Monterey Bay. Detached drifting sporophytes were tracked with radio transmitters to follow drifter trajectories and to measure drifting speed. Experimental drifters (ED) experienced a 74% reduction in frond length after 35 days, a 76% reduction in average frond number after 70 days, and a reduction in average sorus area by 83% after 28 days. Although zoospore production was reduced following detachment, sporophytes remained fertile with high zoospore germination success as long as sori were present (125 days). Zoospore production and germination success for natural and BCD was similar to ED. The average displacement of radio-tagged drifters was 7.12 km·day−1, suggesting that a sporophyte adrift for 125 days disperses viable propagules (zoospores) over 890 km (±363). Dispersal of propagules is important for population restoration, distribution, and genetic diversity. Such dispersal distances are long enough to connect potentially all Northern Hemisphere Macrocystis populations across a generational timescale and may facilitate inter-hemispheric gene flow. [ABSTRACT FROM AUTHOR]

Abstract: Southern Monterey Bay was the most intensively mined shoreline (with sand removed directly from the surf zone) in the U.S. during the period from 1906 until 1990, when the mines were closed following hypotheses that the mining caused coastal erosion. It is estimated that the yearly averaged amount of mined sand between 1940 and 1984 was 128,000 m3/yr, which is approximately 50% of the yearly average dune volume loss during this period. To assess the impact of sand mining, erosion rates along an 18 km range of shoreline during the times of intensive sand mining (1940–1990) are compared with the rates after sand mining ceased (1990–2004). Most of the shoreline is composed of unconsolidated sand with extensive sand dunes rising up to a height of 46 m, vulnerable to the erosive forces of storm waves. Erosion is defined here as a recession of the top edge of the dune. Recession was determined using stereo-photogrammetry, and LIDAR and GPS surveys. Long-term erosion rates vary from about 0.5 m/yr at Monterey to 1.5 m/yr in the middle of the range, and then decrease northward. Erosion events are episodic and occur when storm waves and high tides coincide, allowing swash to undercut the dune and resulting in permanent recession. Erosion appears to be correlated with the occurrence of El Niños. The calculated volume loss of the dune in southern Monterey Bay during the 1997–98 El Niño winter was 1,820,000 m3, which is almost seven times the historical annual mean dune erosion of 270,000 m3/yr. The alongshore variation in recession rates appears to be a function of the alongshore gradient in mean wave energy and depletions by sand mining. After cessation of sand mining in 1990, the erosion rates decreased at locations in the southern end of the bay but have not significantly changed at other locations. [Copyright &y& Elsevier]

Abstract: Nonlinear aspects of sea surface temperature (SST) in Monterey Bay are examined, based on an 85-year record of daily observations from Pacific Grove, California. Oceanic processes that affect the waters of Monterey Bay are described, processes that could contribute to nonlinearity in the record. Exploratory data analysis reveals that the record at Pacific Grove is non-Gaussian and, most likely, nonstationary. A more recent test for stationarity based on a power law approximation to the slope of the power spectrum indicates that the record is stationary for frequencies up to ∼8 cycles per year (∼45 days), but nonstationary at higher frequencies. To examine the record at Pacific Grove for nonlinear behavior, third-order statistics, including the skewness, statistical measures of asymmetry, the bicorrelation, and the bispectrum, were employed. The bicorrelation revealed maxima located approximately 365 days apart, reflecting a nonlinear contribution to the annual cycle. Based on a 365-day moving window, the running skewness is positive almost 80% of the time, reflecting the overall impact of warming influences. The asymmetry is positive approximately 75% of the time, consistent with the asymmetric shape of the mean annual cycle. Based on the skewness and asymmetry, nonlinearities in the record, when they occur, appear to be event-driven with time scales possibly as short as several days, to several years. In many cases, these events are related to warm water intrusions into the bay, and El Niño warming episodes. The power spectrum indicates that the annual cycle is a dominant source of variability in the record and that there is a relatively strong semiannual component as well. To determine whether or not the annual and semiannual cycles are harmonically related, the bispectrum and bicoherence were calculated. The bispectrum is nonzero, providing a strong indication of nonlinearity in the record. The bicoherence indicates that the annual cycle is a major source of nonlinearity and further implies that the annual and semiannual cycles are harmonically related. Based on the wavelet power spectrum (WPS), the appearance of the semiannual cycle is transitory; however, pathways between the annual and semiannual cycles appear at certain times when nonlinear interaction between them could occur. Comparisons between the WPS and the running skewness suggest that there is a tendency for periods when pathways exist, to coincide with increased positive skewness, and, often, with El Niño warming episodes. The Hilbert–Huang transform, a relatively new tool for nonstationary and nonlinear spectral analysis, was used to further examine the origin of the semiannual cycle. The time-dependent Hilbert spectrum reveals large and erratic variations in frequency associated with semiannual cycle but far greater stability associated with the annual cycle. As a result, the time-integrated Hilbert spectrum does not indicate the presence of a semiannual cycle. The method of surrogates from the field of nonlinear dynamics was also employed to test the Hopkins record for nonlinearity. Differences between the data and the surrogates were found that were statistically significant, implying the existence of nonlinearity in the record. Using the method of surrogates together with a one-year moving window, El Niño warming episodes appear to be a likely source of nonlinearity, consistent with the other analyses that were performed. Finally, the influence of stochastic variability due to serial correlation in the data was examined by comparing standardized statistics for the observations and for simulations based on an autoregressive model whose properties were obtained from the observations. The magnitude of the variability for the simulations was found to be far less than that associated with the original data, and thus stochastic variability does not appear to be a factor that significantly affects the interpretation of our results. [Copyright &y& Elsevier]

Abstract: We report on a direct and autonomous measure of new production based on time series observations with ISUS nitrate sensors deployed for several years on oceanographic moorings offshore of Monterey Bay, California. The amplitude of diel cycles of surface nitrate is correlated with rates of primary production measured by 14C uptake. The drawdown of nitrate averaged over a year is about 70% of the fixed nitrogen needed for biomass production. Phytoplankton biomass predicted from the diel nitrate uptake and a fixed rate constant for nitrate loss (grazing and export) matched observations over the annual cycle. New production rates determined with the moored sensors are highly correlated with nitrate concentration and the intensity of upwelling. The implication is that arrays of moorings with chemical sensors can now be used to estimate new production of biomass and ecosystem processes over multiple temporal and spatial scales. [Copyright &y& Elsevier]

Abstract: A Raman spectrometer extensively modified for deep ocean use was used to measure synthetic hydrates formed in an ocean environment. This was the first time hydrates formed in the ocean have been measured in situ using Raman spectroscopy. Gas hydrates were formed in situ in the Monterey Bay by pressurizing a Pyrex cell with various gas mixtures. Raman spectra were obtained for sI methane hydrate and sII methane+ethane hydrate. Gas occlusion resulting from rapid gas growth of methane hydrate was measured immediately after formation. The Raman shift for methane free gas was coincident with that of methane in the small 512 hydrate cage. The methane Raman peak widths were used to discriminate between methane in the free gas and hydrate phase. Methane+ethane sII hydrate was formed for 43 days on the seafloor. In this case, gas occlusion was not measured when the gas hydrates were allowed to form over an extended time period. Equivalent Raman spectra were obtained for the in situ and laboratory-formed sII methane+ethane hydrates, under similar p, T, and x conditions. With the Raman spectrometer operating in the ocean, seawater contributes to the Raman spectra obtained. Both the Raman bands for the sulfate ion and water were used to qualitatively determine the distribution of water phases measured (hydrate, seawater) in the Raman spectra. [Copyright &y& Elsevier]

Abstract: The exclusively deep-sea ascidian family Octacnemidae comprises several genera in which the oral siphon has hypertrophied to form two large lips which create an “oral hood” capable of capturing motile prey. Megalodicopia hians is typical of this carnivorous family and has been reported to prey upon small epibenthic crustaceans. Distribution of M. hians in the Monterey Canyon system (36°45′N, 122°00′W) (California) was determined with remotely operated vehicles. M. hians was found sparsely to depths of at least 3800m throughout the canyon; however, abundance was greatest within the oxygen-minimum zone (400–800m). Eggs, sperm, and recently fertilized embryos were obtained repeatedly from adults returned to the laboratory in vivo, indicating that this species free-spawns routinely. Overall egg diameter (ovum plus chorion, plus follicle cells) was 175–190μm—considerably smaller than previously reported for this species. Embryonic development at temperature and oxygen concentrations equivalent to the oxygen-minimum zone was 2–4d and, embryos gave rise to typical phlebobranch “simple” tadpole larvae. Larval period was extremely variable, and settlement/metamorphosis occurred up to 3 months post-hatching. These results are discussed within the context of settlement-site selection and fertilization ecology of the species. [Copyright &y& Elsevier]

Abstract: What most clearly distinguishes near-shore and off-shore currents is their dominant spatial scale, O (1–30)km near-shore and O (30–1000)km off-shore. In practice, these phenomena are usually both measured and modeled with separate methods. In particular, it is infeasible for any regular computational grid to be large enough to simultaneously resolve well both types of currents. In order to obtain local solutions at high resolution while preserving the regional-scale circulation at an affordable computational cost, a 1-way grid embedding capability has been integrated into the Regional Oceanic Modeling System (ROMS). It takes advantage of the AGRIF (Adaptive Grid Refinement in Fortran) Fortran 90 package based on the use of pointers. After a first evaluation in a baroclinic vortex test case, the embedding procedure has been applied to a domain that covers the central upwelling region off California, around Monterey Bay, embedded in a domain that spans the continental U.S. Pacific Coast. Long-term simulations (10years) have been conducted to obtain mean-seasonal statistical equilibria. The final solution shows few discontinuities at the parent–child domain boundary and a valid representation of the local upwelling structure, at a CPU cost only slightly greater than for the inner region alone. The solution is assessed by comparison with solutions for the whole US Pacific Coast at both low and high resolutions and to solutions for only the inner region at high resolution with mean-seasonal boundary conditions. [Copyright &y& Elsevier]

Abstract: Observations of animals in the deep ocean typically require the use of bright lights that can damage eyes and disrupt normal behaviors. Although the use of infrared light is an effective means of unobtrusive observation on land, it is far less effective in the ocean where long wavelength light is rapidly attenuated by seawater. Here we describe in situ observations of the behavior of the sablefish, Anoplopoma fimbria, around a baited site under different lighting conditions. Fish were observed with low-light-level imaging that had adequate sensitivity to compensate for the attenuation losses associated with the use of long wavelength light in water. ROV-based experiments compared the number of sablefish seen around bait, illuminated alternately with red vs. white light. Significantly more fish were seen under red light than white light with the average number of sablefish observed per 10min viewing interval under red light being 38.9 (±18.5 SD) compared to 7.5 (±7.1 SD) under white light. Under both red and white light sablefish spent only brief periods in the illumination field (10.5s [±8.7 SD] under red light and 6.6s [±8.7 SD] under white light). It appeared that sablefish were responding to competing drives of attraction to the bait and avoidance of the lights and that the avoidance was greater for white light than for red light. Observations were also made with the newly developed deep-sea observatory, Eye-in-the-Sea, using long wavelength LED illumination. The onset of LED illumination did not generally produce a startle response from fish around the bait, and in some cases invoked no response at all. However, in the majority of cases the fish moved out of the circle of red-light illumination during the 7.5s recording period, indicating that the light was detectable and aversive to these fish. This was true with both 660 and 680nm LED illuminators. We conclude that while a sharper short-wavelength cutoff of the illumination source is required to achieve truly unobtrusive observation, red light is nonetheless significantly less disruptive than white light for observing deep-sea fish behavior, and can provide adequate illumination when used in combination with image-intensified cameras. [Copyright &y& Elsevier]

Abstract: The subsurface plumbing system of ancient seeps of hydrocarbon-rich gases and fluids is partially preserved by seep deposits in Miocene rocks of the Coast Ranges and on the seafloor of the Monterey Bay region in central California. The fossil seep-related deposits are of two types: authigenic carbonates and intrusions of oil-saturated sandstones. Both types occur in fractured and faulted siliceous mudstone and porcelanite layers of the organic-rich Miocene Santa Cruz Mudstone. They are associated with tectonic structures indicating deformation, and are located in the proximity of faults. The morphology of the seep carbonates is characterized by strong asymmetries and by holes, pipes and other types of fluid conduits with orientations parallel to the directions of the local fracture- and fault-sets, thus suggesting structural control over pathways of fluid migration. The dominant direction of the conduits in the seep carbonates and of the intrusive dikes (northeast–southwest) differs from the dominant orientation of the tectonic structures of the San Andreas Fault System (northwest–southeast). Previous interpretations of these ancient seep-related deposits suggested that lateral changes of the thickness of the Cenozoic marine host sediments favored fluid migration from basin depocenters located offshore toward basin margins. Different driving forces for fluids have been hypothesized including hydrocarbon generation, differential compaction, and tectonic compression. Most of the fossil seeps are located on structural highs of the basement and adjacent to offshore basins that form elongated depressions oriented northwest–southeast. Previously unidentified structures that offset the basement along northeast–southwest trends (cross-setting faults) paralleling the orientations of the conduits of the seep carbonates and the dikes of oil-saturated sandstones were also recognized. Tectonic deformation, block rotations (documented by local clockwise rotations of paleomagnetic directions in the Coastal Ranges) and cross-faults were probably produced during the Late Miocene and Pliocene to accommodate the shear stress between conjugate faults during eastward shifting of the activity of the San Andreas Fault System. Comparison with previous studies on ancient seep deposits, regional geology and offshore tectonic data, suggest that the fluids that sourced the seeps were driven by episodes of inverse tectonics, during which previously extensional depositional basins were involved in episodes of tectonic compression. Tectonic deformation created cross-faults in rotated blocks, which could have acted as important conduits for the flow of hydrocarbon-rich fluids and gases and fostered the injection of liquefied sands. [Copyright &y& Elsevier]

Abstract: Microstructure measurements taken on the Monterey Bay continental shelf, within 4km of the shelf break, reveal a complex mixing environment. Depth- and time-averaged dissipation rates and diapycnal diffusivities were elevated above observations made over other continental shelves with no significant topography, but were below those influenced by topographic features. The close proximity of the shelf break/canyon rim, locally generated internal tides, and nonlinear internal waves all contributed to the elevated turbulence. The complex bathymetry associated with Monterey Submarine Canyon allowed an internal tide to be generated at depths greater than 1500m, as well as at the shelf break. The observed velocity field was normally dominated by upward energy propagation from the local shelf break generated internal tide, but near low tide downward energy propagation from a surface reflection of the internal tide generated below 1500m was observed. Turbulent dissipation rates were not well parameterized by either the open-ocean Gregg–Henyey model or the recently developed MacKinnon–Gregg shelf model. Like its application on the New England shelf, the MacKinnon–Gregg model had the correct functional dependence on shear and stratification (dissipation increasing with increasing shear and increasing stratification), however, the magnitude and range of values were too small. The most surprising finding was the presence of what we believe to be large, high-aspect-ratio, downslope-propagating nonlinear internal solitary-like waves of elevation. Upon reaching the canyon rim, these waves propagated into deep water and transformed into waves of depression. On the shelf south of the canyon, the waves of elevation accounted for 20% of the observed turbulent kinetic energy dissipation. Off the shelf, where the solitary-like waves changed to downward displacement, their average dissipation increased 10-fold to , and accounted for nearly half the dissipation in the upper 150m. [Copyright &y& Elsevier]