Recent csgc_rcr items

Navigating Shallow Streams: Effects of Changing Stream Water Depths on Outmigration of Endangered Coho Salmon

Fri, 31 Jul 2026 00:00:00 +0000

Declining streamflow from water management and climate change threatens fish migration. In coastal California, USA, we evaluated the effects of receding streamflow on the seaward migration of juvenile Coho Salmon (Oncorhynchus kisutch) in four streams over 10 years (2010–2020). We monitored the movement of juveniles tagged with passive integrated transponders and measured depths at riffle crest thalwegs (RCTs), the shallowest channel feature that fish must navigate. Each stream exhibited a unique relationship between RCT depth and flow, relating to its geomorphic characteristics, producing distinct ranges of water depths among streams. During the peak migration period, juveniles moved over a wide range of depths (interquartile range 5.8–19.2 cm), with greater depths occurring in wet years than in dry years. However, the depths at which fish were detected were significantly deeper than continuous, observed depth measurements during the same period. We found the greatest differences...

Global priorities for ocean sustainability from Early Career Ocean Professionals.

Fri, 31 Jul 2026 00:00:00 +0000

Intergenerational diversity is central to achieving long-term ocean sustainability. As such, one of the main goals and challenges in the UN Decade of Ocean Science for Sustainable Development (2021–2030) is fostering engagement and leadership across career stages and from diverse sectors. To understand the knowledge and professional development needs of the next generation, we surveyed the perspectives of 1344 Early Career Ocean Professionals (ECOPs) across 108 countries and territories. We assess the survey results, reflect on what has been done to address these needs halfway through the Ocean Decade, and suggest areas to further progress. We found that climate change and its social and ecological impacts are the unifying topical priority for ECOPs globally. ECOPs called for support and access to professional development. Despite progress in many initiatives, enhanced opportunities for collaboration across disciplines and sectors, mentorship and professional development, knowledge...

Predicting Shoreline Changes Along the California Coast Using Deep Learning Applied to Satellite Observations

Fri, 31 Jul 2026 00:00:00 +0000

Understanding and predicting changes in shoreline location are critical for coastal planners. In situ monitoring is accurate but not widely available. Satellite observations of shorelines have global coverage, but their accuracy and predictive capacity have not been fully explored. Abundant beach surveys and extensive wave observations in Southern California provide a unique ground truth for the interpretation of satellite-derived recently wetted waterlines. We combine 23 years of waterline position estimates from satellite imagery with nearshore wave hindcasts and tides to train and test a deep neural network (DNN). The trained DNN uses only tides and waves as predictors at transects with satellite coverage and wave estimates to predict beach width and, for the first time, seasonal average beach slopes. Beach width changes hindcast using DNN have at least fair skill (>0.3) for 50% of transects, where the skill was calculated relative to the mean of extensive new in situ survey...

Lessons learned from the PICES FUTURE Program on development of an interdisciplinary international science program to advance ocean sustainability.

Fri, 31 Jul 2026 00:00:00 +0000

Interdisciplinary international science programs that combine environmental, ecological, and social research are pivotal in advancing ocean sustainability by integrating diverse expertise and fostering collaboration across borders. We examine the evolution and accomplishments of the North Pacific Marine Science Organization’s (PICES) Forecasting and Understanding Trends, Uncertainty and Responses of North Pacific Ecosystems (FUTURE) Program, designed to understand and communicate the future of North Pacific ecosystems under various natural and anthropogenic forces. The program’s unique application of the North Pacific Social-Ecological-Environmental Systems (SEES) framework has aimed to facilitate interdisciplinary collaboration and enhance our comprehension of ecosystem responses to climate variability. Through a combination of systematic review and quantitative text analysis of research outputs, we evaluate the program’s success in addressing its scientific objectives, and identify...

Living in the ‘Blue Zone’ of a sea-level rise inundation map: Community perceptions of coastal flooding in King Salmon, California

Fri, 31 Jul 2026 00:00:00 +0000

As sea-level rise (SLR) inundation maps proliferate, it is important to study their politics – both how they are created and how they act upon and shape various lives and places. This paper uses the example of King Salmon, CA – a rural, low-income residential area projected to be one of the most at risk to SLR on the US West Coast – to examine how a community responds to external projections showing SLR risk to their homes and businesses. Through interviews with 17 King Salmon community members and observation of a county-hosted ‘communities at risk’ workshop, we examined the community’s social context, their past experiences with flooding, and their reaction to SLR projection maps including what next steps they would like to see taken. Residents expressed a strong connection to the place, noting that it is one of the few affordable places to live on the coast in California. We found that residents already live with regular flooding during larger tides of the year and have taken...

Proteinaceous deep sea coral amino acid isotope records reveal climate-driven decadal-scale planktic ecosystem fluctuations

Fri, 31 Jul 2026 00:00:00 +0000

Decadal-scale climate variability drives important fluctuations in nutrient availability and productivity in highly productive eastern boundary current pwelling ecosystems, but the relatively brief duration of most monitoring efforts limits understanding of these dynamics. When applied to high-resolution paleoarchives such as deep-sea proteinaceous coral skeletons, stable carbon and nitrogen isotope (δ13C and δ15N) analysis can provide useful new insight into biogeochemical and ecological changes beyond the instrumental record. However, interpretation of bulk δ13C and δ15N records is often complicated by multiple possible drivers of variability. Here, we addressed these challenges by applying both bulk and compound-specific amino acid δ15N and δ13C analysis to two bamboo coral specimens from Sur Ridge on the central California margin, generating sub-decadal resolution records spanning c. 1810 to present. Our overarching goals were to first test amino acid δ13C and δ15N proxies...

A laser-equipped chamber for the assessment of sprint swimming traits in fishes

Fri, 31 Jul 2026 00:00:00 +0000

Sprint swimming performance in fishes is relatively understudied despite its critical role in predation attempts, prey evasion, spawning events, and overcoming hydraulic challenges. Sprint swimming is characterized by fast acceleration, over a short distance and of limited duration. The bulk of sprint performance research uses analysis of high-speed recordings of fish behavior. While behavioral video analysis has improved, it is still expensive in both processing time and computational resources, limiting the ability to develop reaction norms for sprint performance which necessitate large sample sizes. Here we present a laser-gated sprint performance chamber (SPC) that improves upon past designs by introducing an adjustable number of lasers (≤ 25) that facilitates greater resolution on sprint performance. Use of customized arrangements can facilitate measurement of novel performance metrics of interest to a range of key questions (e.g., fatigue rate, residual anaerobic capacity,...

Size at maturity, reproductive cycle, and fecundity of the southern California brown box crab Lopholithodes foraminatus and implications for developing a new targeted fishery,

Fri, 31 Jul 2026 00:00:00 +0000

The brown box crab Lopholithodes foraminatus is a member of the king and stone crab family (Lithodidae) that occurs in deepwater along the eastern Pacific coast. Historically, landings in California have been low for this species, but an increase in fishing pressure prompted the state to designate it as an emerging fishery and implement an experimental fishery program. With no known biological studies of California brown box crab, essential fisheries information is needed to evaluate the feasibility of a new targeted fishery.

Targeted and nontargeted approaches to uncover complex halogenated pollutants in the historically endangered California brown pelican

Fri, 31 Jul 2026 00:00:00 +0000

Historically, California brown pelicans experienced reproductive failure and population decline induced by the pesticide dichlorodiphenyltrichloroethane (DDT). Although the population recovered after the 1972 DDT ban, nontargeted analytical methods have identified over 45 DDT-related compounds (DDT+) and other typically unmonitored halogenated organic compounds (HOCs) in regional upper trophic level wildlife species, presumably originating from the persistent and chemically-complex DDT manufacturing waste deposited in the Southern California Bight (SCB). However, there is limited data on DDT+ in previously endangered bird populations, including the brown pelican. We identified 183 HOCs in seven brown pelican liver samples (131 ± 48, mean ± SD) via nontargeted analysis. Seventeen DDT+ compounds were identified, including four tris(4-chlorophenyl)methane (TCPM)-related compounds, and 17 polychlorinated terphenyls (PCTs), all of which were not assessed in prior pelican research....

Juvenile life history, migration, and habitat use of natural-versus hatchery-origin Chinook Salmon

Fri, 31 Jul 2026 00:00:00 +0000

Objectives Our overall objective was to directly compare the early life history and migration patterns of hatchery- and natural-origin fish and determine when hatchery fish provide good surrogates for natural-origin winter-run Chinook Salmon Oncorhynchus tshawytscha in the Sacramento River system. Specifically, our objectives were to compare the juvenile freshwater habitat use, residence time in freshwater habitats, and size at age and relative growth of juveniles. Methods Using otoliths that were collected from adult carcasses, we reconstructed the freshwater life history of hatchery- and natural-origin fish through microstructural and chemical analyses. We analyzed the otolith strontium isotope chemistry and daily increment widths to characterize habitat use, migration timing, and growth. Results Following their hatchery-rearing period, hatchery fish had much shorter residence times (11 d, SD = 16 d) in the river than natural-origin fish (129 d, SD = 37 d). Beyond the reduced...

Variation in Salmon Migration Phenology Bolsters Population Stability but Is Threatened by Drought

Fri, 31 Jul 2026 00:00:00 +0000

Intrapopulation variation in movement is common in nature but its effects on population dynamics are poorly understood. Using movement data from 3270 individually-marked fish representing nine cohorts of coho salmon (Oncorhynchus kisutch) in California, we show that bimodal intrapopulation variation in the timing of juvenile down-migration from their natal habitat and subsequent residence in non-natal habitat affects growth, emigration timing, and the abundance and stability of adult returns. Non-natal fish (early down-migrants) exhibited more variable growth and more variable but earlier emigration to the estuary than natal fish (late down-migrants). While natal rearing was more common, non-natal fish were overrepresented among adult returns, and total returns were 1.4 times more stable than natal returns alone. Our results demonstrate that variation in migratory behaviour bolsters population stability. However, non-natal rearing is reduced in low water years, suggesting that...

Characterizing morphology of Egregia menziesii (Laminariales) in California over 2 centuries using historical and contemporary herbarium specimens.

Fri, 31 Jul 2026 00:00:00 +0000

The canopy-forming feather boa kelp Egregia menziesii exhibits remarkable morphological variability across its geographic range. Regional morphotypes of Egregia were once considered separate species, but they were not determined to be genetically distinct; instead, their morphology was thought to reflect local physical or environmental conditions. Although morphological variation in Egregia has long been observed and was previously characterized through field surveys in the early 2000s, we revisited this topic using digital morphometrics (i.e., image analysis) of 1624 macroalgal herbarium specimens from California dating back to the 19th century. We observed that the morphology of Egregia (rachis texture, lateral blade shape, and blade or pneumatocyst density) varied along a latitudinal gradient and could be predicted by seawater temperature and wave height. We also identified some region-specific morphological changes in recent decades. Further, the monthly presence or absence...

Risky main stems are a poorly understood constraint on salmon recovery in coastal California rivers

Fri, 31 Jul 2026 00:00:00 +0000

Objective: Investment in salmon habitat restoration often focuses on natal streams, with a goal of improving access for spawning fish and increasing early life survival of juveniles. This work is justified by a large body of research; however, return on investment in natal streams (at least in terms of increased adult abundance) has, so far, been marginally successful at best. The factors that constrain salmon populations may shift in space and time, and accurately tracking these constraints requires monitoring the full spatial and temporal scope of the salmon life cycle. In particular, juvenile salmon emigration through main-stem rivers to the ocean is not well studied and is poorly understood. Low emigration survival can prevent successful upstream habitat restoration from being realized as increased adult recruitment. Methods: We present acoustic telemetry studies from two coastal California rivers to estimate seaward emigration survival of Coho Salmon Oncorhynchus kisutch...

Centering knowledge co-production in sustainability science: Why, how, and when.

Fri, 31 Jul 2026 00:00:00 +0000

Solving complex sustainability problems requires novel, creative approaches. One such approach is knowledge co-production, where individuals with diverse expertise collaborate to generate knowledge in support of transformative solutions. Although the concept is not new, there is growing interest in using knowledge co-production in sustainability science, yet relatively few resources offer a practical guide, rooted in theory, to help researchers and practitioners understand when and how to co-produce in the context of sustainability science. This paper synthesizes the existing literature across multiple disciplines to present a novel framework and actionable strategies for effective knowledge co-production in sustainability. The wheel of knowledge co-production, the conceptual framework presented, emphasizes the importance of iterative phases of building relationships, assessing available resources, involving diverse participants, considering context, and working together with...

RipScout: Realtime ML-Assisted Rip Current Detection and Automated Data Collection using UAVs

Fri, 31 Jul 2026 00:00:00 +0000

This article presents RipScout, a system for realtime rip current detection and data collection using drones equipped with machine learning (ML). No internet connection is required. RipScout achieves realtime performance by using lightweight ML models that fit the constraints of limited mobile computing re- sources with the drone controller. We compared different ML models trained to detect either one or two types of rip currents. The best model was then selected for RipScout. The system was evaluated with three ML models, with the EfficientDet D2 model achieving the highest accuracy of 93.1% for multiclass detection while maintaining realtime processing at an average speed of 17 frames per second. When a rip is detected along a flight path, the drone hovers in place and collects a video clip of a predefined length, followed by circling around the detected rip using prespecified radii and heights to collect video samples from different vantage points and elevations. An important...

Regional governance solutions for sea-level rise adaptation: Perspectives from Humboldt Bay, California.

Fri, 31 Jul 2026 00:00:00 +0000

Sea-level rise (SLR) is a complex challenge which could require the development of new special-purpose governance arrangements that allow for better coordination across jurisdictions and levels. This paper explores perspectives related to regional coordination for SLR adaptation in Humboldt Bay, California. Humboldt Bay is experiencing one of the fastest rates of SLR on the West Coast and exists in a complex regulatory environment with over 20 government entities, three Tribes, and numerous community members and groups connected to the issue. Through a mixed-methods approach that included 46 semi-structured interviews with and a survey of 107 coastal professionals connected to the Bay, we sought to capture local perspectives related to the barriers and opportunities for SLR adaptation, potential regional governance solutions for SLR, and the incorporation of community and equity considerations into SLR planning. Respondents identified several barriers including competing priorities...

The essential role of large research vessels in marine ecosystem observations and ocean sustainability.

Fri, 31 Jul 2026 00:00:00 +0000

Our understanding of marine ecosystems and ability to manage them sustainably has come from multidisciplinary observations made repeatedly over long periods of time. These long-term ecosystem observations depend on the capabilities of large research vessels, which play an essential role in the collection of global ocean observations. Research vessels serve as large, stable platforms for collecting high volume samples from the surface to the seafloor that provide uniquely valuable in situ marine ecosystem information. Additionally, they serve as mobile laboratories enabling the collection, preservation, processing, and analysis of unique samples and data, such as chemical, biogeochemical, and biological parameters. Given their capacity for, and repeated use in, collecting comprehensive marine ecosystem observations—across geology, physics, chemistry, and biology—large research vessels provide insight into long-term regional ecosystem dynamics. They also act as platforms-of-opportunity...

Sea Grant Programs Build Resilience to Coastal Climate Hazards.

Fri, 31 Jul 2026 00:00:00 +0000

Sea Grant programs across the United States and its territories are working with coastal communities to enhance their resilience to hazards and weather extremes exacerbated by climate change. Drawing on the expertise of the authors, many of whom have multiple years or decades of experience in the Sea Grant network, the article identifies five key strategies that Sea Grant programs employ to support the process of coastal hazards and extreme weather adaptation and resilience-building. The application of these strategies, most of which have their roots in the historical legacy of extension, are then illustrated through summaries of current Sea Grant activities and projects, showcasing how they have been applied in real-world situations. These strategies allow Sea Grant programs to fill a unique and valuable niche in national efforts to enhance coastal resilience. The article concludes with a discussion of emerging challenges and recommendations for strengthening Sea Grant’s capacity...

Anatomy of a range contraction: Flow-phenology mismatches threaten salmonid fishes near their trailing edge

Fri, 31 Jul 2026 00:00:00 +0000

Climate change is redistributing life on Earth, with profound impacts for ecosystems and human well-being. While repeat surveys separated by multidecadal intervals can determine whether observed shifts are in the expected direction (e.g., poleward or upslope due to climate change), they do not reveal their mechanisms or time scales: whether they were gradual responses to environmental trends or punctuated responses to disturbance events. Here, we document population reductions and temporary range contractions at multiple sites resulting from drought for three Pacific salmonids at their ranges’ trailing edge. During California’s 2012 to 2016 historic multiyear drought, the 2013 to 2014 winter stood apart because rainfall was both reduced and delayed. Extremely low river flows during the breeding season (“flow–phenology mismatch”) reduced or precluded access to breeding habitat. While Chinook (Oncorhynchus tshawytscha) experienced a down-river range shift, entire cohorts failed...

Fisheries of the Middle: Building collaborations between seafood and agriculture to revitalize and enhance mid-scale food production.

Fri, 31 Jul 2026 00:00:00 +0000

Fisheries of the Middle: Building collaborations between seafood and agriculture to revitalize and enhance mid-scale food production.

Sea level rise impacts on Coastal Access

Fri, 31 Jul 2026 00:00:00 +0000

Climate change and associated sea level rise (SLR) will have substantial impacts on coastlines worldwide, threatening beaches, infrastructure, economies, and communi- ties. In California, communities and individuals rely on the state’s public coastal access to physically reach and use the beaches and nearshore waters. Such use constitutes a key component of the state’s ocean-dependent coastal tourism and recreation sec- tor, and contributes significantly to state and local economies, coastal culture, and individual’s coastal attachment. This study investigates the impacts of SLR on coastal access, first by using geospatial tools to develop a higher resolution database of the location and elevation of coastal access sites (opportunities, amenities, and facilities, including parking) at various coastal access sites statewide. Then, using the Coastal Storm Modeling System (CoSMoS) SLR run-up model, we project the loss of coastal access opportunities due to SLR. We find that impacts...

Spatiotemporal models reveal dynamic growth patterns in US West Coast groundfish

Fri, 31 Jul 2026 00:00:00 +0000

Objective Variability in somatic growth of marine fish can affect their reproductive potential and survival and, therefore, the productivity of a population. Understanding how growth might vary among species can improve predictions of population status and responses to environmental change. Our objective was to characterize the variability in growth and body condition of groundfish species along the U.S. West Coast to support their monitoring and assessment. Methods We used geostatistical models to estimate growth rate and body condition, two interrelated traits associated with somatic growth, across space and time for nine commercially important U.S. West Coast groundfish species. We fit generalized linear mixed models with Gaussian Markov random fields to biological data collected from annual bottom trawl surveys to estimate variability at a 4- × 4-km spatial resolution. Results Our models uncover spatiotemporal variability in growth rate and body condition in all nine groundfish...

Collaborative fisheries research reveals reserve size and age determine efficacy across a network of marine protected areas

Fri, 31 Jul 2026 00:00:00 +0000

A variety of criteria may influence the efficacy of networks of marine protected areas (MPA) designed to enhance biodiversity conservation and provide fisheries benefits. Meta-analyses have evaluated the influence of MPA attributes on abundance, biomass, and size structure of harvested species, reporting that MPA size, age, depth, and connectivity influence the strength of MPA responses. However, few empirical MPA evaluation studies have used consistent sampling methodology across multiple MPAs and years. Our collaborative fisheries research program systematically sampled 12 no-take or highly protective limited-take MPAs and paired fished reference areas across a network spanning 1100 km of coastline to evaluate the factors driving MPA efficacy across a large geographic region. We found that increased size and age consistently contributed to increased fish catch, biomass, and positive species responses inside MPAs, while accounting for factors such as latitude, primary productivity,...

Artificial intelligence literacy for ocean professionals is needed for a sustainable future

Fri, 31 Jul 2026 00:00:00 +0000

Artificial intelligence literacy for ocean professionals is needed for a sustainable future

Environment-driven trends in larval abundance predict fishery recruitment in two saltwater basses

Fri, 31 Jul 2026 00:00:00 +0000

Environmental and biological factors influencing fish larvae can drive fishery cohort strength, yet larval abundance is typically a better indicator of spawning biomass. Under a changing ocean, studies that explore the relationships between environmental variables, larval abundance, and fishery recruitment remain valuable areas for ongoing research. We focus on a popular, recreational-only, multispecies saltwater bass fishery (genus Paralabrax) whose population status and recovery potential are uncertain. We resolved Paralabrax spp. larval data to species over a 54-year period (1963–2016) and used species distribution models to (i) generate and test species-specific standardized indices of larval abundance as indicators of adult stock status and fishery recruitment and (ii) evaluate long-term spatiotemporal trends in their population dynamics relative to environmental variables and climate forcing. Contrary to initial hypotheses, species-specific larval abundance predicted future...

Coastal Flood Hazard Workshop: Advancements in Bridging Scales and Disciplines for Future Risk Assessment

Fri, 31 Jul 2026 00:00:00 +0000

This workshop brought together researchers with technical expertise in predicting and evaluating coastal flood hazards and potential impacts in a changing climate with the goal of assessing state-of-the-art methods, determining knowledge gaps, and identifying future research pathways that can inform community-level flood risk and adaptation planning.

Marine Protected Areas and Fishing Community Well-Being: An Example from Statewide Socioeconomic Monitoring of the California MPA Network.

Fri, 31 Jul 2026 00:00:00 +0000

As marine protected areas (MPAs) continue to proliferate as an ocean conservation tool, it is important to understand their socioeconomic outcomes, both in the short-term following implementation and in the long-term as they become a more permanent part of the ocean landscape. This paper presents results from an effort to conduct long-term socioeconomic monitoring of commercial fishing communities in relation to California’s statewide MPA network, which was fully implemented in 2012 and consists of 124 MPAs covering 16% of state waters. To assess commercial fishing community perceptions of well-being and outcomes from the MPA network, we held virtual focus groups in 18 major port-based commercial fishing communities across California with a total of 85 participants from 2020 to 2021. Focus groups had both quantitative and qualitative components, with participants rating their fishing community and engaging in discussions on topics related to their environmental, economic, and...

SmartCS: Enabling the Creation of ML Powered Computer Vision Mobile Apps for Citizen Science Applications without Coding

Fri, 31 Jul 2026 00:00:00 +0000

It is undeniable that citizen science contributes to the advancement of various fields of study. There are now software tools that facilitate the development of citizen science apps. However, apps developed with these tools rely on individual human skills to correctly collect useful data. Machine learning (ML)–aided apps provide on-field guidance to citizen scientists on data collection tasks. However, these apps rely on server-side ML support, and therefore need a reliable internet connection. Furthermore, the development of citizen science apps with ML support requires a significant investment of time and money. For some projects, this barrier may preclude the use of citizen science effectively. We present a platform that democratizes citizen science by making it accessible to a much broader audience of both researchers and participants. The SmartCS platform allows one to create citizen science apps with ML support quickly and without coding skills. Apps developed using SmartCS...

Investigating eye lens composition for stable isotope analysis in fishes: a comparison between Chondrichthyes and Actinopterygii

Fri, 31 Jul 2026 00:00:00 +0000

Life history ecology provides a framework for understanding the complex interactions between organisms and their environments but is challenging to resolve for long-lived and migratory species. In fishes, life history is predominantly explored with stable isotope analysis (SIA) of accretionary tissues, such as otoliths. An alternative archival tissue validated for SIA in Teleosts (i.e., ray-finned fishes) is the proteinaceous eye lens and its growth layers (laminae). Here, we aim to expand the SIA of laminae to include Chondrichthyans (cartilaginous fishes; sharks, skates, rays, sawfish, and chimeras). We observe that urea in the eye lens drives patterns of elemental composition (i.e., C:N ratio) for Chondrichthyes, but the isotopic effect of urea is negligible. Teleost fishes exhibit consistent C:N ratios across eye lenses, while Chondrichthyan eye lens laminae C:N ratios decrease from the inner post-apoptotic laminae to outer pre-apoptotic laminae. After confirming the presence...

Seasonal variation and response of surf zone fish assemblages to environmental variables in the Northeast Pacific

Fri, 31 Jul 2026 00:00:00 +0000

Located at the land-sea interface, the highly dynamic sandy beach and surf zone ecosystem is one of the coastal zones used most intensely by humans (e.g., recreation, fishing, tourism). Surf zones are also important as fish habitat; however, the factors structuring fish assemblages in the surf zone are relatively understudied due to challenges associated with sampling this dynamic environment. To investigate temporal influences on surf zone fish communities, we evaluated seasonal trends in the fish assemblage and associations with environmental conditions using baited remote underwater video stations (BRUVS) at four beaches on the Northeast Pacific coast (California, USA) from July 2020 to June 2021. Our study region is characterized by strong seasonality in productivity (due to spring upwelling) and the wave climate (in response to winter storms), making it an ideal location for evaluating seasonal change in surf zone fish. We found that surf zone fish assemblages exhibited marked...

Time-varying flow-ecology relationships for an endangered fish population: Longfin Smelt in the San Francisco Estuary

Fri, 31 Jul 2026 00:00:00 +0000

Major estuaries globally are experiencing fast-paced changes in hydrology and ecosystem dynamics. However, connecting alteration of river flow regimes to estuarine fish population dynamics remains a challenge, partly due to the untested assumption that flow regimes, fish dynamics, and the resulting flow–ecology relationships are stationary (i.e., have no systematic changes in mean or variance over time). Here, we studied the endangered population segment of Longfin Smelt (Spirinchus thaleichthys) in the San Francisco Estuary, which depends on seasonal river flows to reproduce. We used extensive biomonitoring data (1980–2020) and two time-series modeling techniques, namely multivariate autoregressive state-space (MARSS) models and dynamic linear models (DLMs), to understand how population dynamics respond to interannual flow variation, and whether flow–ecology relationships have changed over time. MARSS outputs showed that population trajectories are best explained by a combination...

First controlled out of season spawning for California yellowtail (Seriola dorsalis)

Fri, 31 Jul 2026 00:00:00 +0000

The ability to control egg production and have a consistent supply of high quality eggs is critical to the commercial success of any farmed marine finfish species. Here we describe the first documented controlled spawning of California yellowtail (CYT; Seriola dorsalis). The aim for this study was to shift volitional spawning six months ahead of when natural spawning typically occurs for the species using photothermal manipulation. Over the course of one year we tracked spawning for two sibling groups of F1 generation broodstock and recorded relevant metrics for all spawn events (egg production, viability), eggs (egg and oil diameters, hatch rates), and larvae (notochord length at hatch, yolk sac volume, survival to first feeding). The first group was subjected to natural day length and temperature conditions (Natural) and produced eggs from March through October in 2023. The second group had a shifted day length and temperature regime (Controlled) designed to stimulate spawning...

Management considerations for establishing a coastal acidification monitoring system from U.S. Coastal Acidification Networks

Fri, 31 Jul 2026 00:00:00 +0000

Ocean acidification (OA), caused by the uptake of anthropogenic carbon dioxide, is a concern for ocean resource users in coastal regions where the phenomenon is compounded by variable processes. Sustained OA monitoring systems are critical for characterization of baseline ocean conditions and identification of changes and impacts to coastal ecosystems and communities. Establishing an OA monitoring network is best accomplished through iterative planning, sustained funding, and comprehensive understanding of the coastal system. This paper offers decision-making considerations for entities interested in establishing a local to regional scale OA observing system. Such considerations include which carbon system parameters can be measured in each system, which sensors and platforms will provide applicable information for interested partners, and best practices for observing data management. Because every region faces unique circumstances, we present context-specific examples of effective...

How California Sea Grant’s State Fellowship Program Fuels Careers in Coastal Conservation and Management

Fri, 31 Jul 2026 00:00:00 +0000

California Sea Grant’s State Fellowship Program, modeled after NOAA Sea Grant’s highly successful John A. Knauss Marine Policy Fellowship Program, provides hands-on experience in the planning, implementation, and management of marine, coastal, and/or watershed resource policies and programs in the state of California. The program matches graduate students who have recently completed their degrees with hosts in municipal, state, and federal agencies and in research and con- servation organizations in California for a 12-month paid fellowship. Over 300 fellows have been matched with over 40 unique hosts since its launch in 1987. Many alumni are now employed in key positions in government at the state and federal level, with 80% of participants in a given year going on to jobs in policy and/or resource management after completing their fellowships. This article provides a brief history of the program and testimonials from past fellows and hosts, and explores the program’s important...

Lessons learned from integrated long-term monitoring of a coho salmon population complex in the Russian River watershed

Fri, 31 Jul 2026 00:00:00 +0000

In California’s Russian River watershed, home to imperiled salmon and steelhead populations, an intensive long-term monitoring program plays an integral role in supporting species recovery. The program conducts life cycle and basinwide monitoring of natural- and hatchery-origin coho salmon using PIT antenna arrays, downstream migrant traps, snorkel counts, electrofishing, and spawner surveys paired with environmental monitoring. The program has also served as a foundation for targeted research by providing baseline data and monitoring infrastructure. Long-term and consistent tracking of population metrics has indicated modest but meaningful positive trends in abundance, but has also revealed unanticipated bottlenecks to population recovery, many of which are related to low streamflow. Monitoring has also revealed complex movement patterns of juveniles and adults throughout the watershed that have broadened our understanding of salmon life history diversity and the importance of...

Mobilizing ocean observations for marine ecosystem sustainability and resilience: A case study of the California Cooperative Oceanic Fisheries Investigations (CalCOFI)

Fri, 31 Jul 2026 00:00:00 +0000

The ocean is rapidly changing through warming, sea-level rise, ocean acidification, declining oxygen concentrations, and altered circulation patterns, which are reshaping marine ecosystems worldwide. These changes necessitate a complete and holistic view of affected marine ecosystems. Long-term ocean monitoring programs are crucial for understanding these changes and guiding sustainable management. The California Cooperative Oceanic Fisheries Investigations (CalCOFI)*1, initiated in 1949, is one of the world's longest-running and most comprehensive marine ecosystem observing programs. CalCOFI collects extensive ocean data across all Essential Ocean Variables in the Southern California Current four times a year (Gallo et al. 2022). This encompasses over 36 physical and chemical parameters, 2,500 biological parameters, and 50,000 environmental DNA sequences, measured simultaneously (Satterthwaite et al. 2025). These data have illuminated long-term ecosystem patterns, supported marine...

Persistent kelp forests during a massive decline reveal the importance of land-sea connectivity

Fri, 31 Jul 2026 00:00:00 +0000

A fundamental goal in ecology is to understand the drivers of stability in natural ecosystems in the face of disturbances. However, this is challenging when biotic and abiotic stressors operate simultaneously across multiple spatial scales. Such is the case for bull kelp forests (Nereocystis luetkeana) in northern California, where losses of predators combined with marine heatwaves have led to shifts from kelp forest to sea urchin barren states. However, despite the >90% loss of bull kelp forests since 2014, some patches remain. Here, we investigate the bull kelp community assemblage in these remnant patches as well as the drivers of bull kelp forest resistance. We used a combination of in situ field surveys (years 2020–2022), remote sensing data (years 2016–2022), and a laboratory grazing experiment with urchins (Strongylocentrotus purpuratus). We found that, in addition to the two dominant states (kelp forest vs. urchin barren), there is a third community state dominated...

The cross-cutting role of Ocean Decade Challenge 7 in achieving a sustainable and resilient global ocean observing system

Fri, 31 Jul 2026 00:00:00 +0000

With more than 90% of global warming occurring in the ocean, sea level rise doubling in the past 30 years, and the ever-increasing frequency and intensity of extreme events, ocean observations are essential for understanding and addressing some of these most pressing global challenges. Known observational needs can be addressed immediately by upgrading and expanding ocean observing capacity in under-observed areas such as polar regions, island nations and territories, coastal areas of developing countries, rapidly changing coastal systems, and the deep ocean. Enhancing existing and developing new cost-effective technologies for a range of user needs to maximize the reach of essential observations, supported by standardization and best practices for interoperability. Improved spatial and temporal coverage is urgently needed but also needs to be co-designed and fit-for-purpose. Democratizing access to ocean data and integrating artificial intelligence and machine learning into data...

Building bridges for ocean sustainability: The evolution and impact of the Early Career Ocean Professional (ECOP) Programme

Fri, 31 Jul 2026 00:00:00 +0000

Since its endorsement as a global network Programme in June 2021, the Early Career Ocean Professional (ECOP) Programme has been instrumental in supporting ocean professionals worldwide through funding, training, networking opportunities, and career development initiatives. Rooted in the vision of elevating diverse perspectives, the ECOP Programme fosters knowledge exchange between experienced professionals and ECOPs to promote ocean sustainability. As the UN Decade of Ocean Science for Sustainable Development (2021-2030) enters its fourth year of implementation, the ECOP Programme has grown and diversified to a formidable extent, both geographically and thematically. With over 5,200 ECOPs from 151 countries and overseas territories, the global ECOP community is currently dispersed across five regional nodes and more than 40 national hubs. This commentary brings some of the most active ECOP nodes into the limelight, amplifying their collective efforts to better understand, engage,...

Response of eelgrass (Zostera marina) to an adjacent Olympia oyster restoration project

Fri, 31 Jul 2026 00:00:00 +0000

Recent restoration efforts for the native Olympia oyster, Ostrea lurida, are commonly motivated by potential return of oyster-associated ecosystem services, including increased water filtration. The potential impact of such restoration on another species of ecological concern, eelgrass, Zostera marina, is unclear, but has been hypothesized to be positive if oyster filter feeding increases light penetration to eelgrass. For two years after construction of an oyster restoration project, we assessed the response of adjacent eelgrass (impact) compared to control and reference eelgrass beds by monitoring changes in light intensity, eelgrass shoot density, biomass, leaf morphometrics, and epiphyte load. We observed lower light intensity consistently over time, including prior to restoration, near the constructed oyster bed relative to the control and one of the reference locations. We also observed minor variations between control and impact eelgrass morphology and density. However,...

Toward social-ecological indicator integration in managing oceans and coasts.

Fri, 31 Jul 2026 00:00:00 +0000

A holistic understanding of social-ecological systems is essential to foster resilient, adaptive, and sustainable marine ecosystems and human communities. Yet, the integration of social and ecological dimensions is still developing within natural resource management, as are the indicators necessary to monitor them. In this study, we assess the integration of social and ecological indicators in marine management through a case study exploring the use of and degree of linkage between social and ecological indicators in US federal environmental and ocean resource agencies. Using a survey, we collected indicator sets or reports developed by these US federal agencies and found that 7 out of 11 total reports contained both social and ecological indicators. Within those reports, there were 333 social indicators. Only 35% (116) of the social indicators could be directly linked to commonly monitored ecological indicators. Social-ecological connections were focused on many themes, including...

Effects of Freshwater Flow and Population Connectivity on Benthic Community Dynamics in the San Francisco Estuary

Thu, 23 Jul 2026 00:00:00 +0000

Climate change and water diversions have greatly modified freshwater outflow into the San Francisco Estuary, changing the Estuary’s salinity regime. These climate- and water diversion-driven changes in salinities may have a wide range of impacts on important components of the San Francisco Estuary including the distribution of threatened/endangered species, the success of habitat restoration and the management of invasive species. Previous work has shown significant variation in the recruitment and survival of numerous species throughout the Estuary linked to freshwater outflow levels.

Adaptive Management of Marine Protected Areas: Predicting Responses to MPA Implementation for Comparison to Monitoring Data

Fri, 15 Dec 2017 00:00:00 +0000

Adaptive Management of Marine Protected Areas: Predicting Responses to MPA Implementation for Comparison to Monitoring Data

Noroviruses in coastal waters: Implications for seafood cultivation and human health

Tue, 2 Sep 2014 00:00:00 +0000

Noroviruses in coastal waters: Implications for seafood cultivation and human health

Controlling Marine Invasive Species: The case of the Indo-Pacific Lionfish Invasion in the Southeast U.S. and Caribbean

Wed, 21 May 2014 00:00:00 +0000

Our hypothesis is that modeling features common to marine biological invasions, like the ability of the invader to disperse over long distances, will call for invasive Indo-Pacific lionfish (Pterois volitans and P. miles) control policies that diverge from those that are efficient based on models geared towards terrestrial and freshwater species, and that these differences will be economically significant.

Controlling Marine Invasive Species: The case of the Indo-Pacific Lionfish Invasion in the Southeast U.S. and Caribbean

Fri, 16 May 2014 00:00:00 +0000

Exploting marine actinomycete diversity for natural product discovery

Fri, 16 May 2014 00:00:00 +0000

The project hypotheses have not changed. We continue to address questions related to the diversity and distributions of MAR4 actinomycetes in marine sediments, the relationships between who these bacteria are (phylogeny), the types of secondary metabolites they produce, and the mechanistic biochemistry responsible for their biosynthesis.

Assessing selected Pacific Oyster stocks for disease resistance in Tomalas Bay, California

Thu, 1 May 2014 00:00:00 +0000

Assessing selected Pacific Oyster stocks for disease resistance in Tomalas Bay, California

MPA-Based Collaborative Techniques to Improve Management of Nearshore Fisheries

Thu, 1 May 2014 00:00:00 +0000

MPA-Based Collaborative Techniques to Improve Management of Nearshore Fisheries

Patch Dynamics of Nutrients, Fecal Indicator Bacteria and Chlorophyll near the Tijuana River

Mon, 8 Apr 2013 00:00:00 +0000

The overall project goal is improved understanding of the physical and biological controls on nearshore (0-15 m water depth) patchiness of nutrients, fecal indicator bacteria (FIB) and chlorophyll (chl) near the Tijuana River.

Investigating Sources, Transformations and Fates of Brominated Compounds in the Coastal Environment

Thu, 4 Apr 2013 00:00:00 +0000

Methoxylated and hydroxylated polybrominated diphenyl ethers (MeO- and OH-PBDEs) and polybrominated dibenzo-p-dioxins (PBDDs) found in marine biota in the coastal environment are not derived from the anthropogenic, PBDE flame retardant compounds.

Sea Urchin Gonad Index a Key to Understanding Secondary Production in the Restoration of Giant Kelp Forests off Palos Verdes

Fri, 15 Mar 2013 00:00:00 +0000

Red and purple sea urchins (Strongylocentrotus franciscanus and S. purpuratus) that live in persistent barrens are perennially starved and will have lower gonad indices (the proportion of the weight of the whole urchin that is comprised of the weight of its gonad) than their counterparts living in persistent kelp forests. Establishing sea urchin gonad indices can be use as a measure of fishery-related secondary production in nearshore rocky reef ecosystems because gonad condition is linked to the quality of the urchin's diet and correlated with environmental conditions on a fine spatial scale.

High-Throughput Molecular Identification of Fish Eggs and Larvae

Wed, 6 Mar 2013 00:00:00 +0000

Ichthyoplankton surveys can reveal the location, timing and intensity of spawning activity for many fish species and are widely used to assess fisheries resources. However, the utility of these surveys is limited by the fact that many eggs and larvae cannot be identified to the species level using morphology alone. This project was motivated by the hypothesis that fish eggs and larvae can be more accurately identified by species specific DNA sequences than by morphology alone.

Cross-shelf Larval Migrations Regulating Larval Supply and Connectivity in a Network of Marine Reserves

Wed, 16 Jan 2013 00:00:00 +0000

1. Does larval transport and recruitment vary markedly across an upwelling cell? 2. Do interspecific differences in larval behavior affect transport and recruitment? 3. How far from natal populations do larvae with different dispersal “strategies” travel at and away from a major upwelling center? 4. How should spatial variation in larval transport affect the placement, size, spacing and evaluation of MPAs across upwelling cells?

Connectivity of West Coast Marine Sanctuaries: Tracking Sooty Shearwaters Throughout Dynamic Upwelling Ecosystems in the California Current System

Fri, 4 Jan 2013 00:00:00 +0000

We propose that as a super-abundant, top-level-predator, Sooty Shearwaters are an ideal California Current Ecosystem (CCE) bioindicator species. Sooty Shearwaters dominate the CCE avifauna during the spring-summer 'upwelling season' and depend on massive amounts of energy-dense forage fishes (anchovy, sardine, krill). We hypothesize that Sooty Shearwater distribution (and abundance), and residency patterns, are related to upwelling dynamics (i.e., offshore transport, upwelling retention, wind-stress curl) that structure and control bottom-up productivity and energy transfer through the CCE foodweb.

Making Restoration More Efficient: Testing the Contributions of Planting Diversity and Introduced Plant Legacy Effects to Recovering Coastal Ecosystems

Tue, 27 Nov 2012 00:00:00 +0000

Hypothesis: Plant invaders with an architecture that is novel to the invaded system, will dramatically alter the abiotic and biotic environment through changes to physical properties, primary production food sources and/or living space.

Hypothesis: The addition of organic litter and higher planting diversity, characteristics of a mature system, would lead to faster ecosystem development of soils, plant communities and invertebrate communities after the removal of plant invaders than no litter addition and a monoculture.

Reefs that Rock and Roll: Critical Assessment of Rhodolith Bed Habitat

Thu, 2 Aug 2012 00:00:00 +0000

The main hypotheses of this proposal are that 1) a novel benthic marine habitat exists, rhodoliths, exists that has been unrecognized in prior surveys and 2) that human induced disturbance is degrading this common coastal California benthic habitat - rhodolith beds. These beds are diverse and threatened marine habitats that are common in Southern California should be included in coastal protection, monitoring and management decisions. By determining the distribution, measuring habitat metrics and determining the common sources of disturbance in beds around Catalina Island, the information can be used to inform the Southern California MPA process.

Paradigm or Paradox: Can we Attribute Species Changes to Global Climate Change in Light of Decreasing Water Temperatures in Central California?

Wed, 11 Jul 2012 00:00:00 +0000

The main goal of this study was to gather information about historical changes in water temperature and species composition, in order to identify variables that will enable us to predict changes in water temperatures and species abundances in California caused by global climate change. Our primary objectives were to (1) review the existing published and unpublished data sets to refine our understanding of trends in sea surface temperature in central California; (2) review fish and climate data sets to determine if we could identify how species abundances changed relative to changes in water temperatures and basin-scale environmental indices; and (3) identify recent changes in species abundances in central California that are related to water temperatures.

Long-term Faunal Changes in California Nudibranchs: Climate Change and Local Ocean Health

Wed, 25 Apr 2012 00:00:00 +0000

(1) The abundance, species richness, and community composition of nudibranchs in central California has changed significantly in the past 30 to 70 years.(2) The observed changes are consistent with those predicted by climate variability on interannual and decadal time scales. Specifically, during warm phases: (a) the proportional abundance and speciesrichness of southern species should increase, as northern species decline, and (b) geographic ranges should shift poleward. The reverse of these should occur during periods of cooling. Further, these changes should be apparent at multiple, widespread sites (otherwise, more localized environmentalfactors, and not broad scale climate factors, would be implicated as the cause).(3) Long-term, anthropogenic climate warming is superimposed on natural climate variation, and its biological signal (similar to that described above for natural periods of warming) should be apparent bycomparing the abundance, species richness, and community composition...

Estimating the Impact of Invasive Spartina densiflora on Primary Productivity in Humboldt Bay

Tue, 17 Apr 2012 00:00:00 +0000

Invasive dense-flowered cordgrass (Spartina densiflora) is impacting the primary productivity of Humboldt Bay salt marshes.

A Comprehensive Oyster Disease Survey in California

Fri, 6 Apr 2012 00:00:00 +0000

The goal of this project was to investigate and document the presence of disease agents in cultured and wild oyster populations throughout California. This is the first comprehensive survey to be conducted since that of Katkansky and Warner in the late 1960s to early 1970s (Katkansky and Warner, 1974). Particular emphasis was placed on detection of the agent of Denman Island Disease (Mikrocytos mackini, Farley et al., 1988). This pathogen of the Pacific oyster (Crassostrea gigas) was detected in the State of Washington in 2002, and many California oyster growers receive seed from Washington State. All major populations of farmed and feral commercial oysters and wild native oysters Ostrea lurida were targeted for sampling. Sufficient numbers from each population were collected so that relatively rare pathogens should have been detected when they are present.

Parasites as Indicators of Coastal Wetland Health

Fri, 6 Apr 2012 00:00:00 +0000

Trematodes can provide a powerful and cost-effective ecological indicator tool to assess and monitor biodiversity in estuarine habitats.

Solid Phase Absorption Toxin Tracking (SPATT) and Nutrient Loads: Testing a New Tool for Algal Toxin Monitoring in Fresh, Brackish and Coastal Ecosystems

Thu, 5 Apr 2012 00:00:00 +0000

We are interested in testing a new methodology called Solid Phase AbsorptionToxin Tracking (SPATT), which is a man-made resin that passively captures algal toxins in water; it can be thought of as a man-made, passive, sentinel “mussel”.This technology was developed in New Zealand (MacKenzie et al. 2004), and is inlimited use in the UK (Turrell et al., 2007) and Australia (Takahashi et al.,2007), but has not yet been tested in the US. Our hypothesis was that this resin, deployed using the same methodology as described by others (outside the US), would passively capture domoic acid, providing an integrated time-series of toxin levels in the coastal ocean.

A Novel Approach to Evaluating Patterns of Vertical Distribution in Cryptic Larvae: Application of Fluorescence in situ Hybridization (FISH) and a Large-Particle Cell Sorter

Wed, 4 Apr 2012 00:00:00 +0000

We hypothesized that differences in the distribution of adult mussels are the result of differences in the selection pressures ontheir larvae, such that the vertical distribution of larvae from the inner bay species (M. senhousia) facilitates bay retention, while that of the open-coast species (M. californianus) enhancesalongshore dispersal.

Transferrable Antibiotic Resistance Plasmids in Urban Coastal Wetlands

Tue, 3 Apr 2012 00:00:00 +0000

The overarching hypothesis driving this research is that antibiotic resistance genes released into the natural environment through urban storm water may persist, creating a reservoir of resistance genes that have the potential to return to the human community through various vectors such as birds, insects, and fish. The specific aim of this Program Development grant is to assess the diversity of multidrug-resistance plasmids in sediments of two urban wetlands.

Collaborative Fisheries Research in Support of Ecosystem-‐Based Salmon Management in Northern California

Tue, 3 Apr 2012 00:00:00 +0000

The state of the Chinook salmon (Oncorhynchus tshawytscha) fishery in California is imperiled. One of the proposed mechanisms for recent population declines and fisheries closures is environmental variation having deleterious effects on prey availability and the ocean survival of Sacramento River fall Chinook (Lindley et al. 2009). To address this hypothesis, we analyzed collaborative fisheries research data (stomach samples obtained from commercial and recreational fisherman) on Chinook salmon diet in central California during the early-mid 1980s and mid 2000s. We compared this information with historic diet records for this population from 1955. Salmon diet composition changed significantly through time, with a decline in diet diversity. Specifically, previously important prey groups including juvenile rockfish (Sebastes spp.), krill (Euphausiidae), Pacific herring (Clupea pallesi) and market squid (Loligo opalsecens) were either greatly reduced...

Evaluating the Functional Recovery of Restored Coastal Wetland in Southern California

Tue, 3 Apr 2012 00:00:00 +0000

Within the Huntington Beach Wetlands (HBW), we hypothesized that Brookhurst and Magnolia Marshes (marsh areas isolated from tidal influence for approximately 100 years) would have significantly different physical characteristics (salinity, temperature, moisture, sediment parameters), more terrestrial plant, algal, invertebrate and microbial communities and altered food web structure from neighboring Talbert Marsh (a marsh area whose tidal connect was restored 20 years ago). In addition, we hypothesized that once Brookhurst Marsh was restored (Summer 2009), these differences would decrease and with time, resemble those of Talbert Marsh. This restoration of structure and function will occur on differing time scales; we predicted that physical parameters would quickly become similar while algal, invertebrate and microbial communities would begin to change on a month-year time scale. Changes to the plant community and the food web structure are anticipated to occur on a year-decadal...

Shelter Use, Movement, and Home Range of Spiny Lobsters in San Diego County

Tue, 3 Apr 2012 00:00:00 +0000

The California spiny lobster is an ecologically and economically important species in southern California coastal waters. In San Diego County, commercial lobster landings average approximately 500,000 pounds per year with a subsequent value of ca. $5 million, and recreational fishing for lobsters is a valued part of life in San Diego for many people. Lobsters are a major predator of benthic invertebrates along the southern California coastline, and they act as a keystone species by preying upon competitively dominant mussels on rocky shorelines and sea urchins that consume kelp, thereby promoting the existence of diverse shoreline communities. Despite the fact that P. interruptus has supported a fishery in California for over 100 years and may presently be overfished, we have relatively little fishery-independent information on lobster population dynamics and behavior that could be used to implement conservation efforts. Our goal in this research was to fill some of...

Economic Evaluation of Tradable Property Rights

Tue, 3 Apr 2012 00:00:00 +0000

Economists have for decades advocated transferable property rights, in which the total annual allowable catch is divided into shares, which are then tradable, as a market mechanism to decrease overcapacity. Tradable property rights, or individual transferable quotas (ITQs), are a significant departure from command-and-control regulations that impose combinations of gear restrictions, season limitations, license limitations and trip limits. While in theory tradable property rights have clear economic advantages over command and control, Federal fisheries managers face the challenge of evaluating and ranking regulatory options in a world of complexity and uncertainty.

The goal of this project is to describe the changes in the composition of the Mid-Atlantic surf clam fishery, which has been regulated with first command and control and then tradable property rights. The data analysis indicates that while there were changes in the structure of the clam industry, the introduction...

Ecology and Trophic Interactions of Jumbo Squid (Dosidicus gigas) in the California Current Ecosystem

Fri, 16 Mar 2012 00:00:00 +0000

Humboldt squid have recently demonstrated a range expansion into the waters off California from the previous northern extent of their range in Mexico. In this new environment, we expected the vertical and horizontal migratory behavior and the diet to be generally similar those previously documented in Mexico. However, we also expected significant differences in diet and reproductive activity, with potentially great impacts on ecosystems in the California Current System. In particular, consumption of numerous ecologically and economically important species could greatly affect both nearshore and offshore environments and fisheries in the California Current System. We hypothesize that mechanisms driving the range expansion include tolerance of environmental variability and flexibility in diet.

Validation of a New Method for Population Assessment of Pacific Salmonids Using Genetic Markers

Wed, 8 Feb 2012 00:00:00 +0000

The goal of the proposed research project is to evaluate a novel method of efficient genetic tagging through an experiment with Chinook salmon (Oncorhynchus tshawytscha) from California’s Central Valley. The proposed parentage-based tagging (PBT) experiment has four components: marker discovery, development of analysis tools, implementation of the parent database, and assignment of known offspring and mixed fishery samples. Utilizing new methods for large scale parentage assignment, the collection of genetic information from a parental breeding generation can be used to “tag” the offspring cohort. When this is done at a hatchery or at a weir, the entire breeding population of a stock or population can be sampled, and the entire next generation tagged. Offspring can be non-lethally sampled during their seaward migration, in fisheries, and upon return to spawn (at hatcheries or instream). Genotyping is followed by high confidence parentage assignment wherein...

Krill and Krill Predators: Ecosystem-Based Management in the Gulf of the Farallones-Cordell Bank Krill Production Domain

Mon, 6 Feb 2012 00:00:00 +0000

We will test the primary hypothesis that coastward advection of bottom cold-salty water during intense wind-driven upwelling provides conditions conducive forE. pacifica(the more oceanic species) to move onto the continental shelf where they become abundant and available to predators “early” in the season each year. As a corollary, we will test the hypothesis that as upwelling relaxes “later” in the season each year,E. pacificamoves offshore where it is less available to predators, andT. spinifera(the more coastal species) develops, becoming the dominant euphausiid in shelf waters and predator diets.

Novel, Post-Translationally Modified Peptide Antibiotics from Solitary Tunicates

Mon, 6 Feb 2012 00:00:00 +0000

Although the pharmaceutical industry has “mined” the world of soil bacteria,streptomycetes and fungi to find novel antimicrobial molecules, the emergence of resistant superbugs necessitates identifying new antibiotic sources. Recent research into the innate immune system has focused attention on antimicrobial peptides – molecules that equip animals to resist infection without assistance from antibodies and other accoutrements of adaptive immunity. In recent years, potent antimicrobial peptides have been identified in the blood cells (hemocytes) of horseshoe crabs, shrimp, mussels and tunicates ("sea squirts"). Our studies centered on three tunicates (Styela clava, Styela plicata and Ciona intestinalis) that are abundant in Southern California's shallow waters.

The Role of Symbiotic Metabolites in the Development of Toxic Phytoplankton Blooms

Fri, 3 Feb 2012 00:00:00 +0000

Most phytoplankton, including the toxic species of interest, cannot be grown axenically and require cohabitabing,associated, or symbiotic bacterial partners. However we have been able to prepare stable binary cultures of phytoplankton of interest with just a single species of bacteria (most of which are species of Marinobacter). While we recognize the culturable bacteria that we have isolated and are now studying are not necessarily qualitatively orquantitatively representative of the bacterial population associated with the phytoplankton in the wild, the ability to produce viable binary phytoplankton/bacterial cultures represents a critically important experimental tool. While other non-culturable bacteria could be quantitatively more important inhabitants of the "phycosphere" in the wild, our ability to ascertain the specific chemical determinants supplied by these bacteria and necessary tophytoplankton survival would be severely limited or impossible with such a heterogeneous...

Parentage in White Sturgeon

Wed, 1 Feb 2012 00:00:00 +0000

We hypothesize that the addition of six microsatellite loci to an existing panel of eight microsatellite loci will increase the accuracy rate of parentage assignment of farmed white sturgeon to 95%.

Development of Novel Stable Isotope Approaches to Evaluate Carbon Flow in a Restored Coastal Wetland in Southern California

Thu, 19 Jan 2012 00:00:00 +0000

We hypothesized there would be differences in the microbial and infaunal communitiesprimarily responsible for degrading macrophyte vs. microalgal carbon. Specifically we predicted that:

The invertebrate community degrading macrophyte-derived carbon will be significantly different from those degrading algal-derived carbon.

The microbial communities (bacteria and fungi) degrading macrophyte-derived carbon will be significantly different from those not using this carbon source.

Climate change and restoration factors affecting fecal pathogen dynamics in wetland systems

Mon, 19 Dec 2011 00:00:00 +0000

This project has three main hypotheses: 1) Increased water temperatures, decreased salinity, and increased flow rate will enhance transport of protozoal oocysts through wetland systems. 2) Larger vegetation, increased vegetation density, and increased wetland length will enhance retention of protozoal oocysts in wetland systems. 3) Factors found to maximize protozoal retention in the laboratory-based models will also significantly affect protozoal transport in a natural and constructed wetland.

Exploring the Impact of Avian Predators on Central California Salmonids

Wed, 12 Oct 2011 00:00:00 +0000

Avian predators, Western Gulls in particular, are having significant impacts on juvenile salmonid populations along the central California coast. Exclusion efforts can reduce predator impact and increase juvenile salmonid survival.

Extending the Use of Solid Phase Adsorption Toxin Tracking to the Land-Sea Interface

Mon, 3 Oct 2011 00:00:00 +0000

Harmful algal blooms (HABs) are an escalating problem in coastal ecosystems, inflicting massive economic losses on commercial fisheries and causing death and illness to both humans and marine fauna. Paralleling the rise of marine HAB problems, cyanobacteria (previously identified as "blue-green algae") have a worldwide distribution and can form extensive blooms in freshwater and estuarine habitat. Microcystins are fast becoming a global health concern, with severe and recurrent blooms with toxin elaboration reported globally, including central California. Until recently, microcystin intoxication was considered a public health issue mainly of freshwater habitat, reflected by the vast body of published literature on potential human health risks due to microcystin exposure in rivers, lakes, reservoirs and freshwater aquaculture. In contrast, monitoring of marine water and seafood for similar risks has been limited, despite confirmation of outflows of microcystin-contaminated freshwater...

Developing the capability to monitor and predict upwelling along the California coast using an ocean circulation model

Thu, 22 Sep 2011 00:00:00 +0000

Coastal ocean forecasting models can be used to monitor and predict coastal upwelling.

Trophic ecology of the Gopher Rockfish (Sebastes carnatus): providing baseline information for monitoring marine protected areas

Tue, 30 Aug 2011 00:00:00 +0000

Gopher Rockfish diets will differ inside vs. outside of marine protected areas (MPAs) due to higher Gopher Rockfish densities inside MPAs.

Detecting, Characterizing and Determining the Biological Response to Regime Shifts off the California Coast

Tue, 9 Aug 2011 00:00:00 +0000

First, using one method of change detection analysis called the cumulative sum, it is possible to detect and characterize regime shifts along the California coast using sea surface temperatures (SSTs) and other variables. Second, physically-determined regime shifts and changes in ocean climatology, determined largely through detailed temperature time-series, can be linked to corresponding changes in biological communities, particularly phytoplankton, which exhibit rapid generation times.

Harnessing the Pharmaceutical Potential of Marine Cyanobacteria

Mon, 11 Jul 2011 00:00:00 +0000

We hypothesize that the secondary metabolite pathways in cyanobacteria can be manipulated by applying transcriptional promoters, either of a genetic or chemical nature (elicitors), to produce more secondary metabolites with potential pharmaceutical utility.

Understanding connectivity to sustain and manage coastal resources

Thu, 17 Mar 2011 00:00:00 +0000

We seek to test hypotheses about rates of self seeding, the role of passive circulation and behavior in larval transport, and to identify regional source and sink populations in mytilid mussels. We assessed temporal variability in connectivity patterns for Mytilus spp, using experiments conducted previously (in 03, 04, 05, 06, and 07) and during this grant (08–10), compared results to passive transport predictions corrected for larval supply, and synthesize the information to generate generalized conceptual models of open coast, inner and outer bay connectivity patterns in Southern California.

Transport of Ghost Shrimp as Live Bait: Potential Effects on Impacted Southern California Populations

Wed, 2 Mar 2011 00:00:00 +0000

The bait industry in Southern California imports live ghost shrimp, Neotrypaea californiensis, from Oregon and Washington. Though ghost shrimp occur naturally in Southern California, southern populations may be genetically different from northern ones.

A Field Experimental Investigation of the Effects of Black Brant Geese Grazing on Eelgrass Growth and the Animals in an Eelgrass Bed

Thu, 10 Feb 2011 00:00:00 +0000

Eelgrass (Zostera marina) beds and other seagrass ecosystems around the world are recognized for their trophic support, nursery, refuge, water quality and recreational functions (Williams and Heck 2001).

Ecological Impacts of Beach Grooming on Exposed Sandy Beaches

Tue, 8 Feb 2011 00:00:00 +0000

Kelp and phytoplankton washed ashore by tides and waves support a rich diversity of shore life. On many of the most popular sandy beaches in California, however, local municipalities regularly rake up litter and kelp in a process called beach grooming. The ecological consequences of this process on plants and animals that live and forage in regularly raked areas are evaluated. The information gathered may help guide and improve the state's beach maintenance practices.

Dispersion in the Surfzone: Tracer Studies for Water Quality and Ecology

Mon, 18 Oct 2010 00:00:00 +0000

Measurement of the spatial and temporal scales of nearshore chlorophyll-a (chl) is critical to our ability to understand or predict dense, and potentially harmful blooms of phytoplankton along the California Coast. Patchiness in chl may result from patchiness in nutrient availability, swimming or sinking, predation, or transport and mixing by breaking waves, currents, internal waves and tides. We performed a study during the Fall 2006 Huntington Beach (HB06) experiment to investigate the biological and physical factors that affect phytoplankton patchiness. Autotrophic phytoplankton require light and nutrients to survive. However, the nearshore euphotic zone (the critical depth for photosynthesis) is often nutrient-depleted due to uptake and planktonic growth. In order to sustain populations, phytoplankton rely on delivery of new nutrients from below the euphotic zone through upwellling or vertical mixing. or 2) terrestrial sources (from rain, ground water, tidal flushing or...

California spiny lobsters and benthic community structure in Southern California: top-down and bottom-up interactions

Fri, 1 Oct 2010 00:00:00 +0000

We hypothesize that: spiny lobster movement behavior is governed by a combination of forces acting from the bottom-up (i.e. food availability) and from the top-down (i.e. risk of predation); and that spiny lobsters significantly influence the structure of benthic communities in kelp forest and seagrass habitat.

Understanding submarine groundwater discharge and its influence on coastal water quality along the California Coast

Fri, 25 Jun 2010 00:00:00 +0000

We proposed directed field and modeling research to address the following hypotheses: (H1) Submarine groundwater discharge (SGD), its quality, and the percentage that is fresh versus saline, is modulated by season, tides, and wave conditions; (H2) the chemical (nutrient, carbon, trace metal) and biological (human health indicators) composition of SGD is affected by land use and geology; (H3) human health indicators and nutrients can be freely transported through the beach aquifer and are not removed via interactions with the sediments, and (H4) SGD impacts the water quality of the nearshore environment at a level comparable to surficial runoff.

Investigating the Limits of Native Oyster Recovery and Restoration

Thu, 3 Jun 2010 00:00:00 +0000

The project hypotheses were as follows: A. Oyster recruitment will be higher at inner bay sites than the outer bay sites and density of recruits will be positively associated with adult oyster density. B. Mortality due to predators will be greater in the inner bay than the outer bay sites. C. Introduced predators have a greater per capita impact on oysters than native predators. D. Growth rates of oysters will be higher in the inner bay than the outer bay. E. Mortality due to overgrowth by space competitors will be higher in the inner bay than the outer bay. F. Oyster growth and survival will be higher at inner bay sites and will show a positive linear increase with increasing temperature and phytoplankton abundance.

Nematode Community Analysis for Monitoring Meiofaunal Response to the Bolsa Chica Wetlands Restoration Project

Wed, 12 May 2010 00:00:00 +0000

The Bolsa Chica Wetlands have undergone extensive engineering works in 2004-2007 to restore different levels of tidal action in different sectors of the wetlands. Different properties of nematode communities can be used to make management decisions and evaluate restoration success. Published studies have shown among others that nematode abundance increases, while their diversity and evenness decrease, in conditions of nutrient enrichment. From past observations we hypothesize that the following spatial and temporal patterns will occur in Bolsa Chica:

- From the beginning of our sampling efforts, we expect to find that Outer Bolsa Bay harbors fewer nematodes, but more species and more equitable numbers per species, compared to Inner Bolsa Bay.

- As the effects of tidal restoration kick in, we expect to find progressively more species and evenness but lower abundance in the full tidal restoration area.

- As the effects of tidal restoration kick in, we expect...

Sec.I: Age, growth, and radiometric age validation of the blackgill rockfish, Sebastes melanostomus; Sec.II: Age validation of the canary rockfish (Sebastes pinniger) using the disequilibria of lead-210 and radium-226

Wed, 24 Mar 2010 00:00:00 +0000

Abstract Section I: As nearshore fish populations decline, many commercial fishers have shifted effort to deeper continental slope habitats to target fishes for which biological information is limited. One such fishery that developed in the northeastern Pacific Ocean in the early 1980s was for the blackgill rockfish, Sebastes melanostomus, a deep- dwelling (300-800 m) species that congregates over rocky pinnacles, mainly from Southern California to southern Oregon. Growth zone-derived age estimates from otolith thin sections were compared to ages obtained from the radioactive disequilibria of 210Pb, relative to its parent, 226Ra, in otolith cores of blackgill rockfish. Age estimates were validated up to 41 years, with a strong pattern of agreement supporting a longevity exceeding 90 years. Age and length data fitted to the von Bertalanffy growth function indicate blackgill rockfish are slow-growing (k = 0.040 females, 0.068 males) and that females grow slower than males, but...

Understanding the Pathogenesis of Streptococcus iniae Infection in Fish and Development of an Effective Vaccine for Use in Aquaculture

Tue, 23 Mar 2010 00:00:00 +0000

S. iniae infection has emerged as a serious fish health and economic problem in intensive U.S. aquaculture operations. Current antibiotic options are few and possess severe practical limitations and potential adverse environmental impacts. We believe the major factor contributing to the large burden of S. iniae disease in aquaculture is the lack of fundamental knowledge of S. iniae virulence factors and the fundamental pathogenesis of infection.

Tackling Ecological Complexity and Climate Change: Matches and Mismatches in the Seasonal Cycle of California's Marine Flora and Fauna

Tue, 23 Mar 2010 00:00:00 +0000

Matches and mismatches in predator needs and prey availability account for changing reproductive success of top predators (fish and seabirds) in the California Current Large Marine Ecosystem (CCLME).

Assessing changes in life history traits and reproductive function of CA sheephead across its range: historical comparisons and the effects of fishing

Thu, 4 Mar 2010 00:00:00 +0000

Project Hypotheses The specific predictions can be summarized as: P1: Life history parameters will vary across the range of this species and spatial differences in life histories will be determined by population density, sex ratios, environmental factors, and fishing pressure. P2: Fish collected in this study will be smaller and younger than fish collected from previous times (historical collections from 1970-1980) and the effects will be greatest at sites where fishing is intense (i.e. southern California vs. Baja California). P3: Fish collected in this study will change sex from female to male at a younger age and smaller size than previous times, especially at sites where fishing is intense (as predicted by size advantage model). P4: As a result of P3 (females mature younger and smaller), operational sex ratios will increase (also predicted by size advantage model). P5: Stricter harvest limits may have initiated recovery in heavily exploited populations and may result...

Binational Studies Leading to an Ecosystems-based Management Strategy for Common Thresher Shark in the Southern California Bight (SCB).

Thu, 4 Mar 2010 00:00:00 +0000

Survey of the Mexican SCB Sector Artisanal and Commercial Shark Fisheries Hypotheses: a) Common thresher sharks represent a substantial portion of the catch of artisanal and commercial shark fisheries in the Mexican SCB sector. b) Exploitation of common threshers and other elasmobranchs is important to the economy of northern Baja California and, by extension, is directly linked to U.S. fishery management. Mexican SCB Longlining Survey Hypotheses: a) Thresher shark nursery grounds extend south throughout the Mexican sector of the SCB. b) Juvenile threshers in Mexican SCB waters will exhibit seasonal patterns of abundance similar to those observed in the California SCB (i.e. higher abundance in early Spring and Summer when pupping is thought to occur). Tracking and Archival Tagging Hypotheses: a) Juvenile thresher sharks utilize distinct inshore areas as nursery grounds and have a strong preference for continental shelf waters. b) Within these nursery grounds, juveniles have...

Enhancement of fertilization success in abalone: Increasing effectiveness of transplanting and out-planting recovery strategies

Fri, 29 Jan 2010 00:00:00 +0000

This study tests the very general hypothesis that field fertilization success in red abalone is a predictable function of the hydrodynamic regime, and the density, sex ratio and spacing of animals within aggregations.

Project Goals and Objectives (1) To determine the hydrodynamic mechanisms that facilitate fertilization of abalone inhabiting coastal waters; (2) To establish the optimal adult density, spacing and sex ratio to maximize fertilization success within a given flow regime; (3) To identify optimal field environments for transplanting or out-planting abalone aggregations, as well as natural abalone distributions that likely experience little or no reproductive success.

Enhancement of Growth Rates and Swimming Performance in Juvenile Marine Finfish in Aquaculture

Wed, 27 Jan 2010 00:00:00 +0000

We hypothesize that exercise enhances growth of hatchery-reared white seabass by reducing stress and modulating key growth-regulatory factors, and that this will be associated with positive effects on swimming performance. It is secondarily hypothesized that positive effects of exercise on growth and swimming performance will be applicable to other marine finfish, including California yellowtail and California sheephead.

Assessing Withering Syndrome Resistance in California Black Abalone: Implications for Conservation and Restoration: Part II

Wed, 27 Jan 2010 00:00:00 +0000

Hypothesis: Quantitative real-time PCR can be used to quantify loads of the WS rickettsial bacterium (infection intensity) in abalone.

Hypothesis: Juvenile black abalone recruiting on the California Channel Islands are more resistant to WS than are black abalone in northern Central California that have not experienced high disease (WS) selection pressure.

NOTE: only abstract of study available at this time pending publication of papers. For further information, please contact Carolyn S. Friedman (carolynf@u.washington.edu) or Glenn VanBlaricom (glennvb@u.washington.edu ).

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Time-varying flow-ecology relationships for an endangered fish population: Longfin Smelt in the San Francisco Estuary

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Controlling Marine Invasive Species: The case of the Indo-Pacific Lionfish Invasion in the Southeast U.S. and Caribbean

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A Comprehensive Oyster Disease Survey in California

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Solid Phase Absorption Toxin Tracking (SPATT) and Nutrient Loads: Testing a New Tool for Algal Toxin Monitoring in Fresh, Brackish and Coastal Ecosystems

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