Recent csgc items

Readying California Fisheries for Climate Change

Mon, 18 Aug 2025 00:00:00 +0000

This document provides scientific guidance to the California Department of Fish and Wildlife (CDFW) regarding the potential impacts of climate change on California fisheries and recommendations for building resilience to buffer climatic forces. At CDFW’s request, the California Ocean Protection Council (OPC) provided funding to the Ocean Science Trust (OST) to convene an OPC Science Advisory Team (OPC-SAT) Working Group with relevant ecological, social science, and governance expertise. This guidance was prepared by OST and the OPC-SAT Working Group in partnership with CDFW, in adherence with the requirements in the OPC Staff Recommendation: “California State Fisheries Management: Current Efforts and Future Needs.” This project was developed for consideration by the California Department of Fish and Wildlife (CDFW) to help inform the state’s process to amend the Marine Life Management Act (MLMA) Master Plan. Products from this project have been submitted to CDFW for review and...

California’s Experience with Dunes and Coastal Resilience: A Synthesis Report of the 2021 Coastal Dunes for Resilience Workshop

Wed, 18 Dec 2024 00:00:00 +0000

The California Dune Science Network (Network) is a collaborative effort to expand understanding of coastal dunes and their role in building a resilient, transitional, and adaptive coast for future generations. In an effort to foster knowledge-sharing across these sites and disseminate information and lessons learned, the Network hosted a virtual Coastal Dunes for Resilience Workshop on December 8th and 9th, 2021. The workshop featured recent dune research, information about nature-based dune and resilience projects, and collaborative learning opportunities at California's pilot project and natural dune sites. It also engaged diverse perspectives on coastal resource stewardship, public access, and culturally inclusive climate adaptation approaches and how these play a role in the success of coastal dune resilience efforts.

Binational Coastal Resilience Assessment

Wed, 18 Dec 2024 00:00:00 +0000

Binational Coastal Resilience Assessment

Compartiendo la Costa: Oportunidades y estrategias para la resiliencia costera en la región San Diego-Baja California

Mon, 9 Dec 2024 00:00:00 +0000

El propósito de este documento es compartir una visión estratégica para mejorar la resiliencia costera en la región de San Diego-Baja California a través de la colaboración binacional basada en una evaluación de necesidades liderada por California Sea Grant y Climate Science Alliance.La visión de este documento identifica oportunidades clave y estrategias accionables que integran la investigación científica, el conocimiento tradicional y prácticas innovadoras para apoyar a las comunidades y ecosistemas costeros. Al fomentar asociaciones transfronterizas, expandir las capacidades de investigación y comprometer a diversos actores, este documento tiene como objetivo guiar los esfuerzos hacia un futuro más resiliente para nuestra costa compartida.

California’s Experience with Dunes and Coastal Resilience: A Synthesis Report of the 2021 Coastal Dunes for Resilience Workshop

Mon, 9 Dec 2024 00:00:00 +0000

The California Dune Science Network (Network) is a collaborative effort to expand understanding of coastal dunes and their role in building a resilient, transitional, and adaptive coast for future generations. In 2021, the Network documented at least nineteen sites in California where coastal dunes were in planning stages or had already been restored or constructed to increase resilience. The Network acknowledges that this list may be incomplete and welcomes suggestions for additional dune sites and resources. In an effort to foster knowledge-sharing across these sites and disseminate information and lessons learned, the Network hosted a virtual Coastal Dunes for Resilience Workshop on December 8th and 9th, 2021. The workshop featured recent dune research, information about nature-based dune and resilience projects, and collaborative learning opportunities at California's pilot project and natural dune sites. It also engaged diverse perspectives on coastal resource stewardship,...

EVALUATING SOCIOECONOMIC DIMENSIONS FOR A RESILIENT SHELLFISH MARICULTURE INDUSTRY IN HUMBOLDT BAY: ASSESSING THE STRENGTHS, VULNERABILITIES, AND POTENTIAL OF HUMBOLDT’S EXPANDING INDUSTRY

Mon, 9 Dec 2024 00:00:00 +0000

For nearly 90 years the shellfish mariculture industry in Humboldt Bay has coexisted with various stakeholder groups and the Bay’s delicate ecology. Presently, the shellfish mariculture industry in Humboldt Bay is composed of six shellfish producing businesses ranging in operational size from small-scale to large-scale. Commercial shellfish production from Humboldt Bay yields over 70 percent of California’s mature, market-sized, Pacific oysters (Crassostrea gigas) and Kumamoto oysters (C. sikamea). Shellfish growers in the Bay also produce seed from Pacific oysters, Kumamoto oysters, and Manila clams (Tapes semidecussata).

As the mariculture industry in Humboldt Bay is poised to expand its footprint, very limited data about the industry have been made available for planners and decision makers. The purposes of this thesis were to: (1) Gather reliable socioeconomic data about

the state of the mariculture industry in Humboldt Bay. (2) Evaluate the industry’s

strengths...

Molluscan Shellfish Aquaculture in Federal Waters of the Exclusive Economic Zone (EEZ): Agencies, Industry, and Academia Working Together on Compliance and Permitting Requirements

Mon, 9 Dec 2024 00:00:00 +0000

Approximately 91% of the seafood products sold in the United States are imported, and roughly

half of those imports are produced by aquaculture.5 These seafood imports total 2.45 million

metric tons, 89,000-90,500 metric tons of which is comprised of molluscan shellfish (e.g. oysters,

mussels, clams, and scallops).6 These imports have contributed to a significant seafood trade

deficit, which ballooned to $14 billion in 2016.7 Increased domestic aquaculture production has

the potential to reduce this reliance on seafood imports, which could result in an estimated

additional 50,000 full-time and part-time jobs8 if United States “offshore” aquaculture production

is doubled.9 Furthermore, it has been suggested by some as a way to reduce the carbon footprint

associated with imported seafood.10

While the potential for increased domestic molluscan shellfish marine aquaculture production11

has been the subject of high-level...

DETERMINING POPULATION STRUCTURE, REPRODUCTIVE POTENTIAL, AND HABITAT ASSOCIATIONS OF PINTO ABALONE (HALIOTIS KAMTSCHATKANA) IN SOUTHERN CALIFORNIA

Mon, 9 Dec 2024 00:00:00 +0000

This study provides the first assessment of demographic and habitat information

for pinto abalone (Haliotis kamtschatkana) in San Diego, California, two decades after

the closure of all abalone fisheries in southern California. SCUBA surveys conducted

from June 2014 to December 2016 indicate that current low densities (0-0.03

individuals/m2) were far below critical thresholds identified for other abalone species

(0.15-0.30 abalone/m2) for successful spawning and recruitment. A broad range of sizes

were represented (13-146 mm), however, only 95 individuals were found. Some sites

showed significant aggregation of adult (> 50 mm) pinto abalone, 30% of adults had a

nearest-neighbor within a critical spawning distance of 2 m, and 65% had a neighbor

within 5 m, indicating that at least a small proportion of individuals may be capable of

reproducing successfully. Pinto abalone showed a significant preference for boulder

habitat...

California’s Experience with Dunes and Coastal Resilience: A Synthesis Report of the 2021 Coastal Dunes for Resilience Workshop.

Mon, 9 Dec 2024 00:00:00 +0000

This article provides a synthesis of the virtual Coastal Dunes for Resilience Workshop held on December 8th and 9th, 2021. In an effort to foster knowledge-sharing across these sites and disseminate information and lessons learned, the California Dune Science Network hosted the Workshop that featured recent dune research, information about nature-based dune and resilience projects, and collaborative learning opportunities at California's pilot project and natural dune sites. It also engaged diverse perspectives on coastal resource stewardship, public access, and culturally inclusive climate adaptation approaches and how these play a role in the success of coastal dune resilience efforts.

The Coastal Dunes for Resiliency Workshop provided an initial opportunity for ideas and strategies to be shared amongst the many practitioners working in the coastal resilience space. The workshop highlighted common challenges, needs, and four emerging themes for implementing coastal...

Sharing the Coast: Opportunities and strategies for accelerating coastal resilience in the San Diego-Baja California Region

Mon, 9 Dec 2024 00:00:00 +0000

The purpose of this document is to outline a strategic vision for enhancing coastal resilience in the San Diego-Baja California Region through binational collaboration. It draws from a needs assessment led by California Sea Grant and the Climate Science Alliance. This vision document identifies key opportunities and actionable strategies that integrate scientific research, traditional knowledge, and innovative practices to support resilient coastal communities and ecosystems. By fostering cross-border partnerships, expanding research capabilities, and engaging diverse stakeholders, this document aims to guide efforts towards a more resilient future for our shared coastline.

Building Climate Resilience of Urban Waters, Ecosystems, and Communities

Mon, 9 Dec 2024 00:00:00 +0000

particularly in urban ecosystems. The project site, Manzanita Canyon, is located in the heart of a

“disadvantaged” community in San Diego, California. In urban watersheds such as this, ecosystems

provide services disproportionate to their size, yet are also highly vulnerable to climate change hazards

because of the heavy reliance on services and the relatively degraded state. This two-year project

improved water quality and climate resilience of an urban ecosystem and an underserved community by

engaging 2,253 community members in stewardship activities; restoring 7.56 acres of native coastal

scrub ecosystem, including planting, maintaining and monitoring 1,536 natives; and removing 22 metric

tons (758 m3) of invasive plants and trash. Findings from this project formed the basis of the following

stewardship recommendations:

1. Community engagement was most effective when community-based leaders or organizations

were...

Living Shorelines & Resilience in Southern California: A Summary of a Series of Workshops held as part of The Resilient Coastlines Project of Greater San Diego

Wed, 12 Feb 2020 00:00:00 +0000

In 2016, a series of workshops were held to discuss living shorelines in Southern

California. The workshops specifically focused on the unique benefits, challenges and

opportunities for implementing living shorelines in the region, and the nexus between

nature-based solutions and ongoing local adaptation planning. Approximately 140

participants partook in these dialogues, and some of the key themes that emerged

include:

 Letting nature do the work for you

 Designing for the future

 Integrating nature into shoreline management projects

 Project goals distinguishing living shorelines

 Engineering and urban living shorelines

 Space constraints along urban coastlines

 Permitting pathways to support demonstration projects

 Living shorelines and phased sea level rise planning

 Designing with watersheds and sediment management in mind

 Exploring emerging commercial opportunities

...

Diets and Stable Isotope Signatures of Yellowtail Rockfish (Sebastes flavidus) in Central California

Fri, 20 Sep 2019 00:00:00 +0000

Studies of fish diets can improve the understanding of trophic distributions

and the predatory role of a species in an ecosystem. Identifying the spatial and

temporal variability in the diets of fishes can provide useful information for stock

assessments and management. Yellowtail Rockfish (Sebastes flavidus) are a

commercially and recreationally important fishery species, and abundant along

the central California coast, yet the most recent studies of diets occurred over 20

years ago in Oregon and Washington. To provide current information from

California, I examined the food habits of Yellowtail Rockfish collected near

Cordell Bank, the Farallon Islands, and Half Moon Bay in 2013 and 2014 using

gut content and stable isotope analyses. Yellowtail Rockfish analyzed in this

study were semi-pelagic predators, feeding primarily on tunicates, crustaceans,

and teleosts. Based on δ15N values, fish caught in 2013, on...

Local Seafood Availability in San Diego, California Seafood Markets

Thu, 3 Jan 2019 00:00:00 +0000

Like many developed coastal cities, San Diego, California has strong geographic and recreational ties to the adjacent ocean, but weak culinary ones. Less than 10% of the seafood consumed in the U.S., and San Diego in particular, is domestic. The popularity and abundance of farmers’ markets and other local markets in San Diego indicates an interest among producers and the public alike in cultivating local, diverse food systems, but this trend has been slower to catch on for seafood. The goal of this project was, therefore, to define and begin to understand the influences on the patterns of locally sourced, domestic seafood availability in San Diego. This study focused on seafood availability in seafood markets including researching market websites and contacting seafood counter managers to determine the general frequency (consistent, occasional, none) at which the markets sold seafood produced by San Diego fishermen or aquafarmers. Seafood market locations were mapped, and demographic...

Integrating collaborative data collection with management: A lobster fishery test case

Mon, 9 Jul 2018 00:00:00 +0000

Cost-effective programs for gathering essential fisheries information (EFI) are critically needed to

improve the data-poor state of fisheries in California and worldwide. The California Marine Life

Management Act (MLMA) recognizes this need and requires development of fishery management

plans (FMPs) that identify suitable protocols for collecting data, and use of the best available

scientific information to inform management. Furthermore, in the United States, several state

and federal laws require the engagement of fishermen and others in fisheries management. To

address these needs, we developed a collaborative at-sea sampling program (CASP) by:

• determining the key regulatory, administrative and operational features of established

collaborative fisheries data collection programs,

• developing a robust sampling design with associated protocols for the commercial

California spiny lobster fishery,

• designing,...

Angler exposure to domoic acid via consumption of contaminated fishes

Mon, 9 Jul 2018 00:00:00 +0000

Angler exposure to domoic acid via consumption of contaminated fishes

Collaborative fisheries research to build socioeconomic essential fishery information: A test case

Mon, 9 Jul 2018 00:00:00 +0000

Fisheries are integrated social-‐ecological systems, characterized by dynamic and complex interactions within and between the natural and human environments. California’s 1998 Marine Management Life Act (MLMA) recognizes the role of people in fisheries, and the MLMA Master Plan calls for the inclusion of socioeconomic as well as ecological “essential fishery information” in fishery management plans. However, critical gaps in such information for virtually all fisheries hinder managers’ ability to actively adapt and communities’ ability to plan for the future. This project begins to meet such information needs for the commercial fishery for California halibut, providing an example for other fisheries. We conducted a small collaborative fisheries research (CFR) project that engaged fishery participants, scientists and managers. Our goal was to produce sound social scientific understanding of the human dimensions of the fisheries system that is useful to the fishing, management,...

Figuring Out the Human Dimensions of Fisheries: Illuminating Models

Mon, 9 Jul 2018 00:00:00 +0000

Figuring Out the Human Dimensions of Fisheries: Illuminating Models

Managing Flow Regimes and Landscapes Together: Hydrospatial Analysis for Evaluating Spatiotemporal Floodplain Inundation Patterns with Restoration and Climate Change Implications

Fri, 6 Jul 2018 00:00:00 +0000

Riverine landscapes are shaped by dynamic and complex interactions between streamflow and floodplain landforms, and these physical processes drive productive and diverse freshwater ecosystems. However, human activities have fundamentally altered river-floodplain processes and degraded ecosystems. Flow regime variability has been homogenized and floodplains disconnected from rivers due to dams, diversions, levee building, and land use change. Reconciling competing demands to support ecosystems and resilience to future change is a core scientific and management challenge. This dissertation describes spatiotemporal dynamics of floodplain environments, introducing a method for flood regime classification and establishing a methodological approach for hydrospatial analysis to quantify and evaluate the response of floodplain inundation patterns and related physical habitat to restoration and flow regime change under climate change. It is motivated by the need to develop process-based...

Can the United States have its fish and eat it too?

Mon, 25 Jun 2018 00:00:00 +0000

As domestic affluence increases, nations advocate for conservation policies to protect domestic biodiversity that often curtail natural resource production activities such as fishing. If concomitant consumption patterns remain unchanged, environmentally-conscious nations with high consumption rates such as the U.S. may only be distancing themselves from the negative environmental impacts associated with consuming resources and commodities produced elsewhere. This unintended displacement of ecosystem impacts, or leakage, associated with conservation policies has not been studied extensively in marine fisheries. This paper examines this topic, drawing on case studies to illustrate the ways in which unilateral marine conservation actions can shift ecosystem impacts elsewhere, as has been documented in land use interventions. The authors argue that the U.S. should recognize these distant ecological consequences and move toward greater self-sufficiency to protect its seafood security...

Calcifying algae maintain settlement cues to larval abalone following algal exposure to extreme ocean acidification

Tue, 19 Jun 2018 00:00:00 +0000

Ocean acidification (OA) increasingly threatens marine systems, and is especially harmful to calcifying organisms. One important question is whether OA will alter species interactions. Crustose coralline algae (CCA) provide space and chemical cues for larval settlement. CCA have shown strongly negative responses to OA in previous studies, including disruption of settlement cues to corals. In California, CCA provide cues for seven species of harvested, threatened, and endangered abalone. We exposed four common CCA genera and a crustose calcifying red algae, Peyssonnelia (collectively CCRA) from California to three pCO₂ levels ranging from 419–2,013 µatm for four months. We then evaluated abalone (Haliotis rufescens) settlement under ambient conditions among the CCRA and non-algal controls that had been previously exposed to the pCO₂ treatments. Abalone settlement and metamorphosis increased from 11% in the absence of CCRA to 45–69% when...

Spatial and Temporal Examination of Bivalve Communities in Several Estuaries of Southern California and Northern Baja California, MX

Tue, 19 Jun 2018 00:00:00 +0000

Spatial and Temporal Examination of Bivalve Communities in Several Estuaries of Southern California and Northern Baja California, MX

BASELINE CHARACTERIZATION OF FISH COMMUNITIES ASSOCIATED WITHNEARSHORE ROCKY REEFS IN THE NORTHERN CALIFORNIA MARINEPROTECTED AREA STUDY REGIONS

Tue, 19 Jun 2018 00:00:00 +0000

BASELINE CHARACTERIZATION OF FISH COMMUNITIES ASSOCIATED WITHNEARSHORE ROCKY REEFS IN THE NORTHERN CALIFORNIA MARINEPROTECTED AREA STUDY REGIONS

The Resilience of Marine Ecosystems to Climatic Disturbances

Tue, 12 Jun 2018 00:00:00 +0000

The intensity and frequency of climate-driven disturbances are increasing in coastal marine ecosystems. Understanding the factors that enhance or inhibit ecosystem resilience to climatic disturbance is essential. We surveyed 97 experts in six major coastal biogenic ecosystem types to identify “bright spots” of resilience in the face of climate change. We also evaluated literature that was recommended by the experts that addresses the responses of habitat-forming species to climatic disturbance. Resilience was commonly reported in the expert surveys (80% of experts). Resilience was observed in all ecosystem types and at multiple locations worldwide. The experts and literature cited remaining biogenic habitat, recruitment/connectivity, physical setting, and management of local-scale stressors as most important for resilience. These findings suggest that coastal ecosystems may still hold great potential to persist in the face of climate change and that local- to regional-scale management...

Effects of Flow-Related Variables on Oversummer Survival of Juvenile Coho Salmon in Intermittent Streams

Tue, 12 Jun 2018 00:00:00 +0000

While many studies have established the importance of streamflow as a driver of fish population dynamics, few have examined relationships between survival of juvenile salmonids and flow-related variables in intermittent streams. With predictions for higher frequency of drought conditions due to climate change, and the associated increasing human demand for water during the dry season, understanding fish–flow relationships is becoming increasingly important for the protection of sensitive aquatic species. To examine the effects of low streamflow on juvenile salmonids rearing in small intermittent streams, we estimated survival and collected environmental data in four coastal California watersheds from 2011 to 2013. We used an individual-based mark-recapture modeling approach to evaluate the influence of flow-related variables on oversummer survival of PIT-tagged juvenile Coho Salmon stocked into eight stream reaches. Survival was positively associated with streamflow magnitude,...

Managing Small-Scale Commercial Fisheries for Adaptive Capacity: Insights from Dynamic Social-Ecological Drivers of Change in Monterey Bay

Tue, 12 Jun 2018 00:00:00 +0000

Globally, small-scale fisheries are influenced by dynamic climate, governance, and market drivers, which present social and ecological challenges and opportunities. It is difficult to manage fisheries adaptively for fluctuating drivers, except to allow participants to shift effort among multiple fisheries. Adapting to changing conditions allows small-scale fishery participants to survive economic and environmental disturbances and benefit from optimal conditions. This study explores the relative influence of large-scale drivers on shifts in effort and outcomes among three closely linked fisheries in Monterey Bay since the Magnuson-Stevens Fisheries Conservation and Management Act of 1976. In this region, Pacific sardine (Sardinops sagax), northern anchovy (Engraulis mordax), and market squid (Loligo opalescens) fisheries comprise a tightly linked system where shifting focus among fisheries is a key element to adaptive capacity and reduced social and...

Seasonal fish and invertebrate communities in three northern California estuaries

Tue, 23 Jan 2018 00:00:00 +0000

The majority of Northern California estuaries are small, flooded, river valleys that are largely unstudied due to their small sizes and remote locations. Yet these estuaries serve as important nursery areas for many marine fish species including rockfish, flatfish, smelt, and herring, and they are vital to anadromous species such as Chinook Salmon (Oncorhynchus tshawytscha) and Steelhead (O. mykiss). I sampled the summer and winter fish and invertebrate communities of the Big, Mad, and Ten Mile river estuaries. Fish were sampled via beach seine or fyke net and invertebrates were sampled via benthic cores, June 2014-June 2016. This research is part of a larger suite of studies establishing baseline conditions in Northern California Marine Protected Areas (MPAs). Big and Ten Mile river estuaries in Mendocino County were designated as MPAs in 2012. The Mad River Estuary in Humboldt County was selected as a non-MPA site to investigate its potential as a reference estuary. In the Mad...

Juvenile survival and adult return as a function of freshwater rearing life history for Coho Salmon in the Klamath River Basin

Tue, 23 Jan 2018 00:00:00 +0000

The Scott and Shasta rivers, Klamath River tributaries, experience spatial disparity in habitat quality in spring and summer as a result of historical and current landuse.

Juvenile Coho Salmon (Oncorhynchus kisutch) born in the upper tributary reaches often rear in natal streams before migrating to sea. However, those born in the lower reaches often encounter unsuitable habitat and emigrate during their first spring to seek non-natal rearing habitats. It is assumed that these early outmigrants are population losses. This study evaluated first-summer survival, and contribution to the adult population, of non-natal rearing juveniles in the Klamath River Basin. In the spring of 2014 and 2015 juveniles were tagged using Passive Integrated Transponder (PIT) tags as they were leaving the lower Scott and Shasta Rivers. Movement and survival was subsequently tracked using recapture and detection efforts in potential mainstem summer rearing locations. Strontium microchemistry...

The response of a predatory fish, Opiodon elongatus, to a marine protected area: variation in diet, catch rates, and size composition

Tue, 23 Jan 2018 00:00:00 +0000

Marine Protected Areas (MPAs) are a management tool used to protect and sustain many ecologically and economically important fish species from overexploitation by recreational and commercial fishing. Lingcod (Ophiodon elongatus) and some of its prey species, such as rockfish (Sebastes spp.), are species that are protected from fishing in some California MPAs. Lingcod is an apex predator that consumes a variety of fish and invertebrate species. In this study, I sought to assess the effect of an MPA on the abundance, size and diet of Lingcod. I hypothesized that Lingcod in a no-take MPA would be more abundant and larger than Lingcod in an adjacent reference site (REF) that was open to fishing. Furthermore, I hypothesized that diet would differ between Lingcod in caught the MPA and Lingcod in the REF. I collected Lingcod from the Point Buchon State Marine Reserve (MPA) and an adjacent REF site that was open to fishing. I measured, weighed, sexed, and collected stomach contents from...

Economic effects of Pacific halibut closures on businesses on the North Coast and the age, growth, and reproductive status of Pacific halibut in Northern California and Central Oregon

Tue, 23 Jan 2018 00:00:00 +0000

Traditionally, the recreational fishery for Pacific halibut has been open in California from 1 May through 31 October. In 2014, however, the Pacific halibut fishery was closed in California during the month of August for the first time in history in an effort to reduce harvest and bring total catch closer to what is allocated to our region by the Pacific Fisheries Management Council (PFMC) Catch Sharing Plan. To determine the effects that the closure had on businesses along the North Coast, I conducted an economic impact survey in 2014. The results of the survey showed that fishing-related businesses lost between zero percent and eight percent of their revenue in 2014, as a result of the closure; lodging and traveler service companies lost between 0.3 percent and one percent of their revenue in the same year. None of the businesses changed the number of employees as a result of the closure. We estimated a decrease in revenue for businesses on the North Coast to be between $189,750...

Expectations and adaptation to environmental risks

Tue, 23 Jan 2018 00:00:00 +0000

Expectations and adaptation to environmental risks

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

Studying gravel bars in rivers to identify what features facilitate groundwater exchanges that create good Chinook salmon spawning habitat

Mon, 8 May 2017 00:00:00 +0000

Studying gravel bars in rivers to identify what features facilitate groundwater exchanges that create good Chinook salmon spawning habitat

Optimizing salt marsh harvest mouse conservation through an investigation of demography, habitat use andmulti-species management

Mon, 8 May 2017 00:00:00 +0000

Optimizing salt marsh harvest mouse conservation through an investigation of demography, habitat use andmulti-species management

Examining the effects of perennial pepper weed on tidalmarsh ecosystems and identifying strategies to stop thenoxious weed’s spread

Mon, 8 May 2017 00:00:00 +0000

Examining the effects of perennial pepper weed on tidalmarsh ecosystems and identifying strategies to stop thenoxious weed’s spread

Determining thermal tolerances of longfin smelt and inland silverside and develop biomarkers of thermal stress using new genomics technology

Mon, 8 May 2017 00:00:00 +0000

Determining thermal tolerances of longfin smelt and inland silverside and develop biomarkers of thermal stress using new genomics technology

The Effects of 4-nonylphenol on the Immune Response of the Pacific oyster, Crassostrea gigas, Following Bacterial Infection (Vibrio campbellii)

Thu, 1 Sep 2016 00:00:00 +0000

The Effects of 4-nonylphenol on the Immune Response of the Pacific oyster, Crassostrea gigas, Following Bacterial Infection (Vibrio campbellii)

CREATION AND UTILIZATION OF NOVEL GENETIC METHODS FOR STUDYING AND IMPROVING MANAGEMENT OF CHINOOK SALMON POPULATIONS

Tue, 28 Oct 2014 00:00:00 +0000

CREATION AND UTILIZATION OF NOVEL GENETIC METHODS FOR STUDYING AND IMPROVING MANAGEMENT OF CHINOOK SALMON POPULATIONS

Understanding Food Webs in Shallow Nearshore Waters of the Delta

Fri, 24 Oct 2014 00:00:00 +0000

Understanding Food Webs in Shallow Nearshore Waters of the Delta

Salinity Tolerances and Biomarkers of Salt Stress in Longfin and Delta Smelt

Fri, 24 Oct 2014 00:00:00 +0000

Salinity Tolerances and Biomarkers of Salt Stress in Longfin and Delta Smelt

Controls on the Net Carbon Emissions from Restored Wetland Ecosystems

Fri, 24 Oct 2014 00:00:00 +0000

Controls on the Net Carbon Emissions from Restored Wetland Ecosystems

Modeling Wetland Plant Cover to Assess Ecosystems and Bird Habitats

Fri, 24 Oct 2014 00:00:00 +0000

Modeling Wetland Plant Cover to Assess Ecosystems and Bird Habitats

Unraveling Sources of Food Web Support in the Sacramento-San Joaquin Delta’s Marsh Ecosystem

Fri, 24 Oct 2014 00:00:00 +0000

Unraveling Sources of Food Web Support in the Sacramento-San Joaquin Delta’s Marsh Ecosystem

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

Seasonal variation of diatoms and dinoflagellates in Monterey Bay, CA determined by Chemtax alanysis of HPLC pigment data

Mon, 9 Jun 2014 00:00:00 +0000

Phytoplankton samples were collected off the Monterey Municipal Wharf II at a single location (36º 36’ N and 121º 53’ W) weekly from June 2003 to March 2010. The contribution of five algal groups to total chlorophyll a (chl a) was derived using CHEMTAX from biomarker pigment measurements made via HPLC analysis. The purpose of this study was to specifically define the relative abundances of diatoms and dinoflagellates on a seasonal and interannual basis. Spearman’s rho (ρ) correlation coefficients were calculated to determine the strength of the relationship between the diatoms and dinoflagellates and two environmental variables; sea surface temperature (SST) and upwelling indices (UI). During the summer of 2004 and until the end of 2006, previous studies had suggested that the typical diatom-dominated bay shifted to a dinoflagellate-dominated system resulting from global warming effects on mixed layer stability. The high-resolution (weekly), long-term (2003-2010) sampling regime...

The population dynamics of mitten crab larvae in the San Francisco Bay

Mon, 9 Jun 2014 00:00:00 +0000

The Chinese mitten crab, Eriocheir sinensis, has a history of invasions in numerous countries. In 1992, the Chinese mitten crab was introduced to the San Francisco Bay/Delta system. Since its invasion in the San Francisco Bay, it has become an aquatic nuisance species. Little is known about the population dynamics of the megalopa stage of the Chinese mitten crab in the San Francisco Bay estuary, particularly the megalopa stage. Light traps are often used to sample marine larvae and can provide measures for relative abundance of larvae between sampling locations. As part of an ongoing study to monitor mitten crab larvae in the San Francisco Bay, light trap and plankton tow samples were analyzed formitten crab megalopae and zoeae. In order to implement low cost sampling devices for mitten crab megalopae such as light traps, it is necessary to be able to identify their larvae in collected samples. Thus, the main objective of this work was to develop a means to distinguish mitten...

Floodplain restoration planning for a changing climate: Coupling flow dynamics with ecosystem benefits

Mon, 2 Jun 2014 00:00:00 +0000

This dissertation addresses the role that dynamic flow characteristics play in shaping the potential for significant ecosystem benefits from floodplain restoration. Mediterranean-climate river systems present challenges for restoring healthy floodplains because of the inter and intra-annual variability in stream flow, which has been dramatically reduced in an effort to control flooding and to provide a more consistent year-round water supply for human use. Habitat restoration efforts require that this reduced stream flow be altered in order to recover more naturally dynamic flow patterns and reconnect floodplains. This thesis defines and takes advantage of an eco-hydrology modeling framework to reveal how the ecological returns of different hydrologic alterations or restoration scenarios—including changes to the physical landscape and flow dynamics—influence habitat connectivity for freshwater biota. A method for quantifying benefits of expanding floodplain connectivity can...

Interannual-to-Decadal Changes in Phytoplankton Phenology, Fish Spawning Habitat,and Larval Fish Phenology

Thu, 22 May 2014 00:00:00 +0000

Phenology is the study of seasonal, biological events and how they are influenced by climate. Climate change has prompted an earlier arrival of spring in numerous ecosystems. It is uncertain whether such changes are occurring in coastal upwelling ecosystems, because these regions are subject to decadal climate oscillations and regional climate models predict later seasonal upwelling. To answer this question, chapter 1 investigated decadal changes in the phenology of 43 larval fish species in southern California. The first principal component of this dataset showed a progression towards the earlier appearance of larvae, although 18% of phenological events exhibited seasonal delays. These changes were best explained by a secular trend towards earlier warming of surface waters. Species with earlier phenology were characterized by an offshore, epipelagic distribution, while fishes with delayed phenology were more likely reside in coastal, demersal habitats. Chapter 2 focused on improving...

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.

Human dimensions perspectives on the impacts of coastal zone marine renewable energy

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

Climate change and soaring energy costs have fueled attention to renewable energy. In coastal areas, the potential to harness the clean power of offshore wind, wave, and tide is irresistible. Our extensive coasts and oceans offer what appears at first glance to be virgin territory for development of energy producing facilities. A closer look,however, reveals that these areas are teeming with productive activity, activity that cannot be ignored in planning and implementing marine renewable energy (MRE) development and production.

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

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

Wed, 30 Apr 2014 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.

The effects of freshwater flows on the native Olympia oyster in San Francisco Estuary

Mon, 16 Dec 2013 00:00:00 +0000

After heavy winter storms, salinity levels in the San Francisco Estuary can drop precipitously, stressing and sometimes killing organisms such as the native Olympia oyster (Ostrea conchaphila ) and invasive Mediterranean mussel (Mytilus galloprovincialis ).

Phytoplankton and bacteria nutrient use: impacts of nutrient loading on the base of the food web

Mon, 16 Dec 2013 00:00:00 +0000

Treated municipal wastewater contains a form of nitroge known as ammonium. When discharged into waterways, this ammonium may alter phytoplankton (algal) communities and potentially degrade available food resources for zooplankton and other organisms.

Saving San Francisco Bay-Delta native fishes: hatchery management and reinintroduction strategies

Mon, 16 Dec 2013 00:00:00 +0000

Several native fish species in the San Francisco Bay-Delta and Central Valley have experienced dramatic population declines and could realistically go extinct in the wild.

The effects of bifenthrin pesticide on the reproductive health of steelhead under hypersaline conditions.

Mon, 16 Dec 2013 00:00:00 +0000

Salmon and steelhead in the San Francisco Bay-Delta face many challenges, including exposure to pesticides in runoff and municipal wastewater discharges.

Detecting changes at the base of the pelagic food web in the San francisco Estuary.

Mon, 16 Dec 2013 00:00:00 +0000

Since about 2004, populations of delta smelt, longfin smelt, juvenile striped bass, and threadfin shad have dropped significantly in the Sacramento-San Joaquin Delta for no obvious or as yet substantiated reason.

South Coast Seafood

Wed, 28 Aug 2013 00:00:00 +0000

Commercial fisheries are an important part of California's economy. In 2011, approximately $201 million dollars in ex-vessel revenue (the amount paid directly to fishermen) came from commercial fishery landings, and more than 120,000 jobs on and off the water were supported by the state's seafood industry (NOAA 2011). Fishing communities from Crescent City to San Diego are the centers of this activity, providing a diverse supply of seafood and a visual reminder of California's maritime heritage.

Santa Barbara Channel Seafood

Wed, 28 Aug 2013 00:00:00 +0000

Central Coast Seafood

Wed, 28 Aug 2013 00:00:00 +0000

North Coast Seafood

Wed, 28 Aug 2013 00:00:00 +0000

Quagga and Zebra Mussel Eradication and Control Tactics

Mon, 5 Aug 2013 00:00:00 +0000

Aquatic invasive species (AIS)continue to threaten coastal and marine habitats in California. The goal of this project is to conduct research and develop outreach materials that help agencies, groups and individuals prevent, eradication and control AIS. Current objectives include: 1) investigate recruitment dynamics of quagga mussels in southern California to provide baseline informaiton on infestations in various locations, inform monitoring efforts and to identify factors influencing the success of mussel populations in California, 2) conduct research to evaluate additional eradication and control tactics for development of IPM strategies for lakes, reservoirs and irrigation canals, including the use of fish biological control agents for management of quagga (and zebra) mussels, 3) evaluate IPM strategies for control of Asian kelp, Undaria pinnatifida, including the use of invertebrate biological control agents.

Geophysical Constraints on Sediment Dispersal Systems

Wed, 17 Apr 2013 00:00:00 +0000

Geophysical and geological approaches were employed to understand sediment dispersal systems and their response to various forcing functions (i.e., sea level member marine environments were studied; one with high precipitation and sediment discharge (Gulf of Papua, Papua New Guinea) and the other with low precipitation and sediment discharge (Oceanside Littoral Cell). The high-sedimentation rate in the Margins Source-to-Sink (S2S) program, we acquired CHIRP and core data across the GoP continental shelf that complemented onshore and offshore research in the region. CHIRP seismic data imaged three Holocene sedimentary lobes. The older Central lobe is downlapped by two younger lobes to the north and south. Sediment analysis showed that the older Central lobe has an elemental signature similar to the younger Northern lobe with both sourced from the Purari River watershed and lobe migration appears to be climatically controlled. The Southern lobe has elemental signatures more consistent...

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.

Epidemiology of Fecal Protozoa at the Human, Animal, and Environmental Interface

Fri, 22 Mar 2013 00:00:00 +0000

Cryptosporidium and Giardia are important disease agents for both humans and animals worldwide. Unlike many pathogens, their capacity for surviving in soil and water for extended periods of time enables environmental transmission. Both parasites replicate within warm-blooded vertebrate hosts and are excreted as an environmentally resistant oocyst or cyst, respectively. New hosts become infected through ingestion of oocysts or cysts in contaminated water, food, or soil. The objective of this thesis work was to utilize an epidemiologic approach to identify environmental factors associated with the prevalence of Cryptosporidium and Giardia spp. in California coastal wetlands, as well as to ascertain the prevalence and identify potential transmission pathways within the animal community in the Virunga Massif, Rwanda.

Because Cryptosporidium and Giardia are waterborne parasites, key factors in wetland ecology were examined for their impact on parasite levels in water. First,...

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.

Hydrologic System Response to Environmental Change: Three Case Studies in California

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

Hydrologic systems are vulnerable to anthropogenic and natural environmentalchanges. When these changes impair a system’s ability to function and serve as aresource, then restoration or mitigation may be needed. Successful management offreshwater resources requires a quantitative understanding of hydrologic processes and dynamics, and an assessment as to how hydrologic systems may respond to futurechanges. Some systems are sufficiently large or complex so as to defy direct control or restoration, but people can still benefit from understanding that will allow more reliable and thoughtful resource use, as part of a comprehensive management approach. The three chapters presented in this thesis examine hydrologic system response to a variety of environmental changes, including: (1) a recovering riparian wetland located downstream of a dam, (2) an overdrafted and seawater intruded coastal groundwater basin, and (3) a region experiencing an increase in the intensity of extreme precipitation...

The Coastal Boundary Layer: Pattern, Mechanism, and Ecological Effects of Decreased Alongshore Transport

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

Dispersion of planktonic propagules connects shoreline populations of many marine species, and considerable effort has been directed at understanding this process. However, gaps in knowledge persist. In particular, relatively little information has been available regarding transport over the innermost portions of the continental shelf and its impacts on larval distributions and population connectivity. I quantified velocity in nearshore waters at 5 sites along the California coast and investigated characteristics relevant for dispersing larvae. Mean depth-averaged velocities increased with distance from shore at all sites. This repeated and consistent “coastal boundary layer” (CBL) pattern exhibits a logarithmic profile that resembles that associated with the “law of the wall” of smaller-scale turbulent boundary layers, despite differences in spatial dimension and governing physics. A tentative scaling of dominant terms in an alongshore momentum balance suggests nontrivial...

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.

A Field-Calibrated Model of Pioneer Riparian Tree Recruitment for the San Joaquin Basin, CA

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

In the Central Valley of California, Populus fremontii ssp. fremontii, Salix gooddingii, and Salix exigua dominate the near-river forests. Historically, seedling recruitment for these disturbance-adapted species coincided with spring floods. Changes in flow timing and magnitude due to river regulation have decreased the success of seedling cohorts and contribute to the decline of pioneer riparian tree populations.

In order to address gaps in our understanding of these species and their potential restoration strategies, I rigorously quantified and field-calibrated a conceptual model of seedling recruitment using field and laboratory studies. Results indicate that these species do not maintain a seed bank and that vegetation competition does not limit seedling recruitment in the first year. Abundance was correlated with soil moisture and with low bank elevation. However, overwinter mortality was nearly complete.

Results...

Effects of Tissue Nitrogen and Media Nitrate on Trace Metal Uptake and Trophic Transfer by Ulva spp.

Tue, 30 Oct 2012 00:00:00 +0000

A general survey of trace metal content in Ulva spp. (Linnaeus) around Moss Landing, California was carried out. The next objective was to evaluate whether tissue nitrogen or media nitrate affects metal uptake (As, Pb, Mn, Zn) by Ulva spp. under eutrophic conditions. Additionally, the role of metal burden in the invertebrate Idotea resecata as a function of metal content in its diet was examined. Mean trace metal concentrations in Ulva differed significantly among sites in Moss Landing, California. Laboratory measurements using samples from 15 sites along the central California coast revealed a significant positive correlation between Ulva spp. tissue nitrogen and both arsenic and manganese uptake. No relationship was found between tissue nitrogen and lead or zinc, but a significant positive correlation with the relative change in manganese and lead was observed. Though statistically insignificant, a regression analysis revealed a logarithmic relationship between media...

Sacramento River Steelhead: Hatchery vs. Natural Smolt Outmigration

Tue, 9 Oct 2012 00:00:00 +0000

The Sacramento River steelhead trout (Oncorhynchus mykiss) is a threatened species whose numbers are supplemented by the release of captive-bred juveniles. Each year, the Coleman National Fish Hatchery alone produces 600,000 yearling steelhead smolts and releases them into Battle Creek, a tributary of the upper Sacramento River. Smolts are young, silver trout (or salmon) that are ready to migrate to sea for the first time. The hatchery operations are mitigation for loss of natural steelhead in their historic spawning grounds. Coleman is one of several hatcheries in the Sacramento River basin that cultures steel- head for mitigation purposes.

Copper Toxicity in the San Francisco Bay-Delta

Tue, 9 Oct 2012 00:00:00 +0000

San Francisco Bay has high dissolved copper concentrations—relative to nearby coastal waters—that often approach federal water quality standards put in place to protect sensitive marine life. But, how toxic is this copper?

Previous studies by other researchers have suggested that metal-binding compounds known as ligands can “grab up” more than 99.9 percent of the total available dissolved copper in seawater, rendering that copper biologically unavailable. Microorganisms that need trace amounts of copper for growth cannot readily obtain it in its ligand-bound form.

Invasive Spartina densiflora Brongn. Reduces Primary Productivity in a Northern California Salt Marsh

Mon, 13 Aug 2012 00:00:00 +0000

Comprehensive primary productivity measurements of the impact of invasive species are important environmental indicators. This study obtained measurements of the impact of invasive Spartina densiflora on the primary productivity of a Humboldt Bay (California) salt marsh using above and belowground biomass measurements coupled with paired closed-chamber carbon dioxide flux measurements. Compared to samples dominated by native vegetation, samples dominated by S. densiflora displayed higher aboveground net primary productivity, lower belowground net primary productivity, lower net primary productivity, and lower net ecosystem exchange measurements; thus, S. densiflora colonization reduced primary productivity. Benthic macroalgal cover was a strong predictor of net ecosystem exchange. In plots dominated by S. densiflora, less benthic macroalgae was present and less photosynthetically active radiation reached the substratum. Therefore, increased...

Assessing Trophic Ecology and Nutritional Status of Marine Mammals with Bulk and Compound-Specific Amino Acid Isotope Analysis

Thu, 9 Aug 2012 00:00:00 +0000

Compound-specific isotope (CSI) analysis is rapidly growing tool in the field of ecology to assess the trophic position and foraging behavior of an animal. Only a handful of studies have examined the values and patterns of carbon and nitrogen amino acid isotopes ( δ 13C-AA and δ 15N-AA), and have primarily been done on plankton and other low trophic position organisms. Since AA data separate into unique biochemical groupings, much more detailed information is revealed than the widely used bulk isotope technique - such as source of diet (offshore vs. coastal), base of the food web, trophic positions, and an animals physiology. To examine the usefulness and power of the CSI method, we tested how δ 13C-AA and δ 15N-AA patterns and values appear in several populations of harbor seals (Phoca vitulina) off the California coast, primarily comparing seals from San Francisco Bay (SFB) and the Channel Islands (CI).

In Chapter 1, we compared bulk isotopes...

Physical and Biological Dynamics of Surfzone Bacterial Pollution: Sources, Transports, and Removal Mechanisms

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

Nearshore concentrations of fecal indicator bacteria (FIB) are controlled by a complex array of physical and biological processes. The studies herein evaluate the contribution of several such process to coastal FIB dynamics using laboratory studies, mathematical modeling, and fieldwork. Two field sites are discussed; Border Fields State Beach (BFSB) and Huntington Beach, both sites of chronic FIB contamination in Southern California. At Huntington Beach field measurements of alongshore currents and horizontal diffusion were used to parameterize a suite of individual based particle tracking models. These models were used diagnostically to evaluate the contribution of physics and mortality to FIB dynamics. Advection and diffusion were found to explain a significant fraction of surfzone FIB decay, but played a lesser role offshore, suggesting that offshore FIB loss may be dominated by mortality rather than physics. No single mechanism was identified that best-explained FIB mortality...

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.

Climate Change and Tidal Marsh Plant Communities in the San Francisco Bay-Delta

Fri, 20 Jul 2012 00:00:00 +0000

Sea levels in California, south of Cape Mendocino, are predicted to rise between 90 and 95 cm between 2000 and 2100, with a range as high as 167 cm and as low as 42 cm, according to a 2012 report by the National Academy of Sciences.

Whatever the ultimate rise in sea level is, it will largely control the fate of tidal marsh habitats in the San Francisco Bay-Delta.

Tidal marshes are wetlands periodically inundated by tidal flows and, unlike mudflats, are vegetated. They provide overwintering and foraging habitat for resident and migratory birds, and are a buffer against floods and storm surge. They also filter and remove pollutants.

Only about 5 to 10 percent of the delta’s historic tidal marshes remain. Most fringe an aging collection of levees. Former wetlands— now diked, behind levees and dry—are sinking and below sea level by as much as 20 m in some places.

Plans are underway to restore thousands of acres of tidal marshes. Whether these marshes are...

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.

Movements and Habitat Use of Female Leopard Sharks in Elkhorn Slough, California

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

From May 2003 to February 2005,20 female leopard sharks (78 -140 cm TL) were tagged with acoustic transmitters in Elkhorn Slough, California, and their movements and habitat use were examined using acoustic tracking techniques. Nine sharks were manually tracked for 20-71.5 h, and 11 sharks were monitored for 4-443 d using an array of acoustic receivers. Use of different regions in Elkhorn Slough by tagged sharks changed seasonally and was associated with changes in temperature, salinity, and dissolved oxygen. Sharks used Elkhorn Slough National Estuarine Research Reserve (ESNERR) extensively throughout the year, but especially during the spring and summer. ESNERR appeared to be important as both a foraging and nursery area, likely due to the abundance of intertidal mudflats. Movements and habitat use were tidally influenced, and likely were related to the distribution of important prey items in Elkhorn Slough.

Detecting Endocrine Disruption in the Sacramento- San Joaquin Delta

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

In 2001, the EPA began restricting the use of organophosphate pesticides in bug sprays and strips to protect the health of humans and other mammals. Their main replacement has been another class of highly toxic pesticides known as pyrethroids.

The pyrethroid molecule is basically a chemically stabilized version of the natural pyrethrin molecule found in mums (yes, the flowers). In its modified form, it is more persistent in the environment, more hydrophobic (it will stick to sediment) and more toxic.

Vertebrates, including humans, have enzymes that can break down low doses of pyrethroids but they tend to have endocrine- disrupting effects. Both the pesticides and the compounds produced during their metabolism can potently mimic sex hormones.

Fishes are particularly sensitive to endocrine disrupting compounds (EDCs), due to their size and continuous exposure via contaminated water. Fish exposed to EDCs may display a variety of physiological and behavioral abnormalities,...

Movements of Lingcod (Ophiodon elongatus) Tagged in Carmel Bay, California

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

Movements of 30 lingcod (Ophiodon elongatus) tagged with acoustic transmitters were monitored over one year using an array of acoustic receivers in Carmel Bay, California. For all tagged lingcod, residence times in the array varied from 3.8 to 100%of their respective days at liberty. On average, lingcod spent 42.5 ± 17.9 (SE) consecutive days in and 8.1 ± 1.5 (SE) consecutive days out of the array. Residency significantly decreased with total length for female lingcod, while a significant relationship was not exhibited for male lingcod. Large female lingcod, at lengths > 90% maturity, spent the least amount of time in the array but were present during the fall spawning season and briefly during the spring. There was an observed decline in residency in April for males and small female lingcod, the timing of which coincided with the post nest-guarding dispersal period for males and with the return of large females into the array. Large female lingcod were recorded...

Late Holocene Stratigraphy, Humboldt Bay, California: Evidence for Late Holocene Paleoseismicity of the Southern Cascadia Subduction Zone

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

Late Holocene stratigraphy representing rapid episodic subsidence is found in synclines of Humboldt Bay, California. These synclines are associated with the Cascadia subduction zone fold and thrust belt, which bends eastward in Northern California. In the axes of the synclines, repeated sequences of intertidal muds overlying saltmarsh to lowland peat deposits represent episodes of rapid submergence followed by gradual emergence. Observations of the contacts between the peats and overlying muds are abrupt (<1 cm). The rapid submergence most likely represents coseismic subsidence associated with large magnitude earthquakes. The evidence for these submergence events is found within both the northern Freshwater syncline and the southern South Bay syncline.

Radiocarbon dating indicates at least eight rapid episodic subsidence events during the past 3500 years. Rapid episodic events have occurred for the following age ranges: 0-300, 500-800, 1050-1350 (2 events), 1600-1900,...

Deomographic Statistics and Annual Molting Probabilities of the Adult Female Dungeness Crab (Cancer Magister) in Northern California

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

Adult female Dungeness crabs (Cancer magister) can be inseminated only while in a soft-shell condition immediately after molting. Population modelers have therefore assumed that all adult female Dungeness crabs undergo an annual molt. Based on this assumption, a tag-recovery project was initiated in northern California to determine demographic statistics of the adult female stock. Of 12,037 adult female crabs tagged and released, recoveries of 492 crabs in the commercial fishery showed that a large proportion of adult female Dungeness crabs fail to molt annually and that extrusion of viable eggs does not require annual molting and mating.

A size-specific annual molting probability estimator was developed which accounts for commercial gear selection biases. Estimates using this technique showed that annual molting probabilities decline with increasing adult female size and become zero above 155 mm. Therefore, size and age are weakly correlated. Size-related population...

Chinook Salmon Spawning Behavior: Evidence for Size-Dependent Male Spawning Success and Female Mate Choice

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

The spawning behavior of unmanipulated groups of tagged and untagged chinook salmon was observed during three spawning seasons on Bogus Creek, Siskiyou County, California. Individually recognizable male and female chinook salmon were observed daily throughout their lives on the spawning grounds. Male chinook salmon were observed to compete for access to females. Larger than average sized males were observed to be in primary (dominant) status with females much more often (44 percent of observations) than smaller males (8 percent). In 35 observed spawnings, primary males always appeared to spawn, and entered the nest first or at the same time as the first satellite male in 27 of the 29 spawnings involving more than one male. Individual large males were observed to spawn as a primary male on three occasions, and may have spawned as a primary male on up to 12 occasions.

Female chinook salmon exhibited significantly more aggressive behavior toward smaller males and more courting...

Factors Affecting Methylmercury Accumulation in the Food Chain

Tue, 26 Jun 2012 00:00:00 +0000

The common scientific wisdom is that dissolved organic debris (from rotting dead plant material, for example) reduces the biological activity, and hence toxicity, of heavy metals such as mercury. Prior to the start of this project, however, a study showed that organic debris could also sometimes enhance build up of the toxic form of mercury in phytoplankton. This toxic form is called methylmercury (MeHg). It is produced in the aquatic environment by sulfur-reducing bacteria and biomagnifies through aquatic food chains.

What Controls Harmful Algal Blooms and Toxicity in the Sacramento-San Joaquin Delta?

Wed, 20 Jun 2012 00:00:00 +0000

This project shows that harmful algae like it hot. All things being equal, surface water temperature is the best predictor of whether a harmful algal bloom will form in the Sacramento-San Joaquin Delta, though flow dynamics, nutrient pollution and microbial associations also may play a role.

An Evaluation of the Use of Mating Marks as an Indicator of Mating Success in Male Dungeness Crabs

Wed, 13 Jun 2012 00:00:00 +0000

Dungeness crab (Cancer magister) fisheries of the eastern Pacific, from Alaska to central California, have a minimum size limit, measured as carapace width (CW), to ensure that all harvested males have had the opportunity to participate in at least one mating season as sublegal-sized crabs. Dependable indicators of female mating activity have been revealed, but mating activity of males has only been indirectly inferred through examination of so-called "mating marks", presumably created during the premating embrace between a male and female. Previous researchers found that mating marks were present on a higher percentage of sublegal-sized males than on legal-sized males, leading to implications that in a fished population large females may go unmated, and cause a reduction in overall egg production. I present results from laboratory experiments designed to discover the process of mating mark formation, along with at-sea observations documenting the occurrence of mating...

Residence of Juvenile Chinook Salmon, Oncorhynchus tshawytscha, in the Smith River Estuary, California, 1998–2000

Wed, 13 Jun 2012 00:00:00 +0000

Wild juvenile chinook salmon appear to spend an extended period of time in the estuary of the Smith River, California. Based on recovery patterns of freeze-branded juveniles released from June through August, 2000, mean estuarine residence time ranged from 8.3-13.8 d during June and July, and increased to an estimated 38.3 d for fish marked and released in August. Based on computer simulations of the process of estuarine entrance and exit, and on evidence of estuarine growth of juvenile Chinook salmon, it appears that these estimates of mean residence times were negatively biased. True mean residence times calculated in other studies may also be considerably longer than those estimated using existing published methods.

Rowdy Creek Hatchery rears large numbers of chinook salmon and many are released as fingerlings into the Smith River estuary during May–June. In 1999, about 13% of Rowdy Creek fingerlings were marked with a left maxillary clip, whereas in 2000 about 22%...

From ‘Omics to Otoliths: Establishing Menidia Species as Bioindicators of Estrogenic and Androgenic Endocrine Disruption.

Mon, 7 May 2012 00:00:00 +0000

A large body of work has established a link between endocrine disrupting compounds (EDCs) and physiological abnormalities in fishes. EDCs, which include pesticides such as pyrethroids, can mimic, synergize or antagonize the effects of endogenous hormones. Both theory and empirical data confirm that EDCs can also cause fish population decline. However, to date few studies have attempted to link realistic environmental EDC mixtures with responses at multiple tiers of the biological hierarchy, including population level impacts. Additionally, although EDCs currently areknown to impact a wide array of fishes, most studies continue to use a few standardlaboratory denizens. A need exists for an estuarine model fish, particularly consideringthat estuaries are utilized by many fish species for part of their lives and are subject to many EDC inputs. Silversides (Menidia spp.) are well appointed for this role.Furthermore, the San Francisco Bay (SFB) estuary, home to introduced silversides,represents...

Design and Performance of the COOPS Sun Photometer

Wed, 2 May 2012 00:00:00 +0000

The scattering of light in the atmosphere by aerosols has significant implications to the measurement of ocean color by satellite. Determining the effects of this scattering by measuring aerosol optical thickness (ζ_a) and sky radiance requires a Sun Photometer. The COOPS Sun photometer was designed and constructed using a commercially available two channel CCD spectrometer, tracking telescope, and Gershun Tubes fabricated at Moss Landing Marine Laboratories. The instrument was then calibrated using the high altitude Langley method. The performance of COOPS was evaluated using an industry standard CIMEL CE 318N (serial #59) as a reference. Measurements of ζ_a by both instruments were compared and the results how deviations as a function of wavelength, channel, and day of measurement. COOPS was accurate to within 2% for select sequences of measurements at 440 nm while measurements at the longer wavelengths of 675 and 870 nm showed potential for similar accuracy....

The Comparative Genomics of Salinispora and the Distribution and Abundance of Secondary Metabolite Genes in Marine Plankton

Tue, 1 May 2012 00:00:00 +0000

This dissertation is based on a bioinformatics approach to study microbiology, ecology, evolution, marine biology and secondary metabolites. Comparative genomics was applied to identify the similarities and differences between two marine Actinobacteria Salinispora tropica and S. arenicola. The first step in this analysis was to identify orthologous genes between the two species and create a gene-by-gene alignment of the genomes in order to identify synteny of orthologs. The second step was to identify all secondary metabolite gene clusters and mobile genetic elements followed by a thorough analysis of the evidence for horizontal gene transfer. The first two steps reveal that the main differences between these species lie on genomic islands that harbor secondary metabolites and mobile genetic elements. The Salinispora genomes were used as the basis for comparison against other Actinobacteria to identify possible marine adaptation genes. Several marine adaptation...

Larval Behavior and Natural Trace Element Signatures as Indicators of Crustacean Population Connectivity

Mon, 30 Apr 2012 00:00:00 +0000

In an era of increasing governmental protection of marine resources and accelerating climate change, knowing how benthic populations of marine organisms are connected is of paramount importance. However, little is known about connectivity in the nearshore environment, particularly at ecologically and demographically relevant scales. Because the dispersive larval stage is the key to understanding population connectivity, my dissertation focused on developing a new technique for tracking larvae and determining how larval swimming behaviors can influence their cross-shelf distributions in the dynamic upwelling environment of northern California. This information is relevant not only to the applied fields of invasive species management, stock assessment, and marine protected area establishment, but also to the academic pursuit of understanding how life evolved in the sea.

In Chapters 1 and 2, I focused on investigating the role of swimming behavior in regulating larval transport...