Romberg Tiburon Center for Environmental Studies

Image: Ripples on water

SF State's bayside marine and estuarine research facility.

Rosenberg Institute Seminar Series at the Romberg Tiburon Center-Abstracts Archive


The Barbara and Richard Rosenberg Institute for Marine Biology and Environmental Science Seminar Series brings leading local, national, and international scientists to a public forum at RTC to speak about the latest advances in science.

See abstracts or brief descriptions for past seminars below.


Spring 2017

1/25: Investigating the diet of sea-floor microbes: Clues from isotopic and molecular composition of pore-water dissolved organic matter

Tomoko Komada, Professor, Department of Chemistry & Biochemistry, Romberg Tiburon Center and San Francisco State University

Marine dissolved organic matter (DOM) is a globally significant carbon reservoir, yet the mechanism of DOM accumulation remains unclear. Microbial processes within the seafloor have long been known to produce DOM, but the significance of this flux is not well understood, because of limited knowledge about the composition and reactivity of DOM generated within the sediments. We address this knowledge gap through isotopic and chemical analyses of pore-water DOM in two California Borderland basins with contrasting depositional patterns. At both sites, pore-water DOM consists of a complex mixture of labile to refractory moieties with variable radiocarbon ages. The composition of bulk DOM varies within and across sites, but the refractory component shows striking similarity regardless of site and sediment depth, and has an older radiocarbon age than bulk DOM. These findings suggest that sediments are important sources of pre-aged DOM that accumulates in the deep sea.


2/8: Shedding light on symbioses: lessons from a bioluminescent vertebrate-microbe association

Alison Gould, Postdoctoral Researcher, UC Berkeley

Virtually all organisms are dependent on symbioses with microorganisms for their success, yet the processes by which these essential interactions are established and maintained over time remain largely unknown. I present a pairwise symbiosis between a coral reef cardinalfish and a luminous bacterium as a model association to investigate the ecological mechanisms that help to maintain symbiont specificity over host generations. To do so, I integrate field studies to define key attributes of the host’s behavioral ecology and life history in Okinawa, Japan with recently developed genomic methods (restriction site-associated sequencing, “RAD-Seq”) to test the hypothesis that the fish’s ecology genetically structures populations of its facultative symbiont over time and space, consequently promoting the specificity of the association. Results indicate that resident populations of adult fish enrich the surrounding reef water daily with their excess luminous symbionts and that larval fish disperse significant distances as a cohort to non-natal reefs and acquire a symbiont from the locally enriched water near their settlement site. Ultimately this study highlights the role of a host animal in structuring natural populations of its bacterial symbiont, thereby promoting the specificity of this bioluminescent vertebrate-microbe symbiosis over host generations.


2/15: Linking sensory neuron plasticity to adaptive, injury-induced behavior in cephalopods

Robyn Crook, Assistant Professor of Biology, San Francisco State University

Most animals will experience sub-lethal injury at least once in their lives. Injured animals incur multiple fitness costs, including increased predation risk, decreased foraging efficiency and reduced reproductive success. Behavioral changes that offsets these costs, even partially, are therefore likely to 1) be under strong selection, 2) be highly conserved and 3) produce measurable adaptive benefits. Although injury-induced behaviors are common and widespread, their neural mechanisms remain poorly understood. Work in my laboratory at SF State aims to identify the mechanisms and functions of injury-induced behaviors in cephalopod molluscs. Cephalopods’ soft bodies are vulnerable to injury, their behavior is highly plastic, and their nervous system is comparably complex (but independently evolved and structurally unique) to that of vertebrates. However, many cellular mechanisms of plasticity are conserved among molluscs and vertebrates. Thus cephalopods are uniquely placed to provide novel insights into strongly selected, highly conserved mechanisms of injury-induced behavior that in mammals may include pain, anxiety and other complex affective states. Recent studies combine electrophysiological manipulations of plasticity in nociceptive input, with measurements of changes to neural signal controlling motor circuits. In behavioral studies, we are looking at the duration and context of injury-induced behaviors that alter defense, foraging and reproduction, to measure the fitness costs of injury and the adaptive value of injury-induced neural and behavioral plasticity.


2/22: Sea-level rise and Pacific coast salt marshes: impacts on plant productivity, community structure, and decomposition

Christopher Janousek, Research Associate, Department of Fisheries and Wildlife, Oregon State University and Western Ecological Research Center, USGS

Salt marshes provide valued ecosystem functions and services including food web support, storm protection, nutrient cycling, and carbon sequestration. These functions and services may be threatened by sea-level rise if vertical marsh accretion cannot keep pace with rising water levels. Through observational, experimental, and modeling approaches we are assessing inundation and salinity effects on plant growth, plant fecundity, vegetation composition, and decomposition of plant organic matter across the Pacific coast. Our on-going work suggests the following general conclusions: (i) Inundation and salinity effects on plant growth vary by species, suggesting that marsh vulnerability likely varies spatially and that local marsh species composition may change with relative sea-level rise. (ii) Increasing salinity may interact with rising seas to lower plant productivity and reduce plant diversity. (iii) The cycling of salt marsh carbon through decomposition may be affected by a suite of abiotic and biotic factors including inundation, salinity, plant abundance, and plant composition. Our results help further understanding of how marsh structure and function may be impacted by climate change at local and regional scales along the Pacific coast. Such information is critical for informed tidal marsh management, habitat restoration, and adaptive responses to coastal climate change.


3/1: Restoration of native species in highly modified estuaries

Chela Zabin, Smithsonian Enviromental Research Center

Restoration frequently occurs in habitats that have been dramatically altered by human activities, including the introduction of non-indigenous species (NIS). NIS can pose threats to native species as competitors, predators, or ecosystem engineers. When eradication of NIS is not tractable, one potential tool for restoration practitioners is to take advantage of environmental conditions that alter the impacts of NIS on species targeted for restoration. I’ll discuss investigations of this option for native oyster (Ostrea lurida) restoration in three California bays and implications for restoration design.


3/8: Indigenous Knowledge of Marine Systems from Coastal Tribes and Canoe Cultures
Melissa K. Nelson, Ph.D., Associate Professor of American Indian Studies, SFSU

Pacific Ocean Tribes from the Coast of California to the Islands of Hawaii and around the Pacific Rim have long-term ecological knowledge and marine management systems.  They harvest fish, seafood, and seaweed for food, navigate their canoes through coastal waters, and hold a deep cultural and spiritual connection to the Ocean through intergenerational practices based in ethical values imbedded in oral traditions.  This talk will highlight coastal environmental changes and share tribal responses to climate disruption with particular attention to the iconic abalone, access to seaweed, and revitalization of canoe traditions. 


3/15: The economics of sea level rise: A case study in southern Monterey Bay

Philip King, Ph.D., Associate Professor in Economics at San Francisco State University

A brief overview of the issues involved in any economic analysis of sea level rise, followed by a specific application in southern Monterey Bay. The study examines the benefits and costs of differing adaptation strategies over four reaches in southern Monterey Bay. The economic benefits include recreation, ecological value and protection of private and public property. Under a wide range of plausible scenarios and assumptions, we find that coastal armoring is not cost effective. In most cases, retreat is the best option.


4/5: Ocean acidification: Science, solutions, and stepping out of our comfort zones
Tessa Hill, UC Davis
Recent work has focused on the potential consequences of reduced ocean pH that result from ongoing influx of anthropogenic carbon dioxide (CO2) into seawater (termed 'ocean acidification', or OA). Research along the West Coast has brought into sharp focus the potential local consequences of highly acidified seawater for aquaculture operations and California ecosystems more broadly. In response, states have mobilized in developing policy and science recommendations, with research efforts shifting to defining strategies for coping with this issue. For example, seagrass beds have been highlighted as potential "OA refugia" for their capability to buffer acidified waters. These ecosystem services are based upon the assumption that seagrasses fix carbon through photosynthesis, thereby effectively reducing the CO2 load in seawater, and that seagrass beds can also 'trap' carbon in below-ground sedimentary reservoirs.In this talk, I will review some of the science of OA, potential local solutions including the role of vegetated habitats, and provide a call for marine scientists to step out of our 'comfort zones' in addressing problems of major societal significance.

4/26: Applications of endocrinology to the management of commercially important crustaceans in Alaska

Sherry Tamone, Professor of Biology, University of Alaska Southeast

Commercially important crustaceans in Alaska include but are not limited to red king crab, snow crab, Dungeness crab, Tanner crab and Northern spot shrimp. Crab fisheries are size selected male only fisheries while all sexes of shrimp may be harvested. The Tanner crab (Chionoecetes bairdi) and northern spot shrimp (Pandalus platyceros) both undergo male specific sexual differentiation that is important to their life history and to the fishery, and these life history events can be studied through their endocrinology. Molting hormones (ecdysteroids) regulate growth in all crustaceans. In crabs such as Tanner and snow crabs, these hormones can be used in association with morphometrics to distinguish terminally molted male crabs, a life history stage distinguished by an allometric increase in chelae size. Sexual differentiation of male crustaceans is mediated by the insulin-like androgenic gland hormone (IAG), a product of the androgenic gland (AG). The role of this hormone is to promote the male phenotype during the life history of the animal. For gonochoristic species such as C. bairdi, and protandric species such as P. platyceros, IAG is thought to be the hormone responsible for promoting spermatogenesis and secondary sexual characteristics (such as the large claw morphology of C. bairdi). In protandric shrimp, in which functional males become functional females, the mechanism for transition from male to female is hypothesized to be the degeneration of the AG; thus elimination of IAG. Professor Tamone will present data on our current understanding of the endocrine basis for sexual differentiation in Tanner crab and spot shrimp.


5/10: Population Dynamics of Green Tide Macroalgae in the Central Sf Bay

Rosemary Romero, PhD Candidate, Dept. of Integrative Biology, UC Berkeley

Blooms of green macroalgae, known as Green tides, have been increasing in frequency and intensity world-wide over the last decade. Nuisance green tides can outcompete seagrass beds for light and their decay results in toxic anoxic conditions. Green tides are predominantly composed of macroalgae belonging to the genus Ulva, including many species commonly found in the San Francisco Bay. These algae are thought to exhibit large blooms due to a combination of broad physiological tolerances to environmental conditions, rapid growth rates, and high reproductive potential, all of which can lead to population eruptions, especially under eutrophic conditions.  Investigations of the dynamics of nuisance green macroalgae have focused on post-recruitment processes such as herbivory, while less is known about the roles of propagule availability and dispersal traits in bloom initiation and persistence.

Fall 2016

8/24: Untangling factors shaping community response to extreme events in coastal marine ecosystems

Laura Jurgens, Smithsonian Environmental Research Center

A worldwide upsurge in extreme events, including heat waves, storms, and harmful algal blooms (“red tides”) poses escalating threats to species and ecosystems. Scientists increasingly recognize that such rapid, severe perturbations may have even more severe ecological consequences than gradual shifts in stressors such as temperature and ocean chemistry. I use an approach that integrates ecomechanics, community ecology, and animal physiology to explore key factors that shape ecological responses to such events in coastal marine ecosystems. These include how the physical structure of habitat-forming species can both buffer and exacerbate population risk from heat waves, how the spatial dynamics of a HAB-driven mass mortality may alter species' recovery trajectories, and how predators can affect the ways tropical marine communities respond to acute disturbances like hurricanes.


8/31: Transcriptomics in environmental physiology and finding the ‘genes that matter’ for environmental adaptation

Tyler Evans, Department of Biological Sciences, California State University East Bay
Transcriptomics (quantifying changes in the cellular mRNA pool) is a popular approach for exploring how organisms respond to environmental change. Broadly, my research uses transcriptomic approaches to determine the mechanistic basis of environmental tolerance and identify genotypes and phenotypes sensitive or resistant to abiotic change. Along with collaborators, I have used transcriptomics to explore the effects of ocean acidification on early life stage purple sea urchins, resolve spatial and temporal patterns of environmental stress in wild migrating salmon, and understand the mechanistic basis of differing salinity tolerance in oysters. While transcriptomics provides a sensitive means for identifying gene transcripts regulated by the environment, uncertainty remains as to whether genes differentially expressed in response to environmental change are actually most important for coping with that change (i.e. the ‘genes that matter’). As the accessibility of transcriptomics continues to increase, it becomes necessary to better understand the relationship between gene expression and fitness.


9/7: To salinity and beyond: microbial diversity and carbon cycling in San Francisco Bay wetlands

Dr. Susanna Theroux, Southern California Coastal Water Research Project

Wetland restoration efforts in San Francisco Bay aim to provide an effective long-term carbon storage solution and a mechanism to reverse land subsidence caused by a centuries of industrial and agricultural development. However, predicting the net greenhouse gas (GHG) flux in newly restored wetlands is notoriously difficult in part due to our limited understanding of carbon cycling in wetland microbial communities. Using high-throughput DNA sequencing, we were able to link belowground microbial communities with their aboveground GHG production in a suite of sites in San Francisco Bay ranging from freshwater marsh to hypersaline salt ponds. While salinity was responsible for large shifts in microbial community composition, outlier sites with anomalously high methane production harbored novel and unexpected methane-producing species. By shining a light on the microbial dark matter underfoot, we are better able to understand how these dynamic populations and their complex environments will respond to a warming planet.


9/28: Climate change impacts on coastal ecosystems: are they detectable already?

Dr. Bruce Menge, Oregon State University

Society’s greatest environmental challenge is confronting the impacts of climate change. In this talk, I present evidence indicating that Oregon’s coastal climate has already begun to change. Upwelling has intensified, wave height has increased, oceanic water temperature has increased while coastal water temperature has decreased, oxygen levels in the ocean have decreased, coastal waters have become more acidified and less amenable to calcification of marine organisms. Associated with these environmental changes are ecological changes: declines in mussel abundance and increases in macroalgae abundance, die-offs from hypoxia, relocations of fish populations, and failure of oyster recruitment. Research goals in response to actual or expected changes include modifications of oyster fishery practices, determination of adaptation potential for marine species, determination of ecosystem resilience, and identification of more and less threatened areas of coastline.


10/5: Predator-Prey Dynamics Reveal Hidden Structure in the Sea

Dr. Kelly Benoit-Bird, Oregon State University

The average concentrations of biota in the ocean are generally low, a critical problem for ocean consumers. When we examine the biology with new tools guided by the predators themselves, we find that instead of being relatively devoid of life, the ocean is peppered with narrow hot-spots of activity. From the surface ocean to the deep sea and animals ranging from plankton and fish to squid and whales, small patches of plenty have impacts on ecosystems disproportionate to their contribution to the total biomass. These small aggregations provide the key to solving the experimentally demonstrated feeding paradox as well as providing a mechanism for evolution in an apparently isotropic environment where there are no obvious barriers to gene flow, Hutchinson’s “Paradox of Plankton”.


10/12: Conservation genetics of aquatic vertebrates: challenges and opportunities

Dr. Susana Caballero, Biological Sciences Department, Universidad de los Andes, Colombia

High genetic diversity in natural populations has been regarded as a key component to the adaptive potencial of a species, particularly under a global change scenario.  In this talk we review and explore ways to study and evaluate genetic diversity and population structure in aquatic vertebrales, particularly river dolphins, sharks and river turtles found in South America and we further investigate how results from these studies can be integrated into conservation priorization at local level.


10/19: Exploring Parts Unknown: The Biodiversity and Evolution of Sea Anemones

Dr. Meg Daly, Ohio State University

The sum of our knowledge of invertebrate biodiversity is but a drop in the ocean: not only do many species remain undocumented, but those we have named are often known only in very limited ways.  Although the magnitude of the task of documenting marine diversity is daunting, the opportunities and impact of doing so are unparalleled in terms of fundamental discovery about evolution and ecology.  Using actiniarian sea anemones as an example, I will highlight the ways in which species description, anatomical study, and genomic data can provide new perspectives on the history and function of marine systems.


10/26: Long-Term Monitoring of Environmental Stressors in NOAA’s Estuarine Research Reserves

Dr. Matthew Ferner, Research Coordinator, San Francisco Bay National Estuarine Research Reserve

We live in a world increasingly characterized by environmental change. Our response to these changes and their impacts depends on our ability to detect and understand them. Despite repeated calls from scientists and managers for more long-term environmental monitoring, adequate funding to implement such efforts is often beyond the capacity of individual research projects and agency programs. Empowered by the Coastal Zone Management Act of 1972, coastal states around the country have partnered with the National Oceanographic & Atmospheric Administration (NOAA) to support long-term environmental monitoring across a national network of Estuarine Research Reserves, including one in San Francisco Bay headquartered at the Romberg Tiburon Center. Dr. Ferner will share his perspective on this federal-state partnership and provide local and national examples of the value of long-term monitoring in estuaries. He will also highlight opportunities for scientists, students, teachers and the public to get involved in this monitoring network.



Dr. Phil McGillivary, US Coast Guard Pacific Area & Icebreaker Science Liaison

Field campaign results and future capabilities are reported for networked systems of multiple autonomous underwater vehicles (AUVs), autonomous surface vessels (ASVs), and unmanned aircraft systems (UAS) off the California and Iberian coasts, in both arctic and Antarctic ecosystems, and for coral reef ecosystems. We highlight how Integrated networks of unmanned systems provide cost-effective time series monitoring of coastal ecosystems, including response to, and recovery from short-lived coastal maritime events. A focus is on discussion of data communication technologies, methods of data archiving, and use of data analysis software to assist with real-time anomaly detection and visualization. This latter capability is critical to enabling autonomous adaptive sampling of events over appropriate temporal and spatial scales. Examples are provided of how autonomous systems integration into ocean observing systems can improve socially relevant measurements of ocean and climate dynamics.


11/9: Managing the high seas for ecological, economic and social sustainability

Dr. Rashid Sumaila, University of British Colombia
Increasingly, fishing vessels are exploiting fish on the high seas, a part of the ocean that is relatively less effectively managed. This has led to the overfishing of many economically important high seas fish stocks. For example, overall, stocks of tunas and their relatives have declined on average by 60% during the last half century. It has, therefore, recently been suggested that a possible solution is to high seas fisheries mismanagement is to close it to fishing. My talk explores the economic and equity implications of this proposal, and come to the conclusion that closing the high seas could be both catch and revenue-positive while reducing inequality in the distribution of fisheries revenues among the world’s maritime countries.


11/30: Linking sediment flux to marshes with dynamics in Bay shallows: Observations from China Camp and San Pablo Bay

Jessie Lacy, Pacific Coastal and Marine Science Center, US Geological Survey

Salt marsh provides critical estuarine habitat and shoreline protection, and is highly vulnerable to sea-level rise. Marsh resilience to sea-level rise depends on sediment supply from adjacent waters. We are investigating the influence of tides and wind waves on sediment supply to the salt marsh in China Camp State Park, adjacent to San Pablo Bay, in northern San Francisco Bay.  I will discuss two indicators of sediment supply:  suspended-sediment flux through the mouth of a narrow tidal creek traversing the marsh, and suspended-sediment concentration (SSC) over the marsh plain and adjacent mudflat. As Bay waters move into the marsh with the flooding tide, the physical processes governing suspended sediment shift, primarily due to the presence of vegetation. Waves are attenuated, and particle trapping and settling create gradients in SSC across the marsh. Understanding these processes can inform prediction of marsh resilience and priority setting in marsh restoration and conservation.

Spring 2016

3/16: Under pressure: Climate Change, Upwelling, and Eastern Boundary Upwelling Ecosystems

Marisol Garcia Reyes, Farallon Institute

Understanding how upwelling is impacted by natural and anthropogenic climate change is a vital step in maintaining a productive and healthy ecosystem in the Eastern Boundary Upwelling Ecosystems (EBUE) of the world.  In this seminar we will talk about two aspects of an interdisciplinary project that investigates the past, present and future of coastal upwelling, and how its variability impacts the ecosystem.  First, we will review how upwelling favorable winds are being impacted by climate change, from the well-known Bakun hypothesis to emerging alternative mechanisms and evidence.  Second, we will explore how, through a comparative analysis between the California and the Benguela EBUE, we can investigate global climate change impacts on upwelling ecosystems.


3/30: Good Friends: Growth and Flowering Responses of Eelgrass to Grazing by Brant Geese

Frank Shaughnessy, Department of Biological Sciences, Humboldt State University

Eelgrass makes up nearly all of the diet of brant geese on west coast of North America and there are several lines of evidence indicating that this is a coevolved plant-animal relationship. Brant could therefore affect the ability of an eelgrass bed to support juvenile crabs and rockfish. But what does the plant think about losing photosynthetic surface area to a bird? Our first experiment in Humboldt Bay, California tested the hypotheses that eelgrass growth is altered by grazing induced canopy thinning, brant feces, or the interaction between these two factors. The treatment that combined grazing (i.e. leaf clipping) and brant feces resulted in the fastest leaf growth and eventually the most flowering. The second experiment tested the hypothesis that an intermediate combination of clipping and feces would result in faster eelgrass growth relative to ‘no brant’ or ‘intense grazing’ treatments. This hypothesis was supported. Implications of this study are that, so long as brant do not damage shoot apical meristems, their grazing increases plant productivity and likely sexual reproduction, which in turn means that an eelgrass bed with brant should have a more productive detrital pathway than a bed without the bird.


4/6: Epigenetic regulation and local adaptation in marine mussels

Sean Place, Sonoma State University

Two populations of the marine mussel, Mytilus californianus, reside along the Oregon coast and experience marked differences in environmental and oceanographic conditions despite being only 65Km apart. Previous research suggests these populations experience high levels of gene flow resulting in genetically homogenous populations. As a result, it is assumed differences in physiological responses to environmental conditions are plastic and can be adjusted over time. Yet a number of studies have identified physiological differences that appear to be maintained for extended periods of time even under common garden conditions. This would suggest the potential for local adaptation exists within this broadly distributed species. In this study we used a reciprocal transplant design to examine these populations for signs of local adaptation by characterizing growth, gene expression, and global DNA methylation levels across populations. Our results indicated physiological plasticity cannot fully compensate for changes in growth conditions and that these populations may be adapted for optimal growth at the site from which they originated. These populations also displayed different levels of DNA methylation, which we postulate may provide a mechanism for local adaption to occur in these populations while maintaining genetic homogeneity.


4/20: Empowering Stakeholders and Decision Makers with Natural Capital Information

Gregg Verutes, Natural Capital Project, Stanford University

People depend on nature to sustain and fulfill human life, yet the values of nature are typically ignored in decisions. Mapping and modeling ecosystem services can help highlight the diverse benefits provided to people by nature (what and where) and explore how those benefits might change under different management options--thus bringing information about nature’s values into decisions in practical ways.  
The Natural Capital Project develops science-based approaches and tools to collaborate with decision-makers and provide the information they need to make informed development decisions while strengthening local capacity to create and use natural capital information.  Gregg will share real-life examples highlighting key methods and tools used in our coastal-marine engagements.  Case studies include statewide prioritization of nature-based adaptation strategies in coastal California, identifying areas for mangrove protection and restoration in the Ca Mau province of Vietnam, and coastal zone management in the Galapagos National Park and Marine Reserve. 

4/27 Science Talk: Tipping Points, Adaptation and Transformation in Coupled Human-Ocean Systems
Anne Salomon, School of Resource & Environmental Management, Simon Fraser University
Ecological surprises challenge science and society. While the nature and timing of abrupt changes in ecological organization and function remain poorly understood, emerging evidence points to the existence of regime shifts across a variety of ecosystems worldwide. Yet, unraveling the mechanisms governing their behavior is notoriously difficult because it requires understanding ecological and social phenomena that occur on very different scales of space and time. By way of 3 case studies, I will discuss key characteristics of coupled human-ocean systems and factors that confer their resilience to disturbance. First, research on sea otter recovery in British Columbian kelp forests has reveal evidence of abrupt changes, nonlinear trophic dynamics and the alteration of reef-wide community niches. Occupational multiplicity, experimentation and knowledge exchange offer mechanisms by which to cope with these sudden shifts. Second, recent evidence suggests that prehistoric clam gardens, intertidal rock walls built by indigenous people of the northeastern Pacific during the Holocene, increased clam production and in combination with a diversity of resource use and governance protocols, offered an adaptive strategy that enhanced food security. Finally, by reconstructing historical baselines and simultaneously assessing change in both the social and ecological resilience of the Pacific herring fishery in British Columbia, we were able to pin point sources of conflict and opportunities for governance transformation. Collectively, these case studies reveal that a diverse portfolio of use and management approaches, polycentric governance systems, and learning platforms offer a fruitful ways to enable adaptation and transformation in coupled human-ocean systems.


5/4: Near-shore Carbon Dynamics in the Context of Anthropogenic Ocean Acidification

Andreas J. Andersson, Associate Professor, Scripps Institution of Oceanography

Concerns have been raised on how near-shore marine ecosystems will be affected by ocean acidification resulting from increasing atmospheric CO2, but until recently, the influence of natural variability and processes affecting near-shore carbon chemistry have been largely overlooked. Here, I present results from a number of near-shore environments ranging from coral reefs in Bermuda to estuaries in Southern California, illustrating the dynamic and sometimes surprising nature of these environments. Observations from Bermuda demonstrate how shifts in reef biogeochemical processes towards increasing calcification and heterotrophy cause seawater acidification events. These shifts appear linked to offshore productivity and ultimately controlled by large-scale climatological and oceanographic processes. Similarly, seasonal acidification events of near-shore environments in Southern California appear strongly linked to the intensity and duration of upwelling of deep water, which ultimately is controlled by the coastal wind field and atmospheric processes. In contrast, export of estuarine waters from a salt marsh estuary in this region, partly counteracts surface seawater acidification by the addition of high loads of total alkalinity to the near-shore environment.


5/11: Moving beyond Drosophila envy: the genetics of speciation in a marine invertebrate

Suzanne Edmands, USC Dornsife College of Letters, Arts & Sciences

Most progress in speciation genetics has come through work on model systems like Drosophila, with particular emphasis on the special role of sex chromosomes.  A more comprehensive understanding will require studies of alternative systems with different sex determination mechanisms, such as those found in a wide variety of marine invertebrates, reptiles and plants. I will discuss results of breeding and molecular assays in the copepod Tigriopus californicus designed to test explicit predictions about the mechanics of speciation in the absence of sex chromosomes. This includes predictions concerning the number of incompatibilities, the level of conflict between nuclear and mitochondrial genes, the importance of sterility vs. viability problems and the cause of sex-specific hybrid dysfunction in the absence of sex chromosomes.

Fall 2015
8/26: When Integrated Taxonomy Fails to Integrate: Molecular Insights Into Morphological Character Evolution in Octocorals 
Dr. Catherine McFadden, Harvey Mudd College 
The National Science Foundation has awarded Harvey Mudd College Department of Biology Chair Cathy McFadden a $494,481 collaborative grant with the American Museum of Natural History (AMNH) to study how environmental conditions in the distant past may have affected the evolutionary development of corals and sea anemones—research that will help shed light on how current climate change endangers coral reefs and the rich sea life they support. "One of our main goals is to figure out how these groups with very different types of skeletons are related to one another," McFadden said. "Which groups evolved from others and in what order, and at what point in the past. In particular, we want to know whether the evolution of a particular type of skeleton, or the loss of a skeleton, correlated with past environmental conditions." Understanding these evolutionary relationships has proven difficult for scientists so far, because corals and sea anemones belong to one of the oldest groups of multicellular animals, believed to have evolved over 600 million years ago.

9/2: Global Change Impacts on Wetland Vulnerability to Sea Level Rise
Dr. Patrick Megonigal, Smithsonian Environmental Research Center

Coastal wetlands are economically important ecosystems that are under threat from a wide range of anthropogenic activities, all of which interact with ongoing and accelerating sea level rise. Despite the precarious geomorphological setting where these systems form, there are relatively few examples of historical marsh loss because of fascinating feedbacks between flooding, plant growth and elevation change that tend to stabilize submerging wetlands. It is unclear how these feedbacks are influenced by a host of global-scale changes that are underway. Plant productivity is a key feedback on marsh elevation that responds to rising atmospheric carbon dioxide, nitrogen availability and other global-scale changes. Such processes have been the focus of ongoing research at the Smithsonian Environmental Research Center for nearly three decades. Anthropogenic effects on sediment availability, wetland migration inland, and environmental attitudes that influence land use are all heavily influenced by human socioeconomic systems. Recent efforts to monetize the “blue” carbon sequestration capacity of tidal wetlands represents one example of how social and economic policies will ultimately shape the future of these enigmatic ecosystems.


9/9: Tree rings and Climate: The tree ring divergence problem and a proposed solution 

Dr. Zan Stine, San Francisco State University

Annual growth ring variations in Arctic trees are often used to reconstruct the temperature history of the Earth. However, in the later half of the 20th century, tree-ring estimates systematically underestimated increases in high-latitude surface temperature, a phenomenon sometimes known as "the divergence problem". At the same time, large-scale declines in sunlight reaching the Earth's surface were observed, a phenomenon known as "global dimming". In general the growth of Arctic vegetation is limited both by temperature and light availability, suggesting that variations in atmospheric transmissivity may also influence tree-ring characteristics. We show that Arctic tree-ring density is sensitive to changes in light availability across two distinct phenomena: explosive volcanic eruptions and the recent epoch of global dimming. In each case, the greatest response is found in the most light-limited regions of the Arctic. Essentially no late 20th century decline in tree-ring density relative to temperature is seen in the least light-limited regions of the Arctic. 


9/16: Achieving resilient fisheries in a dynamic world: lessons from response diversity
Dr. Elena Finkbeiner, Center for Ocean Solutions
Small-scale fisheries are critical for securing livelihoods for millions of people around the world, yet are increasingly vulnerable to external drivers of change such as globalization and climate change. There is an imminent need to redirect management goals towards facilitating resilient small-scale fisheries capable of adapting in a constantly changing world. This research explores the link between diverse and flexible access to marine resources in small-scale fisheries and the ability for fishers to adapt and respond in a changing environment. A comparative case study approach was used to explore these objectives across fishers’ and fishing cooperatives in Bahia Ulloa, Baja California Sur, Mexico, using diverse techniques, such as interviews and the collection of fisheries catch and economic data. Overall, this research suggests that with greater attention to access, equity, and participatory governance, small-scale fisheries in Mexico and beyond will be better equipped to sustain livelihoods and the environment in a changing world

9/23: Using Science to Empower Communities and Improve Marine Protected Areas in East Africa

Dr. Jennifer O’Leary, California Polytechnic University

Marine protected areas (MPAs) are an important marine management tool for conserving ecosystems and ecosystem benefits. However, globally, many MPAs are not managed using science-driven approaches, and can be at risk due to local and global threats. By addressing local threats, managers can make ecosystems more resilient to global threats such as climate change. Since the 1960s, East Africa has been ahead of many nations in establishing marine protected areas (MPAs), but has not been as effective in managing them for long-term sustainability in the face of external threats. To promote managers ability to recognize and address threats, we developed a pilot program in adaptive management for Kenyan national marine protected areas.


9/30: Sampling Uncharted Waters: Examining Longfin Smelt Rearing Habitat in Fringe Marshes of the Low Salinity Zone
Lenny Grimaldo, ICF International

Despite a rich monitoring history (> 40 years) for invertebrates and fish in the San Francisco Estuary, very little is known about how invertebrates and fish use tidal marshes along the axis of the low salinity zone.  Our study investigated the abundance and distribution of larval fish communities in fringe marshes and shallow waters of Suisun Bay (between Antioch and Benicia) that have been overlooked by the long-term monitoring programs. Larval Longfin Smelt were widely distributed in shallow waters and tidal marshes of the low salinity zone.  During some sampling periods, Longfin Smelt densities in tidal marshes were similar or higher than densities observed in the channel stations of the California Department of Fish and Wildlife Smelt Larval Survey.  In addition, most the Longfin Smelt had yolk-sacs, indicating they hatched near our sampling sites. Our study indicates that tidal marshes from the Suisun Bay area provides key rearing habitat for Longfin Smelt.  Information from our study could be used to guide future restoration in the area, design additional monitoring stations for the larval fish surveys, and understand the role of food generated within marshes to support secondary production in adjacent open waters.


10/7: Nitrogen cycling and loss in the Eastern Tropical South Pacific oxygen deficient zone
Dr. Karen Casciotti, Stanford University

The Eastern Tropical South Pacific Ocean is one of three large natural oxygen deficient zones. Nitrogen cycling in oxygen deficient zones leads to production of nitrous oxide (N2O), accumulation of nitrite, and loss of bioavailable nitrogen from the deep ocean nutrient reservoir. We use stable isotopic measurements from a series of cruises in the Eastern Tropical South Pacific Ocean to trace the balance of nitrite oxidation and reduction, which dictates how much bioavailable nitrogen is retained or lost from the region. Our analysis suggests that nitrite oxidation may play an important and largely unrecognized role in the distributions of nitrite and nitrate, as well as their isotopic values in the ocean’s oxygen deficient zones.


10/14: A Latitudinal Approach to Assess Sea-level Rise Vulnerability for Pacific Coast Tidal Wetlands
Dr. Karen Thorne, USGS Western Ecological Research Center

Climate change effects on coastal ecosystems will include rising sea levels and changes in the frequency and severity of storms.  Sea levels are projected to increase up to 167 cm by 2110 along the Pacific coast and storms may increase in frequency and magnitude, threatening the persistence of tidal marshes.  In 2012 we initiated a project that developed a standardized methodology to collect detailed ground data at 18 study sites in Washington, Oregon, and California along a latitudinal and tidal gradient. At study sites we collected local physical and biological data, including elevation, tidal inundation, salinity, vegetation composition and structure, and accretion rates to assess how sea-level rise may alter these estuaries in the future. This data was used to calibrate the Wetland Accretion Response Model for Ecosystem Resilience (WARMER) model that projects wetland elevations under sea-level rise scenarios.  This standardized approach allowed site results to be comparable across the coast but site specific enough to assist resource managers with climate change planning.  Multiple factors, including initial elevation, marsh productivity, sediment availability, and rates of sea-level rise affected marsh persistence to 2110 at all sites. Model results showed that sea-level rise vulnerability varied across the Pacific coast estuaries and was driven by local accretion rates, climate and the extent of anthropogenic modification of the estuary. Our models suggests that most tidal wetland study sites have resiliency to sea-level rise over the next 50-70 years, but that sea level will eventually outpace marsh accretion by 2110. Results from stakeholder workshops will also be presented.


10/21: Molecular Diagnostics of Marine Ecosystem Health
Dr. Sara Edge, AMEGEN Consulting

Given the ecological and economic importance of marine ecosystems, a better understanding is needed regarding how organisms respond to toxicants, how toxicants interact with other stressors, and on what scales they most significantly impact marine health. My research integrates genomic analyses, laboratory and field studies to address ecological and biochemical questions related to marine invertebrate and ecosystem health. I identify molecular mechanisms associated with stress or toxicity exposures that can identify routes of toxicity, measure susceptibility, and enable predictions of exposure thresholds. A major focus of this research has been in the transcriptional changes of symbiotic corals and sponges associated with exposure to toxicants such as oil, dispersants and pesticides. This lecture will provide a unique perspective on the stress responses of corals by focusing on the use of genetic and molecular technology borrowed from the field of human diagnostics. Ultimately this can improve our ability to predict how corals will respond to increasing anthropogenic threats and environmental challenges leading to more accurate forecasts of reef health.


12/7: Learning to observe ecology - quantifying processes in coastal ecosystems

Dr. Steven Litvin, Research Coordinator, Marine Life Observatory Program, Hopkins Marine Station

Coastal habitats along the California Current Ecosystems often experience inundations of upwelled waters that are low dissolved oxygen and pH. These events have the potential to influence the structure and function of coastal ecosystems. The ecological consequences of environmental drivers in these systems will be mediated by physiological thresholds and behavioral responses of resident organisms in the context of the spatial and temporal variability of DO, pH and other potential stressors.  I will present two projects supported by the Marine Life Observatory program at the Hopkins Marine Station that address these questions using a novel mix of in-situ monitoring, laboratory experiments and modeling approaches: 1) How physiological limits and in-situ variability in dissolved oxygen impact the behavior and ecology of rockfish and 2) A framework to estimate impact of environmental and local anthropogenic stressors (fishing) on population dynamics of abalone.


Spring 2015

1/28: The Biomechanics and Physiological Ecology of Ram-feeding Marine Vertebrates
Jeremy Goldbogen, Hopkins Marine Station, Stanford University
Gigantic ram filter feeders have evolved independently in several lineages of bony fishes, birds, sharks, and whales, but the physiological mechanisms of this feeding mode are virtually unknown. Here I present an integrated approach towards understanding the biomechanics and physiological ecology of ram feeding in the world’s largest whales, with an emphasis on the scaling of feeding performance and the energetic limits to extreme body size.


2/18: The biogeochemical cycling of iron in the ocean: insights from marine particles
Phoebe Lam, UC Santa Cruz
Particulate iron is a significant fraction of the total iron pool in the ocean, usually accounting for at least a third and often the majority of the total iron pool.  Most iron studies to date have focused on the dissolved iron fraction, but studying the particulate iron fraction has the advantage of providing insight on its source and internal cycling through its mineralogy. Here I describe the use of synchrotron x-ray techniques to determine the chemical speciation of marine particulate iron, and the implications for source, internal cycling, and bioavailability of iron.

2/25: Diverse physiological roles of proton pumps in marine organisms 
Martin Tresguerres, Scripps Institution of Oceanography, UC San Diego
Vacuolar H+-ATPase is an evolutionarily conserved enzyme that "pumps" protons into vesicles or from cells into internal fluids or out to the external environment (hence its common name, "proton pump"). Depending on the cell type, its intracellular localization, and its functional association with other proteins, proton pumps may be involved in diverse physiological functions. This presentation will discuss some recently established roles of proton pumps in pH regulation in shark gills, carbon concentrating mechanisms and bio-mineralization in corals, bio-demineralization in deep sea bone-eating worms, and water and solute transport across the intestine of bony fish. 

3/4: Species-specific responses of juvenile rockfish to ocean acidification
Cheryl Logan, CSU Monterey Bay
The North American west coast provides a natural experimental system for testing the effects of ocean acidification on marine organisms. Congeners with varying exposures to acidic waters during spring upwelling may have different physiological tolerances. Rockfish (Sebastes spp.) provide an excellent comparative study system comprising >100 species with diverse life history traits and niches. We compared physiological and gene expression differences between juvenile winter- and spring- spawning rockfish, blue (Sebastes mystinus) and copper rockfish (S. caurinus), respectively, after chronic exposure to four pCO2 treatments. Copper rockfish exhibited a decrease in critical swimming speeds and aerobic scope at the highest pCO2 treatment, whereas blue rockfish showed no significant response. RNAseq transcriptome analyses of muscle tissue from the same individuals showed that the species exhibit divergent gene regulation strategies for coping with high pCO2. Among pCO2 treatments, each species had 100s of differentially expressed genes, but fewer than 20 were common to both species. Transcriptome profiles of physiologically tolerant rockfish may help explain the mechanistic basis underlying their increased ability to compensate against the effects of elevated pCO2. Our study highlights the need for integrative comparative studies for assessing the adaptive capacity of fishes in responding to ocean acidification.  

3/11: An interdisciplinary study of fish mortality events in the intermittent Pescadero estuary 

Chandra Richards, UC Berkeley
Pescadero Natural Marsh Preserve is an extensive marshland ecosystem and complex intermittent estuary located along the Pacific coast of California. The estuary experiences physical separation from the ocean (closed state) and later reconnects with the ocean (open state), so it is susceptible to fluctuations in sulfur (S) oxidation state and concentration, salinity, biogeochemical conditions, sedimentation, and hydrologic regimes. Die-offs of federally protected and threatened steelhead trout have drastically increased near-annually since 1995, occurring unexpectedly with the first breach of the sandbar closure, and have been more regular in Pescadero than in other nearby California estuaries. Culminating in an interdisciplinary study of physical, biological, and geochemical interactions, this review seeks to understand the estuarine influences impacting fish die-offs, specifically physical dynamics, biological responses, and watershed processes. It will also include an analysis of Pescadero’s current state in predicting if mitigation practices will reduce and eliminate recurring die-offs and restore the watershed to pre-existing wetland conditions.

4/15 Public Forum: Deep-Ocean Industrialization and Biodiversity Challenges in the 21st Century
Lisa Levin, Scripps Institution of Oceanography, UC San Diego
One of the greatest challenges of the 21st century is managing our deep ocean sustainably, for it is vast, remote, difficult to access, and highly vulnerable to increasing human disturbance and changing environmental conditions. Advanced technology and our increasing need for food, energy and raw materials is creating a growing demand for deep-sea resources. It is also driving our increasing abilities to extract them from greater depths. The deep ocean covers two thirds of our planet and provides key ecosystem services, including those that drive global biogeochemical cycles that sustain virtually all life in the sea. Using the wealth of the deep ocean sustainably and wisely for human benefit while conserving its unique attributes, including its biological diversity and the key ecosystem functions and services it provides, will require public awareness and appreciation of deep-sea ecosystems, as well as new cross-disciplinary conversation and interdisciplinary research.

4/22: Coping with toxic foods:  using transcriptomics to investigate the effect of Alexandrium fundyense on the physiology of a marine copepod
Petra H. Lenz, Pacific Biosciences Research Center, University of Hawaii at Manoa
Large herbivorous calanoid copepods such as Calanus finmarchicus are important links in pelagic communities, consuming phytoplankton and being preyed upon by many invertebrate and vertebrate pelagic species. Increases in ambient temperatures and changes in the phytoplankton dynamics have raised questions regarding this species’ physiological response to a changed environment.  However, C. finmarchicus inhabits a 3-dimensional space spanning thousands of kilometers horizontally and a kilometer in depth across the open ocean, rendering it relatively inaccessible for studies its physiological ecology across habitat, season, climate (decadal oscillations, global climate change) and other environmental factors.  Transcriptomics offers a new approach to obtaining physiological data, and next-generation sequencing has opened opportunities for developing genomic resources for non-model species that are of biological and economic interest, but which lack reference genomes.  Among environmental stressors that could impact species like C. finmarchicus are harmful algal blooms.  These are predicted to increase in frequency and magnitude potentially leading to major changes in herbivore communities.  Harmful algal blooms do not appear to be lethal to copepods, however little is known about their effect on copepod physiology and overall fitness.  In the Gulf of Maine, red tides, caused by blooms of the dinoflagellate, Alexandrium fundyense, are of particular concern.  In feeding experiments using naturally occurring concentrations of A. fundyense, survival of copepods in the experimental group did not differ from controls. Nevertheless, evidence of physiological impact was apparent in reduced egg-production and hatch-success rates.  Using global gene expression, biological processes responsive to the alga were identified at both low and high exposure to A. fundyense. The results suggest that C. finmarchicus exposed to even low doses of the dinoflagellate show broad physiological responses beyond what have been readily observed previously.

5/13: Differential sensitivity of coccolithophore species to OA gives insight to future changes in their community structure
Magdalena Gutowska, MBARI & GEOMAR
It has recently been proposed that coccolithophore species were differentially affected by environmental changes over the Paleocene-Eocene Thermal Maximum (PETM). Based on coccolithophore cell geometry, Gibbs et al. (2013) concluded C. pelagicus showed indications of slower reproduction during this period of rapid ocean warming and acidification. It is suggested that this is indicative of its limited physiological ability to adapt. In light of anthropogenically induced changes in the future ocean, a deeper understanding of the variability underlying coccolithophore responses is important. The work I’ll be discussing examines calcification rates as well as changes in coccolith morphology in the Coccolithales species Coccolithus pelagicus ssp. braarudii (strain PLY182g) over a broad pCO2 range (55 to 4500 µatm). Evidence now exists from both the paleorecord, as well as from physiological studies, that a restructuring of coccolithophore communities can be expected in the future due to the differential sensitivity of key species to rapid environmental change. This information needs to be considered when modeling future changes in carbonate production and export by phytoplankton

The Seminar Series is supported by generous contributions from the Barbara and Richard M. Rosenberg Institute at the Romberg Tiburon Center, San Francisco State University
Back to RTC Home page



SF State Home