EOS Center

Bob Bowers, Research Scientist, LBNL, Joint Genome Institute  

Applying single cell genomics to microbial communities at the JGI

Abstract: This seminar traces my journey to the DOE Joint Genome Institute, highlighting how microbial diversity has shaped my research, from algal genomics and airborne microbial ecology to lowbiomass communities and viral detection. I’ll describe my role in JGI’s singlecell and metagenome groups, including bioinformatics user support, then delve into two case studies: coniferneedle phyllosphere microbiomes and untargeted singlecell sequencing at Dewar Creek hot spring. Finally, I’ll showcase R&D on Primary Template Amplification and Atrandi SPC microfluidics for massively parallel singlecell workflows, including an upcoming application to resolve novel microbial populations across groundwater temperature and sulfur gradients at Henry Coe State Park. 

Bio: Robert (Bob) Bowers is a Research Scientist at the Joint Genome Institute (Berkeley, CA). As a microbiologist, his interests span microbial genomics and evolution, community ecology, and host–microbe interactions. His career has ranged from algal genomics and viral detection strategies for human and animal viruses to highthroughput microbial ecology leveraging cuttingedge sequencing platforms and bioinformatics. Most recently, he’s focused on singlecell approaches to recover more complete microbial genomes, including their mobile genetic elements and potential symbionts from diverse environmental samples. 

Roxanne Beltran, Assistant Professor of Ecology and Evolutionary Biology, University of
California, Santa Cruz

Unraveling individual and environmental drivers of life history trait variation in long-lived vertebrates

Abstract: Environmental variation across temporal and spatial scales shapes individual differences in traits and causes resource acquisition and allocation to fluctuate dramatically. Technological advancements including animal-borne sensors have ushered in a research renaissance showing that differences across individual animals are much more common than previously recognized. Despite this progress, critical knowledge gaps remain regarding the drivers and impacts of trait variation in wild animals - what are the secrets to individual fitness that translate to population persistence in wildlife? I investigate the ecological and evolutionary underpinnings of individual variation in elephant seals - a species that has rebounded from near extinction. I combine mark-recapture methods with cutting-edge biologging to test and refine ecological theories by identifying the physiological, anatomical, behavioral, phenological, and life-history traits shaped by developmental stages and environmental conditions. In this talk, I will highlight how my lab group’s research advances the understanding of individual-environment interactions and their impacts on populations and communities. I will also discuss future research directions, including the importance of comprehensive trait data collection and collaboration. Finally, I will underscore how integrating long-term ecological research with inclusive, field-based education programs can foster scientific discovery and promote equity in STEM. 

Bio: Dr. Roxanne Beltran is an assistant professor of Ecology and Evolutionary Biology at the University of California, Santa Cruz. She studies species interactions and global change in the open ocean, through the lens of marine mammal movement, behavior, and demography. Her research leverages the six-decade mark-recapture program of northern elephant seals at Año Nuevo in California along with environmental and biologging data to understand the role of among-individual variation in ecological patterns and evolutionary processes. Roxanne’s lab group integrates research with education activities to foster a highly collaborative community of undergraduate and graduate students, technicians, and postdoctoral researchers. She also advocates for diversity, equity, and inclusion in STEM - particularly in field settings - by undertaking and implementing research on education equity. 

Dan Okamoto, Assistant Professor, University of California, Berkeley

Addressing climate change and spatial structure in temperate nearshore ecosystems  

Abstract: Nearshore marine ecosystems are among the most productive ecosystems on the planet, host diverse assemblages of ecologically, economically, and culturally important species, and also lie on the front lines of climate change. Yet like many ecosystems, classic models of organismal and ecological dynamics have often underpredicted effects of harvest and climate on both ecosystems and people. I will present recent work showing how measuring and modeling processes such as energetic plasticity, acclimatization, consumer-resource dynamics, and metapopulation structure can substantially improve our understanding of how individuals, populations, and ecosystems respond to climate change and harvest for the benefit of people.  

Bio: Dan Okamoto is an assistant professor in the Department of Integrative Biology at the UC, Berkeley.  He is a statistician, modeler, and field ecologist.  His group studies how trophic interactions, climate, and fishing affect dynamics of populations and communities, especially species like sea urchins, kelp, abalone, and forage fish. He enjoys working with communities and managers to improve fisheries and conservation. He received his PhD from UCSB, an MSc from the University of Alaska Fairbanks, a BS from the University of Washington, and worked as a post-doctoral researcher at Simon Fraser University, the Hakai Institute and at Florida State University. 

Allison Moreno, Assistant Professor, University of California, Santa Cruz 

Southern California Respiration Quotient Controls 

Abstract: Southern California Bight coastal waters are dynamic and strongly influenced by a changing climate. An increased respiration quotient has been found during high temperature and low nitrogen conditions. These observations are specific to open ocean conditions, and their applicability to coastal environments is uncertain. To disentangle the controlling factors in a coastal environment, we examined environmental conditions, particulate organic matter, and the respiration quotient over five years in the Southern California Bight. Our study revealed clear seasonal variation in environmental conditions and biological parameters. We detected higher than previously reported respiration quotient ratios. We found a strong inverse relationship between respiration quotient, nitrate and chlorophyll. Our findings also suggest that changes in community structure, triggered by nutrient shifts and a local oil spill, affected the range in respiration quotient and explains some of the variability measured. Coastal environments are more complicated than open ocean measurements, with wider implications.  

Bio: An Assistant Professor at UC Santa Cruz. My journey is simple on paper but complex and I would have it no other way. I love complexity, which is why my lab focuses on marine biogeochemistry and its connection to deoxygenation and climate. Although my lab is just starting it is a trifecta- lab work, being out in the field, and hanging with our computers modeling new ideas. At the center of all we do is the respiration quotient and phytoplankton physiology. Everywhere I go, I come with my life experiences and am who I am- a scientist and bold Chicana.  

Susanna Theroux, Principal Scientist, Southern California Coastal Water Research Project (SCCWRP) 

Are we there yet? Advancing DNA methods for informing environmental management and policy 

Abstract: Environmental DNA (eDNA) methods are revolutionizing the way we monitor biodiversity in California. However, the adoption of eDNA methods for informing environmental management decision-making has been slowed by a lack of standardization among researchers and poor communication with user communities. To help expediate the transition from research to implementation, we initiated a series of studies to bring the gap between eDNA researchers and environmental managers. These studies ranged across a diversity of habitats and management concerns, from harmful algal blooms to endangered Southern California steelhead. This presentation will review the myriad of successes and obstacles faced when operationalizing a novel tool for routine applications and will highlight future directions for advancing the adoption of eDNA methods. 

Bio: Susie Theroux is a Principal Scientist at the Southern California Coastal Water Research Project (SCCWRP) where she leads the environmental DNA (eDNA) research program. Dr. Theroux specializes in developing molecular methods for biomonitoring and bioassessment and leads the California Water Quality Monitoring Council’s Molecular Methods Workgroup. Prior to joining SCCWRP, Dr. Theroux was a postdoctoral fellow at the Department of Energy’s Joint Genome Institute and received her doctorate from Brown University and the Woods Hole Marine Biological Laboratory.  

Wim Kimmerer, Adjunct Professor Emeritus, EOS Center, SFSU

Apparent competition among four copepod species in the San Francisco Estuary, an estuarine food desert 

Abstract: The San Francisco Estuary (SFE) is home to nine copepod species, most introduced 3-4 decades ago. We analyzed potential interactions among four of these introduced species that are abundant during spring-summer in the Low-Salinity Zone (LSZ), the rearing habitat for larval delta and longfin smelt. Since 1987, grazing by the introduced clam Potamocorbula amurensis reduced summer phytoplankton biomass and productivity in the LSZby ~10-fold. The resulting chronic food limitation, together with consumption of copepod nauplii by clams, restricted copepod abundance to low levels during summer of every year since 1987, and produced a “food desert” for young smelt. Eurytemora carolleeae, introduced to the Estuary before monitoring began, was highly abundant year-round in the LSZ until it declined sharply in 1987, and it is now abundant only in spring. The other three copepod species are subtropical and most abundant during summer: Pseudodiaptomus forbesi (detected in 1988) at salinity less than ~2, and Limnoithona tetraspina (1993) and its predator Acartiella sinensis (1993)in salinity of 0.5–10. Since 1993 abundance patterns of these four copepods overlap in season and salinity, superficially suggesting competition. However, this is a case of “apparent competition”, because competition for food is ruled out by the distinct diets and incomplete spatial overlap among the four species. Rather, abundance of each species is influenced by a combination of temperature, freshwater flow, feeding by clams on microplankton and copepod nauplii, and predation. The ability of estuarine copepod species to co-occur may generally be explained better by considering the broader hydrodynamic, thermal, and predatory environment than by competition. 

Bio: Dr. Wim Kimmerer is a Research Professor of Biology (Emeritus) at the Estuary and Ocean Science Center of San Francisco State University. He has a Bachelor’s degree in chemistry from Purdue University and a Ph.D. in biological oceanography from the University of Hawaii. Previous positions include a stint in U.S. Navy nuclear submarines, a three-year fellowship at the University of Melbourne, Australia, and a position at a consulting firm in central California. In 1994 he established a zooplankton laboratory at the EOS Center focused mainly on the San Francisco Estuary, studying both the basic ecology of zooplankton and fishes in the estuary, and management concerns such as the maintenance of declining and listed species and the influence of human activities. Current focuses of the laboratory include interactions between physical dynamics of the Estuary and the distribution and dynamics of planktonic organisms, the planktonic food web effects of introduced species, and effects of variation in freshwater flow on fishes, particularly the endangered longfin smelt. He is Principal Investigator of several large projects in the Estuary, including a study of the dynamics of longfin smelt, temporal transitions among a suite of introduced estuarine copepods, and a study of copepod movements into and out of a large tidal wetland. He served as Co-founder and later President of the California Estuarine Research Society, Chair of the Estuarine Ecology Team, Interagency Ecological Program (1995–2015), Co-Chair of the Science Board, CALFED Bay-Delta Ecosystem Restoration Program, and Science Advisor to the San Francisco Bay Subtidal Habitat Goals Project. In 2012 he received the Brown-Nichols Science Award presented by the Delta Science Program for significant research and application of science to manage the estuary, and in 2013 received the Conservation Achievement Award from the Cal-Neva Chapter of the American Fisheries Society. He is a Fellow of the California Academy of Sciences.

Zachary Gold, Lead Molecular Ecologist - Ocean Molecular Ecology Program, NOAA Pacific Marine Environmental Laboratory

Leveraging eDNA to Survey Large Marine Ecosystems in the Northeast Pacific

Abstract: Environmental DNA (eDNA) is a powerful, cost effective, and scalable tool enhancing marine ecosystem monitoring programs across NOAA. This talk highlights our progress operationalizing eDNA approaches at scale across the West Coast Ocean Acidification, Ecosystem Fisheries Oceanography Coordinated Investigations (EcoFOCI), and California Cooperative Oceanic Fisheries Investigation (CalCOFI) cruises to generated robust marine biodiversity inventories co-located with high resolution physical and chemical hydrographic measurements. Our work highlights the power of eDNA approaches to better characterize marine ecosystem shifts across key environmental thresholds. Critical to enhancing these efforts are the integration and synthesis of eDNA data sets across ocean observing platforms being led by the West Coast Ocean Biomolecular Observation Network. Ultimately, rigorous adherence to open science principles and wide spread adoption of standards and best practices are critical to effectively mobilize trusted biomolecular observations of marine biodiversity. Such efforts directly support the National Aquatic eDNA and National Ocean Biodiversity Strategies. 

Bio: Dr. Zachary Gold is the Ocean Molecular Ecology Program Lead at the NOAA Pacific Marine Environmental Laboratory in Seattle. His research seeks to leverage the advances in molecular biology to scale biological analyses with physical and chemical processes and allow for characterization of marine ecosystems response to climate change.  

Sarah Cohen – Coastal Estuarine Population Connectivity and Environmental Stress

Julie Gonzalez – Towards More Holistic Conservation and Restoration Approaches

Ellen Hines – Bycatch Risk Assessment for Chilean Fisheries and Marine Mammals with Varying Data

Michelle Jungbluth and Sean Jungbluth – Marine and Estuarine (Zoo)plankton Ecology

Wim Kimmerer – Density Dependence in Pelagic Estuarine Populations

Stuart Siegel – Nature-Based Shoreline Protection Along the Mid and Upper Intertidal

Anne Simonis – You Can Learn a Lot by Listening…

Frances Wilkerson – Nutrients, Phytoplankton, HABs and Primary Productivity

Jaime Jahncke, PhD, Director, California Current Group, Point Blue Conservation Science and Adjunct Professor at San Francisco State University’s Estuary & Ocean Science Center

From Peru to California: How ocean processes influence prey and predator abundance in coastal areas? 

Abstract: This presentation examines the interplay between ocean processes and the abundance of prey and predators in coastal ecosystems, with a focus on regions in Peru and California. The talk explores how physical oceanographic processes influence prey availability and seabird distribution, highlighting findings from long-term studies on seabird diet, foraging ecology, and ecosystem dynamics. The work of Point Blue Conservation Science, particularly at the Farallon Islands and within the Greater Gulf of the Farallones, is showcased as a model for understanding and addressing environmental challenges. Research emphasizes the impacts of climate change, marine heatwaves, urban pollution, and human activities on marine biodiversity and ecosystem health. Dr. Jahncke also discusses innovative approaches, including automated surveys, drones, and machine learning, to enhance data collection and analysis. The talk concludes with a call for collaborative, science-based strategies to advance ocean conservation and build resilience in the face of climate and human pressures. 

Bio: Dr. Jaime Jahncke is the Director of the California Current Group at Point Blue Conservation Science and an Adjunct Professor at San Francisco State University’s Estuary & Ocean Science Center. With over 30 years of experience in marine bio-oceanography, Jaime’s work focuses on understanding and conserving marine wildlife and ecosystems. He collaborates with diverse partners to develop science-based solutions for ocean resilience, sustainable fisheries, and biodiversity conservation. Committed to advancing equitable and innovative approaches, Jaime strives to integrate research, policy, and community engagement to protect marine habitats and support coastal communities.