seminar

Sarah Goodnight, Ecologist/Postdoctoral Fellow, Smithsonian Environmental Research Center

Cross-habitat detection and monitoring of marine invertebrate invasions in California: a 12-year synthesis 

Abstract: California’s estuaries are hotspots of species invasions due to high commercial and recreational activity, which vector nonindigenous species (NIS) into vulnerable nearshore ecosystems. Comprehensive monitoring across habitats is critical for detecting new introductions and evaluating the impacts of NIS on native communities. This talk presents data from a long-term monitoring program conducted by the Smithsonian Environmental Research Center (SERC) and Moss Landing Marine Lab (MLML) in collaboration with California’s Department of Fish and Wildlife (CDFW) that aims to detect invertebrate invasions in California’s estuaries and evaluate geographic patterns in NIS community structure and overall prevalence. Using these data, we report novel NIS detections in California from the past 12 years, examine the key vectors driving these introductions, and determine which habitats are reservoirs of NIS across the state. We also investigate native vs. NIS community structure and patterns of diversity across spatial and temporal scales.  

Bio: Sarah is a postdoctoral ecologist at the Smithsonian Environmental Research Center (SERC) who is interested in leveraging non-indigenous species (NIS) monitoring data to examine how NIS community structure varies across different environments and spatial scales, and how NIS presence impacts native diversity. Prior to her work at SERC, Sarah completed a postdoc at George Mason University and her PhD at Florida Atlantic University, where her research focused on interactions between hosts and their native and invasive parasites. She specializes in invertebrates in her research (but has a soft spot for amphibians).  

Abreanna Gomes, Senior Natural Resource Coordinator with the Kashia Pomo Band of Pomo Indians

Marine Monitoring and Restoration of the Kashia Coastline

Abstract: As a member of the Tribal Marine Stewards Network (TMSN), Kashia Band of Pomo Indians (KBPI) is among an alliance of Tribal Nations reclaiming our right to manage and steward ocean and coastal territories. Returning management to Tribes ensures indigenous knowledge drives decision-making, resulting in healthy and viable communities and ecosystems for future generations. Today Kashia people steward the ocean, engaging in multiple marine monitoring and restoration efforts throughout the Sonoma County coast. Current activities include 3D habitat mapping of the rocky intertidal using high resolution imagery, monthly marine biotoxin monitoring for Tribal shellfish consumption, monthly beach watch surveys and annual kelp mapping. Kashia is also conducting a seaweed tending project to monitor the impact of traditional harvesting practices. Among other activities includes pursuing the development of an Aquaculture Farm and Restoration Center and a Kashia Dive Team.

Bio: Abreanna Gomes, a Kashia Tribal member, graduated from the University of California Davis with a B.S in Environmental Science and Management and a minor in Native American Studies. She has been working with the Kashia Department of Environmental Planning and Natural Resources (KDEPNR) since 2016, first as a Water Resource Technician and later as the Senior Natural Resources Coordinator. She has in the field experience monitoring Tribal lands and natural resources in both upland and coastal habitats. In recent years she has helped build and manage many of the Tribe’s coastal monitoring programs and youth programming opportunities. She maintains a FAA remote pilot certificate, which is used to conduct annual kelp drone surveys to assess current conditions of kelp beds and monitor kelp growth and recovery. She is in charge of coordinating much of KDEPNR’s fieldwork. 

Alex Braud, Coastal Geospatial Scientist, San Francisco Estuary Institute

Mapping Resilience: How Better Data Supports Nature-Based Solutions

Abstract: Regional, accurate, and repeatable data are foundational to science-based coastal planning. San Francisco Bay faces mounting pressure from sea level rise, and understanding where nature-based solutions can work and how well requires knowing where coastal habitats exist, how they're distributed across the tidal frame, and how they're changing over time. Elevation relative to the tides controls habitat type and drives sediment dynamics, making it a key variable for assessing marsh condition, sea level rise vulnerability, and restoration potential. This talk covers ongoing work at SFEI to build and continuously improve Bay-wide geospatial datasets and tools that support regional monitoring programs and resilience metrics designed to inform decisions across a range of scales and applications, from project prioritization and restoration tracking to shoreline planning. Topics include automated habitat mapping, a multi-agency lidar coalition, and satellite-derived intertidal elevation mapping that integrates imagery with local water level data. 

Bio: Alex Braud is a Coastal Geospatial Scientist at the San Francisco Estuary Institute, where he works at the intersection of coastal science, geospatial analysis, and resilience planning for San Francisco Bay. He develops remote sensing and modeling tools to monitor wetland change, sediment dynamics, and shoreline resilience, while contributing to the science-policy interface that drives coastal adaptation decisions. Alex holds master's degrees in Environmental Studies and Public Administration from the College of Charleston and bachelor's degrees in Geography and Disaster Science from LSU. He previously served as a NOAA Coastal Management Fellow at the SF Bay Conservation and Development Commission. 

Paula Pappalardo, Biologist - Data Scientist, Smithsonian Environmental Research Center

Using metabarcoding to detect species of concern

Abstract: Accurate species identification is critical for biodiversity research and conservation. Early detection is especially important for invasive species management, particularly in marine systems where eradication after establishment is rarely feasible. DNA metabarcoding provides a powerful and scalable approach for surveying communities and detecting non-native species at sentinel sites. However, uncertainty in taxonomic assignment and interpretation of metabarcoding signals can lead to false positive detections, with potentially serious consequences for managers and stakeholders. In this talk, I will discuss how sampling design influences non-native species detection, approaches to optimize taxonomic assignment, and methods for assessing confidence in species identifications derived from metabarcoding data. 

Bio: Paula is an ecologist at the Smithsonian Environmental Research Center who works on identifying invasive species from biodiversity surveys using metabarcoding and eDNA techniques. Her research focuses on biodiversity assessment in estuarine and marine systems, synthesizing data on species traits, distributions, and environmental conditions to understand the processes shaping biodiversity. Paula enjoys collaborative, multidisciplinary research and develops analytical methods and tools related to her work.

Christopher Francis, Professor of Earth System Science & Oceans, Stanford University

Dynamics and Activity of Ammonia-Oxidizing Archaea Blooms in South San Francisco Bay 

Abstract: Ammonia-oxidizing archaea (AOA) play a critical role in the biogeochemical cycling of nitrogen in estuaries, including San Francisco Bay (SFB). Based on metagenomic and 16S rRNA gene amplicon sequencing, we observed massive AOA ‘blooms’ in South SFB, which account for >20% of the overall microbial community and co-occur with weeks of high nitrite concentrations. We also observed pronounced nitrite peaks occurring in the autumn for 7 of the last 9 years, suggesting that seasonal AOA blooms are common in South SFB. To elucidate the dynamics and activity of nitrifying microorganisms over the course of an AOA bloom, we measured nitrification rates, quantified AOA abundance, and analyzed both metagenomic and metatranscriptomic data during the autumn of 2018 and seasonally throughout 2019. Overall, our work reveals that AOA are not only abundant but also highly active during blooms, oxidizing large amounts of ammonia to nitrite—a key intermediate in the microbial nitrogen cycle. 

Bio: Christopher Francis received his Ph.D. from Scripps Institution of Oceanography before moving to Princeton University, where he was a postdoctoral fellow in microbial biology and geosciences working with Dr. Bess Ward. In 2003, Dr. Francis joined Stanford University where he is currently a Professor in the Department of Earth System Science as well as the new Oceans Department where he serves as Associate Chair. His research program is focused on the molecular, genomic, biogeochemical, and ecological aspects of the microbial cycling of nitrogen, with particular emphasis on coastal and estuarine systems, including San Francisco Bay, Elkhorn Slough, and Monterey Bay. 

Jan Walker, Senior Ecologist, Southern California Coastal Water Research Project (SCCWRP)   

Monitoring for management: A modular, ecosystem function-based assessment framework for estuarine condition 

Abstract: The California Estuary Monitoring Program (CalEMP) is an ongoing, statewide effort to assess the quality and condition of California estuaries by leveraging regional and local monitoring programs and projects. The program is designed to evaluate estuarine health and condition using a standardized, comprehensive, function-based assessment framework. Building an estuarine assessment program around a modular, function-based framework addresses several key challenges to large scale monitoring, such as comparability across heterogeneous environments and differing management needs. A function-based approach provides a way to accommodate different estuary types and assimilate data from diverse monitoring programs. The modular nature of the approach provides flexibility for implementing agencies to address both local and regional needs concurrently, thereby encouraging broad adoption. Program partners have collaboratively developed assessment frameworks, standardized monitoring protocols, data structures, and quality control measures to ensure consistency and comparability across projects and sites. 

Bio: Jan Walker is an estuarine and coastal ecologist at the Southern California Coastal Water Research Project (SCCWRP). She specializes in developing assessment tools and programs for coastal ecosystems, specifically estuaries, beaches, and dunes. Over the last decade, she’s been focusing on developing condition assessment tools for estuaries and other marine habitats, as well as causal assessment methodologies to identify and predict potential stressors to these ecosystems. Currently, she is building a binational, state, and regional monitoring program for estuaries in California and Baja California, Mexico.  

Prior to SCCWRP, she received her B.S. in environmental science at the University of Virginia and her Ph.D. in marine ecology from the joint doctoral program at University of California, Davis and San Diego State University. 

Sophie George, Faculty Fellow, University of Washington; Professor Emerita, Georgia Southern University

Simulated and natural Marine Heatwaves affect multidimensional trait space of  Pisaster ochraceus (Echinodermata: Asteroidea) larvae 

Abstract: Marine heatwaves (MHWs) periods of exceptionally warm temperatures are becoming a huge concern in the Pacific Northwest due to devastating consequences on marine invertebrates. They are linked to sea star wasting disease the cause of massive declines in Pisaster ochraceus in the region. This study documents the characteristics of MHWs at Friday Harbor in the Pacific Northwest and assesses their effects on larval morphology. In 2024, sevenMHWs were detected in the San Juan Channel at Friday Harbor; two severe, one strong, and four moderate.  Simulated and natural MHWs accelerated development and led to distinct larval morphologies. MHW larvae were longer and wider with longer and narrower stomachs while controls were longer and narrower with rounder stomachs. Seven and 40-day MHWs led to significant morphological heterogeneity in multidimensional space at the end of simulated MHWs and during and after natural MHWs indicating high sensitivity to unstable environmental conditions.

Bio: Sophie George obtained her PhD at the University of Paris in Biological oceanography.  She was a postdoctoral fellow at Friday Harbor Laboratories, University of Washington and at Harbor Branch Oceanographic Institution at Fort Pierce, Florida. She taught at Georgia Southern University for over 25 years and spent 6 years as a program director at NSF. She has mentored 95 students including 17 REU students. She is currently investigating the effects of marine heatwaves on the morphology and swimming behavior of several echinoderm larvae including the sea star Pisaster ochraceus. She co-Chair’s the Marine Star Specialist Group, International Union for the Conservation of Nature. 

Durrell Kapan, Senior Research Fellow, Entomology and Center for Comparative Genomics, Cal Academy  

From collections to regeneration the Xerces/Silvery Blue project

Abstract: Biodiversity is in crisis, and insects–key architects of ecosystem function–are declining rapidly. This talk tells a San Francisco story that begins with loss: the extinction of the Xerces blue butterfly, widely regarded as the first North American invertebrate driven extinct by human-caused habitat destruction. It then pivots to hope, showing how museum collections can become engines for regeneration. Using the California Academy of Sciences’ collections, ancient DNA, and ecological modeling, we asked: What was Xerces, what was its ecological “job,” and what species could serve as its avatar in restored habitats? Genomic comparisons with its closest living relative, the Silvery Blue, combined with host-plant, habitat, and climate data, pointed us to cool, foggy coastal Monterey County populations as the best surrogate. I’ll share updates from a translocation program moving these Silvery Blues to restored dunes in San Francisco’s Presidio, where partners and volunteers who help release and track butterflies have documented egg-laying, survival, and local emergence. 

Bio: Durrell D. Kapan, Ph.D. is an evolutionary ecologist at the California Academy of Sciences Institute for Biodiversity Science and Sustainability. His research integrates insect genomics, population genetics, and data science to understand biodiversity patterns, resilience, and conservation outcomes. He works across scales—from museum collections and genomic datasets to field surveys and ecological modeling—and collaborates with partners spanning NGOs and state and federal agencies. Durrell also mentors undergraduate and graduate students and helps translate research into on-the-ground restoration and decision support for biodiversity and climate resilience. 

Laura Guertin, Distinguished Professor of Earth Sciences, Penn State Brandywine  

Stories of communicating scientific ocean drilling, from text to textiles 

Abstract: Tales of adventures at sea are disseminated in the popular press (social media, magazines, books, etc.), while the completed analyses of deep-sea samples are published in scholarly reports and peer-reviewed journals. This presentation will highlight specific examples of how scientific ocean drilling expeditions have been shared from historic oceanographic expeditions and the more recent IODP Expedition 390. This presentation will include audio/video clips, select quilts from the Stories of the South Atlantic quilt collection, and why it is important for all scientists to be storytellers of their work.  

Bio: Distinguished Professor Laura Guertin (Penn State Brandywine) holds a Ph.D. in Marine Geology & Geophysics from the University of Miami's Rosenstiel School. She is a Fellow of the Geological Society of America and the American Association for the Advancement of Science. In addition to sailing on two NOAA vessels and JOIDES Resolution, her science communication experiences include serving as the geoscience education and educational technology blogger with the American Geophysical Union for nine years, initiating and managing the growing scientific ocean drilling audio archive Tales from the Deep, and quilting science stories, including a 19-quilt collection from IODP Expedition 390.  

Stuart Siegel, PhD, SPWS 

Two Birds, One Ecosystem – Bringing Nature-Based Solutions to the SF Estuary 

Abstract:  The San Francisco Estuary, like most estuaries globally, faces a combination of large-scale historic habitat loss and the modern threat of rising sea levels. This estuary has spent decades restoring its lost estuarine ecosystems and is a leader in driving the science and practice of large-scale restoration forward. The region’s citizens walk their talk – voters have passed billions in statewide and regional bonds and taxes. The region is very focused on planning for rising sea levels – every city and county in California must have its adaptation plan adopted by 2034 and the bay area is moving fast. The Bay Conservation and Development Commission recently estimated a $109 billion price tag, likely an underestimate. The January 2026 tidal flooding has been a wake-up call. Enter estuarine ecosystems – subtidal mudflats, eelgrass beds, oyster reefs, tidal marshes, upland ecotones, open waters, and in some places beaches and creek mouths. These habitats give us many “ecosystem services” in addition to their myriad ecological functions. “Nature-based” shoreline protection is recognized as a significant and vital service in high demand today. Delivering on this opportunity is the challenge. There is science and adaptive management – what works where, under what circumstances, what do our projects teach us, how do we disperse knowledge. There is engineering – converting knowledge into constructable designs. There is regulatory – the webs of environmental regulation in the U.S. derive from hazards of the past not the present. There is the funding – planning, design, permitting, construction, assessment. And there is the land and project sponsors – some entity must step up and make projects happen. And we are rising to these challenges – making projects happen in ways and places previously thought out of our reach.  

Bio: Dr. Siegel focuses on the intersection of climate change adaptation, ecosystem conservation, restoration, and resilience, natural and nature-based infrastructure, and regional planning, with a focus on the San Francisco Estuary. Over his 40-year career, Dr. Siegel has worked on numerous restoration projects large and small, integrating innovative “nature-based” strategies that utilize marsh ecosystems to yield ecological benefits, carbon storage, and flood and erosion protection for the built environment. He has served as a lead science advisor for the Suisun Marsh Plan, Delta Vision’s ecosystem team, and the Delta Regional Ecosystem Restoration Implementation Plan, and the Integrated Regional Wetland Monitoring Pilot Project. He regularly serves on project and regional technical advisory and steering committees. Dr. Siegel is the Coastal Resilience Specialist for the SF Bay NERR and Adjunct Professor in SFSU’s School of the Environment. Dr. Siegel is a Senior Professional Wetland Scientist and received his Master’s and Ph.D. in Geography and his B.A. in Environmental Science and B.S. in Chemistry, all from UC Berkeley.