Under Pressure: Coastal upwelling and Climate Change – September 6th, 2018

Marisol Garcia-Reyes, Farralon Institute
Moss Landing Marine Labs Seminar Series - September 6th, 2018

Hosted by the Physical Oceanography Lab

MLML Seminar Room, 4pm

Open to the public

Marisol has studied coastal upwelling for over 10 years, focusing on its variability, and how it relates to climate (García-Reyes et al., 2015) and its marine ecosystem (García-Reyes et al., 2013). She has a background on physics and atmospheric sciences, but she's an oceanographer at heart. Her current research includes a comparative study on climate impacts on the California and Benguela upwelling ecosystems (see CalBenJI project), and development and analysis of Indicators of ocean and climate variability in California (see the MOCI project)

Under Pressure: Coastal Upwelling and Climate Change

Is your research subject, life or hobbies part of the California Current or coast? Do you wonder (and get asked) how is it impacted by climate change? This seminar is for you. Back to the basis of coastal upwelling. We will explore the following questions: How coastal upwelling, the process that brings nutrient rich water to the coast and fuels a rich marine ecosystem, depends on global climate? How is this a global phenomena? How it is and will be impacted by climate variability and change? What do we know and what do not know about these changes? And how they impact our coast and our lives?

Using Transcriptomics and Reverse Genetics to Understand Cnidarian-Dinoflagellate Symbiosis – September 13th, 2018

Phillip Cleaves, Stanford University
Moss Landing Marine Labs Seminar Series - September 13th, 2018

Hosted by the Invertebrate Zoology & Molecular Ecology Lab

MLML Seminar Room, 4pm

Open to the public

Using Transcriptomics and Reverse Genetics to Understand Mechanisms of Cnidarian-dinoflagellate Symbiosis

Phillip A. Cleves1, Cory J. Krediet1, Erik M. Lehnert1, Benjamin M. Mason1, Marie Strader2, Mikhail Matz2, and John R. Pringle1

1Department of Genetics, Stanford University, Stanford, CA, USA

2Integrative Biology, The University of Texas at Austin, Austin, TX, USA


The endosymbiosis between corals and dinoflagellate algae (genus Symbiodinium) is essential to the energetic requirements of coral-reef ecosystems.  However, coral reefs are in danger due to elevated ocean temperatures and other stresses that lead to the breakdown of this symbiosis and consequent coral "bleaching".  Despite its importance, the molecular basis of how corals establish and maintain a healthy symbiosis is poorly understood, in part because of the lack of a tractable genetic model organism. The small anemone Aiptasia is symbiotic with Symbiodinium strains like those in reef-building corals but has many experimental advantages over corals, making it an attractive laboratory model for cnidarian symbiosis.  To explore the possible transcriptional basis of heat-induced bleaching, we used RNA-Seq to identify genes that are differentially expressed during a time course of thermally stressed symbiotic and aposymbiotic Aiptasia strains. We observed a strong upregulation of hundreds of early stress response genes at time points long before bleaching begins in symbiotic anemones. The putative promoters of these early stress response genes are enriched for NFKB and HSP1 transcription factor binding sites suggesting that many of these stress response genes share core transcriptional inputs. The overall expression patterns were similar between the symbiotic anemones and the aposymbiotic anemones, indicating that many of the expression changes are not specific to the presence of the algae. However, blocking protein synthesis or HSP1 DNA binding with pharmacological inhibitors during this up-regulation results in more severe bleaching suggesting this symbiont-independent early stress response is protective against thermal stress and bleaching.

Genetic tools are needed to allow rigorous functional testing of the roles in symbiosis of candidate genes and pathways. As a first step in developing transgenic methods for Aiptasia, we have successfully expressed the photoconvertible Kaede fluorescent protein in larvae by microinjection of capped mRNA into 1-cell zygotes obtained by spawning in the laboratory.  This technique should allow both expression of tagged proteins for localization studies and the overexpression of candidate genes to analyze gain-of-function phenotypes.  In addition, we have promising results for two different methods for analyzing loss-of-function phenotypes in Aiptasia.  First, we have microinjected zygotes with translation-blocking morpholinos targeting the FGF1a gene, which has been shown to be required for apical-tuft formation in another anthozoan.  Preliminary results show apparent loss of apical-tuft formation in successfully injected larvae, suggesting that the Fgf1a protein was effectively knocked down.  Meanwhile, we have successfully used the CRISPR-Cas9 technology to create genetic changes in embryos of the coral Acropora millepora.  Through the establishment of both gain-of-function and loss-of-function methods in both Aiptasia and corals, Aiptasia will be a uniquely powerful genetic model organism (with year-round spawning) for the study of cnidarian-Symbiodinium symbiosis, and the discoveries made can be validated using similar technologies in corals.


We thank the Gordon and Betty Moore Foundation and the Simons Foundation for support.


Scientific Art… or Artistic Science? – September 20th, 2018

Ron Holthuysen, Scientific Art, Inc.
Moss Landing Marine Labs Seminar Series - September 20th, 2018

Hosted by the Phycology Lab

MLML Seminar Room, 4pm

Open to the public

In 1980, Ron Holthuysen  founded Scientific Art Studio.  After teaching, biology, chemistry and physics for a few years, he decided to follow his desire to create natural history exhibits.  There was not really a job in which he could explore and combine his interests in taxidermy, wild life photography, film, design, history, paleontology, geology, sculpture, painting, engineering, teaching and be an inventor all at the same time.  Ron has always had the need to involve himself in a wide range of fields, and to challenge himself with interesting projects.  The result is Scientific Art Studio as it is now.

During the last 35 years, under the name of Scientific Art Studio He has been able to take on and, mostly to great satisfaction of his clients, finalize projects of a very wide variety.  From Natural History exhibits to special effects for motion pictures and television, from Museum taxidermy to mechanical costumes for a Las Vegas show, from the restoration of artifacts to the design of rock show stages, and much more.  The source of his inspiration and the focus of his interest has been always Nature in its broadest embrace.  It gives Ron great satisfaction to reconstruct extinct animals and plants, to work with scientific specialists and to dabble in whatever  draws his attention.

Scientific Art or Artistic Science ?

The initial reaction of members of the Scientific World and of the Art World often is to distance themselves from one another’s realm of interest.


A world of exactness and no fuzzy, artsy stuff.

Rigid discipline.


Seeking for the absolute freedom of self expression.

No restraints.

Absolute separate worlds, right ?

Think again or better: Look , listen, smell and feel again.

Science and Art are, in my opinion, co-dependent siblings.

Both realms study and investigate and interpret the world we live in.

This talk features the some of the  visualizations and interpretations of our world through Scientific Art (or Artistic Science)

Watch Ron’s MLML seminar presentation below:

Coral Reefs, Climate Change, and Atoll Sustainability: How long will atolls be able to sustain human habitation? – October 4th, 2018

Curt Storlazzi, USGS
Moss Landing Marine Labs Seminar Series - October 4th, 2018

Hosted by the Geological Oceanography Lab

MLML Seminar Room, 4pm

(or Watch it Live here!)

Open to the public

Curt received his BSc from the University of Delaware in 1996, his PhD from the University of California at Santa Cruz in 2000, and has been a research geologist in the U.S. Geological Survey’s (USGS) Coastal and Marine Geology Program since 2003.

Curt’s research focuses on the quantitative study of hydrodynamics, sediment transport, and geomorphology in coastal and marine environments across the Pacific, Atlantic, Arctic, and Indian Oceans.

Currently, Curt is the Chief Scientist of the USGS Coral Reef Project and leads a research team of 13 PhD- and MSc-level scientists that examines the geologic and oceanographic processes that affect the sustainability of US coral reefs and reef-lined coasts, authoring more than 130 scientific papers, reports, and book chapters on these topics.

Curt is on the steering committee for the US Coral Reef Task Force and regularly contributes scientific review for the US Global Change Research Program, NOAA’s National Marine Sanctuary Program, the National Park Service, the USFWS Landscape Change Cooperatives, and theUSGS Climate Science Centers.

Coral Reefs, Climate Change, and Atoll Sustainability:
How long will atolls be able to sustain human habitation?

Although absolute rates of sea-level rise (SLR) and projected 2100 global sea levels are still under deliberation, the models consistently suggest that eustatic sea level will be considerably higher by the end of the century and rates of SLR will far outstrip vertical coral-reef accretion rates, which will have a profound impact on coral reef-lined islands. Atoll islands are low-lying carbonate Holocene features, many of which have maximum elevations of less than 4 m, that support 1000 year-old cultures, yet the amount of land and water available for human habitation, water and food sources, and ecosystems is limited and extremely vulnerable to wave-driven flooding and inundation from SLR. The USGS is leading a multi-agency, multidisciplinary effort to understand how SLR and climate change may impact low-lying atoll islands in Micronesia using field observations and global climate model outputs to drive coupled hydrodynamic and hydrogeologic models for a number of SLR and climate change scenarios. Rising sea levels and climate change will reduce the ability of coral reefs to mitigate wave-driven flooding in the future, leading to more frequent, persistent, and extreme marine flooding and overwash on atoll islands, damaging infrastructure, habitats, and agriculture. More importantly, the increased marine flooding, along with decreased precipitation, will result in salinization the islands’ limited freshwater drinking supplies with such frequency that the freshwater resources will not be able to recover. Our findings suggest that such “tipping points” – when the islands can no longer sustain a freshwater lens and thus human habitation – will likely occur in decades, not centuries as previously thought, which will result in significant geopolitical issues when it becomes necessary to abandon and relocate island-states.

More info on:

Coral Reefs: https://coralreefs.wr.usgs.gov/

Sea-level Rise and Atolls: https://walrus.wr.usgs.gov/climate-change/atolls/

Watch Curt’s MLML Seminar Presentation Below:

Are they really ‘species’? (Potential) cryptic speciation of the common and abundant ctenophore, Bolinopsis infundibulum – October 18th, 2018

Shannon Johnson, MBARI
Moss Landing Marine Labs Seminar Series - October 18th, 2018

Hosted by the Invertebrate Zoology & Molecular Ecology Lab

MLML Seminar Room, 4pm

(or Watch it Live here!)

Open to the public

Bolinopsis (Ctenophora: Lobata) are common, relatively large, and abundant comb jellies found throughout the world ocean. Bolinopsis infundibulum is thought to occur in most northern latitudes, and B. vitrea in tropical latitudes. Sequence data from conservative loci such as 18S rRNA revealed little to no differentiation within the genus and is unresolved for lobate ctenophores in general. In contrast, sequence data from the mitochondrial locus Cytochrome-C-Oxidase subunit I, (COI) revealed species-level differentiation amongst ocean basins for both taxa. Sequence data from the 28S rRNA, Internal transcribed spacer (ITS) rRNA, and Histone-3 (H3) nuclear loci, also confirmed patterns of species-level differentiation. Sequences also revealed a new lineage of Bolinopsis from the Pacific Ocean. Bolinopsis n.sp. included two closely related, yet distinct mitotypes that were sympatric in the Monterey Bay, California (USA). The sympatric lineages were often collected together and did not segregate by depth or geography.  Nuclear genomic RAD sequencing on a small subset of individuals revealed potential cytonuclear disequilibrium and hybridization between the two mitotypes, lending evidence to the presence of a cryptic species complex. Further genomic sequencing and Sanger sequencing, coupled with morphological investigations are underway to determine if genetic differentiation is reflected phenotypically.

Shannon is an MLML Alum!  Check out her alumni interview on The Drop-In Blog!

Watch Shannon’s MLML Seminar Presentation Below:

Differential effects of nitrate, ammonium and urea as N sources for microbial communities in the North Pacific Ocean – October 25th, 2018

Irina Shilova, Second Genome
Moss Landing Marine Labs Seminar Series - October 25th, 2018

Hosted by the Chemical Oceanography Lab

MLML Seminar Room, 4pm

(or Watch it Live here!)

Open to the public

Irina Shilova is a Microbial Ecologist and Bioinformatician with advanced education in Molecular Biology and Microbiology and extensive experience in the field, lab and meta‘omics data analysis. She has developed and implemented novel molecular tools and informatics approaches to study responses of microbial communities to environmental stimuli. Irina is dedicated to mentoring and science outreach and passionate about the microbial world and striving towards constant improvement and learning.

Differential effects of nitrate, ammonium and urea as N sources for microbial communities in the North Pacific Ocean

Nitrogen has long been known to limit phytoplankton growth and productivity in large regions of the oceans. Likewise, the form and supply of N are important controls on microbial community composition, activity and ultimately ecosystem function. However, the effect of different chemical nitrogen species on complex natural phytoplankton communities in the open ocean is not well-known. We investigated the effect of nitrate, ammonium, and urea on microbial and phytoplankton community composition (cell abundances and 16S rRNA gene profiling) and functioning (photosynthetic activity, carbon fixation rates) in the transitional zone of California Current system and oligotrophic waters of the North Pacific Ocean. All nitrogen substrates tested significantly stimulated phytoplankton growth and productivity. Urea resulted in the greatest (>300%) increases in chlorophyll a and productivity at two experimental stations, largely due to increased abundances of Prochlorococcus. Two abundant clades of Prochlorococcus, High Light I and II, demonstrated similar responses to urea, suggesting this substrate is likely an important N source for natural Prochlorococcus populations. The timing and magnitude of response to nutrient amendments varied with geographic location due to the differences in phytoplankton community composition and nutrient status among and within these communities. Finally, both the oligotyping approach applied for 16S rRNA gene sequences and the gene-targeted transcription (microarray) approach showed that sub-populations of Prochlorococcus and Synechococcus had different responses to nitrogen sources. Our results provide support for the hypothesis that changes in nitrogen supply would likely favor specific populations of phytoplankton in different oceanic regions and thus, affect both biogeochemical cycles and ecological processes.

Environmental Data Justice at the Hunters Point Naval Shipyard (and DISCUSSION afterwards) – November 1st, 2018

Lindsey Dillon, Science and Justice Research Center, UCSC
Moss Landing Marine Labs Seminar Series - November 1st, 2018

Hosted by the Fisheries & Conservation Biology Lab

MLML Seminar Room, 4pm

(or Watch it Live here!)

Open to the public

Lindsey Dillon is an Assistant Professor of Sociology at UC Santa Cruz. She received a PhD in Geography in 2014 and held a postdoctoral fellowship in American Studies. Her works looks at the intersection of urban geography, environmental justice social movements, and the politics of knowledge. At UCSC she serves on the steering committee of the Science and Justice Research Center.

Environmental Justice at the Hunters Point Shipyard

This talk explores the politics of environmental data at the Hunters Point Shipyard, in southeast San Francisco. The shipyard is a Superfund site and currently undergoing cleanup and redevelopment as a landscape of condominiums, offices, and waterfront parks. The construction activity produces health hazards for the neighboring Bayview-Hunters Point community, which has struggled against environmental racism for decades. I explain environmental data justice (a concept I am helping to develop with other colleagues, based on our work advocating for better data practices under the Trump administration) and I explore whether and how this applies to a particular case in Hunters Point: the attempt to demolish Candlestick Park by exploding it, and the political organizing that stopped this from happening.