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Emma Choi researched fish spawning trends in the Marine Protected Area off La Jolla by using DNA techniques in the Burton Lab. This consisted of collecting fish eggs, amplifying their DNA by PCR, and sending the DNA out to be sequenced for identification. This molecular method of identifying fish eggs complements data regarding local fish species obtained by diver surveys.
Mentors: Elena Duke, Graduate student, and Ron Burton, CCE-LTER Associate
Fernando Gil created a quality control program with MATLAB, using several live scripts in the Martz Lab, to calculate the alkalinity of seawater samples from the underway CalCOFI samples. After creating a 3-point regression and applying corrections, he calculated the pH of the seawater from various CalCOFI stations off the coast of southern California. Fernando also created a chart to show which components of this system were functioning at any given time along the path of the cruises.
Mentor: Todd Martz, CCE-LTER Associate
Sara Ramirez at habitat suitability modeling for the California market squid in the Miller Lab, and applied the concept to spawning suitability. Because market squid are restricted by their environment during spawning, the model was constructed using the species-environment relationships of bathymetry, substrate affinity, and temperature - ranking spawning zones on how suitable it is based on those criteria.
Mentors: Nathali Cordero-Quiros, Graduate student, and Art Miller, CCE-LTER Co-PI
Niv Anidjar measured dissolved iron concentration in seawater samples in the Barbeau Lab, taken during process cruise P1706. He used these concentrations along with ADCP velocity data in order to determine values for cross-shore advective flux of dissolved iron, as these measurements are useful for understanding changes in distribution of primary producers. Iron is episodically the limiting nutrient in the CCE, which can restrict growth of plankton.
Mentors: Kiefer Forsch, Graduate student, and Kathy Barbeau, CCE-LTER Co-PI
Kellie Lemoine studied the role of siderophores in microbial iron acquisition in the Barbeau Lab. Siderophores are compounds that strongly bind and transport iron in microorganisms. Through experimentation in the lab, she found that siderophores may play a significant role in helping bacteria take up inorganic iron in the California Current Ecosystem, an area where upwelling may be a source of sedimentary iron.
Mentors: Lauren Manck and Sara Rivera, Graduate students, and Kathy Barbeau, CCE-LTER Co-PI
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Cristina Curiel analyzed physical and biological model data results generated by an ocean computer model (Darwin model) from the CCE region. She worked in Art Miller’s group, defining characteristics of different phytoplankton and zooplankton groups. Her project focused on ocean eddies, and the associated edges of the eddies known as fronts, comparing computer model results with field measurements. analysis, under iron limited conditions.
Mentors: Art Miller, CCE-LTER Co-PI
Gabriela Haddad studied spawning patterns of fish in two habitats of our local Marine Protected Area, using DNA sequencing to identify fish eggs in the Burton Lab. Fish species compositions, spawning periods and habitats, and environmental effects were analyzed for nearby kelp forest and Scripps pier samples.
Mentors: Mentors: Elena Duke, Graduate student, and Ron Burton, CCE-LTER Associate
Aysell Medina studied heterotrophic bacteria from the CCE-P1706 coastal filaments cruise, working in the Aluwihare Lab. She measured bacterial abundance and size in comparison with previous years. She used a variety of lab techniques, including DNA staining to calculate the carbon content for each cell.
Mentors: Sara Rivera, Graduate student, and Lihini Aluwihare, CCE-LTER Co-PI.
Kaytlyn Taglialavore working in the Aluwihare Lab, analyzed seawater's Fluorescent Dissolved Organic Matter (FDOM) characteristics in the California Current Ecosystem on samples collected during the CCE-P1706 cruise. She subsequently used MATLAB to identify key chemical components within the CCE's FDOM and focused her analysis on the distributions of these components relative to distance offshore, DOC concentration and depth.
Mentors: Brandon Stephens, Graduate student, and Lihini Aluwihare, CCE-LTER Co-PI
Maggie Wang analyzed Synechococcus diversity in the California Current Ecosystem using filters collected at sea at four different locations on the P1604 cruise. She worked in the Palenik Lab and used molecular techniques to compare inshore vs. offshore clades of cyanobacteria as well as variations with depth.
Mentors: Maitreyi Nagarkar, Graduate student, and Brian Palenik, CCE-LTER Associate
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Bretton Coppedge studied iron uptake in a marine bacterium, Alteromonas macleodii, and created a gene similarity network that helped identify which genes Alteromonas most likely uses to take up iron. She also analyzed the expression of these genes through qPCR analysis, under iron limited conditions.
Mentors: Lauren Manck (Grad student) and Kathy Barbeau (CCE LTER Co-PI)
Elena Duke researched the spawning activity of fish populations in two of San Diego’s Marine Protected Areas using DNA barcoding techniques. She was able to decipher seasonal changes in spawning activity from the data and changes in community composition over time.
Mentors: Alice Harada (Grad student) and Ron Burton (CCE LTER Assoc. PI)
Wiley Wolfe's goal this summer was to determine the short-term chemical spatiotemporal variability of Agua Hedionda Lagoon. He did this using a paddle board with a WavepHOx sensor attached, along with a GPS watch to record the time and location of each measurement.
Mentors: Taylor Wirth (Staff Res. Assoc.) and Todd Martz (CCE LTER Assoc. PI)
India Dove analyzed multi-decadal changes in microplastic sedimentation rates in the anoxic Santa Barbara Basin, researching whether microplastic sedimentation rates changed over a century timescale and whether there was a distinct time horizon when plastic first emerged in the sediments. She enumerated, imaged, measured, and recorded various characteristics in over 1,100 microplastic pieces extracted under the microscope.
Mentors: Jennifer Brandon (Grad student) and Mark Ohman (CCE LTER Lead PI)
Brooke Rasina focused her study on the heterotrophic bacteria in the California Current Ecosystem, testing whether El Niño had an effect on bacterial abundances and bacterial carbon content. The abundance and carbon data from Process cruise P1604 (El Niño year) were compared to similar data from P0605 (normal year), P0704 (normal year) and P1408 (“Blob” year).
Mentors: Sara Rivera (Grad student) and Lihini Aluwihare (CCE Co-PI)
Casey Graff studied machine learning techniques for the automatic classification of digital zooplankton images. He wrote computer algorithms to help classify and quantify plankton images to further understand plankton distributions, create oceanographic models, and study population ecology. Automating this process can help save significant time and resources.
Mentors: Jeff Ellen (Grad student) and Mark Ohman (CCE LTER Lead PI)
Jennifer Beatty estimated the ciliate biomass in the California Current during the “Blob” (P1408) and El Niño (P1604) warm water anomalies. Ciliates are heterotrophic plankton that represent up to one third of the heterotrophic biomass in the California Current. They are extremely fragile, so she used a different filtering process than other plankton, counted ciliate cells and calculated the carbon biomass from each cruise year.
Mentors: Ali Freibott (Grad student) and Mike Landry (CCE LTER Lead PI)
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Linda Tong studied mesozooplankton grazing via gut fluorescence in the Ohman lab this summer. She analyzed zooplankton gut samples from CCE Process Cruise P1408, examined possible factors affecting spatial variability in mesozooplankton grazing, and sought to determine an appropriate metric for approximating the factor of food concentration. Linda gained invaluable experience and knowledge, and a better appreciation for the CCE through her work.
Mentors: Jenni Brandon, Graduate student & Mark Ohman, CCE-LTER Head PI
Raul Martinez performed trace metal analysis in the Barbeau lab this summer. Specifically, he collected and looked at copper levels in San Diego Bay and off the SIO pier to determine levels of toxicity. The study included characterizing copper-binding organic ligands with electrochemical measurements using CLE-ACSV. Raul gained a better understanding of chemistry and how data are analyzed to determine copper and ligand concentrations.
Mentor: Angel Ruacho, Graduate student
Maria Winters worked in the Miller lab on a physical oceanography modeling project regarding eddies. She analyzed output from a combined biological-physical model of the CCE, which represented changing populations of plankton in the CCE over time, as well as changing physical variables. Maria improved her MATLAB skills, which helped to better understand and improve the model to represent the CCE, one of the most productive ecosystems in the world.
Mentor: Art Miller, CCE-LTER Co-PI
Vivian Han focused her studies in the Palenik lab on the population dynamics and the clade distribution of Synechoccocus, an ecologically important cyanobacteria. She collected seawater samples at the SIO pier, and used genetic techniques to create the clade libraries. Vivian also investigated whether Gymnodinium, a genus of photosynthetic dinoflagellates, grazed on Synechoccocus via co-culture experiments.
Mentor: Maitreyi Nagarkar, Graduate student & Brian Palenik, CCE-LTER Assoc-PI
Abdalrahman Alrayyes worked with the CalCOFI folks (Goericke lab) as a data analyst sorting through decades of pH data to confirm that the data were true from CalCOFI cruises, or to decipher new relationships that could allow one to better understand the ocean’s chemistry. He ended up investigating how factors such as nitrate and oxygen contents are related to pH after discovering the pH sensors were faulty, having to draw on theoretical data to make calculations.
Mentor: Ralf Goericke, CCE-LTER Co-PI
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Kyra Rashid worked the first part of the summer in Mike Landry’s Lab, investigating how climate change influenced microplankton community distribution and dynamics through work in the lab. She spent the last month at sea on the CCE P1408 Process Cruise and became familiar with the design, execution, and analysis of dilution experiments which are a means of calculating community growth and grazing rates, as well as taking part in various types of oceanographic sampling with the scientists.
Mentor: Ali Freibott, Graduate student
Kari Ann Yoshida spent the summer performing guided research in Brian Palenik’s Lab on the survival of the marine cyanobacterium, Synechococcus, at differing ocean depths. She created various clone libraries of Synechococcus DNA by isolating specific sequences extracted, amplified, and cloned through molecular methods, and observed relative preferences of clades in surface and deeper waters.
Mentor: Maitreyi Nagarkar, Graduate student
Jasmine Tan worked in Farooq Azam’s Lab measuring protein synthesis rates of bacteria and converting synthesis rates into bacterial carbon productivity via leucine incorporation and centrifugation. She also tested how to best store bacterial samples, and spent the last month on the CCE P1408 Process Cruise, collecting seawater samples from various depths at different stations in the CCE for later analysis.
Mentor: Byron Pedler Sherwood, Post-doc
Taylor Wirth spent the summer working in the Todd Martz Lab, where autonomous ocean sensors are developed, most notably the SeapHOx pH & oxygen sensor. Taylor designed a lighter, smaller, and more hydrodynamic housing for this sensor (called WavepHOx), along with a rechargeable battery pack, which can be used on Wave Gliders and SUPs in the near-shore environment. Taylor also participated in some local field testing of the WavepHOx!
Mentor: Phil Bresnahan, Graduate student
Maya Land worked in Mike Landry’s Lab earlier in the summer, learning a relatively new method of secondary production estimation of the molting enzyme, chitobiase. She implemented this method on the CCE LTER research cruise in August (P1408) to measure the chitobiase-based production rates of crustacean zooplankton communities.
Mentor: Moira Décima, Post-doc

Alicia Highland researched mesozooplankton grazing rates across oceanic fronts in the California Current Ecosystem (CCE), with major emphasis on pelagic copepods. The aim of the research she conducted was to determine whether zooplankton grazing upon phytoplankton changes along the frontal boundaries, and utilized the gut fluorescence method in order to measure chlorophyll pigments.
Mentor: Dr. Mark Ohman
Ana-Patricia Lopez learned how to use an ecosystem model for quantifying spatial structures of phytoplankton and their relationship to ocean currents, waves and ocean fronts, through data manipulation of large data sets. This helped her learn whether the simulations resembled real observations and how to diagnose the physical controls of the ecosystem.
Mentor: Dr. Art Miller
Anna Cassady studied the effects of secondary metabolites from each of four strains of the marine cyanobacterium, Synechococcus, in supernatant on the development of other strains. She also measured the effect these secondary metabolites had on sea life communities off the SIO pier. The experiment was monitored by using both microscopy and flow cytometry in the lab.
Mentor: Dr. Brian Palenik
Emma Nuss investigated the relationship between biological activity in the ocean and physical processes, in particular eddy currents, by studying the output of a Darwin model. Her main question focused on what happens to phytoplankton in an eddy off the Southern California Coast.
Mentor: Art Miller
Jenny Couture worked on a project that investigates our ability to assess the state of the ocean. More specifically, she carried out a meta-analysis on Pacific Ocean observation programs to determine where and how the physics, chemistry, and the biology of the ocean are measured. While some measurements were adequate, biological monitoring was severely lacking or inconsistent in her findings.
Mentor: Dr. Tony Koslow
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Aarani Arulmoli studied how bacteria are involved in the biogeochemical cycling of iron, using metagenomic analysis of the microbial community in environmental samples, and in iron addition grow-out incubations. Aarani constructed a clone library using various DNA techniques in the Barbeau Lab, becoming familiar with each step in the process to prepare plasmids for analysis, along with how to make phylogenetic trees to evaluate bacterial community composition.
Mentor: Dr. Kathy Barbeau
Dustin Chen tested the validity of the “school trap” hypothesis of three fish species (Pacific sardine, chub and jack mackerels) in the Checkley Lab, using MATLAB to analyze a dataset containing egg and larval concentration data spanning from 1951 to 2010. Historical habitat overlap between sardine and either mackerel species were investigated using correlation analyses with three proxies for sardine population levels. Dustin also started a diet comparison study of locally collected Pacific sardine and chub mackerel.
Mentor: Rebecca Asch, Graduate student
Jonathan Cheng spent the first part of the summer in the Azam Lab studying marine bacteria and the role they play in the biogeochemistry of the ocean. He focused on measurement rates of bacterial carbon production, using a radioisotope incorporation technique. Jon then participated on the 30- day CCE process cruise (P1208), gathering and filtering samples for bacterial community growth analysis, along with helping out other CCE scientists on their shipboard projects.
Mentor: Ty Samo, Graduate student
David Muller worked in the Martz Lab, which specializes in developing autonomous chemical sensors for the ocean, mainly to measure pH. David spent many hours overhauling the software that interfaces with an autonomous SeapHOx instrument package (3 sensors and a converter) and updated an older computer to run the software. He honed his software skills putting all the code together and learned a lot about electrical engineering and digital circuit design as well!
Mentor: Dr. Todd Martz
Carole Wang interned the first part of the summer in the Palenik Lab focusing on Synechoccocus, a marine cyanobacterium. She tested whether external stressors (sugars and other chemicals) to Synechoccocus cultures could induce or disrupt the formation of micro-colonies (clumping behavior), analyzed with epifluorescence microscopy and fluorometer readings. Carole also participated in the month-long CCE process cruise (P1208), assisting the Landry Lab with water sample collection from the CTD Rosette and from drifters – for phytoplankton and grazers’ incubation studies.
Mentor: Dr. Brian Palenik
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Kayla Blincow analyzed data collected from the Oozeki net (on CalCOFI cruises) to map euphausiid communities in the California Current. She also went to sea for several weeks on a CalCOFI cruise (1108) as the “Oozeki technician.” Continuing with her project back at SIO, she identified euphausiids to the species level and counted the number of each species from the cruise samples, estimated the abundance of each type of species, and mapped their community structure based on where the sample was collected.
Mentor: Dr. Tony Koslow
Lisa Della Ripa conducted research which involved comparing and assessing the trophic positions of zooplankton in three different biogeochemical environments, using various lab techniques. She spent one month at sea in the CCE study area, and a week at sea in Hawaii. Lisa investigated differences in δ15N between the 0.2-2 mm size fractions and in the source nitrogen between the three regions and assessed whether the absolute trophic positions were different between regions.
Mentor: Dr. Mike Landry
Evelyn Hunter created a database which included data from the ALF (Advanced Laser Fluorometry) device and underway data from CCE-LTER cruises. She wrote and ran functions in MATLAB to consolidate and organize numerous smaller text files into one complete file, which were then imported into a Microsoft Access database. Evelyn also assisted with some CCE process cruise (P1106) preparations.
Mentor: Dr. Ralf Goericke
Melinda Lopez spent the summer creating additional software functionalities for a program running within an autonomous instrument package (SeapHOx), constructed in the Martz lab. She was able to program, calculate, and display the pH by using certain measured or user input pH calibration sensor coefficients (i.e. temperature and salinity).
Mentor: Dr. Todd Martz
Wendy Plante participated on a one-month research cruise (P1106) and studied the role of Iron in the CCE study area. She assisted in casting the trace metal clean rosette, filtered samples, and ran experiments to examine how Iron affected the prevalence of primary producers. Back at SIO, Wendy ran Iron (II) lifetime experiments and compared the oxidation rate of Iron (II) in the water samples collected on the ship.
Mentor: Dr. Kathy Barbeau
Ellen Umeda also participated on the CCE Process cruise (P1106) for one month. She assisted with the deployment and recovery of the bongo and MOCNESS tows, anesthetized and size fractioned the zooplankton samples caught, and placed them in liquid nitrogen for gut fluorescence and biomass analysis. Back on land, Ellen compared vertical distribution and life history stages of pyrosomes – for which she sorted, measured, and calculated densities from the MOCNESS tows.
Mentor: Dr. Mark Ohman
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Kayla Busby examined the seasonal and geographical diversity of Synechococcus sp. CC9311, using qPCR techniques, with a focus on the environmental prevalence of an operon that is upregulated in this abundant marine cyanobacterium in response to copper shock. Samples from the SIO pier, local estuaries and coastal sites were analyzed.
Sponsor: Dr. Brian Palenik's lab
Ross Castillo used numerous techniques required to better understand aspects of iron cycling in marine systems. He combined wet lab experiments with bioinformatics when developing degenerate primers and identifying proteins of interest to study acquisition of heme as an iron source by marine bacteria.
Sponsor: Dr. Kathy Barbeau's lab
Chelsea Didinger participated on a research cruise. She assisted with equipment deployments and recovery, sample preservation, and designed and ran experiments to measure the ammonium excretion rate of euphausiids using a fluorometric method. Back in the lab at SIO, she also conducted excretion experiments with copepods.
Sponsor: Dr. Dave Checkley's lab
Danielle Lara examined concentrations of carbohydrate levels in seawater samples, collected on a 2008 CCE LTER Process cruise, using diverse lab techniques. Concentrations at various depths of the water column were then examined for trends. Sponsor: Dr. Lihini Aluwihare's lab
Emilie Schnarr compared oceanic and reef-associated zooplankton selected by the yellowtail damselfish from various reef habitats surrounding the island of Moorea. By examining stomach contents with a microscope and prey item size with ZooScan and ZooProcess, the number, diversity, type, and size of zooplankton was determined.
Sponsor: Kate Hanson (Graduate student)
*Laura Cummings and Hank Lin were partner REUs from the NSF-sponsored Computer Vision Coral Ecology project. Sponsors for Laura and Hank were Graduate student Ben Neal (Scripps Photobiology Group, G. Mitchell Lab) and Post-doc Tali Treibitz (Computer Science Engineering, UCSD), respectively.*

Nadija A. Anderson investigated the role of iron and silica as limiting nutrients for phytoplankton growth in the California Current Ecosystem, and analyzed samples using nutrient-amended incubation studies on the Scripps pier.
Sponsor: Kathy Barbeau's lab
Emily Botts compared the diversity of coastal versus offshore populations of the marine cyanobacteria - Synechococcus, a diverse genus of phytoplankton, from a CalCOFI cruise using the high-resolution melting technique of DNA.
Sponsor: Brian Palenik's lab
James Hayes gathered information management materials from 26 LTER sites, which involved documenting information systems development, data handling, and changes associated with technology and with the roles of information management. His work will support research on the development of site-based infrastructure.
Sponsor: Karen Baker's Informatics Team
Patricia Lee quantified the total organic carbon (TOC) content in samples that were collected on a CCE LTER 2008 Process cruise, using a high-temperature catalytic oxidation (HTCO) method and a nondispersive infrared sensor.
Sponsor: Lihini Aluwihare's Lab
Junna Murakawa analyzed the grazing rates of mesozooplankton (sized ~ .2 mm to 5mm) from various locations within the CCE (2008 Process cruise) by looking at the level of extracted chlorophyll a pigments from phytoplankton remaining in their guts.
Sponsor: Mark Ohman's lab
Robert Peterson implemented a geographic dictionary (a gazetteer) designed to be integrated into an existing information system and also initiated development of a history module that incorporates a timeline of events designed to enable the capture of project narratives.
Sponsor: Karen Baker's lab
Tim Stillinger worked on correlating in situ acoustical backscatter data of zooplankton samples collected with an Acoustic Doppler Profiler (ADP) to zooplankton biomass estimates, which required digitizing zooplankton samples with Zooscan and identifying many, many species.
Sponsor: Mark Ohman's lab
Elliot Weiss extracted water-soluble photosynthetic pigments called phycobiliproteins, from Scripps pier water samples using modified lab techniques, and used relative fluorescence to determine their presence (community structure) over the course of the summer.
Sponsor: Greg Mitchell's Lab
Sean Wiley gained loads of experience with the Ocean Informatics Team - programming languages, designing and implementing programs (information and data associated with the LTER Network), technical skills to program backend databases/software, as well as interact with the users of the databases/software.
Sponsor: Karen Baker's Informatics Team

Todd Langland studied the relationship between size measurements of zooplankton using a Zooscan machine, and the carbon and nitrogen content of the organisms.
Sponsor: Mark Ohman's lab
Mary McCormick researched how changing environmental factors alter food webs by analyzing the nitrogen isotopes in tissues of three species of small animals that are common in the California current.
Sponsor: Michael Landry's lab
Lisa Kamino examined the quality of nitrogenous marine organic matter by identifying retention times and content of amino acids in water samples, and studied the cycling of organic N in marine environments.
Sponsor: Lihini Aluwihare's lab
Emy Daniels focused on identifying grazers of an important marine bacterium, Synechococcus - and created a DNA "library" of ciliates using PCR and cloning techniques. Emy also participated in a CalCOFI-LTER research cruise, helping scientists with various hydrographic projects at sea.
Sponsor: Brian Palenik's lab
Brian Pearson created and improved upon a method to test for the presence of phycobiliproteins (photosynthetic pigments) in ocean samples. It was then used as a biochemical method to validate a new, faster instrument in identifying phycobiliproteins, found mostly in cyanobacteria and red algae.
Sponsor: Greg Mitchell's lab
Randelle Bundy investigated iron light co-limitation of deep chlorophyll max communities.
Sponsor: Kathy Barbeau's lab
Kate Tsyrklevich focused on mesozooplankton grazing as assessed from gut fluorescence measurements.
Sponsor: Mark Ohman's lab