Undergraduate Research Opportunities Center

Download the document below for a detailed description of project, qualifications, and mentor expectations:

Mentor Intake Form - Rachel Brooks

Canary Rockfish

Present fishery management strategies are concentrated on species-specific stock assessment models, which are often (due to data limitations) based on the assumption that life history and demography traits are stable and invariant across species range. Mounting evidence suggests that geographic and habitat-specific variation in demographic rates and life history traits may be more common than previously though and a significant source of stock structure. Despite this potential source of stock variation, most fisheries stocks are managed over broad geographic areas with minimum size limits and catch limits applying equally in all areas.

The goal of this research project is to gather information that can be used to improve fisheries management, by quantifying geographic- and habitat-specific variation in demography and life history traits of canary rockfish (Sebastes pinniger) along the U.S. West Coast. Life history parameters such as length-at-age, length-at-maturity, fecundity, and condition of canary rockfish will be compared between soft-bottom and high relief rocky habitats as well as between well-known biogeographic break points along the U.S. West Coast. The collection methods primarily focus on hook-and-line fishing and chartered sport fishing vessels (CPFV). The study will be conducted over the summer of 2017 from Washington to Southern California and lab work could extend through the summer and into fall.

Objectives:

• Determine the length at age, length at maturity, fecundity, and condition of canary rockfish in soft bottom and high relief rocky bottom habitats

UROC Researcher role & qualifications:

The UROC Researcher will assist with field sampling on CPFV’s and lab work over the course of summer and possibly into fall 2017. There are 9 anticipated ports that we hope to cover in the early summer: 3 in Washington (Neah Bay, La Push, Westport), 3 in Oregon (Newport, Coos Bay, Brookings), and 3 in Northern California (Eureka, Fort Bragg, Bodega Bay). During late summer and early fall, depending on the UROC Researcher's availability, we will also be fishing in southern California (Santa Barbara, Ventura, Long Beach).

During on-board sampling the UROC Researcher will assist with fishing, descending bycatch, entering data, organizing and transporting gear, and interacting with volunteer anglers. Between fishing days, the UROC Researcher will assist in fish dissections by taking morphometric measurements, extracting otoliths for aging, preserving gut contents and tissue samples for diet/stable isotope analysis, collecting gonads and liver for fecundity and condition indices.

Potential independent projects for the UROC Researcher to pursue include identification of geographic variation in canary rockfish distribution, diet, or condition OR investigation of fishing parameters in canary rockfish catch (catch per unit effort, bycatch, gear usage) along the coast.

Qualifications:

• Applicant must be willing to travel mid-June through early August in an MLML vehicle with other researchers
• Applicant must be comfortable with participating in fish dissections (including handling a scalpel or fillet knife)
• Applicant must have experience using word and excel
• Applicant must have experience working with boats, be familiar with proper boat etiquette, and willing to work at sea in adverse weather conditions
• Applicant must be able to assist in recording data, descending bycatch, fishing for rockfish, and taking morphometric measurement while at sea
• Applicant must be confident in handling various fish species (will be taught the proper handling techniques)
• Applicant must be comfortable with identifying various fish and invertebrates
• Applicant must be comfortable conversing with various deckhands, captains, and volunteer anglers about the project

Snorkeling to catch fish

Measuring fish size

Fishing

June Shrestha preparing samples for analysis

This project focuses on fish excretion in kelp forests in central California and southern California. We are taking an interdisciplinary, ecological approach to elucidate 1) how fish-derived nutrients cycle through the nearshore temperate marine systems and 2) how human activities - such as fishing and subsequent establishment of marine reserves - affect this critical biogeochemical cycle.

In temperate marine ecosystems, nutrient recycling via fishes may contribute a significant portion to the total nutrient supply to the ecosystem (via their excretion), yet relatively little is known about the magnitude and variability of this recycling regime. Studies indicate that fishes are responsible for significant fluxes of nutrients in oligotrophic (nutrient poor) systems through physiological processes of consumption, storage, and excretion. More recent studies focusing on biogeochemical cycling in tropical systems estimate nitrogen input by fishes to be 25 times higher than all other sources combined. To date, this mode of nutrient recycling has only been documented in oligotrophic systems; however, the structure and function of nearshore temperate kelp communities may rely on fish-derived sources of nutrients.

Objectives:

• Quantify rates of nutrient excretion as a function of body size for the dominant kelp forest fishes in California
• Calculate the nutrient excretion rates for complete fish assemblages
• Utilize fish survey data to estimate how nutrient fluxes vary in kelp forests across large spatial scales to assess the potential significance of fish-derived nutrients at the ecosystem level.

UROC Researcher role & qualifications:

The UROC Researcher will assist with efforts to quantify excretion rates of kelp forest fishes in Monterey Bay. Majority of work will be in the field (75%) however some work in the laboratory may be required (25%).

Field Work (75%):

• Fishing - Gear: hook-and-line, gillnets, etc.; Fish identification;
• Fish and handling
• Water filtration and water changes
• Collect water samples for nutrient analysis
• Data recording
• Maintain cleanliness of boats and state vehicles as needed

Laboratory Work (25%):

• Prepare water samples and reagents
• Run samples through handheld fluorometer and spectrophotometer

Qualifications:

• Applicant must have experience from a college level chemistry lab and will be trained in seawater sample analysis
• Applicant must have the ability to work in diverse outdoor conditions on a small boat, and be able to lift 30 lbs
• Applicant must have a willingness to learn fish identification; marine kelp forest fishes taxonomic experience preferred
• Applicant must be willing to work on a small boat and work through any sea worthy situations
• Applicant must be willing to travel; the second half of the summer will be at Santa Catalina Island
• Applicant is not required to be an AAUS certified diver but there are opportunities for those that are
• Fishing skills preferred

This three-year project focuses on the impacts of size-selective mortality on sex-changing fishes. The project will conduct field experiments to manipulate the form (selection for large, small, or random-sized individuals) and intensity (0%, 50%, and 80% removal) of size-selective mortality on the demography of three hermaphroditic goby species that differ in their pattern of sexual allocation. The results will be used to parameterize models of size-selective mortality to predict long-term population dynamics.

This project has four Principal Investigators from multiple research institutions that will each focus on different parts of the study. Dr. Scott Hamilton and Stephen Pang from MLML will investigate the effects of male limitation on hermaphroditic species. To do this, field experiments will be used to determine the sex ratios and male abundance at which males limit population reproductive output across our two hermaphroditic study species.

Objective:

• Determine the effects of male limitation on hermaphroditic species populations

Former UROC Researcher Tyler Gerome surveying one of our artificial reefs in Big Fisherman’s Cove, Santa Catalina Island.

Principal investigator Mia Adreani (California State University, Northridge) tagging bluebanded gobies that will be outplanted onto our artificial reefs.

UROC student Katherine Neylan collecting bluebanded gobies from natural reefs for use in our manipulative field experiment.

UROC Researcher role & qualifications:

The UROC Researcher will be primarily helping with the field experiments. Scientific diving will be the majority of the work. As such, an AAUS certification is mandatory. Artificial reefs will be constructed, stocked with fish, and monitored throughout the summer for changes in abundance, growth, and reproductive effort in relation to the intensity and form of size-selective harvesting imposed. Fish outplanted on each reef are periodically re-collected and sexed. The UROC student will also help with evaluating the proportion of unfertilized eggs at each reef.

Qualifications:

• Applicant must be willing to spend long days in the field throughout the summer. This is a very field work intensive research opportunity.
• Student must be willing to spend the entire summer on Santa Catalina Island off the coast of Southern California. Transportation to the island from San Pedro will be provided but transportation to Southern California from Northern California and back will need to be coordinated by the student, though there may be opportunities for carpooling with other researchers.
• Applicant must be an AAUS certified diver and should have some diving experience with field work
• Student with some computer skills, statistical background, and laboratory skills preferred

This research project is an eco-physiological study that focuses on the adaptive capabilities of kelps. A UROC Researcher would assist with an investigation examining how a local kelp species, Pterygophora californica, stores and allocates compounds seasonally, and how this can be affected by wave disturbance. Our goal is to examine the areas of the algal thallus used as sources and sinks and determine how this physiology may aid in its recovery from disturbances. In addition, we plan to physically depict the presence of storage areas and how they are changing temporally.

These topics will be investigated using a subtidal biomass removal and growth experiment and through harvesting and analyzing kelp specimens using several methods. Analyses will include CHN analysis, sugar analysis, and photosynthetic pigment analysis. This laboratory based work also has the potential to include a live specimen tagging experiment using a radioactive isotope.

UROC Researcher Role and Qualifications:

UROC students would be involved in both laboratory and field based components of the project. They would be expected to be involved with each of the following:

- subtidal biomass removal and growth experiment

- field data collection

- kelp harvesting

- sample prepping for analyses

- data entry

Qualifications:

• This research opportunity welcomes applicants who have AAUS scientific diving certification but this diving certification is not a requirement. Only students who wish to dive with Lindsay will need the certification.
• Student must be curious about the natural world and willing to learn
• Student must have some experience with Excel, Powerpoint, and professional email communication
• Student must have basic hands-on outdoor experience
• Student does not need prior boating experience but it would be advantageous
• Student will be required to provide their own transportation. Dive preparation, sample processing, and laboratory analyses will all take place in Moss Landing. Diving will occur approximately once a month, and lab analyses will vary. When samples are taken after diving, there will be several days of lab work following, and in between there will be opportunity for data analysis.

Larval rockfish

NOAA Southwest Fisheries Science Center in Santa Cruz

Kristin Saksa with a gopher rockfish

This research examines the effects of ocean acidification (OA) and hypoxia on gravid female rockfish and their larvae. An increase in upwelling and rising of the Oxygen Minimum Zone (OMZ) off the California coast have led to coastal ocean conditions that are increasingly acidic (lower pH)and hypoxic (lower dissolved oxygen content). We will primarily use hook and line fishing to collect Gopher rockfish (Sebastes carnatus) and Brown rockfish (Sebastes auriculatus). Rosy rockfish (Sebastes rosaceus) larvae will be sampled from gravid females that are currently at the NOAA Southwest Fisheries Science Center in Santa Cruz.

Objectives:

• To determine the effect of OA and hypoxia on gravid female rockfish throughout the larval gestation period.
• To determine the effects of OA and hypoxia on embryo development, larval survival, metabolic performance and olfactory capabilities of three rockfish species with different life histories.
• To examine patterns of larval gene expression and enzyme activity levels associated with exposure to OA and hypoxia.

UROC Researcher Role and Qualifications:

The UROC student’s anticipated role is to assist with animal husbandry at the NOAA-SWFSC aquarium in Santa Cruz. Husbandry entails monitoring and recording the pH/DO/temperature, feeding rockfish, cleaning tanks, and assessing the health of adult rockfish. The UROC student will help run larval survival trials and identify larval mortalities in the low pH/low DO treatment tanks. They may also assist on rockfish parturition days by counting larvae for seeding trial tanks and collecting fecundity samples. There will be a need for UROC student assistance with olfaction swim trials by setting up scent tanks for lingcod,surf perch, and jellyfish. The UROC student would also be involved in transferring fish larvae into the Y-choice swim flume for olfaction trials. Daily responsibilities will be highly dependent on rockfish parturition schedule.

Qualifications:

• Some experience in aquarium or aquaculture facility preferred but not required
• Student must be willing to travel to the NOAA Southwest Fisheries Science Center in Santa Cruz regularly. All work days, besides fishing trips out of the Monterey wharf, will take place at the NOAA facilities.
• Student must be willing to participate in fishing trips to collect fish. Experience collecting live specimens from the field is beneficial but not required.
• Student must be willing to handle and care for adult and larval rockfish
• Student must be willing to learn taxonomic fish identification, which will be beneficial when on field fish collection trips

The giant kelp (Macrocystis pyrifera) is a foundation species that promotes biodiversity,

ecosystem resilience, and provides consumable biomass to consumers in the form of fixed organic

carbon. This foundation species has been extensively studied over the last century. However,

attempts to make predictive ecosystem models have been futile. This is because models have failed

to incorporate all trophic and physical dynamics of the system simultaneously. My study aims to

break apart some of the physical and biological aspects of M. pyrifera by using artificial kelp as a model system.Experiments in a flume have shown evidence that the structure of M. pyrifera is capable of diverting water flow vertically, and thus, can act as a transport mechanism of consumable particulates through the water column.

This research project investigates a novel organic carbon transport mechanism within giant kelp beds. I will be testing this mechanism using an array of sensors deployed within the artificial kelp plots which measure water flow, particle distribution, planktonic community, and organic carbon. Knowing how the presence of giant kelp affects food ability and transport to consumers is critical for understanding how these ecosystems function.

Currently, the research focus is on the analysis of water samples collected from the previous field season. This analysis will consist of microscopy imaging and program coding to determine particle distribution in relation to organic carbon signals through the water column. The goal is to quantify and identify the phytoplankton and other planktonic organisms within each sample. To process the data from a variety of sensors, python and java script will be developed in order to automate data computation. Later, there are plans to continue some data collection in the field. This would involve deploying and retrieving sensors from a research vessel.

Objectives:

• Calculate the contribution of organic carbon by phytoplankton within kelp beds.
• Determine if there is a stratification or mixing of particles through the water column.

UROC Researcher Role and Qualifications:

Microscope imaging will require Licea software use on windows PC (training will be provided). These images will then need to be analyzed using particle analyzer in ImageJ software. Some basic coding will need to be written in python to automate processing hundreds of .csv files obtained from oceanographic sensors.

Students role will be to help process data files into manageable formats for statistical analysis. The student will also aid in imaging samples under high power microscope which will be used for particle size and distribution analysis.

Qualifications:

• Student must be familiar with basic microscopy techniques. Training on the use of Licea microscopy software will be provided
• Student will be trained in image analysis using particle image analyzer in ImageJ software. This may require that some basic python code be written automate the processing of .csv files. Experience with any of these processes or software programs is highly desirable but not necessary.
• Familiarity with diatom identification is a plus but not necessary