Pacific Islands Fisheries Science Center Young Scientist Opportunity Projects

Project 1: Using environmental DNA to assess marine biodiversity in Hawaiʻi 

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Mentors: Dr. Jamison Gove, Dr. Jonathan Whitney, Andrea Schmidt (CIMAR)

Background: Effective biodiversity monitoring is vital to understanding and predicting how human and natural stressors influence the taxonomic composition of marine ecosystems. Current underwater coral reef survey techniques primarily document the presence of conspicuous species and do not characterize lower trophic levels such as algae, plankton, and cryptobenthic fauna. 

Thus, a large fraction of the total biodiversity on a given reef remains under sampled. This biodiversity may impact the underlying biophysical and ecological processes driving marine ecosystem function. Utilizing environmental DNA (eDNA) coupled with metabarcoding, we can now more holistically survey whole reef ecosystems (from microbes to mammals) across a range of reefs, allowing us to better understand gradients in biodiversity and the associated underlying drivers. 

Objectives: PIFSC’s Hawaiʻi Integrated Ecosystem Assessment (IEA) recently led a multi-disciplinary and collaborative research expedition focused on assessing biodiversity of shallow-water coral reefs in West Hawaiʻi. The internship will directly support data analysis and interpretation of the eDNA samples collected from this expedition. The selected intern will be exposed to and support the following research efforts: summarizing coral reef species across the study domain; comparing methodological approaches for sampling eDNA; creating species groups based on ecological and cultural relevance; quantifying and comparing biodiversity using a variety of species diversity metrics; assessing biodiversity based on variations in habitat, ocean conditions, and human impacts; and comparing eDNA results with concurrently collected visual benthic and fish survey data. 

Duties and Responsibilities: 

• Candidate will work with the research team to further refine the project scope based on the candidate’s skills and interests.
• Meet regularly with mentors to ensure the project is progressing and the goals of the internship are being met. 
• Produce a document on the project findings.
• Contribute to the development of a manuscript that supports the objectives of the project. 
• Present findings as part of a symposium with other NOAA summer interns.

Qualifications: 

• Applicants should have experience and/or strong interest studying coral reef ecosystems including an interest in quantitative community ecology. 
• An interest in using genomics, and in particular, eDNA to assess biodiversity.
• Strong quantitative skills including proficiency in Microsoft Office software (particularly Excel), some experience with command line programming such as R or Matlab, and a capacity to work with large data sets. 
• Good organizational skills, attention to detail, and ability to focus on repetitive tasks.
• Strong work ethic and a willingness to learn.
• Ability to work both independently and as part of a team.
• Ability to be flexible and adapt to a changing work environment.

Project 2: Transitioning the Hawaiian Monk Seal Biological Specimen Database

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Mentors: Vikram Khurana, Claudia Cedillo, Lizabeth Kashinsky (CIMAR)

Background: The Hawaiian Monk Seal Research Program (HMSRP) conducts research to develop and test targeted recovery strategies to conserve the Hawaiian monk seal population. Our scientists work to enhance the recovery of Hawaiian monk seals by investigating threats to their survival and working to mitigate factors impeding species recovery. As a part of the program's disease surveillance and outbreak preparedness efforts, HMSRP researchers collect biological specimens (e.g., blood, tissues, swabs, etc) and health data. The data is compiled using paper or electronic data sheets and manually entered later into a central database. HMSRP connects the samples to patient history information, lab diagnostics, field specimen collection and necropsy sample entry. The current specimen database documents, categorizes, archives locations and tracks over 80,000 samples for the HMSRP. The Protected Species Support Program (PSSP) works in collaboration with HMSRP to transition the current specimen archiving database system to a program-specific designed Microsoft Access database (will be referred to as Access database) to better suit the specific and unique needs that arise with protected species work. 

Objectives: The key objective of the selected intern will be to assist the transition of the HMSRP specimen data into a new Access database, which is a vital aspect of specimen data organization. The primary activities related to this objective will be to export data forms and fields into Excel files and work with program staff to transition into and build the new Access database. This includes troubleshooting HMSRP’s current centralized specimen database during the exporting process. They will also assist in quality control while transitioning the data as well as refinement of data fields. As part of the PSSP team, a PYSO Intern will work closely with the HMSRP and also develop an understanding of how the specimen data relate to research and conservation efforts for the species. In addition, the intern will have opportunities to learn about wildlife, fisheries research, and endangered species conservation, including broad exposure to other Hawaiian monk seal research areas and stranding response efforts as they arise.

Duties and Responsibilities: 

• Export data fields and data from current database.
  • Organize Excel spreadsheets of exported data from the current database in preparation for importing to the new database and organize data in folders by type.
  • Troubleshoot current database issues such as exporting errors and complications utilizing tab delimited files.
  • Assist HMSRP and PSSP partners with the design of data entry fields and forms in Microsoft Access.
• Assists in quality control of data. 
  • Cross references exported data with current database.
  • Assists in corrections and adjustments of data results.
• Meet with Federal and Cooperative Institute for Marine and Atmospheric Research (CIMAR) mentors regularly.
• Take part in HMSRP and PSSP team meetings.
• Participate in and/or observe HMSRP field research and stranding response efforts opportunistically. 
• Present database project as part of a symposium with other NOAA summer interns.

Qualifications:

• Interest in data management, protected species research, and specimen archiving.
• Experience utilizing web-based and database forms including Microsoft Access and Excel.
• Extreme attention to detail.
• Ability to remain focused especially while working with large electronic data sets, troubleshooting technological problems, and quality controlling data.
• Excellent writing and communication skills.
• Strong interest in designing, debugging, and testing databases.
• Interest in protected species conservation and/or veterinary science.

Project 3: PIFSC Research Cruise Operations (GIS) Dashboard: User Friendliness Phase

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Mentors: Dr. M. Kimberly Lowe, LT Kristin M. Sojka and Kyle Koyanagi (CIMAR)

Background: Throughout 2019-2021, several marine mapping applications were developed by staff of the Pacific Islands Fisheries Science Center (PIFSC) using ArcGIS Online ® tools and the NOAA GeoPlatform to provide ready access to geospatially defined fisheries, habitat and protected species research data from the US Pacific Islands Region (PIR).  In 2022, these base layers and live feed sources were compiled into a prototype PIFSC Science Operations Dashboard intended to allow tracking of PIFSC research cruise operations in progress and along with current physiographic and oceanographic data (depth profile, bottom substrate, topography, nutrients, temperature, salinity, etc.). The prototype was completed through an early development stage and shared as a proof of concept with staff at the Pacific Islands Fisheries Science Center (PIFSC), Office of Marine and Aviation Operations (OMAO), and other NOAA users. An important pending step, once in-house testing was complete, would be to configure the dashboard to display the most recent ship location, historical track lines, vessel type, and allow the user to turn off/on the various optional base layers in the most user-friendly format possible.  Then the application would be ready to publish on the NOAA GeoPlatform and be made available to all NOAA users.

Objectives: The selected intern will assist with the development, configuration and refinement of the PIFSC Operations Dashboard to meet project requirements and will package the application for final review and approval by PIFSC and OMAO. All of the data is open source (mostly NOAA), so few additional approvals are required. PIFSC SOD will be responsible for obtaining OMAO’s (another line office) sign off on publishing the application to the NOAA Geoplatform where all NOAA users will have access.

The target audience includes PIFSC Directorate and division staff, as well as participants in a given research cruise during field operations. Users can also upload the locations of new field stations during operations. Once fully configured, it should be visually appealing, intuitive and easy to use. The dashboard’s online documentation will be updated to serve as a reference, so that novice users can look up tips and tricks, understand how to use widgets, and easily navigate the application.

This project is part of the PIFSC Hōkūala Kīkaha Kai Internship, which will give a successful student the opportunity to apply for a position as a biological science technician for up to 2 years following completion of PYSO, with the potential for growth into a permanent position with the Pacific Islands Fisheries Science Center.

Duties and Responsibilities:

• Work with mentor and research team to further refine project scope.
• Complete ArcGIS online training in basic mapping concepts and dashboard configuration.
• Develop and refine Operations Dashboard prototype.
• Complete the online GIS dashboard application, including documentation, using ArcGIS Online.
• Review, test, refine and publish the application on the NOAA Geoplatform.
• Develop project summary findings. 
• Meet regularly with mentors and SOD staff to refine the GIS application.
• Present findings as part of a symposium with other NOAA summer interns.

Qualifications:

• Experience and/or interest in geographic information systems (GIS).
• Experience with computers and proficiency in basic Microsoft Office software (Word, Excel, PowerPoint).
• Capacity to work with large data sets.
• Ability to learn new software (online training in ArcGIS and GIS dashboards will be completed in the first few weeks of the internship).
• Good organizational skills, attention to detail, and ability to focus on repetitive tasks.
• Strong work ethic.
• Willingness to learn.
• Ability to work both independently and as part of a team.
• Ability to be flexible and adapt to a changing work environment.

Project 4: It’s all about the plankton! Exploration of zooplankton communities in the North Pacific Ocean

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Lead Mentors: Dr. Donald Kobayashi (PIFSC/PRP), Dr. Kisei Tanaka (PIFSC/ARP), Dr. Joy Smith (CIMAR/ARP), Dr. Johanna Wren (PIFSC/PRP)

Scientific Advisors: Bruce Mundy, Dr. Jonathan Whitney, Andrea Schmidt, Emily Contreras, Dr. Ryan Rykaczewski

Background: Researchers collected zooplankton across the North Pacific Subtropical Gyre as part of the NOAA PIFSC Bigeye Tuna Initiative, which aims to understand what environmental conditions characterize a suitable nursery habitat for the commercially important bigeye tuna. Zooplankton are critical to ecosystem functioning and provide food to higher trophic levels. Some zooplankton are the early life stages of commercially important species, as well as species of management and conservation concerns. Due to zooplankton’s short life span and sensitivity to fluctuating water conditions, shifts in composition and biomass make them potential bioindicators for environmental change and identifying suitable tuna habitat. Since zooplankton biomass provides an estimate for available food, areas with greater available food may predict areas of greater larval fish recruitment. 

This study aims to link zooplankton biomass and shifts in larval fish species to changes in environmental parameters, both satellite-derived (temperature, chlorophyll-a, mixed layer velocities) and in situ measured variables (oxygen, temperature, salinity, and water chemistry), across a latitudinal gradient in the North Pacific Ocean. Multiple zooplankton samples were collected via 2-m ring nets and stored in ethanol. Zooplankton samples will be measured for total wet biomass, and then microscopy will be used to identify the abundance of selected zooplankton taxa, including both larval fish and invertebrate species. The number of taxa and species will be determined from sorting efforts currently underway, but tentatively could include skipjack tuna (Katsuwonus pelamis) and pelagic molluscs (heteropods and/or pteropods). Biomasses and sizes of the selected taxa will also be enumerated.

Objectives: 

• Compile environmental data for sites where zooplankton were collected. Some data will be from satellite remote sensing, and some will have been collected in situ via oceanographic instruments.
• Prepare a summary of key environmental variables across a latitudinal gradient.
• Analysis of a subset of zooplankton samples collected via 2-m ring nets, specifically identifying larval fish and major taxonomic groups of zooplankton, with counts, biomasses, and sizes.
• Explore statistical analyses to link changes in zooplankton characteristics to environmental conditions.

The project could result in a peer-reviewed scientific publication.

Duties and Responsibilities:

• Analyze global and regional satellite data (e.g. temperature, chlorophyll-a, mixed-layer properties.
• Identify and sort zooplankton under a microscope.
• Compile analysis and findings into a written report.
• Write a news story for the NOAA Fisheries website and social media outlets.
• Present findings as part of a symposium with other NOAA summer interns.

Qualifications: 

• Willingness to spend a substantial portion of the internship in the laboratory analyzing zooplankton samples under the microscope.
• Working knowledge of programming languages such as R and basic statistical methodologies.
• Willingness to conduct ecological analyses of various environmental data using R.
• Ability to accurately collect and analyze information from PIFSC’s Environmental Data Summary (EDS) tool, including climatological data from satellite-derived data products such as sea surface temperature.
• Excellent skills with Microsoft Excel or Google Sheets.

Questions? Please contact pifsc.pyso@noaa.gov.

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