NISTIR 8370 The San Francisco Estuary Institute Collection at the NIST Biorepository Debra Ellisor Nina Buzby Michael Weaver Melissa Foley Rebecca Pugh This publication is available free of charge from: https://doi.org/10.6028/NIST.IR.8370 NISTIR 8370 The San Francisco Estuary Institute Collection at the NIST Biorepository Debra Ellisor Rebecca Pugh National Institute of Standards and Technology Material Measurement Laboratory Hollings Marine Laboratory Charleston, SC 29412 Nina Buzby Michael Weaver Melissa Foley San Francisco Bay Estuary Institute 4911 Central Avenue Richmond, CA 94804 This publication is available free of charge from: https://doi.org/10.6028/NIST.IR.8370 April 2021 U.S. Department of Commerce Gina M. Raimondo, Secretary National Institute of Standards and Technology James K. Olthoff, Performing the Non-Exclusive Functions and Duties of the Under Secretary of Commerce for Standards and Technology & Director, National Institute of Standards and Technology Certain commercial entities, equipment, or materials may be identified in this document in order to describe an experimental procedure or concept adequately. Such identification is not intended to imply recommendation or endorsement by the National Institute of Standards and Technology, nor is it intended to imply that the entities, materials, or equipment are necessarily the best available for the purpose. National Institute of Standards and Technology Interagency or Internal Report 8370 Natl. Inst. Stand. Technol. Interag. Intern. Rep. 8370, 22 pages (April 2021) This publication is available free of charge from: https://doi.org/10.6028/NIST.IR.8370 Abstract The National Institute of Standards and Technology (NIST) has been collaborating with the San Francisco Estuary Institute (SFEI) since 2009, providing biobanking services at the NIST Biorepository in Charleston, South Carolina, in support of their ongoing water quality monitoring program, the Regional Monitoring Program for Water Quality in the San Francisco Bay (RMP). Specimens (bivalve tissue, bird egg contents, fish tissue and sediment) are collected and processed by SFEI-partnering institutions according to their This established protocols and shipped to the NIST Biorepository for archiving. This report outlines NIST’s role in the project, describes collection and processing protocols developed publication by SFEI and their collaborators, details shipping and archival procedures employed by biorepository staff and provides an inventory of the collection maintained by NIST from 2009 to 2020. is available Key words free Biobanking, specimens, SFEI, protocols. of charge from: https://doi.org/10.6028/NIST.IR.8370 i Table of Contents 1 The San Francisco Estuary Institute Project 1 1.1 Background and Responsibilities 1.2 Projected Collections 2 Preparing for a Collection 2 This 2.1 Supplies 2.2 Permits publication 3 Field Collection and Sample Processing 3 3.1 Bivalves 3.2 Sediment is 3.3 Seabird Eggs available 3.4 Sport fish 4 Shipment and Archival 6 free 4.1 Sample Shipment 4.2 Sample Archiving of charge 5 Collection Inventory 7 from: References https://doi.org/10.6028/NIST.IR.8370 List of Tables Table 1. SFEI Projected Project Plan 8 Table 2. Solvent Wash Protocol 9 Table 3. Sampling Sites for RMP Bivalve Monitoring 9 Table 4. Sampling Sites for RMP Seabird Egg Monitoring 10 Table 5. Sampling Information for Sport Fish Monitoring 11 Table 6. Summary of SFEI Specimens Archived at the NIST Biorepository 13 List of Figures Fig. 1 SFEI collaborators and responsibilities 14 Fig. 2 Cryovial with barcode label appropriately applied 14 Fig. 3 PFA jar lid tab with barcode label appropriately applied 15 ii Fig. 4 PFA jar with barcoded tab appropriately inserted into the lid 15 This publication is available free of charge from: https://doi.org/10.6028/NIST.IR.8370 iii 1. THE SAN FRANCISCO ESTUARY INSTITUTE PROJECT 1.1 Background and Responsibilities The San Francisco Estuary Institute (SFEI) is a non-profit research institute in Richmond, California that administers the Regional Monitoring Program for Water Quality in the San Francisco Bay (RMP). The RMP was created in 1993 through San Francisco Bay Regional Water Quality Control Board Resolution No. 92-043 that directed the Executive Officer to This implement a Regional Monitoring Plan in collaboration with permitted dischargers pursuant publication to California Water Code, Sections 13267, 13383, 13268 and 13385. The goal was to replace individual receiving water monitoring requirements for dischargers with a comprehensive Regional Monitoring Program. As such, the RMP has been collecting and archiving tissue and sediment samples for retrospective chemical analyses to assess water quality in San is Francisco Bay and surrounding areas. available Prior to 2010, these samples had been stored at -20 °C at SFEI and collaborator facilities. However, reports from other research groups indicated that a storage temperature of -20 °C may not be suitable for the long-term (> 10 years) stability of chemical contaminants in these free samples. Storage at -80 °C or lower is recommended, with storage at cryogenic temperatures of (≤ -150 °C) believed to allow sample preservation without any major structural or charge biochemical changes over several decades [1],[2]. Since 2010, the National Institute of Standards and Technology (NIST) has been providing banking services to SFEI for long-term archiving of biological and environmental specimens at the NIST Biorepository located in from: the Hollings Marine Laboratory, Charleston, South Carolina. These services include: https://doi.org/10.6028/NIST.IR.8370 1. Providing clean storage containers for sample collection, which include both 22 mL perfluoroalkoxy (PFA) jars and 5 mL or 10 mL polypropylene cryovials 2. Providing pre-printed barcode labels according to information obtained from SFEI or SFEI-affiliated field collectors for sample tracking in the NIST Biorepository database 3. Providing long-term archival of samples in liquid nitrogen vapor-phase freezers and maintaining samples according to NIST Biorepository standard operating procedures 4. Shipping samples banked from SFEI-administered programs to testing laboratories upon request 5. Maintaining an electronic database of SFEI samples, including sample identification information and sample location tracking information A 25-year plan was developed for service from 2009-2034 (Table 1). Though the collaboration began in 2010, the previous year’s collection (2009) was incorporated into the NIST Biorepository as well. Every five years, the agreement is revisited by both NIST and SFEI and the terms agreed upon. If changes are made during the span of the five-year agreement, amendments are drafted and included to incorporate changes in collection, funding or other necessary details. 1 1.2 Projected Collections The RMP is responsible for the collection of bivalve, bird egg, sediment and sport fish specimens. SFEI also collects sport fish specimens for the California Surface Water Ambient Monitoring Program (SWAMP), which are included in the archive. Collections are conducted by SFEI or their associated contractors according to protocols developed within their institution. Details regarding each archived collection are outlined below, including projected plans for SFEI collections. Deviations from these plans can occur for various reasons and are This addressed on a case-by-case basis. Current sampling schemes are described by component publication below. • Bivalves, including mussels (Mytilus californianus) are collected from a reference site and deployed for about 100 days at seven fixed locations. Native clams (Corbicula is fluminea) are collected from two sites synoptically with mussel deployments. Bivalve available collection frequencies have varied over time. • Double-crested cormorant (Phalacrocorax auritus) eggs are collected from three fixed sites and Forster’s tern (Sterna forsteri) eggs from a variable number of sites every three years. free • Sediment was historically collected every four years from 27 subtidal locations (seven of fixed sites, 20 random sites). The frequency of subtidal collections decreased to every charge ten years starting in 2018. Sediment samples from the Bay margins were collected in 2015 and 2017 from 40 locations each year. Bay margins collections will continue to be collected every four years. from: • Five to 15 sport fish species are collected from seven popular fishing locations every five years. https://doi.org/10.6028/NIST.IR.8370 • Other SFEI programs, such as SWAMP, have also been included in the collection. The key contacts and collaborators for each collection are outlined in Figure 1. 2. PREPARING FOR A COLLECTION Prior to each collection event, SFEI contacts the NIST Biorepository to notify them of upcoming events and requests clean supplies and labels for shipment to the appropriate collaborator. 2.1 Supplies NIST is responsible for receiving storage containers purchased by SFEI, cleaning these containers and shipping them to field collectors prior to each collection event. Because the main objective of the SFEI collections is to monitor a range of environmental pollutants that have different chemical properties, two different storage container types were chosen at the inception of the collaboration with NIST in order to prevent sample contamination and accommodate various downstream analyses. Samples are stored in either 22 mL PFA jars or polypropylene cryovials (either 5 mL or 10 mL volumes). Polypropylene cryovials are