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Moira Décima1, Deborah Steinberg2 and Linsey Sala1
1Scripps Institution of Oceanography, UCSD
2Virginia Institute of Marine Science

Biological collections are a critical component of scientific infrastructure. They are at the core of innovative research on globally relevant issues by serving as archives of Earth’s natural heritage, and are powerful assets used in all types of formal and informal educational settings. They support research on basic biological structures and processes, as well as deepen our understanding of evolution, biodiversity, and global environmental change. One key, unappreciated aspect of biological collections is how they often advance science in ways that were not anticipated by their collectors. In fact, the development of new technologies allowing deeper investigations into physical specimens continues to increase the value of biological collections over time. A vital point to acknowledge in our current times with global climate change is that an increasing number of collected species will no longer exist in nature – our biological collections holding the record of their passing time on earth.

Important contributors to biological collections are two pelagic LTERs: the California Current Ecosystem (CCE) and the Palmer Antarctica (PAL) sites, established to investigate the effects of multiple scales of climate forcing on pelagic ecosystems along California and the Antarctic Peninsula, respectively. These programs have collected thousands of plankton samples for ongoing studies of pelagic ecology and oceanography and provide a rich repository for investigating the multiple effects of anthropogenic influences on the marine pelagic ecosystem, including climate change.

The California Current Ecosystem (CCE) LTER site was established in 2004 on the shoulders of the CalCOFI (California Cooperative Oceanic Fisheries Investigations) program, an oceanographic monitoring program that was started in 1949 after the crash of the sardine fishery The Scripps Institution of Oceanography’s Pelagic Invertebrate Collection (SIO-PIC) at the University of California, San Diego houses the zooplankton samples from CalCOFI and CCE LTER. The collection, however, predates these programs, dating back to the turn of the 20th century, when zooplankton samples began to be collected the year Scripps was founded in 1903. Systematic samplings of small areas of the California Current were conducted during the first 4 decades of the century, followed by a rapid expansion of sampling in the post WWII years. This included expanded sampling in the California Current but also open ocean expeditions to various areas round the world, including the ocean North Pacific, the Indo Pacific and Antarctica. SIO-PIC currently houses approximately 148,000 bulk net tow samples and 40,000 reference specimen lots. This is one of the largest university-based collections of pelagic invertebrates in the world. Approximately 87,000 zooplankton samples have been collected as part of CalCOFI and CCE LTER that reside and are maintained in SIO-PIC.

Credit: Scripps Institution of Oceanography at UC San Diego; Linsey Sala

Figure 1: Inside the Pelagic Invertebrate collection, in 1911 (top) and 2024 (bottom).

Although CalCOFI was initially established as an ichthyoplankton monitoring program, the zooplankton samples collected through this program have shed light on a multiplicity of ecosystem-level processes. Decades of sampling allowed scientists to detect widespread shifts in the California Current ecosystem and krill communities in response to multidecadal and El Niño Southern Oscillation (ENSO) forcing, as well as secular long-term changes in gelatinous zooplankton1-6. Samples stored in the collections also allow for other assays, such as biochemical analyses enabling investigations into the effects of past ENSO events on isotopic baselines and foodweb structure7-9, or dietary studies focusing on gut contents of stored specimens. Importantly, subsequent studies using samples within the collections were able to shed light on phenomena and impacts of anthropogenic forcing that were not part of the original sampling intention. For example, gut contents of zooplankton indicated that a harmful algal bloom was likely responsible for ‘Hitchcock’s birds’, with high abundances of Pseudo-nitzschia (producers of domoic acid) as the culprit of erratic seabird behavior that inspired the famous film10. Investigations into microplastics found that these have been prevalent in the ecosystem since at least the 1980s11, and ubiquitous in the guts of salps – a type of generalist particle-feeding zooplankton12. Blue whale migration timing was related to variability in spring krill biomass, with decadal-scale increases in temperature leading to earlier whale arrivals and an extended residence time in Southern California13. These are just a few examples of studies that have capitalized on specimens archived within the Collections holdings.

Credit: Photo Credit: Linsey Sala

Figure 2: Examples of reference zooplankton specimens archived at PIC.

The Palmer Antarctica (PAL) LTER was established in 1990 to investigate the effects of climate change on the marine pelagic ecosystem west of the Antarctic Peninsula. Long-term warming, as well as sub- decadal climate oscillations, affects the population dynamics and life history strategies of organisms in this highly productive ecosystem through modulation of the amount and timing of sea ice. PAL includes over three decades of sampling the pelagic food web in the region – from bacteria, phytoplankton, zooplankton, penguins, to whales. As part of this effort, long-term or sub-decadal trends tied to climate have been documented in zooplankton including the keystone species Antarctic krill (Euphausia superba), gelatinous salps, and pteropods (pelagic snails)14-16. Thousands of zooplankton samples have been collected along the Antarctic Peninsula as part of PAL LTER and are stored both in the Smithsonian National Museum of Natural History and at the Virginia Institute of Marine Science (VIMS) 

Credit: Andrew Corso, CC BY-SA 4.0.

Figure 3: Larval fish specimens from PAL-LTER in VIMS Nunally Ichtyology Collection

Unanticipated in the PAL sampling program and for our physical collections was the interest in, and usefulness of, the zooplankton samples for the study of the ecology and life history of larval fishes (‘bycatch’ in our plankton net tows) in the region. Funding that leveraged PAL LTER zooplankton samples plus those from other regions was secured in the mid-2010’s to expand and digitize the larval fish collection as part of the Nunnally Ichthyology Collection at VIMS. The study of these museum-archived larval fishes, sorted from the PAL LTER plankton collection, led to the description of previously undocumented life history stages of known fish species17, the discovery of a new species18, and documentation of warmer sea surface temperature and decreased sea ice leading to reduced larval abundance of Antarctic Silverfish (Pleuragramma antarctica) – an important food source for penguins and other higher trophic levels19. The PAL LTER larval fish time series is now the longest running, fisheries-independent collection of Antarctic fishes in the world.

The bulk net tow samples that both of these LTER sites collect refer to the mixed community of zooplankton retrieved by a plankton tow, while reference or voucher specimens refer to individual zooplankters that have been sorted out and identified to different taxonomic ranks through species level. The reference materials include representative and in some cases exemplar (or type) specimens from groups such as the euphausiids (krill), copepods, chaetognaths, cephalopods, and salps. Reference specimens are key to biodiversity studies, as well as investigations into the taxonomy, anatomy, ecology, and functional morphology of any given species. Taxonomic work conducted within SIO-PIC has led to the creation of formative taxonomic and biogeographic references of different zooplankton groups, including euphausiids20 mysids21, calanoid copepod families Euchaetidae22 and Heterorhabdidae23, cephalopods24, and descriptions of the larval stages of various commercially and ecologically indicative decapod crustaceans25.

The vast expanse of collection holdings means that many specimens have been collected and stored, but with variable information included in databases. This problem, which extends to many collections, is currently being addressed through an NSF-supported Thematic Collection Network (TCN): Digitization of Marine Invertebrate Collections (DigIn). The DigIn consortium is made up of 22 institutions digitizing marine invertebrate specimens from 19 collections across the United States. This project seeks to digitize, standardize, and make 840k specimen lot data and 400K images available online in global data aggregators. SIO-PIC and VIMS will add thousands of reference specimen records to this digitization effort, making unique specimens discoverable online that will enable further scientific investigations.

Closing thoughts: the need for continued Collections support

While the value of biological collections is recognized, recently evidenced by new requirements for NSF proposals to include a specimen management plan, critical support is insufficient to maintain their functioning and growth with continuing sample accession, as budgets supporting research continue to contract in the United States26,27. Their value is only going to increase with the pressing need to investigate ecosystem change in the Anthropocene, since collections are singularly equipped to provide us with key information on physiological, ecological and evolutionary data spanning decades and sometimes centuries28. Sustaining these priceless collections is urgent and needed in the face of declining biodiversity and accelerating global change.

This article part of DataBits, stories about data management, techniques, and tools. DataBits is curated by the LTER Information Managers. For more information and to contribute a DataBits article, reach out to the Network Office or Marina Frantz, current editor of DataBits.


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