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Biological Collections: Ensuring Critical Research and Education for the 21st Century (2020)

Chapter: 4 Building and Maintaining a Robust Infrastructure

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Suggested Citation:"4 Building and Maintaining a Robust Infrastructure." National Academies of Sciences, Engineering, and Medicine. 2020. Biological Collections: Ensuring Critical Research and Education for the 21st Century. Washington, DC: The National Academies Press. doi: 10.17226/25592.
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Suggested Citation:"4 Building and Maintaining a Robust Infrastructure." National Academies of Sciences, Engineering, and Medicine. 2020. Biological Collections: Ensuring Critical Research and Education for the 21st Century. Washington, DC: The National Academies Press. doi: 10.17226/25592.
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Suggested Citation:"4 Building and Maintaining a Robust Infrastructure." National Academies of Sciences, Engineering, and Medicine. 2020. Biological Collections: Ensuring Critical Research and Education for the 21st Century. Washington, DC: The National Academies Press. doi: 10.17226/25592.
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Suggested Citation:"4 Building and Maintaining a Robust Infrastructure." National Academies of Sciences, Engineering, and Medicine. 2020. Biological Collections: Ensuring Critical Research and Education for the 21st Century. Washington, DC: The National Academies Press. doi: 10.17226/25592.
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Suggested Citation:"4 Building and Maintaining a Robust Infrastructure." National Academies of Sciences, Engineering, and Medicine. 2020. Biological Collections: Ensuring Critical Research and Education for the 21st Century. Washington, DC: The National Academies Press. doi: 10.17226/25592.
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Suggested Citation:"4 Building and Maintaining a Robust Infrastructure." National Academies of Sciences, Engineering, and Medicine. 2020. Biological Collections: Ensuring Critical Research and Education for the 21st Century. Washington, DC: The National Academies Press. doi: 10.17226/25592.
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Suggested Citation:"4 Building and Maintaining a Robust Infrastructure." National Academies of Sciences, Engineering, and Medicine. 2020. Biological Collections: Ensuring Critical Research and Education for the 21st Century. Washington, DC: The National Academies Press. doi: 10.17226/25592.
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Page 77
Suggested Citation:"4 Building and Maintaining a Robust Infrastructure." National Academies of Sciences, Engineering, and Medicine. 2020. Biological Collections: Ensuring Critical Research and Education for the 21st Century. Washington, DC: The National Academies Press. doi: 10.17226/25592.
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Page 78
Suggested Citation:"4 Building and Maintaining a Robust Infrastructure." National Academies of Sciences, Engineering, and Medicine. 2020. Biological Collections: Ensuring Critical Research and Education for the 21st Century. Washington, DC: The National Academies Press. doi: 10.17226/25592.
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Page 79
Suggested Citation:"4 Building and Maintaining a Robust Infrastructure." National Academies of Sciences, Engineering, and Medicine. 2020. Biological Collections: Ensuring Critical Research and Education for the 21st Century. Washington, DC: The National Academies Press. doi: 10.17226/25592.
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Page 80
Suggested Citation:"4 Building and Maintaining a Robust Infrastructure." National Academies of Sciences, Engineering, and Medicine. 2020. Biological Collections: Ensuring Critical Research and Education for the 21st Century. Washington, DC: The National Academies Press. doi: 10.17226/25592.
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Page 81
Suggested Citation:"4 Building and Maintaining a Robust Infrastructure." National Academies of Sciences, Engineering, and Medicine. 2020. Biological Collections: Ensuring Critical Research and Education for the 21st Century. Washington, DC: The National Academies Press. doi: 10.17226/25592.
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Page 82
Suggested Citation:"4 Building and Maintaining a Robust Infrastructure." National Academies of Sciences, Engineering, and Medicine. 2020. Biological Collections: Ensuring Critical Research and Education for the 21st Century. Washington, DC: The National Academies Press. doi: 10.17226/25592.
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Page 83
Suggested Citation:"4 Building and Maintaining a Robust Infrastructure." National Academies of Sciences, Engineering, and Medicine. 2020. Biological Collections: Ensuring Critical Research and Education for the 21st Century. Washington, DC: The National Academies Press. doi: 10.17226/25592.
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Page 84
Suggested Citation:"4 Building and Maintaining a Robust Infrastructure." National Academies of Sciences, Engineering, and Medicine. 2020. Biological Collections: Ensuring Critical Research and Education for the 21st Century. Washington, DC: The National Academies Press. doi: 10.17226/25592.
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Page 85
Suggested Citation:"4 Building and Maintaining a Robust Infrastructure." National Academies of Sciences, Engineering, and Medicine. 2020. Biological Collections: Ensuring Critical Research and Education for the 21st Century. Washington, DC: The National Academies Press. doi: 10.17226/25592.
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Page 86
Suggested Citation:"4 Building and Maintaining a Robust Infrastructure." National Academies of Sciences, Engineering, and Medicine. 2020. Biological Collections: Ensuring Critical Research and Education for the 21st Century. Washington, DC: The National Academies Press. doi: 10.17226/25592.
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Page 87
Suggested Citation:"4 Building and Maintaining a Robust Infrastructure." National Academies of Sciences, Engineering, and Medicine. 2020. Biological Collections: Ensuring Critical Research and Education for the 21st Century. Washington, DC: The National Academies Press. doi: 10.17226/25592.
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Page 88
Suggested Citation:"4 Building and Maintaining a Robust Infrastructure." National Academies of Sciences, Engineering, and Medicine. 2020. Biological Collections: Ensuring Critical Research and Education for the 21st Century. Washington, DC: The National Academies Press. doi: 10.17226/25592.
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Page 89
Suggested Citation:"4 Building and Maintaining a Robust Infrastructure." National Academies of Sciences, Engineering, and Medicine. 2020. Biological Collections: Ensuring Critical Research and Education for the 21st Century. Washington, DC: The National Academies Press. doi: 10.17226/25592.
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Suggested Citation:"4 Building and Maintaining a Robust Infrastructure." National Academies of Sciences, Engineering, and Medicine. 2020. Biological Collections: Ensuring Critical Research and Education for the 21st Century. Washington, DC: The National Academies Press. doi: 10.17226/25592.
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Suggested Citation:"4 Building and Maintaining a Robust Infrastructure." National Academies of Sciences, Engineering, and Medicine. 2020. Biological Collections: Ensuring Critical Research and Education for the 21st Century. Washington, DC: The National Academies Press. doi: 10.17226/25592.
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4 Building and Maintaining a Robust Infrastructure The health of biological collections—and, ultimately, of the scientific research that relies on them—is dependent on the underlying infrastructure that assembles, maintains, and provides access to these collections. That infrastructure includes not only the physical space and equipment used to house and maintain the specimens in a collection, but also their accompanying data and the procedures governing their care. It includes the technologies to produce digital data and the cyberinfrastructure to store, analyze, and aggregate data with those of other collections through online portals (see Chapter 5). Finally, biological collections infrastructure includes the trained staff, students, and volunteers who acquire, curate, manage, ensure the quality of specimen and their data and coordinate their scientific and educational uses. Such infrastructure can be expensive and time-consuming to maintain, but the value that biological collections provide to the scientific research and education communities more than justifies these expenditures. For example, an analysis of biological resource centers that collect, certify, and distribute living organisms demonstrated that these institutions amplify the cumulative impact of individual research discoveries and thereby significantly increase the pace and reduce the cost of research (Furman and Stern, 2011). This chapter focuses on the physical infrastructure challenges of ensuring that biological collections remain available and viable for research and educational use. It also touches on an important aspect of the biological collections infrastructure—the mechanisms that ensure that the extended research and the broader education communities have convenient and effective access to the biological specimens maintained in these collections. THE PROMISE OF BIOLOGICAL COLLECTIONS INFRASTRUCTURE It is easy to overlook the importance of infrastructure. When everything is functioning smoothly, infrastructure—whether it is the facilities of a university, the computers and transmission devices underlying the Internet, or the air traffic control system responsible for air travel—tends to be taken for granted. The same is true of the nation’s system of biological collections. When collections are discussed, it is generally in terms of their physical, digital, and intellectual assets and resources used by researchers and others to answer questions about past, present, and future life on Earth. But those resources are available only because of the nation’s biological collections infrastructure, which not only maintains the specimens and associated biological materials and data, but also supports the means in which they are widely shared and distributed. The nation’s biological collections have a dual nature similar to that of biological field stations and marine laboratories, which are both individual entities and “collective elements of the nation’s broader scientific infrastructure” (NRC, 2014b, p. 45). As individual research repositories, each biological collection serves the institution in which it is housed and also serves the broader scientific community. Individual biological collections vary in nature from small, project-based collections with relatively simple infrastructure needs to large repositories of diverse living, fossil, and preserved specimens and their associated data with complex, sophisticated, and ongoing infrastructure needs. Biological collections can also be thought of as a collective system that is a vital component of the nation’s scientific infrastructure. This distributed system is somewhat analogous to the National Radio Prepublication Copy 71

Biological Collections: Ensuring Critical Research and Education for the 21st Century Astronomy Observatory (NRAO), 1 a dispersed set of telescopes that provide resources to astronomy researchers worldwide, as well as to formal and informal educational programs. The capability of distributed biological collections to serve as a collective national resource depends on ongoing digitization efforts and a cyberinfrastructure that allows them to link and integrate their digital data (see Chapter 5). One current difference from the NRAO is that biological collections are managed independently, with each collection in the network largely setting its own strategic plan and being responsible for its own mission, management, and funding. The specific physical infrastructure needs of biological collections vary according to the types of specimens they contain (e.g., size, number, taxonomy, and biosafety level), the maintenance requirements of the specimens (e.g., wet, dry, refrigerated, or frozen), and the intended scientific and educational objectives (see Figure 4-1). The requirements for cryopreserved (frozen) biological collections, for example, are particularly stringent because the specimens and biological material lose their viability or integrity if they thaw. Such collections are often stored in freezers kept at –80oC or in cryogenic storage drawers using liquid nitrogen at –190oC, both of which require constant monitoring and backup generators, particularly for specimens without duplicates housed at another location. At a minimum, all biological collections require a secure facility with the necessary equipment and controls to maintain lighting, temperature, humidity, airflow, and other environmental conditions at the levels required to maintain the specimens and prevent contamination and degradation. Many organisms are represented by a variety of collection types which may require different preservation methods, storage conditions, and locations (sometimes even involving multiple institutions). For example, in addition to herbarium specimens, plants may be represented by separate wood or seed collections, cell or callus cultures, plant genes in bacterial plasmids, frozen or silica-dried leaf tissue, and whole plants in fields, greenhouses, or growth chambers. Mammal and bird collections can include live animals, skin, and skeleton (or fluid- preserved) voucher preparations, frozen tissues, cell cultures, embryos, sperm, karyotypes, diverse sets of endo- and ectoparasites, and more (Galbreath et al., 2019). Ichthyology and herpetology collections contain predominantly ethanol-preserved wet specimens, but also maintain cleared and stained glycerin specimens and skeletal and tissue collections, all requiring different storage conditions. FIGURE 4-1 Different types of specimen storage. (A) Dry storage: fossil shells in drawers at the University of Colorado Boulder Museum of Natural History. (B) Cryogenic storage: microbial strains at the American Type Culture Collection. (C) Liquid storage: specimens in jars at the Florida Museum of Natural History. (D) Greenhouse; Arabidopsis Biological Resource Center at The Ohio State University. Even organisms that appear superficially similar, such as different types of microalgae, may require different types of infrastructure to maintain them as biological collections (see Box 4-1). Due to the wide variety of biological collections, there are many publications that describe specimen-specific infrastructure requirements and baseline standards (see Box 4-2). The basic physical infrastructure requirements also involve a variety of materials, tools, technologies, and other resources necessary to maintain and curate collections. Examples include compactors, digitization infrastructure (cameras, lighting, scanners, printers, etc.), backup generators, safety requirements (e.g., for ethanol or cryogenic 1 See http://public.nrao.edu/about. 72 Prepublication Copy

Building and Maintaining a Robust Infrastructure collection storage), media and reagents to preserve or promote growth, sensors, and alarms to monitor and raise alerts about unauthorized access or fluctuations or unsafe environmental conditions, and tools and technologies to authenticate accessioned material and periodically assess the condition or determine the genetic identity of specimens. An important feature of biological collections is that they—like many culturally and historically important collections—continue to grow. Specimens are added to biological collections through three main mechanisms: (1) field collecting of specimens in previously unexplored ecosystems and resurveying previously sampled ecosystems; (2) generating new, living genetically modified research organisms; and (3) the acquisition of specimens or entire collections by gift, donation, exchange, or purchase. During the 19th century, many of the largest and most ambitious biological collections grew through specific national or international research mandates to catalog all species of a given region, taxon, or clade. Today, many biological collections grow principally as a product of individual research projects or an individual institution’s priorities. The potential ramifications of neglecting the nation’s biological collections infrastructure are wide-ranging, with severe consequences for innovations in biotechnology, medicine, agriculture, energy, and many other sectors built on life science research (Flattau et al., 2007; McCluskey, 2017; Sigwart, 2018). Neglecting infrastructure could also affect research, public services, and private businesses that rely on accurate taxonomic identification, such as forensics, the study of disease outbreaks (human, wildlife, and agriculture), border protection, and the control of invasive species (Cook et al., 2020; McLean et al., 2016). In addition, most natural history collections are non-renewable scientific resources—they cannot be replaced. The loss of individual specimens or entire collections creates unfillable gaps in the knowledge of present and past life on Earth. Institutions that do not provide adequate infrastructure for their biological collections hamper their own missions to advance science and technology, build a highly skilled workforce, and educate the next generation of global citizens. BOX 4-1 Infrastructure and Maintenance of Microalgae Cultures Photo A: Algal culture room, courtesy of UTEX Culture Collection of Algae; Photo B: Courtesy of the National Center for Marine Algae and Microbiota. Microalgae are single-celled photosynthetic organisms that live in a wide range of aquatic and semi- aquatic habitats including lakes, rivers, oceans, snow, and damp soils. Collections of microalgae are used for a variety of research and commercial applications, such as for biofuel production, drug and nutrient development, and cosmetics (Khan et al., 2018). Some species of microalgae can be cryopreserved (frozen), but others must be maintained as live cultures. The UTEX Culture Collection of Algae at the University of Texas at Austin maintains algal live cultures on agar and in liquid, while some are cryopreserved. The Provasoli-Guillard National Center for Marine Algae and Microbiota (NCMA), located at the Bigelow Laboratory for Ocean Sciences in East Boothbay, Maine, is an example of two private culture collections that were developed into a national resource center to meet the needs of the research community. The NCMA maintains the largest and most diverse collection of publicly available marine microalgal strains. Prepublication Copy 73

Biological Collections: Ensuring Critical Research and Education for the 21st Century BOX 4-2 Select Publications About Requirements and Standards for Biological Collections Infrastructure A comprehensive reference for a risk-management approach for all types of collections including fine arts, libraries, and biological Preventive Conservation: Collection Storage collections. It discusses planning and assessment, building design Elkin and Norris (2019) and facilities management, and storage furniture and specimen housing. A comprehensive reference on the living stock collections of 14 The Biological Resources of Model different model organisms. It provides the history of each model Microorganisms organism, how the organisms are being used in scientific research, Jarrett and McCluskey (2019) and the particular requirements and best practices to obtain, maintain, preserve, characterize, and distribute the organisms. A scientific publication that provides recommendations and key Herbarium Practices and Ethics, III considerations for the infrastructure, operation, and services of Rabeler et al. (2019) herbarium collections, including digitization and virtual capabilities. It is the third update of a 1958 publication. ISO 20387:2018: Biotechnology—Biobanking— International standards that define the basic requirements for the General Requirements for Biobanking competence, impartiality, and consistent operation of biobanks. ISO (2018) A comprehensive reference on the technical and managerial requirements for biological repositories, including storage and Best Practices: Recommendations for processing equipment, information management systems, business Repositories, Fourth Edition planning, and specimen collection and access, among other critical ISBER (2018) dimensions. Campbell et al. (2018) provides a brief, accessible guide to new and revised details included in the fourth edition volume. A three-part publication that provides guidance on facilities management, infrastructure, and functions of museum staff to ensure a safe and hazard-free collection. Some of the issues Health and Safety for Museum Professionals addressed include fire protection; occupational and hazards waste Hawks et al. (2010) management; chemical, physical, electrical, and radiation hazards; and energy salvage, field work, conservation, and restoration. This publication is the result of a collaboration between the American Institute for Collaboration and SPNHC. International guidelines that address the full portfolio of infrastructure and management needs to maintain the quality and Best Practice Guidelines for services provided by biological resource centers, including potential Biological Resource Centers approaches to national certification. The guidelines resulted from OECD (2007) discussions of the OECD member countries, key partner countries, and the scientific community to serve as a target for quality management of living stock collections. A comprehensive compendium of 113 articles on the practical Storage of Natural History Collections: applications of storage systems for everything from vertebrate teeth Ideas and Practical Solutions to ethnic costumes to large fossils. Each article was written and Rose and de Torres (2002) reviewed by professionals in the fields of conservation and collections management. A comprehensive reference on a wide variety of collection care and management topics, including environmental controls, pest Managing the Modern Herbarium management, paper conservation, adhesives, destructive sampling, Metsger and Byers (1999) and case studies on moving a herbarium to new quarters. It is the result of a collaboration between the Royal Ontario Museum and SPNHC. 74 Prepublication Copy

Building and Maintaining a Robust Infrastructure CHALLENGES Maintaining a healthy physical infrastructure involves a variety of interrelated challenges. Perhaps the most obvious challenge involving specimens and data is that they need to be preserved indefinitely, beginning with their initial accession and continuing with long-term maintenance for both anticipated and unanticipated uses. Accordingly, the quality of the specimens needs to be carefully and constantly maintained to ensure that findings from past research can validly and reliably be compared with results in any number of future research investigations. These challenges are exacerbated by the fact that healthy collections are continually expanding through the acquisition of new material, which requires a steady increase in physical capacity. Finally, making specimens and data available to researchers and other users, including educators, students, and businesses, is important in maximizing the usefulness and of impact infrastructure considerations for the nation’s biological collections. The following sections describe these challenges in more detail. Collections Require Ongoing Preventive Conservation Without active and ongoing preventive conservation 2, natural history specimens will degrade over time and become less useful for research and education. Fluid-preserved specimens will eventually dry out if not stored in appropriate containers and resupplied with the appropriate liquids, cryopreserved tissues will decay if freezers are not maintained and kept at desired temperatures, dried collections can fall victim to insects and mold, and fossils are subject to Byne’s (Cavallari et al., 2014; NPS Conserve-O- Gram, 2008 3) and pyrite diseases (Cavallari et al., 2014; Larkin, 2011; NPS Conserve-o-gram, 1998 4). Responding to the requirement that collections be viable and pure, living collections also address these issues through quality control processes as described below. Providing ongoing funding for the active care of collections—as well as for the accessioning of new specimens into collections—is a challenge for an institution, especially one charged with the maintenance of many types of scientific research infrastructure. In addition, many biological collections are located in environments that are prone to disaster— natural and human-caused. For example, an attempt to assess risks to herbaria found that about half of all herbaria have at least three risk factors, one of which relates to their location in areas prone to flooding, earthquakes, severe weather (hurricanes, typhoons, etc.), or social unrest, and the other risk factors relate to insufficient staffing and limited utility to modern research because of the collections’ inaccessibility (Thiers et al., 2018). However, even in relatively safe locations, inadequate infrastructure enhances vulnerabilities to natural disasters and theft (Fire at Historic Torrey Hall, 2017 5; Araujo, 2019). Although it may be possible to recover from damage to facilities and equipment, many natural history specimens, including fossils and specimens collected in the past, contain baseline knowledge for historic environmental conditions and prior research that cannot be replaced. The coronavirus disease 2019 (COVID-19) pandemic poses an additional threat. Up to one-third of all museums in the United States may permanently close due to financial losses during the pandemic, potentially leading to the loss or relocation of millions of natural history specimens and fossils (Merritt, 2020). 6 In addition, some living collections cannot be cryopreserved or lyophilized, such as some microalgae or Drosophila species, and require labor-intensive procedures to maintain. When fewer people are allowed to enter the facility during 2 Preventive care is defined as actions taken to minimize or slow the rate of deterioration and prevent damage; it includes activities such as risk assessment, the development and implementation of guidelines for continuing use and care, ensuring appropriate environmental conditions for storage and exhibition, and instituting proper procedures for handling, packing, transport and use (SPNHC, 1994). 3 See https://www.nps.gov/museum/publications/conserveogram/11-15.pdf. 4 See https://www.nps.gov/museum/publications/conserveogram/11-02.pdf. 5 See https://www.uvm.edu/uvmnews/news/fire-historic-torrey-hall. 6 See https://www.youtube.com/watch?v=48rKE129ME4. Prepublication Copy 75

Biological Collections: Ensuring Critical Research and Education for the 21st Century a pandemic, maintenance of these stocks can be impacted and if their transfer is delayed, stocks may lose viability. Sometimes the only solution to failing infrastructure is to transfer specimens wholly or in part to a more stable situation. Usually, the collections transferred are small, although in 2018, the University of Louisiana at Monroe moved nearly 6 million specimens from the herbarium and fish collections to the Botanical Research Institute of Texas and Louisiana State University (the herbarium collection) and to the Tulane University Biodiversity Research Institute (the fish collection). Many collections have been saved from decline or outright destruction when rescued by another institution that was willing to accept responsibility for their care. The U.S. Culture Collection Network published a survey of rescued living microbial collections, including resources at the E. coli Genetic Stock Center, the Fungal Genetics Stock Center, the Phaff Yeast Culture Collection, and the University of Texas Culture Collection of Algae, and described some of the scientific discoveries made since with the rescued specimens (Boundy-Mills et al., 2019). This effort demonstrated the value of having established capacity to ensure that important collections survive when there is insufficient financial support or when senior staff retires or changes institutions. However, transferring collections to a new institution may potentially have negative consequences. Such transfers increase infrastructure, financial, and regulatory requirements at the new institution, break links to historical knowledge about the collection, and can remove the specimens farther from the region where the specimens were collected and, potentially, from the primary users of those collections. Living Stock Collections Require Consistent Quality Control The quality of a living stock collection is a major determinant of whether its specimens can be used for research and of the type of research for which they are most suitable. Specimen quality is critical for ensuring the reproducibility and replicability of research results and reflects on the credibility of collections and their institutions. Quality control, which is similar to preventive conservation for natural history specimens, is the process through which collections personnel seek to ensure that the quality of specimens and reference materials, such as cell cultures, are standardized and maintained. Customers of living stock collections expect that the material they receive will be properly identified as to the species, will possess the expected genetic markers, and will be viable and pure. For these reasons, many living stock collections have staff dedicated to quality assurance. Quality assurance documents and demonstrates control over the quality control processes. Quality assurance facilitates and organizes historical information about the origin and handling of the material and also preserves the traceability of the material. Quality control and quality assurance require performing standardized tests for authentication, sample characterization, replenishment, and long-term stability. Such standardization is based on experience previously gained and includes predetermined ideal ways to identify suitable growth, storage conditions, and protocols to characterize and define the biological materials. These efforts extend not only to handling the materials, but also to shipping the materials to users and receiving incoming materials. Every living collection has taxon-specific minimum categories of quality benchmarks. Jarrett and McCluskey (2019) describe some of the quality considerations for 14 different living model organisms along with descriptions of the facilities and procedures necessary to maintain them. Box 4-3 provides an example of typical minimum categories of quality benchmarks for living microbial collections. There are four key challenges to maintaining quality control of living collections. First, best practices are neither standardized across the living stock collections community nor updated as new regulations and technologies become available. Second, some living collections, such as those of bacteria, yeast, fungi, and other microbes, contain specimens isolated so long ago that they need to be re-identified using current taxonomy and technologies. Third, it is often difficult to confirm genetic markers in materials received from the research community because many living stock collections lack access to specialized personnel, reagents, and equipment for genotyping. Fourth, the equipment and infrastructure to cryopreserve living collections are expensive. Cryopreservation using liquid nitrogen tanks is an 76 Prepublication Copy

Building and Maintaining a Robust Infrastructure effective, but costly, approach to ensuring the longer-term viability of many types of cells and tissues. Many living collections opt for mechanical freezers, which are more affordable but result in a reduction in long-term viability. For some organisms, lyophilization (freeze-drying) may be used, rendering the material stable for long periods of time at room temperature. BOX 4-3 Common Benchmark Categories That Define Quality Control for Living Microbial Collections Culture of Streptococcus aureus grown on blood agar. During growth, this item showed two colony types, suggesting the presence of a contaminant. The arrow shows bigger and pigmented colonies that, after further analysis, were confirmed to be the contaminant. The smaller white colonies were colony-purified for distribution. SOURCE: BEI Resources. Viability. Living collections need to define protocols to confirm that their microbes pass quality control after amplification, preservation, and shipping to the user. Some collections often perform viability testing at intervals during storage. Vertebrate facilities use best practices in alignment with the Animal Welfare Act (https://www.nal.usda.gov/awic/animal-welfare-act), which may include testing for pathogens and health status prior to distribution. Identification. Confirmation of the specimen identity down to the genus and species level (if known) is done for each lot. Accurate identification and characterization of the material are crucial for compliance with regulations related to restricted agents. For example, organisms that can be weaponized are highly regulated and controlled. These collections require a high investment in infrastructure, which explains why these organisms are handled by only very few biological collections. Purity. This category applies to microorganisms as well as larger organisms. Microbes are confirmed pure by standard macroscopic and microscopic techniques as well as molecular assays such as nucleic acid sequencing. Collections of larger organisms such as plant germplasm (http://fps.ucdavis.edu/), zebrafish (zebrafish.org), and Xenopus (https://www.mbl.edu/xenopus) are subjected to a sanitation and/or quarantine process to avoid contamination of the facility. Strain characterization. Some microbiological collections have defined processes to follow, depending on the collection, the organism, the intended use of the material, etc. Unique characteristics of the microorganism need to be confirmed. For example, bacterial isolates for research focused on antibiotic resistance might require confirmation of their antibiotic resistance patterns. Prepublication Copy 77

Biological Collections: Ensuring Critical Research and Education for the 21st Century Collections Need Room to Grow There is a pressing need for the strategic expansion of the nation’s set of biological collections to ensure they adequately represent the diverse array of Earth’s biota across space and time. The continual growth of biological collections is essential for tracking ongoing global change, especially now as the planet’s habitats and physical environments are rapidly shifting. Given the tremendous anthropogenic changes now under way, sampling and archiving the baselines of the presence and distribution of organisms will support future scientists in their efforts to understand changes in biodiversity and organisms’ responses to global change. Likewise, the expansion of living stock collections, including both new types of genetic stocks and new types of products from existing specimens (e.g., tissues, clone libraries, or purified genomic DNA), is essential for many services and areas of research and development, including synthetic biology, microbiome analysis, bioterrorism, and developing crops and livestock able to thrive in an altered climate. Regardless of the reasons, the growth of biological collections requires strategic thinking about infrastructure from multiple angles—the capability to expand space, the development of tools and technologies that help reduce space required for specimen maintenance and storage, and the more effective use of existing space. A collection that has stopped growing is often seen by others in the community as being inactive and thus may be overlooked as a research resource. Some biological collections do not have general growth, or even strategic growth, as part of their mandate. Those biological collections that include growth in their mandate may vary widely in the degree to which they pursue growth. For example, the ornithology collection of the Burke Museum of Natural History and Culture at the University of Washington in Seattle has pursued an aggressive policy of growth since its founding in the 1970s and is now, after five decades of sustained growth, one of the premier ornithology collections in the world. Similarly, the insect and other collections generated by the National Ecological Observatory Network (NEON) 7 are being housed at Arizona State University, which has allocated approximately 10,000 square feet for this purpose (per personal communication, Nico Franz, curator, Hasbrouck Insect Collection, Arizona State University, November 2019). Many living microbial collections include growth within their mission, in part because many scientific journals require that microbial strains used in publicly funded research be made accessible to the research community for future study. Unfortunately, many living collections lack the capacity to accession a high volume of material from publicly funded research, even if collecting such material is within their mission. Addgene, 8 a nonprofit global plasmid repository, is an example of an independent entity that accepts, archives, and distributes thousands of plasmids, viruses, and other materials cited in research publications. However, the Addgene model has not yet been applied to engineered or constructed living strains used in research. Typically, collections growth is the result of funding for specific research projects that have a very specific focus on a particular taxon or on developing a new type of research organisms (e.g., an organism with specific genetic modifications). In other words, growth is typically not the result of a coordinated collecting strategy. As a result, many collections have well-known biases in terms of species, sex, size, or the geographic distribution of specimens, and correcting such biases can be an important motivation for continued growth. Often, the growth of biological collections creates tension between the resources needed to curate and maintain existing collections and the resources needed to house and manage incoming biological material. Additionally, growing biological research collections may compete for space with other institutional functions (e.g., classrooms, research laboratories, and athletics), some of which may be deemed more relevant for immediate revenue generation or the mission of the larger institution. In general, the infrastructure funding programs of NSF’s Division of Biological Infrastructure (DBI) do not include provisions to ameliorate the demands that collections growth places on biological infrastructure. DBI’s Collections in Support of Biological Research (CSBR) program explicitly excludes 7 See https://www.neonscience.org. 8 See https://www.addgene.org. 78 Prepublication Copy

Building and Maintaining a Robust Infrastructure what it deems as “normal” growth, even though there are no clear metrics by which normal growth is determined. NSF provides support for growth in only two situations: when there is an urgent need for an institution to subsume an orphan (abandoned) biological collection, or for new collections produced from national and international initiatives such as NEON. DBI’s Sustained Availability of Biological Infrastructure (SABI) program, established in 2019, only provides support to prevent the loss of “mature” physical infrastructure and cyberinfrastructure. Notably, NSF does not require research proposals that involve collecting or generating new specimens to include support for collections maintenance and growth. All research proposals are required to include a data management plan9 to describe how research results, including data from specimen-based work, will be disseminated and shared. However, there is not yet a requirement for a specimen management plan to describe how specimens and their associated data will be curated, digitized, and cared for over the long term for an established biological collection. Additional discussion about the need for a specimen management plan, including the management of the digital data associated with specimens, and requirements for an accompanying budget to support the management plan, is offered in Chapters 5 and 7, respectively. It is possible that the growth of biological collections is not recognized as a pressing problem and so it has not traditionally been a primary criterion for NSF to grant infrastructure funding. Yet many improvements in infrastructure, including increased space, compactors, and robotic access to specimens and other facilities, can ameliorate the challenges of collections growth. The lower priority placed on growth may have stemmed from the fact that, over the last few decades, collections growth has slowed for many institutions (Malaney and Cook, 2018). The reasons for this slowdown are varied, including a lack of physical space for new collections, an increased reliance on project-based collecting, increased difficulty obtaining permits and navigating the increasingly complex legal issues surrounding biological collecting, the perception of leadership at host institutions that collecting and the fieldwork associated with it is not valuable, and changing societal norms surrounding biological collecting (Antonelli et al., 2018; Bakker et al., 2020; Wallace et al., 2013). Biological Collections Need to Be Accessed Open science 10 is a major, global trend that is changing the culture and practice of science. Open science facilitates the exchange of not only biological materials, but also of ideas, data, and other resources such as databases, journal publications, and analytical software (Becker et al., 2019). In the context of open science there are three interrelated challenges facing the accessibility of biological collections: (1) discoverability, (2) physical access to specimens, and (3) access to digital specimen data (see Chapter 5). Discoverability The lack of a registry or catalog for all biological collections in the United States is an impediment to open science. Some well-curated catalogs exist for particular types of biological collections. For example, the World Federation for Culture Collections (WFCC) maintains both Culture Collections Information Worldwide, 11 a registry of more than 800 culture collections, and the Global Catalogue of Microorganisms, 12 a public online database of bacteria, fungi, and archaea held in more than 130 collections across 49 countries (Wu et al., 2013). However, because many collections do not have an online catalog of their holdings, users need a catalog or registry that provides collection descriptions in order to find specimens relevant for their research; the lack of such a registry or catalog complicates this sort of discovery. 9 See https://www.nsf.gov/pubs/policydocs/pappg19_1/index.jsp. 10 Open science is transparent and accessible knowledge that is shared and developed through collaborative networks (Vicente-Sáenz and Martínez-Fuentes, 2018). See https://doi.org/10.1016/j.jbusres.2017.12.043. 11 See www.wfcc.info. 12 See www.gcm.wfcc.info. Prepublication Copy 79

Biological Collections: Ensuring Critical Research and Education for the 21st Century Access to Physical Specimens Access to specimens and their related data is of crucial importance to many areas of research and innovation, education, and public engagement in science. However, some biological collections lack adequate space, staff, and research tools for users to study specimens on-site. For both natural history and living stock collections, specimens or the associated biological materials are often shipped to users rather than accessed at the collection facility itself, although this may not be possible if a large amount of material is requested or if the specimens are too fragile or bulky to be shipped. Thanks to national or even worldwide networking, some biological collections can facilitate access to samples that are not stored in their own facilities. The management of living material requires specific infrastructure such as a laboratory, a greenhouse, or a vivarium as well as the relevant training and expertise. Some living stock collections are only accessible to registered or qualified users. Direct access is usually restricted when specimens represent endangered species or if the materials pose biosafety or biosecurity risks, in which case the user needs to be prequalified to handle the material appropriately in order to minimize these risks (see Box 4-4). Certain microbes and derivatives could potentially be misused and are under strict regulations and controls. The few collections that manage these agents are also under strict control and regulations. Nonetheless, access to these collections is essential in providing support to the scientific community to develop effective countermeasures and control strategies. Meeting the Needs of a Dynamic Scientific Enterprise The culture and practices in the scientific enterprise are complex and shifting in several ways that have important implications for infrastructure. First, research institutions and funders increasingly emphasize and value convergence of scientific disciplines in order to facilitate collaborative, transdisciplinary research and innovation, particularly to address pressing challenges such as antimicrobial resistance, food security, biodiversity loss, and the independent and sustainable production of energy (Jahn et al., 2012; NRC, 2014a). Research infrastructure that promotes convergence and weakens disciplinary silos typically requires physical space that is easy to access but is outside the domain of any single disciplinary department. A hub-like location, e.g., the University of Idaho’s Integrated Research and Innovation Center, 13 has a variety of design elements that encourage scientists, students, and others to interact formally and informally. Second, institutions that provide formal and informal education programs increasingly support experiential learning in science, technology, engineering, and medicine (STEM) (Monfils et al., 2017; NASEM, 2017). STEM education research provides robust evidence that active learning increases interest in and retention of science (NRC, 2015; and see Chapter 3), thereby making it possible to expand the diversity of the next generation of thinkers who will address ongoing and future challenges facing the planet and human health. In addition, there are growing efforts to cultivate a culture of entrepreneurship and an increasing demand outside of academia for STEM-skilled, workforce-ready graduates. As a result, many colleges and universities are designing (or redesigning) facilities, including research laboratories, classrooms, maker spaces, 14 and informal public gathering spaces that support more immersive transdisciplinary research and experiential learning environments for scientists, students, and learners of all types (e.g., Be a Maker program 15 and the Learning Spaces Collaboratory 16). The Beaty Biodiversity Centre is a successful example of how a natural history collection might effectively integrate research and educational spaces (see Box 4-5). However, building or renovating space to display collections and create immersive and “hands-on” learning opportunities is financially challenging, particularly for smaller biological collections or those 13 See https://www.uidaho.edu/research/entities/iric. 14 Providing the space and the materials for project-based, independent, hands-on experience for students. 15 See https://beam.unc.edu. 16 See https://www.pkallsc.org. 80 Prepublication Copy

Building and Maintaining a Robust Infrastructure that house sensitive materials. In addition, large-scale infrastructure endeavors to build collaborative, transdisciplinary research and learning environments and the ongoing efforts to address infrastructure needs of biological collections are largely disconnected from one another. BOX 4-4 Infrastructure for Biosafety and Biosecurity of Living Collections Physical infrastructure–related challenges faced by living biological collections include compliance with increasingly stringent biosafety and biosecurity regulations set by the Department of Agriculture (USDA) and the Centers for Disease Control and Prevention. Some viruses, bacteria, fungi, parasites, protists, or multicellular organisms are pathogenic to humans, animals, or plants. Pathogenicity greatly affects the physical infrastructure required by living collections, for reasons of both biosafety (protecting the safety of the operator handling the organism) and biosecurity (protecting the general public from accidental or intentional release of pathogenic organisms outside the laboratory). For instance, plant pathogens, especially genetically modified plant pathogens, require special use authorization from USDA’s Animal and Plant Health Inspection Service and must be shipped under a Plant Protection and Quarantine (PPQ) 526 permit. Biosafety Level 1 (BSL1) facilities are used for organisms unable to cause disease in humans, animals, or plants. Precautions and infrastructure requirements are minimally restrictive. Biosafety Level 2 (BSL2) facilities are required for organisms capable of causing disease in humans, animals, or plants but for which the potential diseases are difficult to contract via aerosols. Examples include hepatitis A, B, and C; HIV viruses; and pathogenic strains of E. coli, Staphylococcus, Salmonella, and Candida. BSL2 collections must have personnel trained on how to manipulate pathogenic organisms, the personnel must use protective personal equipment, most of the laboratory manipulations should be done within a biological safety cabinet, and the laboratory must have in place safety protocols for decontamination and routine operations. Biosafety Level 3 (BSL3) facilities are required for organisms that have the ability to infect via aerosols (e.g., Mycobacterium tuberculosis), posing a severe threat to laboratory personnel. All BSL2 requirements are followed plus more stringent control on access to the laboratory. Workers require extensive training and certification to work in a BSL3 laboratory. Personnel are under medical surveillance, and respirators or facemasks are required. A hands-free sink and eyewash station must be available near the exit. To minimize the risk of releasing infectious aerosols, floors, walls, and ceilings must be sealed, the laboratory must have negative airflow, the air needs to be filter-sterilized prior to leaving the facility, and the facility must have two sets of self-closing and locking doors. A biosafety manual details all laboratory operations in compliance with all safety requirements, and all work and quantities of materials manipulated must be documented to assure biosafety. The laboratory must be designed so that it can easily be decontaminated. Biosafety Level 4 (BSL4) facilities are required to manipulate microbes that could easily be aerosol- transmitted and cause severe to fatal disease in humans and for which there are no available vaccines or treatments (e.g., SARS coronavirus, Ebola and Marburg viruses). These are highly regulated and controlled. Personnel are highly trained and must be approved and certified. Personnel wear positive pressure suits and follow all the requirements and procedures for a BSL3 laboratory. Only a few labs, such as the U.S. Army Medical Research Institute of Infectious Diseases at Fort Detrick, Maryland, meet requirements to handle BSL4 organisms. Prepublication Copy 81

Biological Collections: Ensuring Critical Research and Education for the 21st Century BOX 4-5 The Beaty Biodiversity Research Centre’s Integrated Space for Natural History Collections Storage, Research, and Education A B Photo A: Public Display of Fish Research Collections at the Beaty Biodiversity Museum. Photo by Derek Tan, Beaty Biodiversity Museum, Beaty Biodiversity Research Centre, University of British Columbia. Photo B: Young girl gazing at trophy case interpreting Victorian collecting. Photo by Jeff Werner. The Beaty Biodiversity Museum is part of University of British Columbia’s Beaty Biodiversity Research Centre that integrates space for its natural history collection with public displays, laboratories for collections-based researchers and curators, and offices for educators with related meeting and support spaces. The Beaty Biodiversity Museum, which opened in 2010, includes rows of stacking cabinets with windows, offering visitors views of the research collections, in addition to some small exhibitions. The research center participates in undergraduate and graduate education programs as well as workforce training in biodiversity research. Museum programming, such as Researchers Revealed (https://www.zoology.ubc.ca/~biodiv/rr), is designed to support visitors’ understanding of biological collections and their relationship to biodiversity research. THE WAY FORWARD Given the challenges described in the previous section, it is clear that new approaches will be required to maintain and improve the value and effectiveness of the nation’s biological collections. Growing demands on biological collections will require some fundamental changes to the infrastructure supporting these collections—changes that will grow from new approaches to maintaining them. This section outlines some general strategies that will provide overall improvements in the biological collections physical infrastructure. Future-Proof the Infrastructure The environment for biological collections is changing rapidly, from new demands being placed on collections by a steady stream of scientific advances, to the availability of up-to-date technological capabilities, particularly digital ones, and changes in the ways that scientific research and development are conducted (see Chapter 2). The reevaluation of the collections infrastructure is also motivated by the anticipated increase in the rate of species extinctions (Díaz et al., 2019). It is now incumbent on scientists to approach existing and new specimens, especially those from endangered taxa and threatened biomes, as if it is their last opportunity to do so, because it soon may be. Maximizing biodiversity information for future study requires redoubled efforts to document and preserve it, which will result in many new collections that will need to be accommodated in the nation’s biological collections. New methods of propagating living organisms as well as novel methods for preserving tissues and whole organisms may require changes to the current collections infrastructure as well as new curatorial techniques. More robust methods for storage, and the linkage of additional data gathered about endangered and extinct biota, will 82 Prepublication Copy

Building and Maintaining a Robust Infrastructure result in a better understanding of their life histories, habitat requirements, and interactions with other species, and how they reacted to global change in deep time. Guiding this reassessment of current preservation and documentation methods will be the understanding that future knowledge of many species may rely entirely on the specimens and information held in biological collections. Thus, it will be important to ensure that the nation’s biological collections continue to thrive no matter what the future brings. Strategic Planning for Infrastructure Strategic planning gives an organization the opportunity to evaluate or refine its core mission, identify stakeholders, set goals, and determine the strategies and resources that are needed to achieve those goals. In particular, such exercises require foresight and collaboration between research and administrative staff in an institution to guide the way in which infrastructure challenges are addressed. Strategic planning can help identify the financial and other needs of a collection and differentiate the funding needed for ongoing maintenance of the collection from that needed to meet evolving standards, replace aging infrastructure, and accommodate the growth of collections. Initiating the strategic planning process every few years can help identify the potential funding sources for biological collections infrastructure and also identify gaps in funding that will need to be met by other resources during the plan’s duration (Parsons and Duke, 2013). Reflections on the core mission of the collection and its primary and secondary stakeholders will help those in charge of the collection come up with actions to ensure the necessary preventive maintenance and quality control of the specimens, increase the specimens’ accessibility, and anticipate future uses. The planning process should also take into consideration the availability and training needs of collections leadership and staff (see Chapter 6). Many collections already engage in regular strategic planning exercises. For the past several years the Society of Herbarium Curators and iDigBio have sponsored a month-long online course entitled Strategic Planning for Herbaria, which trains representatives from up to 10 herbaria to develop succinct strategic plans that include a vision, mission, strategies, and objectives; strengths, weaknesses, opportunities, and threats (SWOT) analysis; sustainability; and assessment and evaluation. 17 Because strategic planning is a common practice for research institutions and universities, it is critical for a biological collection’s strategic plan to be part of the plan for the larger institution or to at least be closely aligned to the vision, mission, and goals for the larger institution. Developing an individualized strategic plan requires time, training, and input. Biological collections that do not have the resources to develop a plan could be helped if other collections make their strategic plans publicly available. Sharing strategies to achieve a goal is common practice for federal research institutions and is required or promoted by federal funding agencies and certain universities; such examples could inspire and be used by the broader collection community (NCSU 2017–2022 strategic plan from the Department of Biological Sciences; 18 2015–2020 strategic plan for the Virginia Institute of Marine Science 19). Involving an advisory board of experts to help develop and implement the plan could be another way to benefit from the expertise of other biological collections personnel. Emergency Preparedness A disaster preparedness and emergency response plan 20 is considered a core document for natural history collections housed in museums and is required for a natural history collection to be accredited by the American Association of Museums. Developing a contingency and disaster recovery plan is also 17 See https://www.idigbio.org/content/strategic-planning-herbaria-short-course-0. 18 See https://bio.sciences.ncsu.edu/wp-content/uploads/sites/12/2017/08/Biological-Sciences-Strategic-Plan.pdf. 19 See https://www.vims.edu/about/leadership_admin/dean/strategic_plan_2015/index.php. 20 See https://www.aam-us.org/programs/ethics-standards-and-professional-practices/disaster-preparedness-and- emergency-response-plan. Prepublication Copy 83

Biological Collections: Ensuring Critical Research and Education for the 21st Century recommended for living stock collections (Parson et al., 2013). Such a plan includes responses to natural, mechanical, biological, and human-caused emergencies and addresses the needs of staff, visitors, structures, and collections. However, a preparedness and emergency response plan by itself is no guarantee of successful response to a disaster; in the chaos of an actual emergency it may not be possible to access computers or files where a plan is stored. A regular review of the plan, perhaps with response drills, will keep the actions and supplies needed to recover and stabilize collections at hand in the active memory of collections personnel and allow those personnel to continually refine their plan. An understanding of the special needs of collections by local emergency response agencies may add to the success of a disaster response. In the case of a fire at the University of Vermont Herbarium, water damage from hoses was minimized because the local fire department had recently visited the facility as part of a routine check and provided protection against the heat of the fire with padding set onto the tops of the herbarium cabinets (per personal communication, David S. Barrington, University of Vermont, Director, Pringle Herbarium, 2020). Duplicate Specimens Depositing duplicate specimens at different institutions can help ensure that specimens are not lost entirely in the event of a disaster. The deposition of duplicate specimens is an established practice among strains of microorganisms, entomological specimens, and herbaria (Groom et al., 2014; OECD 2007; Rabeler et al., 2019). For living stock collections, the OECD Best Practice Guidelines go a step farther than recommending a duplicate of a specimen be held in a remote location; the guidelines also recommend that specimens be preserved in two or more formats, such as a cryopreserved specimen, lyophilized specimens, or as living cultures. These practices lessen the chance of losses due to power outages, fire, or other types of disasters. For example, copies of several living stock collections are now cryopreserved at the Department of Agriculture (USDA) National Laboratory for Genetic Resource Preservation in Fort Collins, Colorado (McCluskey, 2016), ensuring that these collections can be recovered following a disaster at the home institution. However, it is important to note that the deposition of duplicate specimens is not a practical or even possible solution for many types of biological collections because of already existing issues with space, funding, staffing, and rarity (e.g., dinosaurs or unique culture collection isolates). Nonetheless, when it is possible to have a remote archive of duplicate specimens, this mitigates the risk of specimen loss. Establish Shared Standards and Technologies for Living Stock Collections One way to improve the value of living collections is to have strict and consistent quality standards in place. Such standards can help ensure that resources and data are “fit for purpose”—that is, of the type and quality to meet the specific needs of users (Smith et al., 2014). Many companies and organizations follow ISO (International Organization for Standardization 21) standards, which provide a way to create the documents that provide requirements, specifications, guidelines, or characteristics to ensure that materials, products, processes, and services are a good fit for their purposes. Some ISO standards are specific for biological collections: 1. The ISO standard ISO9001:2015 provides basic guidance to organizations on how to set up a quality management system with commitment from senior management to support the collection. 2. The international biobanking standard ISO20387:2018 provides additional guidance for a culture collection. The guidance in the biobanking standard solidifies what culture collections have been working toward based on best practices of culture collections around the world. 21 See https://www.iso.org/standards.html. 84 Prepublication Copy

Building and Maintaining a Robust Infrastructure 3. A standard that is currently under development, ISO/TC 276 Biotechnology, is intended to bring standardization to the field of biotechnology for biological data and sequence information, which will help to support the information that a culture collection is able to provide. These standards will assure that biological data are accurate and appropriately linked to the specimens and that they are disseminated in correct formats and for appropriate uses. In specific cases, such as when a user needs a stock microbial strain to diagnose a disease, the fit- for-purpose resource may need to be ISO certified. However, in most cases, formalized but non-certified quality control standards and best practices are sufficient assurances of quality. Networks of collections have proven to be particularly effective in raising quality control standards and elevating customer service. For example, the Mutant Mouse Resource and Research Center (MMRRC) is a network of four major collections of mutant mice, with centralized ordering and quality control divisions. WFCC lists 23 regional and international networks of culture collections, including the U.S. Culture Collection Network. Several of these networks, including WFCC, have developed a shared set of best practice guidelines. The Global Biological Resource Centre Network, an OECD-endorsed pilot project, is one particular project that may be a useful model for enhancing quality control in U.S. living stock collections. Arising from networked European Union (EU) collections, the Global Biological Resource Centre Network led to the creation of the EU-funded Microbial Research Resource Infrastructure (MIRRI) project (2012–present). With funding expected to exceed 1 million euros per year, the initial aims for MIRRI were to advance collections to become biological resource centers (BRCs), network BRCs, and interact with the user and regulatory communities (Stackebrandt et al., 2015). Examples of activities that benefited EU collections include the development and implementation of quality control practices to become ISO9001:2015 certified; cooperation on databases, websites, and marketing; and gauging and enhancing user satisfaction. These activities have helped advance the EU bioeconomy, supported innovation, promoted global cooperation, and helped both governments and collections meet global requirements such as the Nagoya Protocol and biosecurity protocols. Comparable efforts in the United States would likely have a similar cost but have not yet been implemented. Establishing a National Registry of Biological Collections A registry of the biological collections held in U.S. institutions would enable users to discover and contact collections with holdings of potential interest, thereby increasing access to them. It would also improve the ability of biological collections with geographic, temporal, or other commonalities to find one another for potential collaboration and to identify the most relevant collections to include in such collaborations. A comprehensive collections registry could also facilitate an assessment of the infrastructure needs of all U.S. collections and perhaps help prioritize grant funding for infrastructure improvement. It might also facilitate the response of the collections community to emergencies caused by natural disasters or infrastructure failure or to anticipate the orphaning of collections and advise on the best options for a collection transfer when needed. The ability of those in charge of a biological collection to compare their collection with others would help inform strategic planning. More communication among collections could lead to the development of more community-wide standards in curatorial practice and data management. The herbarium community already has such a curated registry, Index Herbariorum, which could be a model for a registry that includes all collections (see Box 4-6). WFCC also has a global registry of culture collections. However, the WFCC registry is an opt-in system, which leads to underrepresentation of some countries, underscoring the need for clear criteria for including a collection and for the active curation of registrant information. Prepublication Copy 85

Biological Collections: Ensuring Critical Research and Education for the 21st Century BOX 4-6 Toward a Universal Collections Registry: The Example of the Index Herbariorum Snapshot of the NYBG Steere Herbarium website illustrating the interactive maps, a picture of the herbarium from the outside and the staff working inside the building. See http://sweetgum.nybg.org/science/ih/. Every good ecologist knows that to preserve a species, you need to know what it is, where it is found, and how it interacts with other species in its environment. The same, it happens, is true of biological collections. Since 1935 the Index Herbariorum (IH), a directory to the world’s herbaria, has been the go-to place for information about the world’s herbaria. The IH was begun in the Netherlands, but the New York Botanical Garden assumed responsibility for managing it in the mid-1970s. It became an online resource in 1997. Keeping track of the world’s herbaria is not an easy task—with every week there are new herbaria, new staff, and new holdings to register, and there are closures or mergers of one herbarium with another yearly. But it is essential for botanists and other scientists and researchers to know where to find and how to contact the curators and staff of the roughly 3,300 herbaria in the world today. Collectively, these herbaria contain almost 400 million specimens; the IH also lists approximately 12,000 associated staff, including curators, managers, and other biodiversity experts. Each entry in the IH (http://sweetgum.nybg.org/science/ih) includes the herbarium’s physical location, web address, contents, and history as well as the names, ages, contact information, and areas of expertise of associated staff. The information contained in IH allows herbarium staff not only to address their shipping boxes correctly, but also to find individuals who can identify or evaluate specimens and to find partners for specimen exchange. Biodiversity scientists use IH to find previously collected specimens that are pertinent to their studies. Scientific journals require the use of IH codes in the citation of specimens examined and the designation of type specimens in the description of new species. Collecting permits for national parks and other protected federal lands require that plant and fungal specimens collected on these sites be deposited in IH-listed herbaria. The U.S. Fish & Wildlife Service uses IH as a resource for determining whether an institution should be granted a permit to house endangered species (a CITES permit). IH is also used by the Department of Homeland Security to find specialists for the identification of unknown specimens confiscated at U.S. Customs and Border Protection sites. Several previous attempts to create a global index of all collection types (e.g., GRBio and Biorepositories.org) have failed to produce a comprehensive registry that is regularly updated with current information. iDigBio recently created a static list of collections in the United States, drawing on Index Herbariorum, previous lists, and information gleaned from institutional websites, but this is only a start 86 Prepublication Copy

Building and Maintaining a Robust Infrastructure (see Box 4-7). In collaboration with Index Herbarium, the Global Biodiversity Information Facility (GBIF) plans to create the platform for a comprehensive worldwide biodiversity collections database (Hobern et al., 2019). A registry of U.S. collections could use the GBIF cyberinfrastructure but will still require a significant campaign of outreach to collections institutions to provide data and develop the tradition of updating the index as holdings and staff change. Similarly, an interest group of the Taxonomic Databases Working Group is working on a collections descriptors (CD) data standard for the description of collection-level metadata, 22 which will provide a framework for specimen metadata that needs to be collected in order to provide a full assessment of the strengths and opportunities that these collections may provide to research and education. CONCLUSIONS As long as research, education, and the preservation of natural heritage are national and global endeavors, it will be imperative that the infrastructures for biological collections at both the individual and collective levels are improved and maintained. Given the negative consequences of the nation’s research efforts if biological collections are limited by poor infrastructure or perhaps are lost altogether, it is crucial that proactive measures be taken to strengthen the physical, digital (see Chapter 5), and intellectual (see Chapter 6) assets that support the long-term quality and curation of specimens and their associated data. BOX 4-7 iDigBio Listing of Biological Collections Unspecific or Botanical Gardens, Specialized (e.g. Arboretums, Zoos zooarcheology, Citizen Scientists 4% ichnology) <1% 7% Research Paleontological Institutes 9% 5% Free Standing Museums 13% Herbaria (preserved algae, fungi, plants) University Invertebrate 42% Departments 20% Natural Areas 51% 13% University Museums Vertebrate 14% 22% Type of Biological Collection Affiliation Natural history specimen collections represent a vast distributed network of information on the biodiversity of our planet. Estimates of the total number of specimens held in U.S. collections range from 800 million to 1 billion. The most comprehensive listing of collections for the United States is the iDigBio Collections Catalog (https://www.idigbio.org/portal/collections), which lists approximately 1,600 natural history collections in the United States associated with 729 different institutions. This list includes a large variety of collections of different sizes and affiliations but is not complete and particularly underrepresents small, regional collections and private, personal collections. The charts above show a breakdown of the biological collections in iDigBio by type (generalized categories of taxonomy) and affiliation. “University department” refers to collections held in laboratories or other spaces allocated to an academic department of science. 22 See https://www.tdwg.org/community/cd. Prepublication Copy 87

Biological Collections: Ensuring Critical Research and Education for the 21st Century Due to the diversity of collection types, there is no one-size-fits-all list of physical infrastructure requirements. The assessment of infrastructure needs must take place at the individual level. Unfortunately, most biological collections do not have sufficient resources for preventive maintenance or basic upgrades for existing infrastructure and technologies, let alone for major renovations or new facilities. Thus, biological collections would benefit from individualized strategic plans to outline how day-to-day needs will be met, including issues related to preventive maintenance and quality control, and also how to develop or expand infrastructure to meet future scientific needs. Some aspects of infrastructure will benefit from shared community standards. This is particularly true for quality control for living stock collections, for which consistent genetic identity of the specimens within and between stock collections is crucial for research. Smaller living collections may not be able to afford the staffing and other costs for a quality assurance and quality control system and may not be able to meet the ISO guidelines. Strategic planning will be an important tool in guiding those living stock collections to adopt and maintain nationally accepted quality control standards. In addition, a community approach to developing “next best” protocols and best practices that can be implemented in a way that is commensurate with the available budget could allow such collections to distribute accurately identified pure cultures. For all collection types, a community approach as an additional layer to strategic planning could create mechanisms to pool resources and facilitate the development of best practices and training and ensure that the leadership of biological collections is well equipped to implement those collections’ plans. Biological collections infrastructure also needs to grow in order to keep up with the advance and evolution of scientific research itself. The urgent need to continue collecting will require NSF and other funding institutions, as well as institutions whose mandate includes collecting or generating new types of research specimens, to acknowledge and address growth as an important and necessary component of biological collections in the 21st century. Such institutions will also need to acknowledge the ongoing demands that collections growth places on infrastructure—demands that can only be ameliorated through infrastructure support and improvements. Such an acknowledgment will require the development of clear guidelines and metrics for growth. It will also be important for the infrastructure needs of individual biological collections to be integrated into larger infrastructure initiatives of their host institutions and the community as a whole, especially those initiatives aimed at developing state-of-the-art research hubs that meet the needs of a dynamic scientific enterprise. In such endeavors, the institutional staff charged with maintaining institutional research infrastructure will need to understand the particular needs of biological collections in terms of environmental controls and other sensitivities that can affect preventive maintenance and quality control. Finally, consideration needs to be given to biological collections as a shared and distributed scientific resource for the nation. This will require a consortium to create community-wide mechanisms to pool and share resources. Establishing a registry of biological collections in the United States will be an important step toward cultivating national attention and perspective. Such a registry could be used to conduct periodic community-wide assessments of infrastructure needs. NSF has the opportunity to provide the backbone to cultivate partnerships so that collections across the spectrum are involved in contributing to an emerging consortium. RECOMMENDATIONS FOR THE NEXT STEPS Recommendation 4-1: The leadership (directors, curators, and managers) of biological collections should assess and define the infrastructure needs of their individual facilities and develop comprehensive strategic plans in accordance with those needs and their strategic missions. The strategic plans should outline approaches to: • continually address ongoing preventive maintenance and, in the case of living collections, quality control requirements; and 88 Prepublication Copy

Building and Maintaining a Robust Infrastructure • improve and potentially build new infrastructure, both of which actions are particularly important if collections growth is a component of the strategic mission. The strategic plan should be revisited every 3 to 5 years to ensure that it continues to meet the evolving needs of collections and their users. Recommendation 4-2: Biological collections should take advantage of existing training opportunities and collaborative platforms at the national and international levels, such as those offered through the International Society for Biological and Environmental Repositories and the Organisation for Economic Co-operation and Development certification programs, especially as new aspects of the work evolve, such as regulations compliance, data management, and new techniques and materials for collections storage and documentation. Recommendation 4-3: Professional societies, associations, and coordination networks should collaborate and combine efforts aimed at addressing community-level infrastructure needs of the nation’s biological collections, including: • develop a platform to pool and share resources such as strategic plans, best practices, and training opportunities so that these can serve as resources for the broader biological collections community; • develop and implement strategies to adopt quality control programs to improve uniformity among living stock collections and ensure the availability of high-quality biological resources that best fit the needs of the user; • create a national biological collections registry to document the location, size, and holdings of the collections in the United States. The registry should be curated and updatable. In addition, proactive processes to identify collections should be established, ensuring that collections of all types are well represented in the registry; and • use the national registry to conduct periodic community-wide assessments of needs to inform the development of both individual and community-level strategies to maintain and upgrade infrastructure. Recommendation 4-4: The NSF Directorate for Biological Sciences should continue to provide funding support for biological collections infrastructure and expand endeavors to coordinate support within and beyond the Directorate. Specifically, NSF should: • support new and improved infrastructure to accommodate the pressing needs created by continued collections growth; • require a specimen management plan for all research proposals that includes collecting or generating specimens that describes how the specimens and associated data will be accessioned into and permanently maintained in an established biological collection; and • facilitate the creation and support of an independent consortium to develop collaborative platforms and mechanisms to pool and share resources for strategic planning, preventive maintenance, quality control and assurance, collections growth, establishing a national collections registry, and other community-level assets. REFERENCES Antonelli, A., M. Ariza, J. Albert, T. Andermann, J. Azevedo, C. Bacon, S. Faurby, T. Guedes, C. Hoorn, L. G. Lohmann, P. Matos-Maravi, C. D. Ritter, I. Sanmartin, D. Silvestro, M. Tejedor, H. Ter Prepublication Copy 89

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Biological collections are a critical part of the nation's science and innovation infrastructure and a fundamental resource for understanding the natural world. Biological collections underpin basic science discoveries as well as deepen our understanding of many challenges such as global change, biodiversity loss, sustainable food production, ecosystem conservation, and improving human health and security. They are important resources for education, both in formal training for the science and technology workforce, and in informal learning through schools, citizen science programs, and adult learning. However, the sustainability of biological collections is under threat. Without enhanced strategic leadership and investments in their infrastructure and growth many biological collections could be lost.

Biological Collections: Ensuring Critical Research and Education for the 21st Century recommends approaches for biological collections to develop long-term financial sustainability, advance digitization, recruit and support a diverse workforce, and upgrade and maintain a robust physical infrastructure in order to continue serving science and society. The aim of the report is to stimulate a national discussion regarding the goals and strategies needed to ensure that U.S. biological collections not only thrive but continue to grow throughout the 21st century and beyond.

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