Research Article |
Corresponding author: Shana Hirsch ( slhirsch@uw.edu ) Academic editor: Kristian Meissner
© 2024 Shana Hirsch, Neha Acharya-Patel, Phyllis Akua Amamoo, Giomar H. Borrero-Pérez, Ni Kadek Dita Cahyani, Joape G. M. Ginigini, Kaleonani K. C. Hurley, Manuel Lopes-Lima, Mark Louie Lopez, Ntanganedzeni Mapholi, Koffi Nouho Ouattara, Diana A. Pazmiño, Yoshimi Rii, Fabiano Thompson, Sophie von der Heyden, Mrinalini Watsa, Vanessa Yepes-Narvaez, Elizabeth Andruszkiewicz Allan, Ryan Kelly.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Hirsch S, Acharya-Patel N, Amamoo PA, Borrero-Pérez GH, Cahyani NKD, Ginigini JGM, Hurley KKC, Lopes-Lima M, Lopez ML, Mapholi N, Ouattara KN, Pazmiño DA, Rii Y, Thompson F, von der Heyden S, Watsa M, Yepes-Narvaez V, Allan EA, Kelly R (2024) Centering accessibility, increasing capacity, and fostering innovation in the development of international eDNA standards. Metabarcoding and Metagenomics 8: e126058. https://doi.org/10.3897/mbmg.8.126058
|
Environmental DNA (eDNA) includes a set of rapidly emerging technologies that have the potential to support environmental monitoring and biodiversity conservation through novel, non-invasive, cost-effective and democratic methods and tools. Meanwhile, eDNA researchers are developing international standards for eDNA technologies, methods and data outputs. For eDNA technologies to be accessible, useful and appropriate, we must ensure that any standards developed include a broad conception of users from around the world, a diversity of ecological contexts and locations and, most importantly, a realistic outlook on research capacities and infrastructure. In this article, we assemble perspectives on international standardisation of eDNA from a diverse and global group of users and experts from Africa, South America and the Pacific Islands. The authors of this article collaborated by answering and discussing a set of open-ended questions aimed at eliciting hopes, concerns and experiences regarding eDNA standards. The result is a set of emergent themes and a generative consensus to highlight the need for the creation of adaptable standards, the development of regional capacity, increased sensitising to data sovereignty and the viewing of standardisation as a global capacity-building activity.
biodiversity, capacity-building, conservation, eDNA, environmental DNA, innovation, international standards, monitoring, standardisation
Researchers have demonstrated the utility of environmental DNA (eDNA) technologies and methods for detecting biodiversity, estimating species distributions, locating endangered or invasive species, detecting wildlife microbiota and disease and monitoring conservation across spatio-temporal scales and ecosystems (
With these shifts in the maturity of eDNA and the potential application of these technologies, researchers using and developing eDNA methods and technologies are increasingly discussing the need for and importance of standards (
As of 2024, there are several national efforts aimed at creating standards for eDNA in aquatic environments, including those in Europe, Australia, New Zealand, Canada, China and Japan. There are also nascent efforts to develop international standards for some eDNA methods through the ISO, as well as through the Ocean Biomolecular Observation Network (OBON). The standardisation effort has been largely driven by researchers in the Global North, from countries with the greatest access to state-of-the art technologies, laboratories and funding, such as those in Europe and North America, as well as Japan and Australia (
This is a collaborative manuscript, written by scientists from around the globe. The goal of the project was to understand how efforts to develop international standards (including laboratory protocols, workflows and certifications) might support, or raise concerns for, researchers using eDNA methods and technologies in the Global South and remote (difficult to access) areas. To accomplish this goal, the eDNA Collaborative at the University of Washington engaged with a group of 18 researchers to elicit their perspectives on eDNA standardisation.
An initial set of eDNA researchers and practitioners from South America, Africa, Asia and Pacific Islands (n = 54) were gathered through online research and previous contact with the eDNA Collaborative. From this initial set of contacts, a group of researchers were invited by email to participate in this manuscript as co-authors (see Fig.
This research draws on a rich tradition of qualitative social science methodology. As such, quantifying perspectives or encompassing a representative sample size is not the aim. This mode of qualitative research is common in fields, such as science and technology studies (
The research here uses the interpretive qualitative method of grounded theory (
The notes were then analysed and coded for themes using a standard grounded-theoretical approach (
The results and discussion below represent the collected views of the participant/co-authors, but do not propose a singular perspective or voice. In keeping with qualitative research, the results are not described numerically
There is no universal definition of a “standard.” In this context, we use the ISO definition: “a document, established by consensus and approved by a recognised body, that provides, for common and repeated use, rules, guidelines or characteristics for activities or their results, aimed at the achievement of the optimum degree of order in a given context” (ISO 2019, p. 24). Standards are used in almost all fields and industries to facilitate communication, interoperability of tools or methods and comparability of results. A good standard will ensure reliability and trust. Almost all participants used some form of standard in their work. These range from ad hoc or informal standards such as best-practices and guidelines to more formal protocols such as methods and data requirements to fully formalised standards for lab accreditation or quality assurance or certification, such as those curated by the ISO.
Several participants have adapted national standards to meet their own needs, such as guidelines for PCR analysis and reporting from the Department of Fisheries and Oceans Canada (
Every participant identified benefits (either from existing standards or potential ones) emerging from the creation of international standards. These include several points which centre around reproducibility and collaboration, guidance for research, increasing credibility of eDNA and meeting end goals.
International standards are broadly seen to increase international collaboration by ensuring the results are comparable, reproducible and accurate. When asked how standards currently support their eDNA research or may in the future, almost every participant highlighted the importance of reproducibility or replicability of results. Although reproducibility and replicability are different things (at least at the post-bioinformatics stage), the terms were often used interchangeably. Regardless of the exact meaning and context, these concerns centre around the ability to conduct research in different locations that could be comparable and accurate across time and space. The perceived need to strengthen eDNA research to make it a more credible and trustworthy science that will be accepted by other scientists, decision-makers and resource managers is closely related to this need for reproducibility/replicability as well as interoperability. Several interviewees mentioned that that credibility was important to secure funding for eDNA research and related it to reproducibility and replicability. Some participants also discussed how laboratory certification would be easier with international standards. Realistic and achievable certification and standardisation were also viewed by some as a way to democratise eDNA science by allowing smaller, less well-funded laboratories to gain credibility and stand on par with more prestigious (often better resourced) laboratories and institutions.
In addition, many participants desired clarity and comparability of results across the world and recognised the difficulty of achieving this without standard methods and protocols. Some participants wished for a common nomenclature, clear guides and accepted workflows from sample collection through bioinformatics and data reporting, which would make eDNA methods more accessible to researchers across the world. This, too, was seen to facilitate international collaboration and uptake of eDNA research. Some participants mentioned open access data and software for clarity in workflows and provenance, such as the BioProv for bioinformatics workflows (
There were a variety of opinions that participants expressed about how standards will help or hinder their work. For example, standards may help researchers understand where they can cut costs, making the technology more affordable and accessible, but at the same time, some fear that standards could make research more expensive by requiring particular materials or technologies. Several people discussed how standards could make eDNA tools more effective at developing a baseline understanding about biodiversity and view eDNA as a means to this end, but only if these standards are accessible to communities, managers and those working on the front lines of conservation.
Although there are differences in emphasis and opinion, many participants are aligned in their concerns about international standards. These concerns centre around resources, including 1) cost, accessibility and capacity; 2) data requirements and ownership; and 3) questions about the technical feasibility of standardisation.
Access to the resources necessary to meet standards was a ubiquitous concern across all participants. These resources include finances, access to technologies, materials and equipment, as well as capacity (such as personnel for running a sequencing machine). Participants were concerned that, if the cost is too high, standards will be out of reach, impossible to achieve and elite. Concerns like these, around “setting the bar too high” were expressed by many participants. It is important to note that scientists desire to meet rigorous standards, but it may be physically impossible to access all the resources needed to meet them. Researchers in many parts of the Global South have a difficult time accessing laboratory supplies and when they are obtained, they can be 3–4 times as expensive as they would be when purchased in Europe or North America. They may also take many months to arrive due to customs and shipping delays because there are no regional suppliers. This barrier can make it difficult or impossible for researchers to meet stringent standards or to produce outputs in a timely fashion. In addition, this resource reality means that sending samples overseas for processing may be less expensive than trying to obtain materials and process samples in their labs, although this can be made more difficult by exchange rates, with many Global South currencies considerably weaker against the US Dollar or Euro. Further, shipping samples overseas can lead to potential or perceived issues around experimental and data control that will be discussed later.
Fundamentally, access to materials and technologies is a major barrier to meeting standards, especially if capacity and funding are already stretched. For example, if a high number of biological or technical replicates is required to meet a standard, this may mean that it is too costly to conduct a research project according to those standards. Other participants gave examples of their ongoing difficulties in obtaining reagents or other materials. For some, meeting Canadian or EU standards that include using synthetic DNA for calibration (as opposed to serial dilutions) or using probes in addition to primers for qPCR analysis, is not possible and so standards that require these cannot be met. This type of trade-off is a reality for many researchers in the Global South and remote areas and, in many cases, there is no option, but to adapt protocols and standards to what is available, although this may be problematic during the peer-review process.
Difficulty accessing technology and state-of-the-art equipment was also mentioned by many participants. Laboratory sterilisation was a particular problem identified by a few researchers. There are entire regions (e.g. polar regions, middle jungle and the Amazon Forest) and situations (on research vessels) with no sterile extraction lab and so any standard which requires one would be unattainable. While those doing genetic work aim to have sterile labs, standards that require best practices, such as separating workflows into dedicated and separate rooms, each with their own air sources, can be fundamentally cost prohibitive or physically infeasible. Similarly, researchers in many regions have limited access to sequencers and if they do, a human-centred genomics facility may be all that is available, which is not ideal for eDNA research. Additionally, challenges with access to refrigeration are common, especially when combined with shipping delays. While some of these issues, such as sequencing, are becoming less of a challenge due to developments in portable and affordable sequencing technologies, such as the Oxford Nanopore, these technologies are far from being universally accessible, reliable or applicable. Still, the lack of access to computing power and specialised training necessary for bioinformatics work makes these technologies impractical for many researchers.
Some people pointed out that the goal of eDNA monitoring is to make monitoring more cost effective than traditional monitoring, but if standards require expensive materials, this is directly at odds with this goal. Fundamentally, researchers do not have access to all materials everywhere and this must be considered when developing international standards. There was a common worry that, if international standards are set by those in more developed countries, they will be unattainable by those in less-resourced and accessible areas. Finally, the cost of purchasing the actual standards or obtaining laboratory certification was discussed by some participants as also being a concern.
The second most-common concerns were around the technical issues of creating useful standards. Many participants identified the difficulty of creating a “one-size-fits-all” standard method or protocol ranging from sampling design to data analysis, when it is used to research a wide variety of locations, ecosystems, taxa and applications. The material differences between many study sites are vast–from tropical forests to Arctic deserts and from soil to air to water–and people are concerned that a standard might not translate or be interoperable, across such physical and biological differences.
Different eDNA technologies are also at very different stages of technology readiness, depending on the application and some participants are concerned that standardising at this stage, when many researchers are troubleshooting and experimenting with different techniques, may stifle innovation and may make it difficult for the field to change in the future. People pointed out that the technology is developing at a rapid pace and methods and technologies are still in flux. Further, many locations also lack a local species DNA reference library, which was mentioned by many researchers in this study and has been documented by others (
Data sharing and data standardisation were another set of concerns discussed by almost everyone. While participants regarded data standardisation as important, some also felt that it was costly and time consuming, partly due to the high cost of computing and lack of access to reliable internet connectivity and data servers in some locations, particularly remote islands. Beyond these technical aspects, however, many people discussed data standards in terms of data ownership and control, particularly in relation to genetics. The Nagoya Protocol, which outlines the fair and equitable use of genetic resources, was named as both a difficulty for researchers wanting to ship eDNA samples across borders and recognised as an important consideration for ethical standards development. Some also think that the Nagoya Protocol does not go far enough in protecting genetic resources. While there was no precise consensus amongst participants, many people mentioned the legacy of genetic colonialism, issues with colonial science more generally, intellectual property rights and indigenous sovereignty as being important considerations for standards development, both in terms of genetic resources themselves and the data related to these resources.
Several people discussed the specific issue of data security, describing how eDNA-related data can be very culturally and personally sensitive, particularly in terms of unintentional geo-location of human DNA “bycatch” that could end up in public databases (
Several other concerns around standards were also discussed by some participants. One of these is in relation to publication and that if standards become required for publishing in particular journals or receiving funding from particular sources, this could become a barrier for some researchers. Another concern related to development of standards themselves and that it may be inappropriate to adopt standards from one field and apply them to another. One example would be adopting genomic methods from museum collections or forensics labs, which might not be helpful for those trying to develop genomic methods to be used in the field. Finally, a few participants were concerned about the development of standards that favour private companies, either favouring one over another or stifling experimentation in academic settings by imposing strict, industry or regulatory standards in that context.
In addition to being asked to discuss their perspectives on standards, participants were given an opportunity to talk about access to resources needed more generally. Many of the answers arose in the form of bottlenecks or gaps, in which a research workflow became difficult or impossible without developing alternatives.
One, almost universal concern, for those doing eDNA analysis in the Global South and remote areas was the high cost and difficulty of obtaining reagents, although other materials, such as filters and flow cells, were also mentioned. As discussed above, for some, even basic laboratory equipment is difficult to come by and sequencers were often regionally inaccessible or non-existent, although advances in rapid, in-situ metabarcoding are changing this (
Shipping samples and materials across borders was identified by many participants as being a major, time-consuming and expensive hurdle. Without regional suppliers, shipping times can become prohibitive. There is a general acknowledgement across most participants that there are significant gaps to fill in funding, access and coverage of areas in terms of reference libraries and understanding species and baselines. This includes the High Seas and the Global South, but also many areas of the tropics more generally, where there has been little comprehensive genomic work done. The Barcode of Life Database (BOLD), for example, illustrates a concentration of data in the Global North. Several people discussed the need for experts in specific taxa working to develop rigorous databases on under-represented ecosystems or species. As one participant pointed out: “your sequences are only as good as your libraries”.
Finally, almost half of the participants discussed bioinformatics as being a major bottleneck in their work. The reasons are broad, from difficulties with accessing computing capacity and storage, to lack of expertise and a fast-moving field where pipelines and statistical packages are developing at a rapid rate. Several participants specifically identified the need for training in bioinformatic analyses and the difficulty of retaining people in the bioinformatics field.
A final interview question was related to perspectives on the future of eDNA research, both their own and the field as a whole. As might be expected when speaking to a group of eDNA researchers, everyone expressed a general sense of excitement and optimism for their research and expanding applications for eDNA in the future. People spoke about the fast rate of technological development, with decreasing time to obtain data, possibilities for quantification of organisms and a future where “everything is done in the field”, due to the accessibility of real-time long-read sequencing (
In terms of a cohesive vision for the field, participants discussed the need for people to really “dig in for the long term”, develop expertise and refine methods and protocols. Several people think that this in-depth work is necessary to move the field forward and become more rigorous and trusted. A few participants described a difference in goals between those that are working to develop eDNA as a means to understanding and addressing the biodiversity crisis and those that want to make a profit from the technology, although most people discussed common values across eDNA researchers that is based on openness, collaboration, sharing and even democratic and egalitarian ideals.
It is important to remember that the purpose of this article is not to portray a unified perspective, but instead to describe a diversity of viewpoints, which may, or may not, always be in agreement. Therefore, the outcomes of this paper should not be taken as a collective voice, but instead a collection of voices that offer to broaden scope and ideas in relation to international standards for eDNA.
Many people described the potential positive impacts that international standards could have on their work, but they also illustrated ways that these standards should be adaptable and flexible, having different options or protocols for different contexts and applications. Several examples were provided to illustrate this point, including alternative standards for: in-field (or on a boat or in a kitchen) vs. in-lab. This would include different standards for different processing and analysis goals and flexibility to consider different costs and materials or reagents (such as different Taq polymerases). A common perspective was the need to have pragmatic guidelines that can make research comparable, but that are not so stringent that research (or researchers) are left behind. While flexibility may seem at odds with standardisation, flexibility is actually a well-known property and even purpose for standards, which act as “boundary objects” to enable shared meaning and communication across different communities (
One overarching desire is the need to strengthen regional or in-country capacity for eDNA research. Increasing regional capacity will help avoid imbalances in “parachute” or colonial science (
A recent study by
Further, proficiency testing and obtaining reference materials can be an issue in certifying labs, but this could be done regionally. One example is the National eDNA Reference Centre being established in Australia which will facilitate standardisation, design assays relevant to the region and provide proficiency testing for labs on the continent (
Standards should be developed in a way that provides options, realising that not all data can be geolocated and that some researchers and communities may want to opt-out of publishing sensitive data due to issues of sovereignty or security. Researchers engaging in these conversations in other fields, such as palaeogenomics (or ancient DNA), have identified ways to create more equitable participation of researchers in the Global South by attuning to local implications of research, taking time to develop and implement accountability measures and acknowledging the historical harms caused by scientific colonialism and other forms of exploitation (
Although international standards have no technical requirement to be attainable by all, if a standard is truly an international or “global” standard, eDNA practitioners everywhere should have the capacity to meet it. In other words: while it is important to have a standard, it is more important that everyone can use it within their own situations and contexts. This is especially true because both the biological and social contexts for eDNA research vary across the world and also within locales. The goal of standardisation should be a process-based goal: standardisation itself should build capacity. If eDNA standards are open, accessible and affordable, they can become a powerful tool. Standardisation can help build a strong international network of researchers that rise together to face the biodiversity crisis. This will require the research community to work together to strengthen capacity and support training and mentorship on a global scale, for example, to study climatic and global changes. Importantly, rather than hindering development, dialogues taking place around standardisation of eDNA methods and technologies should act as catalysts and democratising exercises, but in order to do so, dialogue must take place across all hemispheres of the globe and invite a wide range of stakeholders into the conversation.
We gratefully acknowledge The David and Lucile Packard Foundation (grant #2021-72609) for the funding which enabled this research.
The authors have declared that no competing interests exist.
No ethical statement was reported.
The David and Lucile Packard Foundation.
Conceptualization: SLH, RPK, EA. Data curation: SLH. Formal analysis: SLH. Investigation: SLH. Methodology: SLH. Project administration: SLH. Writing - original draft: MLL, SH, RPK, GHBP, MLDL, NKDC, EA, SLH, NAP, PAA, JGMG, KKCH, NM, KNO, DAP, FT, MW, VYN, YR. Writing - review and editing: PAA, DAP, JGMG, YR, KKCH, FT, NM, EA, NKDC, VYN, SLH, MLDL, GHBP, RPK, SH, MLL, KNO, NAP, MW.
Shana Hirsch https://orcid.org/0000-0003-3131-1701
Phyllis Akua Amamoo https://orcid.org/0009-0009-5678-3204
Ni Kadek Dita Cahyani https://orcid.org/0000-0003-4484-6414
Joape G. M. Ginigini https://orcid.org/0000-0002-1726-1771
Manuel Lopes-Lima https://orcid.org/0000-0002-2761-7962
Mark Louie Lopez https://orcid.org/0000-0003-4288-4871
Diana A. Pazmiño https://orcid.org/0000-0001-7082-3254
Yoshimi Rii https://orcid.org/0000-0002-6486-8955
Sophie von der Heyden https://orcid.org/0000-0001-9166-976X
Vanessa Yepes-Narvaez https://orcid.org/0000-0001-7174-5382
Elizabeth Andruszkiewicz Allan https://orcid.org/0000-0002-9675-0003
Ryan Kelly https://orcid.org/0000-0001-5037-2441
All of the data that support the findings of this study are available in the main text or Supplementary Information.
Interview questions
Data type: docx
Explanation note: Contains the questions used in interviews for this research.