Environmental DNA (eDNA) and metagenomics

Environmental DNA or eDNA raises serious ethical complexities relating to human DNA, especially when sampling eDNA on Indigenous lands. This is discussed in a fascinating paper by Matilda Handsley-David and colleagues (see below). But to start with some definitions…

Environmental DNA (eDNA) and metagenomics

Wikipedia offers a good basic definition: Environmental DNA or eDNA is DNA that is collected from a variety of environmental samples such as soil, seawater, snow or even air rather than directly sampled from an individual organism. As various organisms interact with the environment, DNA is expelled and accumulates in their surroundings from various sources. Example sources of eDNA include, but are not limited to, faeces, mucus, gametes, shed skin, carcasses and hair. Such samples can be analyzed by high-throughput DNA sequencing methods, known as metagenomics, metabarcoding, and single-species detection, for rapid monitoring and measurement of biodiversity.

Metagenomic environmental samples also include the DNA of living microbes that inhabit the sample, alongside shed DNA from the sources referred to above. Therefore metagenomic studies are carried out on environments where there are prolific and diverse microbiomes, such as the intestinal tracts of humans and animals. What distinguishes metagenomic samples from DNA sampled directly from an individual organism, is their hybrid nature – metagenomic samples contain the DNA of many different organisms within the same sample, a kind of DNA mash-up.

Metagenomic sampling techniques turned out to be crucial for our residency research. We were very fortunate that Dr Rénee Smith, a genomics scientist from Jimmy’s lab, lent us some of her metagenomics expertise for our DNA extraction and sample preparation. I discuss this in more detail in the Lab Work section of this blog.

Metagenomics and microbial diversity

The drop in the cost of genome sequencing and the widespread use of shotgun and PCR genome sequencing has permitted widespread and relatively ‘unbiased’ sequencing of eDNA collected in environmental samples. This has revealed vast numbers of microorganism species that have never been described or classified, simply because they are resistant to culturing in the lab. Many of these species are being described for the first time through metagenomic sampling of the environment. Metagenomics has made clear that microbial diversity is far more complex than was previously realised using culturing methods.

The ethics of eDNA collection on Indigenous lands

In some climatic conditions human eDNA, and microbial eDNA associated with human life and activities, can persist in soil and sediment samples for centuries beyond the lifespan of the humans concerned.

In a fascinating Nature paper by Matilda Handsley-Davis and colleagues: Researchers using environmental DNA must engage ethically with Indigenous communities, the authors unpack the significant ethical risks and complexities of eDNA and metagenomic studies, especially when carried out on Indigenous lands.

The paper’s abstract explains:

The study of environmental DNA can reveal information about the history and presence of Indigenous communities on their lands — potentially even inadvertently. Better engagement with the ethical aspects of environmental DNA research is required in the field as a whole, and especially for researchers working on Indigenous lands (Handsley-Davis et al, 2021).

Human eDNA can be inadvertently included in eDNA collected from soil or sediment samples, even if the target of the research is microbial or other, non-human DNA:

Increasingly, eDNA research is moving away from metabarcoding and amplicon studies that target specific organismal groups, and towards whole-genome or shotgun sequencing approaches that can reveal the total diversity of DNA present in a sample.

This indiscriminate approach raises key ethical questions, especially in Indigenous contexts. As such, it is critical that ethical questions arising from new approaches to genetic research, such as eDNA analysis, be carefully considered. For example, what are the potential risks and benefits for Indigenous peoples engaging with eDNA research? How should such research be classified, regulated and governed? How can the potential of this new technical approach be communicated without ‘hype’ or over-promising results? (Handsley-Davis et al, 2021).

The authors discuss in detail Indigenous birthing trees:

Some of these questions can be illustrated using the example of the birthing trees that were regularly used by Aboriginal women in southeastern Australia before the expansion of European settlement in the mid-nineteenth century. Women typically gave birth and buried placentas under a birthing tree, and contemporary Aboriginal researchers have used archival records and oral testimony to show that the trees were associated with labour techniques, midwifery and ceremonies surrounding labour and birth. Birthing trees also facilitated connections to land for the mother and baby, and aspects of the traditional practice are still known and used by Aboriginal groups in south-eastern Australia. Acknowledging this historical and ongoing importance of birthing trees for Aboriginal women, we approach this topic as a team of Indigenous and non-Indigenous female researchers drawing collectively on several decades of engagement with Indigenous communities.

Environmental DNA research could provide insight into birthing trees via several mechanisms, investigating questions of mutual interest to researchers and Indigenous communities. For example, human DNA preserved in soil or sediment adjacent to a birthing tree could be revealed, potentially confirming a known birthing site, identifying a previously unknown birthing tree, or demonstrating a connection between a specific family or group and a specific tree. Further, identification of ancient human-associated microbes could provide information on past infections or birth complications. However, such research also presents risks for Indigenous peoples. For example, analysis of soil or sediment samples may not identify human DNA at a birthing tree site, which could potentially be used to argue against land rights claims or the protection of cultural heritage, or eDNA may identify microorganisms associated with potentially stigmatizing diseases, such as sexually transmitted infections. A further risk relates to the use of a Western scientific lens to assess eDNA use. In this example, we see Western science as complementary to Indigenous knowledge, although some may interpret the use of eDNA technology as an implication that Indigenous knowledge is insufficient to inform decision-making about the preservation of birthing trees (Handsley-Davis et al, 2021).

Confounding questions discussed by the authors relate to the ethical regulation of eDNA research. The authors note that discrepancies between Indigenous and non-Indigenous understandings significantly complicate the oversight of eDNA research practices:

Another potential discrepancy between Western and Indigenous viewpoints might arise from the way human and non-human research is distinguished. Human research is typically subject to more stringent ethical requirements and approval from institutional committees, but it is currently unclear if analysis of human DNA isolated from an environmental source would constitute human research.  

Even if no human DNA is isolated from an environmental sample, or if researchers agree to disregard any human DNA detected, Indigenous stakeholders may still have ethical concerns. For example, the cultural significance of non-human animals, water, landscapes and natural phenomena differs between Indigenous and Western contexts, which may complicate existing distinctions between human and non-human research. Because the study of non-human eDNA, including that of animals or plants, could have culturally important implications for Indigenous people, ethical review of such research should implement Indigenous oversight from communities with connections to the land from where eDNA originates (Handsley-Davis et al, 2021).

Thanks to Jimmy and to Bastien Llamas for drawing my attention to this paper, and to Matilda for discussing her research with me, which completely blew open my thinking about the permeability of humans and environment, culture and land, across time and space.


Matilda Handsley-Davis, Emma Kowal, Lynette Russell and Laura S. Weyrich. 2021. “Researchers using environmental DNA must engage ethically with Indigenous communities.” Nature Ecology & Evolution, 5: 146–148. https://doi.org/10.1038/s41559-020-01351-6