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we see everything in front of us with Quick guide


excruciating detail but we do not; we feel
we remember our past like as in a movie
but we do not do that either. Our brain
Environmental DNA
constructs a matrix, our reality.
Both perception and memory rely Emilie A. Didaskalou*, Krijn B. Trimbos
on processing very little information and Kathryn A. Stewart
and filling gaps making unconscious
inferences based on previous What is eDNA? Environmental
experiences. In this matrix created DNA (eDNA) is the genetic material
by our brain, magicians are like Neo, present in an environmental sample
mastering their metier and fooling (Figure 1A). When organisms interact
these assumptions to make us with their environment, they leave
experience what we cannot conceive behind genetic traces in the form
or understand3. Hardly anybody knows of extracellular (free-floating) or
more about attention and misdirection intracellular (within cells, mitochondria
than an experienced magician, and I am or chloroplasts) DNA. These
Figure 1. Neuromagic: exploring the syn- not referring to textbook knowledge, genetic traces are released into the
ergetic links between magic and cognitive but to how it actually works, in real life. environment in many ways, and to be
neuroscience. But magicians are typically not aware honest some can be quite disgusting:
of how far the rabbit’s hole goes and skin, mucus, saliva, sperm, secretions,
of his hands, what he is looking at, and how their mostly intuitive and pragmatic eggs, faeces, urine, blood, root,
so on. This way, seemingly casually he knowledge is based on cognitive leaves, fruit, pollen, rotting bodies
may bias your attention, force a decision neuroscience principles — how we see, and even whole organisms (e.g.,
you are convinced you took freely, or pay attention, decide or remember. microbes).
even make you believe you witnessed Cami and Martinez act like Morpheus,
something that never happened. All explaining in simple terms, and with OK, but what is an environmental
these feats are much more interesting compelling examples, the intricate sample? In the strictest sense,
than unveiling a specific sleight of hands. workings of the matrix in our brain. In environmental samples consist
So, rather than seeking to understand their book, magic acts as a trigger to of water, soil, sediment, snow,
how a magician did a particular trick, learn neuroscience principles that are permafrost, or air. But in a broader
you could delve into all the painstaking presented through a fascinating and sense, eDNA samples can also come
effort he put into making it work. This is refreshing viewpoint, and that should from faeces, feeding traces, spider
exactly what you will find in the superb also be interesting to the lay reader not webs, honey, flowers or surfaces.
new book The Illusionist Brain: The acquainted with the sorcerers’ guild.
Neuroscience of Magic by Cami and If, like me, you are a cognitive What do you measure with eDNA?
Martinez, two seasoned scientists and neuroscientist, just imagine coming Remember the tricorder from the
magic connoisseurs. If you read their up with a behavioural experiment that original Star Trek series? When landing
book, you will not learn a single magic always works — 100% of the time and in parties from the starship Enterprise
trick, but you will discover the theoretical every single subject. That’s what a magic would scout unfamiliar areas and
foundations supporting them all. And the trick does. It doesn’t just apply to a use this futuristic device to perform
foundations of the art of deceiving are, to statistically significant number of people a bioscan of their new surroundings?
a large extent, plain neuroscience. in the audience; it works for everybody. Well, eDNA comes pretty close! It can
“Wake up, Neo…” reads the message In this regard, the book of Cami and measure the presence or absence
on Neo’s computer screen that lead him Martinez lays out the foundations of how of a target species, the species
to meet Morpheus and find out about this is done, and offers the most up to composition of your sample and the
“The Matrix”. It is a sci-fi movie but the date and comprehensive introduction relative abundance or biomass of
idea of the matrix is deeply rooted in to the emerging field of ‘Neuromagic’ species in that sample.
philosophy, going from the notion of a (Figure 1).
brain in a vat, to Descartes’ demon and How do you measure it? First, one
all the way back to Plato’s allegory of the REFERENCES must collect the samples. Sampling
cave (see chapter 4 in Quian Quiroga2). can either be done by direct collection
We don’t live in pods filled with a viscous 1. Tamariz, J. (2014). The Magic Way (Seattle: (e.g., some water, soil), by actively
Hermetic Press).
liquid and cables stimulating our senses 2. Quian Quiroga, R. (2020). Neuroscience Fiction filtering samples (water or air) across
(at least we think we don’t), but the (Dallas, TX: BenBella Books). a membrane, or passively filtering
matrix provides a fascinating metaphor 3. Quian Quiroga, R. (2016). Magic and cognitive by simply placing filters within the
neuroscience. Curr. Biol. 26, R390–R394.
of how the brain works. All what we see, environment to collect DNA. Once
feel and remember is a construction, not the samples are retrieved, the next
Centre for Systems Neuroscience, University
by an architect, an artificial intelligence of Leicester, 15 Lancaster Road, Leicester step is to extract the DNA using the
or an evil genius, but simply by the LE1 7HA, UK. appropriate protocol that provides
activity of our neurons. We believe E-mail: rqqg1@le.ac.uk you with the highest DNA yield while

R1250 Current Biology 32, R1245–R1261, November 21, 2022 © 2022 Elsevier Inc.
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removing enzymes and chemicals A


that might mess up your downstream
analysis. The rest of the workflow
is based on PCR (polymerase chain
reaction) amplification, which boosts
your DNA signal so that you can
detect it. This ranges from quantitative
PCR if you are interested in the
presence or absence of a specific
species, or preparing your samples for
a sequencing run, which can reveal
the species composition within the
clades of your interest, also known as
‘DNA metabarcoding’.

Why is eDNA such a cool tool


to use? Traditional methods of
monitoring biodiversity are mainly
observational. So, aside from obvious B Presence/Absence Species interactions
drawbacks such as identification
bias, and the sometimes-destructive
nature of sampling, traditional
methods also require a high level of
taxonomic expertise which is often
lacking. Plus, identification is usually
time and labour intensive, making Community structure
it costly. On the other hand, eDNA
has been shown to overcome these
hurdles, as samples can be collected
in a non-destructive manner and with
relative ease, and analysis mostly C Origin State
Intracellular
requires only basic laboratory skills.
In fact, methods like metabarcoding
allow you to analyze many samples
or species simultaneously and as
the price of sequencing continues to
decline exponentially, eDNA makes Extracellular
a quick and cost-effective tool
that can be used in a standardized
manner. As a result you can take more
samples in space and time and get a
much better grasp of the species or Fate Transport
community in a location. Likewise,
eDNA’s persistence in the environment Horizontal
varies from hours to weeks in aquatic
environments and from months to
hundreds of thousands of years in
soil and sediment, which allows for
detection of species in the present
and the past. Finally, DNA approaches
pH
have also been proven to be more Vertical
sensitive and can detect elusive
and endangered species, along with Current Biology
species that are difficult to identify or
locate (unreachable habitats). Figure 1. eDNA — applications and ecology.
(A) What is eDNA and where does it come from? (B) eDNA applications. (C) The ecology of eDNA.
What is it used for? Due to its eDNA release by the organism can depend on size or life stage (origin). Similarly, its persistence can
be affected by the form in which eDNA exists in the environment (state) or by the environmental
many advantages, eDNA is used in a
conditions: temperature, UV exposure, pH and microbial activity (fate). Knowledge on how eDNA can
wide range of applications including be transported is also important to determine whether the species detected occurred close to, or far
ancient ecosystem reconstruction, away from, the sampling site and whether they occured in the past or present (transport). Created by
diet analysis, plant–pollinator Emilie A. Didaskalou with BioRender.com.

Current Biology 32, R1245–R1261, November 21, 2022 R1251


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interactions and air quality monitoring. natural world at rates that are difficult Primer
By surveying species across different to monitor with traditional methods.
habitats and taxonomic groups, eDNA
is used to retrieve information on
What we are experiencing now is
that eDNA could supplement, and
Roost making in
the community structure of poorly sometimes even replace, traditional bats
studied habitats, to extend taxonomic monitoring methods that are currently
resolution or diversity estimates of used to inform species and ecosystem
past studies, and to document how management decisions. Filling in Rachel A. Page1,*
communities shift through time in the knowledge gaps concerning and Dina K.N. Dechmann1,2,3,4
response to environmental change, the ecology of eDNA and further
pollution, or restoration efforts. Owing optimizing or resolving technical Structures created by animals can
to its success in detecting species and methodological limitations serve many purposes. Spiders weave
in low concentrations, eDNA is often (e.g., completing our DNA reference intricate webs to trap prey; beavers
used to keep track of the spread of databases, limiting false positives and engineer complex networks of dams
harmful invasive species or to identify negatives) are the most important next to alter waterways; male bower birds
habitats of critical importance to steps. These will allow us to improve construct and decorate elaborate
endangered and otherwise difficult to data interpretation and expand bowers to attract mates. Animal
detect species. Lastly, thanks to the its potential to other applications architecture ranges widely in function,
user-friendly sampling method, eDNA (e.g., population or functional but by far the most common use is
is now also popular in citizen science genetics). Ultimately, technological shelter. Animals can spend a large
and education (Figure 1B). advancements (like Nanopore’s amount of time in their shelters, and
portable real-time sequencer), and the this is often where they both sleep and
What are its limitations? As cool prospect of making eDNA biodiversity rear young, two of the most vulnerable
as it sounds, eDNA is not flawless. data globally accessible, make it a states in animal lives. To optimize
One of its main limitations is the very promising tool for successfully the safety and suitability of refuges
current difficulty in obtaining specific assessing conservation priorities and available to them, many animals have
information beyond the level of biosecurity risk. become architects and create their own
taxonomy, such as age, sex, and size. shelters, ranging from simple holes in
The interpretation of obtained data Where can I find out more? the ground to the large complex nests
also requires a deeper understanding Barnes, M.A., and Turner, C.R. (2016). The ecology of some social insects.
of environmental DNA and implications for
of the ecology of eDNA (where it conservation genetics. Conserv. Genet. 17, Building or modifying a structure to
comes from — origin; it’s physical 1–17. create a refuge, however, requires time
Berry, O., Jarman, S., Bissett, A., Hope, M.,
properties in the environment — state; Paeper, C., Bessey, C., Schwartz, M.K., Hale, and energy, and understanding this
how and where it persists — fate J. and Bunce, M. (2021). Making environmental behaviour in a social and ecological
and how it’s transported) (Figure 1C). DNA (eDNA) biodiversity records globally context is key to understanding
accessible. Environ. DNA 3, 699–705.
Importantly, different practises can Bohmann, K., Evans, A., Gilbert, M.T., Carvalho, the selection pressures that shape
influence eDNA detection, and thus G.R., Creer, S., Knapp, M., Yu, D.W. and de it. Though animal architecture is
Bruyn, M. (2014). Environmental DNA for
laboratory and field protocols often wildlife biology and biodiversity monitoring. taxonomically widespread, reviews of
need to be standardised for different Trends Ecol. Evol. 29, 358–367. animal architecture often focus on birds
species or environments. Likewise, for Cristescu, M.E. and Hebert, P.D.N. (2018). and insects. Few researchers discuss,
Uses and misuses of environmental DNA in
various and quite complicated reasons biodiversity, science and conservation. Annu. let alone parameterize and model,
that would turn this into a slow guide, Rev. Ecol. Evol. Syst. 49, 209–230. the advantages and disadvantages of
Deiner, K., Bik, H.M., Mächler, E., Seymour, M.,
false positives (DNA is recovered Lacoursière-Roussel, A., Altermatt, F., Creer, shelter construction in mammals.
but the species isn’t present) and S., Bista, I., Lodge, D.M., de Vere, N. et al. Bats are the second largest order
false negatives (species are present (2017). Environmental DNA metabarcoding: of mammals with more than 1400
Transforming how we survey animal and plant
but DNA remains undetected) can communities. Mol. Ecol. 26, 5872–5895. species described to date, and exhibit
be introduced into the data during Ruppert, K.M., Kline, R.J., Rahman, M.S. (2019). stunning diversity in ecology, social
Past, present, and future perspectives of
sampling and subsequent analysis. environmental DNA (eDNA) metabarcoding: systems, behaviour, and morphology.
Just to give an example, incomplete A systematic review in methods, monitoring, All bats depend on suitable shelters
DNA reference databases (consisting and applications of global eDNA. Glob. Ecol. or ‘roosts’ as they rest during the day,
Conserv. 17, e00547.
of unique DNA sequences and their Stewart, K.A. (2019). Understanding the effects of and often also between foraging bouts
species identification) can influence biotic and abiotic factors on sources of aquatic at night. Bat shelters have to fulfil
environmental DNA. Biodivers. Conserv. 28,
results enormously. Yet, certain 983–1001. specific microclimate and accessibility
limitations can be overcome during Taberlet, P., Bonin, A., Zinger, L., and Coissac, E. requirements, and their availability both
experimental design and bioinformatic (2018). Environmental DNA: For Biodiversity limits species distribution ranges and
Research and Monitoring (Oxford: Oxford
approaches. University Press). is crucial for successful conservation.
For example, the fact that so many
What is the future of eDNA bats aggregate in just a few suitable
Department of Environmental Biology,
research? It is well known that Institute of Environmental Sciences, Leiden caves has had a dramatic influence
biodiversity is declining worldwide, University, Leiden, Netherlands. on the spread in North America of
and human impacts are altering our *E-mail: e.a.didaskalou@cml.leidenuniv.nl white-nose syndrome, a devastating

R1252 Current Biology 32, R1245–R1261, November 21, 2022 Published by Elsevier Inc.

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