Conservation in a cup of water: estimating biodiversity and population abundance from environmental DNA.

Abstract

Three mantras often guide species and ecosystem management: (i) for preventing invasions by harmful species, 'early detection and rapid response'; (ii) for conserving imperilled native species, 'protection of biodiversity hotspots'; and (iii) for assessing biosecurity risk, 'an ounce of prevention equals a pound of cure.' However, these and other management goals are elusive when traditional sampling tools (e.g. netting, traps, electrofishing, visual surveys) have poor detection limits, are too slow or are not feasible. One visionary solution is to use an organism's DNA in the environment (eDNA), rather than the organism itself, as the target of detection. In this issue of Molecular Ecology, Thomsen et al. (2012) provide new evidence demonstrating the feasibility of this approach, showing that eDNA is an accurate indicator of the presence of an impressively diverse set of six aquatic or amphibious taxa including invertebrates, amphibians, a fish and a mammal in a wide range of freshwater habitats. They are also the first to demonstrate that the abundance of eDNA, as measured by qPCR, correlates positively with population abundance estimated with traditional tools. Finally, Thomsen et al. (2012) demonstrate that next-generation sequencing of eDNA can quantify species richness. Overall, Thomsen et al. (2012) provide a revolutionary roadmap for using eDNA for detection of species, estimates of relative abundance and quantification of biodiversity.

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NEWS AND VIEWS
PERSPECTIVE
Conservation in a cup of water:
estimating biodiversity and population
abundance from environmental DNA
DAVID M. LODGE,*† CAMERON R.
TURNER,*† CHRISTOPHER L. JERDE,*
MATTHEW A. BARNES,† LINDSAY
CHADDERTON,‡ SCOTT P. EGAN,§ JEFFREY
L. FEDER,*,† ANDREW R. MAHON†1and
MICHAEL E. PFRENDER*†–
*Environmental Change Initiative, University of Notre Dame,
Notre Dame, IN 46556, USA, †Department of Biological
Sciences, University of Notre Dame, Notre Dame, IN 46556,
USA, ‡Great Lakes Project, The Nature Conservancy, Notre
Dame, IN, USA,§Advanced Diagnostics and Therapeutics
Initiative, University of Notre Dame, Notre Dame, IN 46556,
USA, –Genomics Core Facility, University of Notre Dame,
Notre Dame, IN 46556, USA
Three mantras often guide species and ecosystem man-
agement: (i) for preventing invasions by harmful spe-
cies, ‘early detectionand
conserving imperilled native species, ‘protection of bio-
diversity hotspots’; and (iii) for assessing biosecurity
risk, ‘an ounce of prevention equals a pound of cure.’
However, these and other management goals are elusive
when traditional sampling tools (e.g. netting, traps, elec-
trofishing, visual surveys) have poor detection limits, are
too slow or are not feasible. One visionary solution is
to use an organism’s DNA in the environment (eDNA),
rather than the organism itself, as the target of detec-
tion. In this issue of Molecular Ecology, Thomsen et al.
(2012) provide new evidence demonstrating the feasibil-
ity of this approach, showing that eDNA is an accurate
indicator of the presence of an impressively diverse set
of six aquatic or amphibious taxa including inverte-
brates, amphibians, a fish and a mammal in a wide
range of freshwater habitats. They are also the first to
demonstrate that the abundance of eDNA, as measured
by qPCR, correlates positively with population abun-
dance estimated with traditional tools. Finally, Thomsen
et al. (2012) demonstrate that next-generation sequenc-
ing of eDNA can quantify species richness. Overall,
rapidresponse’;(ii)for
Thomsen et al. (2012) provide a revolutionary roadmap
for using eDNA for detection of species, estimates of
relative abundance and quantification of biodiversity.
Keywords: biodiversity
invasive species, natural resource management, pyrose-
quencing, qPCR
assessment, biosecurity,eDNA,
Received 10 January 2012; revision received 10 March 2012;
accepted 12 March 2012
Rapid development and application of eDNA
approaches
Recent applications of eDNA have surprised some environ-
mental managers because they seemed to emerge abruptly
from the research phase (Darling & Mahon 2011). Yet the
research that produced these tools illustrates typical and
incremental scientific progress. The term ‘environmental
DNA’ originates from microbiology (Ogram et al. 1987)
and generally means DNA extracted from an environmen-
tal sample without isolating the target organism; for mac-
robiota, an entire organism is often not even present in the
sample. Research targeting ‘macrobial’ eDNA began with
detection of plant DNA in soil (Paget et al. 1998), with the
first metagenetic approach (sensu Creer et al. 2010) to
eDNA also applied to soil (Willerslev et al. 2003). The first
application of macrobial eDNA analysis in an aquatic envi-
ronment detected human, cow, pig and sheep DNA in
river water (Martellini et al. 2005), with the first aquatic
metagenetic approach aimed at riverine fishes (Minamoto
et al. 2011). In this issue, Thomsen et al. (2012) apply the
most current techniques, quantitative real-time PCR (qPCR)
and next-generation sequencing, to demonstrate compel-
lingly the power of the eDNA approach (Figs 1 and 2).
Specifically, results from qPCR provide an index of pop-
ulation size, which is a very important advance over PCR
(Thomsen et al. 2012). In addition, qPCR has a lower detec-
tion threshold than traditional sampling tools, probably
even lower than PCR because of the generally greater sen-
sitivity of qPCR (Thomsen et al. 2012). Finally, using qPCR,
Thomsen et al. (2012), expanding on other recent studies
(Dejean et al. 2011), observed that the rapid degradation of
eDNA in surface water means that the detection of eDNA
indicates the very recent presence of aquatic species. In
80L tank experiments with a toad and a newt species, the
longest that eDNA remained detectable at the highest
organism density after removal of all amphibians was
between 9 and 15 days (Thomsen et al. 2012).
The application by Thomsen et al. (2012) of next-genera-
tion sequencing shows how to move forward from targeted
surveillance of one, or a handful of species, to more accu-
rate estimates of species richness.
Correspondence: David M. Lodge, Fax: 574-631-7413;
E-mail: dlodge@nd.edu
1Present address: Institute for Great Lakes Research, Central Michi-
gan University, Mount Pleasant, MI 48859, USA.
Re-use of this article is permitted in accordance with the Terms
and Conditions set out at http://wileyonlinelibrary.com/online
open#OnlineOpen_Terms
? 2012 Blackwell Publishing Ltd
Molecular Ecology (2012) 21, 2555–2558

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New eDNA tools in the toolbox to facilitate
management goals for species and ecosystems
Some
DNA have involved the detection of faecal pollution
(Martellini et al. 2005) and invasive species (Ficetola et al.
2008; Jerde et al. 2011). With invasive species, finding
incipientpopulationsearly
options to act before a harmful species achieves high
abundance (Robinson et al. 2011). Similarly, identifying
and protecting habitats important to the persistence of
biodiversity is daunting, particularly if threatened or
endangered species are difficult to detect (Goldberg et al.
2011) or restrictions prevent sampling efforts that risk
harm to individual organisms (Beja-Pereira et al. 2009).
Thomsen et al. (2012) and other recent papers (Pfrender
et al. 2010) point the way towards the power of eDNA
for identifying habitats critical to protected species, and
for assessing biodiversity for conservation, remediation
and restoration efforts.
prominentearlyapplications ofenvironmental
providesmanagers with
Trajectory of aquatic eDNA research: extracting more
information more rapidly
We believe that Thomsen et al. (2012) represents a macro-
bial eDNA research agenda that will proceed rapidly along
at least two trajectories: species-specific population surveil-
lance and monitoring; and metagenetic detection of multi-
Fig. 1 The six
Thomsen et al. (2012). From left to right
and top to bottom: Great crested newt
(Trituruscristatus),
spadefoot toad (Pelobates fuscus), adult
Large white-faced darter (Leucorrhinia
pectoralis), Tadpole shrimp (Lepidurus
apus), European weather loach (Misgur-
nus fossilis) and Eurasian otter (Lutra lu-
tra). (Copyright: top left and middle
right, ? http://www.deschandol-sabine.
com;bottom right,
Schulz⁄Polfoto; all other, ? Lars L. Iver-
sen).
speciestargetedin
adult Common
?
Gerhard
Fig. 2 Examples of sampling sites in Thomsen et al. (2012).
Top: Pond habitat for the amphibian species. Bottom: Running
water habitat for the European weather loach. (Copyright: top,
? Lars L. Iversen; bottom, ? Philip Francis Thomsen).
2556 NEWS AND VIEWS: PERSPECTIVE
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ple species simultaneously. Massively parallel technologies
like next-generation sequencing and microarrays can mea-
sure biodiversity across broad taxonomic scales. In compar-
ison with microbial metagenetics, macrobial metagenetics
benefits from a much smaller number of taxa, more reliable
species boundaries and a considerable public database
linkingtaxonomic andgenetic
metagenetics is already transforming the science of biodi-
versity assessment (Anderson-Carpenter et al. 2011).
However, one of the striking gaps in this rapidly grow-
ing field is the dearth of knowledge about how field and
laboratory protocols influence the detection of eDNA
(Goldberg et al. 2011), and how different environmental
conditions affect the production, degradation and detection
of eDNA. For example, a wide range of protocols have
been reported for field sampling (e.g. number and volume
of water samples), filtration (e.g. precipitation vs. various
filters), DNA extraction (e.g. different kits and protocols),
primer design and testing, PCR (e.g. number of reactions)
andconfirmation ofspecies
sequencing). The latter could be an underappreciated prob-
lem when it is critical to resolve among closely genetically
related taxa that could have vastly different repercussions
for management and⁄or biocontrol (Funk & Omland 2003).
Experimentstosystematically
urgently needed. For laboratory protocols, adherence to the
minimum information reporting guidelines for qPCR and
metagenetics (Taylor et al. 2008) would at least make it
more possible to compare protocols among publications
even if the specific effects of different protocols were
unknown.
Environmental DNA analysis is already an essential and
influential tool in water quality monitoring, the early detec-
tion of invasive and other harmful species and the surveil-
lance of imperilled species. With further refinements and
comparisons of field and laboratory protocols, eDNA anal-
ysis will provide more information on taxonomic diversity
and population abundance and find wider applications in
environmental science research. Thomsen et al. (2012) give
us confidence that: (i) eDNA analysis is applicable across
broad taxonomic boundaries; (ii) the presence of eDNA
indicates the recent presence of organisms; (iii) we can
expect to learn more and more about population abun-
dance with qPCR-based eDNA analysis; and (iv) next-
generation sequencing of eDNA will yield increasingly
accurate estimates of species richness. With eDNA, a lot
can be learned from a cup of water.
identities.Macrobial
specificity (e.g. cloning,
compare protocolsare
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DML is interested in the causes of changes in species composi-
tion in communities and the impact of those changes on eco-
system goods and services. CRT is interested in genetic
monitoring for conservation and management of aquatic eco-
systems. CLJ is interested in the application of quantitative
tools for resource management of rare species. MAB is inter-
ested in how dispersal shapes species ranges in human-influ-
enced landscapes. LC is interested in conservation of aquatic
NEWS AND VIEWS: PERSPECTIVE 2557
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biodiversity including management of invasive species. SPE is
interested in population genetics, evolutionary ecology and the
application of genetics to species monitoring. JLF is interested
in how populations adapt to the environment and the conse-
quences of ecological specialization for speciation. ARM is
interested in molecular ecology, phylogeography and methodo-
logical development for genetic monitoring in aquatic and
marine
response to environmental change and the interaction between
evolution and community composition.
ecosystems.MEPisinterestedinadaptation in
doi: 10.1111/j.1365-294X.2012.05600.x
2558 NEWS AND VIEWS: PERSPECTIVE
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