Available via license: CC BY-NC-ND 4.0
Content may be subject to copyright.
1
Title: Environmental (e)DNA detection of the invasive pink salmon Oncorhynchus gorbuscha during
1
the 2017 Norwegian invasion
2
3
Authors: Laura M. Gargan1, Frode Fossøy2, Tor A. Mo2, Jeannette E. L. Carlsson1, Bernard Ball1,
4
Jens Carlsson1
5
6
1Area 52 Research Group, Earth Institute/School of Biology and Environmental Science, University
7
College Dublin, Ireland
8
2Norwegian Institute for Nature Research (NINA), Trondheim, Norway
9
10
Corresponding author: Laura M. Gargan, E-mail: laura.gargan@ucd.ie
11
12
Keywords: Oncorhynchus gorbuscha; invasive species; digital droplet PCR; environmental DNA;
13
Norway
14
15
ABSTRACT
16
The pink salmon Oncorhynchus gorbuscha was introduced from its native range in the Pacific to
17
Northwest Russia several times since the 1950’s. While this species has been regularly observed in
18
rivers in Northern Norway since that time, there has been an upsurge in the numbers of odd-year O.
19
gorbuscha individuals observed in rivers in southern Norway in recent years, and particularly in 2017.
20
Although the wide-scale effects of this species presence are currently uncertain, there are concerns
21
regarding potential competition between O. gorbuscha and native species – most notably the Atlantic
22
salmon Salmo salar. Environmental (e)DNA is becoming a widely used tool to monitor rare and
23
invasive species in aquatic environments. In the present pilot study, primers and a probe were
24
.CC-BY-NC-ND 4.0 International licenseIt is made available under a
(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
The copyright holder for this preprint. http://dx.doi.org/10.1101/651554doi: bioRxiv preprint first posted online May. 31, 2019;
2
developed to detect O. gorbuscha from eDNA samples taken from a Norwegian river system where
25
the species was observed. Water samples were taken at both upstream and downstream locations of
26
the Lysakerelva river during Autumn 2017 (to coincide with spawning) and during late Spring 2018.
27
Autumn samples were positive for O. gorbuscha at both sampling locations, whereas Spring samples
28
showed positive detection of this species in the upstream region of the river, when smolt should have
29
left, or be in the process of leaving the river. These findings reveal that eDNA-based methods can be
30
used detect the presence of O. gorbuscha during their spawning season. This suggests that odd-year
31
populations have the potential to become established in the studied river system. We recommend that
32
eDNA sampling is repeated to determine whether individuals of this odd-year population have
33
survived at sea and return to spawn. Our assay specificity tests indicate that the tools developed in the
34
present study can be used for detection of O. gorbuscha in both Norwegian and other European river
35
systems where presence/absence data is required. We also suggest some modifications to our
36
methodology that may improve upon the detection capabilities of O. gorbuscha using eDNA.
37
38
INTRODUCTION
39
Pink salmon Oncorhynchus gorbuscha (Walbaum, 1792) are native to the Pacific Ocean,
40
where they typically spawn in the freshwater ecosystems of bordering countries between the latitudes
41
of 40o and 70o. This species follows a strict two-year life cycle (Figure 1). Adult O. gorbuscha
42
migrate from the open sea and up-river to spawn in the autumn, after which all spawning individuals
43
die. The juveniles emerge the following spring, ready to migrate down-river and out into the open sea
44
to mature for one winter. They return as adults to freshwater in the next autumn to spawn, thus
45
completing the life cycle (Heard 1991).
46
O. gorbuscha was originally introduced from their native Pacific range to North Western
47
Russia several times since the 1950’s, when fry were stocked in several rivers that drain into the
48
White Sea and the Barents Sea (Bakshtansky 1980). While O. gorbuscha has been regularly found in
49
rivers in Northern Norway since 1960 (Berg 1961), there has been an upsurge in the observations of
50
.CC-BY-NC-ND 4.0 International licenseIt is made available under a
(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
The copyright holder for this preprint. http://dx.doi.org/10.1101/651554doi: bioRxiv preprint first posted online May. 31, 2019;
3
odd-year O. gorbuscha in Norwegian rivers in recent years (Mo et al., 2018), as well as in rivers in
51
the UK and Ireland (Armstrong et al., 2018, Whelan 2017). However, self-reproducing populations
52
have not yet appeared to become established, most likely because they have not adapted time of
53
spawning to match local conditions outside of their native range (Mo et al., 2018).
54
Established populations of O. gorbuscha in rivers in North Western Russia are dominated by
55
odd-year individuals (Gordeeva & Salmenkova, 2011). Thus far, odd-year individuals have been
56
noticeably more abundant throughout their invasive range, with a particularly large number of
57
spawning O. gorbuscha recorded in 2017 (Armstrong et al., 2018, Mo et al., 2018). Therefore, it is
58
these odd-year stocks that are most likely to become established as populations and the next spawning
59
season (which should take place during Autumn of 2019) will be an important time for research
60
scientists to determine the extent of this invasion and its potential ecological effects.
61
Presently, the spawning time of O. gorbuscha in Norway does not appear to overlap with
62
native salmonids (e.g. Atlantic salmon Salmo salar and brown trout S. trutta). However, O. gorbuscha
63
and S. salar have similar preferences for spawning habitats and so there is a risk of competition for
64
optimal spawning sites (Sandlund et al., 2018). While O. gorbuscha juveniles emerge ready to
65
migrate to sea, observations in Norwegian rivers suggest that they spend some time feeding in
66
freshwater (from weeks to months) and during this time there may be interactions between juveniles
67
of native salmonids (Sandlund et al., 2018). However, it is also possible that the eggs and fry of O.
68
gorbuscha can provide a source of food for other native salmonid species (Rasputina et al., 2016). In
69
order to fully assess the impacts of the presence of O. gorbuscha in Norwegian (and other European)
70
rivers, it is first necessary to determine the spatial, as well as the temporal (e.g. time of spawning and
71
migration) distribution of this species.
72
Environmental DNA (eDNA) is a genetic survey method that relies on the detection of taxa
73
from extracellular and intracellular material that is deposited into the environment. Subsequently, this
74
material can be isolated from the environmental sample (such as water, air or soil; Taberlet et al.,
75
2012) and interrogated using genetic markers for multi-species (Thomsen et al., 2012, Hänfling et al.,
76
2016) or targeted species (Ficetola et al., 2008, Jerde et al., 2011, Gustavson et al., 2015) detection.
77
.CC-BY-NC-ND 4.0 International licenseIt is made available under a
(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
The copyright holder for this preprint. http://dx.doi.org/10.1101/651554doi: bioRxiv preprint first posted online May. 31, 2019;
4
While many studies have used quantitative PCR (qPCR) for targeted detection of species in
78
an eDNA sample (Thomsen et al., 2012, Wilcox et al., 2013, Atkinson et al., 2018), more recently the
79
approach of using digital droplet PCR (ddPCR) has been adopted by some researchers (Doi et al.,
80
2015, Nathan et al., 2015, Evans et al., 2017, Baker et al., 2018), with either similar (Nathan et al.,
81
2015) or increased (Doi et al., 2015, Hunter et al., 2017) sensitivity reported for ddPCR platforms
82
compared to qPCR for the analysis of eDNA. ddPCR is a relatively recent technological
83
advancement, allowing for accurate estimation of low copy DNA number (Hindson et al., 2011). It is
84
an absolute quantification method which, unlike qPCR, does not rely on standard curves to estimate
85
target DNA concentration. For DNA samples extracted from environmental water and containing
86
potentially very low copy number of target DNA, the ability of ddPCR to detect rare events in a
87
reaction is of particular interest, especially for invasive species in aquatic ecosystems where they may
88
exist in low abundance and may be difficult to detect using conventional survey methods (e.g. netting
89
and electrofishing).
90
Whether analysis is being carried out using qPCR or ddPCR, eDNA-based detection is
91
becoming increasingly used in aquatic freshwater environments for a range of low abundance or
92
invasive taxa, such as amphibians (Pilliod et al., 2013, Spear et al., 2014), molluscs (Goldberg et al.,
93
2013, Peñarrubia et al., 2016, Carlsson et al., 2017) and crustaceans (Tréguier et al., 2014, Harper et
94
al., 2018), as well as fish (Takahara et al., 2013, Klymus et al., 2015, Davison et al., 2016) –
95
including salmonid species (Gustavson et al., 2015, Atkinson et al., 2018, Rusch et al., 2018). To
96
date, there has been no published studies for implementing eDNA for the detection of O. gorbuscha.
97
We hypothesise that eDNA can be used for detection of non-native O. gorbuscha in running water. In
98
addition, should any eradication measures be employed in the future, eDNA methods could be used to
99
determine the efficacy of such efforts (Banks et al., 2015).
100
This study aimed to address questions relating to the presence and distribution of O.
101
gorbuscha in a Norwegian river, as part of a pilot study employing the non-intrusive and genetic
102
survey method of eDNA collection and analysis. A species-specific probe-based assay was developed
103
for this species and deployed in an urban river system where O. gorbuscha had been previously
104
.CC-BY-NC-ND 4.0 International licenseIt is made available under a
(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
The copyright holder for this preprint. http://dx.doi.org/10.1101/651554doi: bioRxiv preprint first posted online May. 31, 2019;
5
observed. We also developed this assay with the intention that it can be deployed in other European
105
freshwater or marine ecosystems where this species may currently, or potentially, invade. This is of
106
particular relevance for detection of the species during spawning season of this year (Autumn 2019),
107
where it is unknown if the putative increased mortality of O. gorbuscha at sea (resulting from a
108
mismatch between emigration time and food availability; Armstrong et al., 2018) will result in a less
109
significant invasion.
110
111
MATERIALS AND METHODS
112
Water sampling and eDNA extraction
113
For this study, water samples were collected from the Lysakerelva river in the south-east
114
region of Norway (Table 1) during Autumn of 2017 and Spring/early Summer of 2018. This river
115
system runs through a large urban area outside of Oslo and is characterised by a number of natural
116
migration barriers, including waterfalls. The smallest of these waterfalls (Møllefoss) is a few metres
117
in height and is fitted with fish ladders to enable upstream migration. The next waterfall, Granfoss, is
118
sufficiently high (~12-15 metres) as to completely prevent upstream fish migration. In terms of the
119
diversity of fish found in the study area, the Lysakerelva river fish fauna is dominated by S. salar, S.
120
trutta and the European minnow Phoxinus phoxinus (Saltveit et al., 2013). Several O. gorbuscha have
121
previously been caught in the Lysakerelva river (>20 fish; Sandlund et al., 2018).
122
During September 2017, two water samples were taken below Møllefoss and just above upper
123
high tide close to the mouth of the Lysakerelva river, and two water samples were taken immediately
124
below the Granfoss waterfall (~800 metres upstream from the river mouth; Table 1). These samples
125
were taken to coincide with the spawning season of O. gorbuscha. This sampling was repeated the
126
following May, the time period when it is expected that juvenile O. gorbuscha would be undertaking
127
seaward migration (Table 1). In June 2018, two water samples were also taken from the estuary as it
128
was considered possible that O. gorbuscha may also be found in the coastal area after migrating
129
downriver (Heard 1991; Moore et al., 2016). Additional samples (n=4; Table 1) were taken from
130
.CC-BY-NC-ND 4.0 International licenseIt is made available under a
(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
The copyright holder for this preprint. http://dx.doi.org/10.1101/651554doi: bioRxiv preprint first posted online May. 31, 2019;
6
above the Granfoss waterfall in June 2018 as negative eDNA field control samples, as it was expected
131
that no O. gorbuscha would be present at this location due to the barrier of the Granfoss waterfall.
132
For each locality, we filtered two replicate samples of either c. 1 L water on a 0.45 µm
133
cellulose filter (Pall MicroFunnel 300 ST; Pall Corporation, New York, USA; Table 1) or two
134
replicate samples of c. 10 L water on a 2.0 µm glassfiber filter (Merck Millipore, Burlington,
135
Massachusetts, USA; Table 1) using a peristaltic pump (Vampire sampler, Bürkle, Bad Bellingen,
136
Germany). The 0.45 µm cellulose filters were immediately placed in 2 mL tubes with 1440 µL ATL-
137
buffer (Qiagen, Hilden, Germany), whereas the 2.0 µm glassfiber filters were placed in 5 mL tubes
138
with 4050 µL ATL-buffer. All samples were stored at room temperature until further processing in the
139
genetics laboratory. All field equipment (e.g. filtering tubes and collection bottles) was sterilised
140
between collection of each sample using 10% bleach solution for approximately 60 minutes.
141
In the laboratory, 160 µL or 450 µL Proteinase-K (Qiagen) was added to the 2 mL and 5 mL
142
sampling tubes, respectively. All samples were incubated overnight at 56°C. DNA was isolated from
143
0.45 µm cellulose filters using DNeasy DNA Blood & Tissue kit (Qiagen), and from the 2.0 µm
144
glassfiber filters using NucleoSpin Plant II Midi kit (Macherey-Nagel, Düren, Germany), following
145
the manufacturers protocol except that Qiagen buffers were used instead of those supplied with the
146
kit. DNA extracted from the 0.45 µm cellulose filters was eluted in 100 µL AE buffer, whereas DNA
147
extracted from the 2.0 µm glassfiber filters was eluted in 200 µL AE buffer. All samples were re-
148
eluted in order to maximise the output of DNA. Final concentrations of the eluted DNA samples
149
(Supplementary Table 1) were determined using a Nanodrop 1000 Spectrophotometer (Thermo Fisher
150
Scientific, Waltham, Massachusetts, USA).
151
152
Molecular assay development and specificity testing
153
An assay was designed to amplify a 98 bp region of the mitochondrial COI gene of O.
154
gorbuscha (Table 2). This assay consisted of primers and a 5’ VIC labelled TaqMan® minor groove
155
binding (MGB) probe. The primers and probes were designed using Primer3 software (Rozen and
156
.CC-BY-NC-ND 4.0 International licenseIt is made available under a
(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
The copyright holder for this preprint. http://dx.doi.org/10.1101/651554doi: bioRxiv preprint first posted online May. 31, 2019;
7
Skaletsky 2000). Specificity of the assay was checked in-silico, by aligning the primers and probe
157
with the consensus sequence generated from publicly available O. gorbuscha sequences as well as
158
those from other salmonids commonly occurring in the study area (e.g. S. salar and S. trutta). The
159
primer and probe sequences were also checked against the NCBI database to ensure specificity to the
160
target organism. Furthermore, specificity of the assay was checked using qPCR, with tissue-extracted
161
DNA from O. gorbuscha, as well as from S. salar and S. trutta. Tissue-extracted DNA was also
162
acquired and tested by qPCR for rainbow trout (O. mykiss) which, while not a native salmonid, has
163
been widely introduced throughout Europe (Stanković et al., 2015). In addition, DNA extracted from
164
the closely-related chum salmon O. keta tested to check the specificity of the assay. The latter is not
165
currently found in Europe but this species overlaps with O. gorbuscha in its native range.
166
All qPCR reactions took place in a 20 µl reaction volume, containing 10 µl of TaqMan™
167
Environmental Master Mix 2.0 (Thermofisher), 2 µl of each primer (2 µM), 2 µl of probe (2 µM;
168
Applied Biosystems) and 2 µl of template DNA (where extracts were normalised to 34 ng/µl). The
169
PCR program consisted of 50oC for 2 min, 95oC for 10 min, followed by 40 cycles of 95oC for 15 s
170
and 60oC for 1 min. All qPCR reactions were carried out using QuantStudio™ 7 Flex Real-Time PCR
171
System (Applied Biosystems). All qPCR analysis took place in University College Dublin.
172
Potential cross-amplification of other salmonids (O. mykiss, S. salar, S. trutta, Salvelinus
173
alpinus, Salvelinus fontinalis, Salvelinus namaycush and Thymallus thymallus) using the O.
174
gorbuscha assay was also tested using ddPCR at NINA using the same PCR conditions as those
175
detailed in the next section.
176
177
Digital droplet (dd)PCR analysis of eDNA samples
178
Sample collection and eDNA extraction resulted in a total of 14 samples originating from the
179
Lysakerelva river (Table 1). Detection and concentration of target-DNA was assessed using droplet-
180
digital-PCR (QX200 Droplet Digital PCR system with AutoDG, Bio-Rad Laboratories, Hercules,
181
USA). A tissue-extracted DNA sample of O. gorbuscha was included in the analysis, as a positive
182
.CC-BY-NC-ND 4.0 International licenseIt is made available under a
(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
The copyright holder for this preprint. http://dx.doi.org/10.1101/651554doi: bioRxiv preprint first posted online May. 31, 2019;
8
control. A no-template control was also included in the analysis. The eDNA samples, along with
183
positive, negative and no-template controls, were analysed in triplicate with the exception of the
184
samples from 2017 (Table 1), which were analysedsingularly. The ddPCR reactions consisted of 0.9
185
µM forward and reverse primers, 0.25 µM of the probe, ddPCR™ Supermix for Probes (No dUTP)
186
(Bio-Rad Laboratories), dH2O and 5 µL template. In order to assess potential problems with inhibition
187
in our samples we also reran the samples with only 1 µL template. However, we found no indications
188
of inhibition among our samples. To generate droplets, an AutoDG Instrument (Bio-Rad
189
Laboratories) was used, with subsequent PCR amplification in a Veriti96-Well Thermal Cycler
190
(Applied Biosystems). The following thermal cycling conditions were used: an initial denaturation
191
step at 95°C for 10 min, 40 cycles of denaturation at 95°C for 30 sec, annealing and extension at 60°C
192
for 1 min, a final step of denaturation at 98°C for 10 min, and a final hold at 4°C. PCR plates were
193
transferred to a QX200 Droplet Reader (Bio-Rad Laboratories) to automatically detect the fluorescent
194
signal in the droplets. QuantaSoft software v.1.7.4 (Bio-Rad Laboratories) was used to separate
195
positive from negative droplets according to manufacturer’s instructions. A threshold of minimum 3
196
positive droplets were used as a criterion for positive detection Wacker et al. 2019). All ddPCR-
197
analyses took place at the genetic lab at NINA in Trondheim, Norway.
198
199
RESULTS
200
Molecular assay development
201
Testing of the O. gorbuscha assay with non-target salmonids using tissue-extracted DNA and
202
qPCR, revealed that the assay did not cross-amplify S. salar, S. trutta, or O. mykiss. ddPCR testing of
203
non-target salmonid species (O. mykiss, S. salar, S. trutta, S. alpinus, S. fontinalis, S. namaycush, T
204
thymallus) did not produce any detectable amplification. However, amplification was observed for O.
205
keta DNA analysed by qPCR (data not shown). This species is closely related to O. gorbuscha and
206
there are very few nucleotide differences between these species for the COI region targeted by our
207
assay (Supplementary Figure 2). However, this should not present a major concern for researchers
208
.CC-BY-NC-ND 4.0 International licenseIt is made available under a
(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
The copyright holder for this preprint. http://dx.doi.org/10.1101/651554doi: bioRxiv preprint first posted online May. 31, 2019;
9
wishing to apply this assay for O. gorbusha detection in Norwegian and other European locations, as
209
neither O. keta nor other species of Pacific salmon (O. nerka, O. kisutch, O. tshawytscha and O.
210
masoudo) currently occur in these regions.
211
212
ddPCR analysis of eDNA samples
213
An average number of 15,299 droplets were analysed for each sample included in the ddPCR
214
analyses. Using the O. gorbuscha assay in a ddPCR analysis, there was target DNA detected in six out
215
of 14 eDNA samples (Table 3).
216
In Autumn 2017, O. gorbuscha DNA was detected at Granfoss but not at Møllefoss (Table 3,
217
Figure 2). In Spring, target DNA was detected in both samples taken below the Granfoss waterfall,
218
which indicates that there were still young O. gorbuscha in the sampling area that had not yet left the
219
river. No target DNA was found in samples taken near to the mouth of the river in June 2018, which
220
is perhaps unsurprising, considering that upstream and downstream samples were taken 20 days apart
221
and young O. gorbuscha may have already migrated to sea.
222
No detectable target DNA was found in samples taken from the estuary. It is possible that,
223
similar to the samples taken in the downstream region of the Lysakerelva river, young O. gorbuscha
224
may have already migrated out to sea when this sampling took place in the Summer. Alternatively, a
225
lack of detection of O. gorbuscha at this location may be a false negative, as a result of the relatively
226
low number of samples taken over a large sampling area (Table 1).
227
Interestingly, target DNA was also detected in low copy number from one out of four of the
228
control samples above the migration barrier (Figure 2) indicating alternative means of target DNA
229
transport to this site, or contamination of the sample in the field (see Discussion). All no-template
230
controls were negative for target DNA.
231
232
233
.CC-BY-NC-ND 4.0 International licenseIt is made available under a
(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
The copyright holder for this preprint. http://dx.doi.org/10.1101/651554doi: bioRxiv preprint first posted online May. 31, 2019;
10
DISCUSSION
234
The year 2017 was unprecedented in terms of the number of O. gorbuscha that were observed
235
in Norwegian rivers (Mo et al., 2018), as well as in Ireland and Scotland (Whelan 2017, Armstrong et
236
al., 2018). In the present study, we were successfully able to detect O. gorbuscha from environmental
237
water samples in Norway during this invasion. Target DNA was amplified from samples taken in both
238
Autumn (during adult spawning) and the following Spring (during the migration of juveniles),
239
indicating that spawning in the focal river system was successful. However, the survival of juvenile
240
O. gorbuscha at sea is poorly understood and it is unknown whether mortality will limit the ability of
241
this species to return to the river and establish self-reproducing populations.
242
The assay developed and validated in this study not only has applications for monitoring
243
presence of O. gorbuscha spatially and temporally in Norwegian rivers, but also in countries where it
244
currently exists outside of its native range, as well as those where it has not been observed but may
245
potentially occur in the future. Further, this assay can be used to monitor O. gorbuscha presence
246
following any future eradication efforts that may be implemented. While the utility of the assay
247
developed in this study is limited to those areas where O. gorbuscha does not overlap with O. keta,
248
this should not be of concern for researchers using this assay to detect O. gorbuscha within its
249
invasive range as O. keta is not currently found outside the North Pacific.
250
The finding of a positive detection of O. gorbuscha above the impassable barrier of Granfoss
251
waterfall demonstrates the potential drawbacks of using eDNA to infer species presence. There was
252
no indication of contamination in any of the negative controls included in this study. Specificity
253
testing by qPCR and ddPCR revealed that this assay does not amplify COI from other commonly co-
254
occurring native or introduced salmonids. The sample location was the only site visited on the day of
255
sampling, yet it is impossible to rule out contamination of field equipment from previous sampling
256
events downstream of the barrier. It is also possible that an alternative vector, such as predation (by
257
birds for example; Merkes et al., 2014), can explain the detection of target DNA in a location where
258
the organism is not present.
259
.CC-BY-NC-ND 4.0 International licenseIt is made available under a
(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
The copyright holder for this preprint. http://dx.doi.org/10.1101/651554doi: bioRxiv preprint first posted online May. 31, 2019;
11
The results of our pilot study show that this assay can be used to detect the presence of O.
260
gorbuscha in running water. However, we can make some suggestions to increase the efficacy of our
261
approach for future studies. The lack of detection of O. gorbuscha in water samples taken from the
262
estuary and at the mouth of the Lysakerelva river in early Summer indicated that the juveniles had
263
already migrated to sea. We would recommend an increase in temporal sampling, as data derived
264
from these samples may have been able to reveal the timing of juvenile migration to sea, increasing
265
our knowledge about O. gorbuscha behaviour in Norwegian rivers and indicating the extent of
266
potential interactions with local fauna.
267
We detected a mismatch in the forward primer sequence (Supplementary Figure 1), based on
268
the O. gorbuscha consensus sequence generated from publicly available COI records on GenBank.
269
The source of this mismatch is a sequence from an odd-year individual (Accession No. MG951587.1)
270
from the White Sea that was submitted to the NCBI database after the assay was developed and
271
tested. It is therefore possible that this haplotype is found in Norwegian rivers. This mismatch is
272
found on the 5’ end of the forward primer, therefore it is unlikely that our assay efficiency was
273
severely compromised in the present study. However, to ensure optimal efficiency in the assay (and
274
particularly to ensure sensitive detection of the low copy numbers frequently found in eDNA
275
samples), we recommend that the forward primer incorporate a degenerate base at this position should
276
the assay be deployed in other studies. Further, we concur with other eDNA researchers (e.g.
277
Goldberg et al., 2016) that concerted efforts are made to minimise any contamination in the field,
278
through the implementation of careful sterilisation and sampling techniques, as well as the use of
279
strict controls (e.g. field blanks, filter blanks) to monitor for exogenous sources of DNA during the
280
entire eDNA sampling and analysis workflow.
281
282
ACKNOWLEDGMENTS
283
The authors would like to thank Hege Brandsegg for running the ddPCR genetic analysis. We also
284
gratefully acknowledge Sigrid Skoglund for drawing the pink salmon life cycle.
285
.CC-BY-NC-ND 4.0 International licenseIt is made available under a
(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
The copyright holder for this preprint. http://dx.doi.org/10.1101/651554doi: bioRxiv preprint first posted online May. 31, 2019;
12
COMPLIANCE WITH ETHICAL STANDARDS
286
Conflict of interest The authors declare that they have no conflict of interest.
287
Ethical approval All applicable international, national, and/or institutional guidelines for the care and
288
use of animals were followed.
289
290
REFERENCES
291
Atkinson, S., Carlsson, J. E. L., Ball, B., Egan, D., Kelly-Quinn, M., Whelan, K., and Carlsson, J.
292
(2018) ‘A quantitative PCR-based environmental DNA assay for detecting Atlantic salmon (Salmo
293
salar L.)’, Aquatic Conservation: Marine and Freshwater Ecosystems, 28(5), pp:1238–1243.
294
https://doi.org/10.1002/aqc.2931
295
Baker, C. S., Steel, D., Nieukirk, S., and Klinck, H. (2018) ‘Environmental DNA (eDNA) From the
296
Wake of the Whales: Droplet Digital PCR for Detection and Species Identification’, Frontiers in
297
Marine Science, 5. https://doi.org/10.3389/fmars.2018.00133
298
Bakshtansky, E. L. (1980) ‘Pink salmon in the Kola Peninsula’, In: Thorpe JE (ed) Salmon ranching.
299
Academic Press, New York, pp:245–259
300
Banks, J. C., Demetras, N. J., Hogg, I. D., Knox, M. A., & West, D. W. (2016) ‘Monitoring brown
301
trout (Salmo trutta) eradication in a wildlife sanctuary using environmental DNA’, New Zealand
302
Natural Sciences, 41, pp:1–13. https://doi.org/10289/10302
303
Berg, M. (1961) ‘Pink salmon (Oncorhynchus gorbuscha)in northern Norway in the year 1960’, Acta
304
Borealia, A Scientia, Tromsø, 17, pp:1–24
305
Carlsson, J. E. L., Egan, D., Collins, P. C., Farrell, E. D., Igoe, F. and Carlsson, J. (2017) ‘A qPCR
306
MGB probe based eDNA assay for European freshwater pearl mussel (Margaritifera margaritifera
307
L.)’, Aquatic Conservation: Marine and Freshwater Ecosystems, 27(6), pp:1341–1344.
308
https://doi.org/10.1002/aqc.2788
309
Davison, P. I., Creach, V., Liang, W.-J., Andreou, D., Britton, J. R. and Copp, G. H. (2016)
310
‘Laboratory and field validation of a simple method for detecting four species of non-native
311
freshwater fish using eDNA.’, Journal of Fish Biology, 89(3), pp. 1782–1793. doi: 10.1111/jfb.13086.
312
Doi, H., Uchii, K., Takahara, T., Matsuhashi, S., Yamanaka, H. and Minamoto, T. (2015) ‘Use of
313
Droplet Digital PCR for Estimation of Fish Abundance and Biomass in Environmental DNA
314
Surveys’, Plos One, 10(3). doi: 10.1371/journal.pone.0122763.
315
Ficetola, G. F., Miaud, C., Pompanon, F. and Taberlet, P. (2008) ‘Species detection using
316
environmental DNA from water samples’, Biology letters, 4(4), pp. 423–425. doi:
317
10.1098/rsbl.2008.0118.
318
Goldberg, C. S., Sepulveda, A., Ray, A., Baumgardt, J. and Waits, L. P. (2013) ‘Environmental DNA
319
as a new method for early detection of New Zealand mudsnails (Potamopyrgus antipodarum)’,
320
Freshwater Science, 32(3), pp. 792–800. doi: 10.1899/13-046.1.
321
Goldberg, C. S., Turner, C. R., Deiner, K., Klymus, K. E., Thomsen, P. F., Murphy, M. A., Spear, S.
322
F., McKee, A., Oyler-McCance, S. J., Cornman, R. S., Laramie, M. B., Mahon, A. R., Lance, R. F.,
323
.CC-BY-NC-ND 4.0 International licenseIt is made available under a
(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
The copyright holder for this preprint. http://dx.doi.org/10.1101/651554doi: bioRxiv preprint first posted online May. 31, 2019;
13
Pilliod, D. S., Strickler, K. M., Waits, L. P., Fremier, A. K., Takahara, T., Herder, J. E. and Taberlet,
324
P. (2016) ‘Critical considerations for the application of environmental DNA methods to detect aquatic
325
species’, Methods in Ecology and Evolution, 7(11), pp. 1299–1307. doi: 10.1111/2041-210X.12595.
326
Gordeeva, N. V. and Salmenkova, E. A. (2011) ‘Experimental microevolution: Transplantation of
327
pink salmon into the European North’, Evolutionary Ecology, 25(3), pp. 657–679. doi:
328
10.1007/s10682-011-9466-x.
329
Gustavson, M. S., Collins, P. C., Finarelli, J. A., Egan, D., Conchúir, R., Wightman, G. D., King, J.,
330
Gauthier, D., Whelan, K., Carlsson, J., and Carlsson, J. (2015) ‘An eDNA assay for Irish Petromyzon
331
marinus and Salmo trutta and field validation in running water’, Journal of Fish Biology, 87(5),
332
pp:1254–1262. https://doi.org/10.1111/jfb.12781
333
Hänfling, B., Handley, L. L., Read, D. S., Hahn, C. and Li, J. (2016) ‘Environmental DNA
334
metabarcoding of lake fish communities reflects long-term data from established survey methods’,
335
Molecular Ecology, 25(13), 3101-3119. doi: 10.1111/mec.13660.
336
Harper, K. J., Anucha, N. P., Turnbull, J. F., Bean, C. W. and Leaver, M. J. (2018) ‘Searching for a
337
signal: Environmental DNA (eDNA) for the detection of invasive signal crayfish, Pacifastacus
338
leniusculus (Dana, 1852)’, Management of Biological Invasions, 9(9). doi: 10.3391/mbi.2018.9.2.07
339
Hindson, B. J., Ness, K. D., Masquelier, D. a., Belgrader, P., Heredia, N. J., Makarewicz, A. J.,
340
Bright, I. J., Lucero, M. Y., Hiddessen, A. L., Legler, T. C., Kitano, T. K., Hodel, M. R., Petersen, J.
341
F., Wyatt, P. W., Steenblock, E. R., Shah, P. H., Bousse, L. J., Troup, C. B., Mellen, J. C., Wittmann,
342
D. K., Erndt, N. G., Cauley, T. H., Koehler, R. T., So, A. P., Dube, S., Rose, K. A., Montesclaros, L.,
343
Wang, S., Stumbo, D. P., Hodges, S. P., Romine, S., Milanovich, F.P., White, H. E., Regan, J. F.,
344
Karlin-Neumann, G. A., Hindson, C. M., Saxonov, S. and Colston, B. W. (2011) ‘High-throughput
345
droplet digital PCR system for absolute quantitation of DNA copy number’, Analytical Chemistry,
346
83(22), pp. 8604–8610. doi: 10.1021/ac202028g.
347
Heard, W. R. (1991) ‘Life history of pink salmon (Oncorhynchus gorbuscha)’, In: Groot C, Margolis
348
L (eds) Pacific salmon life histories. UBC Press, Vancouver, pp:121–123
349
Hunter, M. E., Dorazio, R. M., Butterfield, J. S. S., Meigs-Friend, G., Nico, L. G. and Ferrante, J. A.
350
(2017) ‘Detection limits of quantitative and digital PCR assays and their influence in presence–
351
absence surveys of environmental DNA’, Molecular Ecology Resources, 17(2), pp. 221–229. doi:
352
10.1111/1755-0998.12619.
353
Jerde, C. L., Mahon, A. R., Chadderton, W. L. and Lodge, D. M. (2011) ‘“Sight-unseen” detection of
354
rare aquatic species using environmental DNA’, Conservation Letters, 4(2), pp. 150–157. doi:
355
10.1111/j.1755-263X.2010.00158.x.
356
Klymus, K. E., Richter, C. A., Chapman, D. C. and Paukert, C. (2015) ‘Quantification of eDNA
357
shedding rates from invasive bighead carp Hypophthalmichthys nobilis and silver carp
358
Hypophthalmichthys molitrix’, Biological Conservation, 183, pp. 77–84. doi:
359
10.1016/j.biocon.2014.11.020.
360
Mo, T. A., Thorstad, E. B., Sandlund, O. T., Berntsen, H. H., Fiske, P., & Uglem, I. (2018) ‘The pink
361
salmon invasion: a Norwegian perspective’, Journal of Fish Biology, 93, pp. 5–7.
362
doi:10.1111/jfb.13682
363
Moore, J. W., Gordon, J., Carr-Harris, C., Gottesfeld, A. S., Wilson, S. M. and Russell, J. H. (2016)
364
‘Assessing estuaries as stopover habitats for juvenile Pacific salmon’, Marine Ecology Progress
365
Series, 559, pp:201–2015. https://doi.org/10.3354/meps11933
366
Nakano, M., Komatsu, J., Matsuura, S. I., Takashima, K., Katsura, S. and Mizuno, A. (2003) ‘Single-
367
molecule PCR using water-in-oil emulsion’, Journal of Biotechnology, 102(2), pp. 117–124. doi:
368
10.1016/S0168-1656(03)00023-3.
369
.CC-BY-NC-ND 4.0 International licenseIt is made available under a
(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
The copyright holder for this preprint. http://dx.doi.org/10.1101/651554doi: bioRxiv preprint first posted online May. 31, 2019;
14
Nathan, L. M., Simmons, M., Wegleitner, B. J., Jerde, C. L. and Mahon, A. R. (2014) ‘Quantifying
370
Environmental DNA Signals for Aquatic Invasive Species Across Multiple Detection Platforms’,
371
Environmental Science & Technology, 48(21), pp. 12800–12806. doi: 10.1021/es5034052.
372
Penãrrubia, L., Alcaraz, C., Vaate, A. B. D., Sanz, N., Pla, C., Vidal, O., and Vinãs, J. (2016)
373
‘Validated methodology for quantifying infestation levels of dreissenid mussels in environmental
374
DNA (eDNA) samples’, Scientific Reports, 6. https://doi.org/10.1038/srep3906
375
Pilliod, D. S., Goldberg, C. S., Arkle, R. S., Waits, L. P. and Richardson, J. (2013) ‘Estimating
376
occupancy and abundance of stream amphibians using environmental DNA from filtered water
377
samples’, Canadian Journal of Fisheries and Aquatic Sciences, 70(8), pp. 1123–1130. doi:
378
10.1139/cjfas-2013-0047.
379
Pinheiro, L. B., Coleman, V. A., Hindson, C. M., Herrmann, J., Hindson, B. J., Bhat, S. and Emslie,
380
K. R. (2012) ‘Evaluation of a droplet digital polymerase chain reaction format for DNA copy number
381
quantification’, Analytical Chemistry, 84(2), pp. 1003–1011. doi: 10.1021/ac202578x.
382
Rasputina, E. N., Shustov, Y. A. and Tyrkin, I. A. (2016) ‘Eggs of pink salmon Oncorhynchus
383
gorbuscha as additional nontraditional food of juvenile Atlantic salmon Salmo salar in rivers of the
384
Kola Peninsula’, Russian Journal of Biological Invasions, 7, pp: 294–296.
385
Rusch, J. C., Hansen, H., Strand, D. A., Markussen, T., Hytterød, S., and Vrålstad, T. (2018)
386
‘Catching the fish with the worm: A case study on eDNA detection of the monogenean parasite
387
Gyrodactylus salaris and two of its hosts, Atlantic salmon (Salmo salar) and rainbow trout
388
(Oncorhynchus mykiss)’, Parasites and Vectors, 11(1). https://doi.org/10.1186/s13071-018-2916-3
389
Sandlund, T., Berntsen, H. H., Fiske, P., Kuusela J., Muladal, R., Niemelä, E., Uglem, I., Forseth,
390
T., Mo, T. A., Thorstad, E., Veselov, A. E., Vollset, K. W. and Zubchenko, A. V. (2018) ‘Pink
391
salmon in Norway: the reluctant invader’, Biological Invasions, doi: 10.1007/s10530-018-1904-z.
392
Saltveit, S. J., Brittain, J. E. and Bremnes, T. (2013) ‘The return of Atlantic Salmon (Salmo salar L .)
393
and improved water quality in urban rivers in Oslo, Norway’, River Res. Applic. 30, pp:571–577. doi:
394
10.1002/rra.2670.
395
Spear, S. F., Groves, J. D., Williams, L. a and Waits, L. P. (2014) ‘Using environmental DNA
396
methods to improve detectability in a hellbender (Cryptobranchus alleganiensis) monitoring
397
program’, Biological Conservation, 183, pp. 38-45. doi: 10.1016/j.biocon.2014.11.016.
398
Taberlet, P. Coissac, E., Hajibabaei, M. and Rieseberg, L. (2012) ‘Environmental DNA’, Molecular
399
Ecology, 21(8), pp. 1789–1793. doi: 10.1111/j.1365-294X.2012.05542.x.
400
Takahara, T., Minamoto, T. and Doi, H. (2013) ‘Using Environmental DNA to Estimate the
401
Distribution of an Invasive Fish Species in Ponds’, PLoS ONE, 8(2). doi:
402
10.1371/journal.pone.0056584.
403
Thomsen, P. F., Kielgast, J., Iversen, L. L., Wiuf, C., Rasmussen, M., Gilbert, M. T. P., Orlando, L.
404
and Willerslev, E. (2012) ‘Monitoring endangered freshwater biodiversity using environmental
405
DNA’, Molecular Ecology, 21(11), pp. 2565–2573. doi: 10.1111/j.1365-294X.2011.05418.x.
406
Tréguier, A., Paillisson, J. M., Dejean, T., Valentini, A., Schlaepfer, M. A. and Roussel, J. M. (2014)
407
‘Environmental DNA surveillance for invertebrate species: Advantages and technical limitations to
408
detect invasive crayfish Procambarus clarkii in freshwater ponds’, Journal of Applied Ecology, 51(4),
409
pp. 871–879. doi: 10.1111/1365-2664.12262
410
Wacker, S., Fossøy, F., Larsen, B. M., Brandsegg, H., Sivertsgård, R., Karlsson, S. (2019)
411
‘Downstream transport and seasonal variation in freshwater pearl mussel (Margaritifera
412
margaritifera) eDNA concentration’, Environmental DNA, doi: 10.1002/edn3.10.
413
Whelan K (2017) ‘Pink invaders’, Off the Scale, issue 18, Sept– Oct 2017, pp. 14–21.
414
.CC-BY-NC-ND 4.0 International licenseIt is made available under a
(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
The copyright holder for this preprint. http://dx.doi.org/10.1101/651554doi: bioRxiv preprint first posted online May. 31, 2019;
15
http://www.offthescaleangling.ie/issue18/offthescale_issue18.pdf. Accessed 22 Mar 2019
415
Wilcox, T. M., McKelvey, K. S., Young, M. K., Jane, S. F., Lowe, W. H., Whiteley, A. R. and
416
Schwartz, M. K. (2013) ‘Robust Detection of Rare Species Using Environmental DNA: The
417
Importance of Primer Specificity’, PLoS ONE, 8(3). doi: 10.1371/journal.pone.0059520.
418
419
420
TABLES AND FIGURES
421
422
423
Figure 1: Life cycle of the pink salmon Oncorhynchus gorbuscha, ill.: Sigrid Skoglund, NINA.
424
425
426
427
.CC-BY-NC-ND 4.0 International licenseIt is made available under a
(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
The copyright holder for this preprint. http://dx.doi.org/10.1101/651554doi: bioRxiv preprint first posted online May. 31, 2019;
16
Table 1: Details of water sampling in Lysakerelva river.
428
Date
Locality
No.
samples
Water
volume
Filter
size
Latitude, Longitude
04.09.2017
Granfoss below waterfall
2
1
0.45µm
59.917894, 10.631348
04.09.2017
Møllefoss below waterfall
2
1
0.45µm
59.914629, 10.636455
31.05.2018
Granfoss below waterfall
2
0.8
0.45µm
59.917894, 10.631348
20.06.2018
Estuary
2
10
2.0µm
59.911005, 10.643129
20.06.2018
Møllefoss below waterfall
2
10
2.0µm
59.914629, 10.636455
22.06.2018
Granfoss above waterfall
2
10
2.0µm
59.918166, 10.630236
22.06.2018
Granfoss above waterfall
2
0.8
0.45µm
59.918166, 10.630236
429
430
431
Table 2: Details of the assay that was designed, tested and deployed for detection of a 98bp region of
432
the mitochondrial COI gene of O. gorbuscha in this study.
433
Primer Type
Name
Sequence 5' -3'
Length (bp)
Forward Primer
PinkF
CACCGCCCTAAGCCTACTAA
20
Reverse Primer
PinkR
AGGCATGGGCTGTAACGATT
20
Probe *
PinkPr
CGCTCTTCTAGGGAATGACCA
21
* 5' VIC labelled reporter dye and 3’ non-fluorescent quencher
434
435
436
Table 3: Detection of O. gorbuscha using eDNA shown as the number of samples that were positive
437
for detection out of the total number of samples analysed by ddPCR.
438
Locality
Date
eDNA detection
Granfoss below waterfall
04.09.2017
1/2
Granfoss below waterfall
31.05.2018
2/2
Granfoss above waterfall
22.06.2018
1/4
Møllefoss below waterfall
04.09.2017
2/2
Møllefoss below waterfall
20.06.2018
0/2
Estuary
20.06.2018
0/2
439
440
.CC-BY-NC-ND 4.0 International licenseIt is made available under a
(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
The copyright holder for this preprint. http://dx.doi.org/10.1101/651554doi: bioRxiv preprint first posted online May. 31, 2019;
17
441
Figure 2: Boxplot showing the number of positive droplets from ddPCR detection of O. gorbuscha in
442
relation to date and locality. The horizontal dashed line indicates the lower threshold of three droplets
443
for assessing a sample as positive. See Table 1 for details of each sample.
444
445
446
.CC-BY-NC-ND 4.0 International licenseIt is made available under a
(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
The copyright holder for this preprint. http://dx.doi.org/10.1101/651554doi: bioRxiv preprint first posted online May. 31, 2019;