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Transport distance of invertebrate environmental DNA in a natural river.

Deiner K, Altermatt F - PLoS ONE (2014)

Bottom Line: We detected D. longispina at all locations and across two time points (July and October); whereas with U. tumidus, we observed a decreased detection rate and did not detect its eDNA after 9.1 km.We also observed a difference in detection for this species at different times of year.Our results indicate that there may be species' specific transport distances for eDNA and demonstrate for the first time that invertebrate eDNA can persist over relatively large distances in a natural river system.

View Article: PubMed Central - PubMed

Affiliation: Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland.

ABSTRACT
Environmental DNA (eDNA) monitoring is a novel molecular technique to detect species in natural habitats. Many eDNA studies in aquatic systems have focused on lake or ponds, and/or on large vertebrate species, but applications to invertebrates in river systems are emerging. A challenge in applying eDNA monitoring in flowing waters is that a species' DNA can be transported downstream. Whether and how far eDNA can be detected due to downstream transport remains largely unknown. In this study we tested for downstream detection of eDNA for two invertebrate species, Daphnia longispina and Unio tumidus, which are lake dwelling species in our study area. The goal was to determine how far away from the source population in a lake their eDNA could be detected in an outflowing river. We sampled water from eleven river sites in regular intervals up to 12.3 km downstream of the lake, developed new eDNA probes for both species, and used a standard PCR and Sanger sequencing detection method to confirm presence of each species' eDNA in the river. We detected D. longispina at all locations and across two time points (July and October); whereas with U. tumidus, we observed a decreased detection rate and did not detect its eDNA after 9.1 km. We also observed a difference in detection for this species at different times of year. The observed movement of eDNA from the source amounting to nearly 10 km for these species indicates that the resolution of an eDNA sample can be large in river systems. Our results indicate that there may be species' specific transport distances for eDNA and demonstrate for the first time that invertebrate eDNA can persist over relatively large distances in a natural river system.

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Observed and predicted detection of eDNA along river transect.Distance along the river Glatt from the source population (Lake Greifensee) at which eDNA for each species (red) Daphnia longispina and (blue) Unio tumidus was detected. Detection rate was determined as the number of positive amplifications of target DNA in three PCR replicates. The colored lines and the shaded area are glm model predictions (mean and standard error respectively) for the two species and time points (Jul: July and Oct: October) respectively. The black dashed line gives the 5% detection threshold. We also give calculated minimal traveling time of river water (and suspended eDNA and other particles therein) over the studied distances.
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pone-0088786-g003: Observed and predicted detection of eDNA along river transect.Distance along the river Glatt from the source population (Lake Greifensee) at which eDNA for each species (red) Daphnia longispina and (blue) Unio tumidus was detected. Detection rate was determined as the number of positive amplifications of target DNA in three PCR replicates. The colored lines and the shaded area are glm model predictions (mean and standard error respectively) for the two species and time points (Jul: July and Oct: October) respectively. The black dashed line gives the 5% detection threshold. We also give calculated minimal traveling time of river water (and suspended eDNA and other particles therein) over the studied distances.

Mentions: Daphnia longispina was detected at all sites (except the expected negative control site) and across the two time points (Fig. 3). Unio tumidus, however, was not detected after 9.1 km downstream distance and was also not detected at 1.6 km in July, but was found in October at this site (Fig. 3). Also, and as expected, U. tumidus was not detected at the negative control site. While both species could be detected in the river, D. longispina had a positive detection for all three PCR replicates for all sites except 3.9 and 9.1 km away from the lake, where only two of the three replicates showed a positive detection. Sequences for the reverse direction of both species had a higher average quality value (81.4% D. longispina, 86.7% U. tumidus) to that of the forward direction (69.4% D. longispina, 79.3% U. tumidus). Additionally, for D. longispina the sequences from amplicons between the two time points indicated a shift in the haplotype detected from the environmental DNA that differed in four base pairs between July and October (Fig. 4). Unio tumidus on the other hand, did not have the same detection levels. Specifically, no site showed a positive detection in all three PCR replicates and there was a decrease in detection rate the further away from the lake the water sample was taken (Fig. 3). All filter, extraction and PCR controls were negative for targeted species eDNA.


Transport distance of invertebrate environmental DNA in a natural river.

Deiner K, Altermatt F - PLoS ONE (2014)

Observed and predicted detection of eDNA along river transect.Distance along the river Glatt from the source population (Lake Greifensee) at which eDNA for each species (red) Daphnia longispina and (blue) Unio tumidus was detected. Detection rate was determined as the number of positive amplifications of target DNA in three PCR replicates. The colored lines and the shaded area are glm model predictions (mean and standard error respectively) for the two species and time points (Jul: July and Oct: October) respectively. The black dashed line gives the 5% detection threshold. We also give calculated minimal traveling time of river water (and suspended eDNA and other particles therein) over the studied distances.
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC3921251&req=5

pone-0088786-g003: Observed and predicted detection of eDNA along river transect.Distance along the river Glatt from the source population (Lake Greifensee) at which eDNA for each species (red) Daphnia longispina and (blue) Unio tumidus was detected. Detection rate was determined as the number of positive amplifications of target DNA in three PCR replicates. The colored lines and the shaded area are glm model predictions (mean and standard error respectively) for the two species and time points (Jul: July and Oct: October) respectively. The black dashed line gives the 5% detection threshold. We also give calculated minimal traveling time of river water (and suspended eDNA and other particles therein) over the studied distances.
Mentions: Daphnia longispina was detected at all sites (except the expected negative control site) and across the two time points (Fig. 3). Unio tumidus, however, was not detected after 9.1 km downstream distance and was also not detected at 1.6 km in July, but was found in October at this site (Fig. 3). Also, and as expected, U. tumidus was not detected at the negative control site. While both species could be detected in the river, D. longispina had a positive detection for all three PCR replicates for all sites except 3.9 and 9.1 km away from the lake, where only two of the three replicates showed a positive detection. Sequences for the reverse direction of both species had a higher average quality value (81.4% D. longispina, 86.7% U. tumidus) to that of the forward direction (69.4% D. longispina, 79.3% U. tumidus). Additionally, for D. longispina the sequences from amplicons between the two time points indicated a shift in the haplotype detected from the environmental DNA that differed in four base pairs between July and October (Fig. 4). Unio tumidus on the other hand, did not have the same detection levels. Specifically, no site showed a positive detection in all three PCR replicates and there was a decrease in detection rate the further away from the lake the water sample was taken (Fig. 3). All filter, extraction and PCR controls were negative for targeted species eDNA.

Bottom Line: We detected D. longispina at all locations and across two time points (July and October); whereas with U. tumidus, we observed a decreased detection rate and did not detect its eDNA after 9.1 km.We also observed a difference in detection for this species at different times of year.Our results indicate that there may be species' specific transport distances for eDNA and demonstrate for the first time that invertebrate eDNA can persist over relatively large distances in a natural river system.

View Article: PubMed Central - PubMed

Affiliation: Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland.

ABSTRACT
Environmental DNA (eDNA) monitoring is a novel molecular technique to detect species in natural habitats. Many eDNA studies in aquatic systems have focused on lake or ponds, and/or on large vertebrate species, but applications to invertebrates in river systems are emerging. A challenge in applying eDNA monitoring in flowing waters is that a species' DNA can be transported downstream. Whether and how far eDNA can be detected due to downstream transport remains largely unknown. In this study we tested for downstream detection of eDNA for two invertebrate species, Daphnia longispina and Unio tumidus, which are lake dwelling species in our study area. The goal was to determine how far away from the source population in a lake their eDNA could be detected in an outflowing river. We sampled water from eleven river sites in regular intervals up to 12.3 km downstream of the lake, developed new eDNA probes for both species, and used a standard PCR and Sanger sequencing detection method to confirm presence of each species' eDNA in the river. We detected D. longispina at all locations and across two time points (July and October); whereas with U. tumidus, we observed a decreased detection rate and did not detect its eDNA after 9.1 km. We also observed a difference in detection for this species at different times of year. The observed movement of eDNA from the source amounting to nearly 10 km for these species indicates that the resolution of an eDNA sample can be large in river systems. Our results indicate that there may be species' specific transport distances for eDNA and demonstrate for the first time that invertebrate eDNA can persist over relatively large distances in a natural river system.

Show MeSH
Related in: MedlinePlus