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Beyond fish eDNA metabarcoding: Field replicates disproportionately improve the detection of stream-associated vertebrate species

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Abstract

Abstract Fast, reliable, and comprehensive biodiversity monitoring data are needed for environmental decision making and management. Recent work on fish environmental DNA (eDNA) metabarcoding shows that aquatic diversity can be captured fast, reliably, and non-invasively at moderate costs. Because freshwater ecosystems act as sinks in the landscape, they also collect traces of terrestrial species via surface runoff or when specimens come into direct contact with water (e.g., for drinking purposes). Thus, fish eDNA metabarcoding data can provide information on fish but also on other, even terrestrial vertebrate species that live in riparian habitats. This data become available and may offer a much more comprehensive approach for assessing vertebrate diversity at no additional costs. Studies on how the sampling strategy affects species detection especially of stream-associated communities, however, are scarce. We therefore performed an analysis on the effects of biological replication on both fish as well as (semi-)terrestrial species detection. Along a 2-km stretch of the river Mulde (Germany), we collected 18 1L water samples and analyzed the relation of detected species richness and quantity of biological replicates taken. We detected 58 vertebrate species, of which 25 were fish and lamprey, 18 mammals, and 15 birds, which account for 50%, 24% and 7% of all native species to the German federal state of Saxony-Anhalt. However, while increasing the number of biological replicates resulted in only 25 % more detected fish and lamprey species, mammal and bird species richness increased disproportionately by 69 % and 84 %, respectively. Contrary, PCR replicates showed little stochasticity. We thus emphasize to increase the number of biological replicates when the aim is to improve general species detections. This holds especially true, when the focus is on rare aquatic taxa or on (semi-)terrestrial species, the so-called ‘bycatch’. As a clear advantage, this information can be obtained without any additional sampling or laboratory effort when the sampling strategy regarding biological replication is chosen carefully. With the consideration of frequent eDNA metabarcoding as part of national biomonitoring programs, the additional information provided by the bycatch can be used to further investigate the state of the environment and its biodiversity on a much broader scale.
ARPHA Conference Abstracts 4: e64815
doi: 10.3897/aca.4.e64815
Conference Abstract
Beyond fish eDNA metabarcoding: Field replicates
disproportionately improve the detection of
stream-associated vertebrate species
Till-Hendrik Macher , Robin Schütz , Jens Arle , Arne Beermann , Jan Koschorreck , Florian Leese
‡ University of Duisburg-Essen, Essen, Germany
§ German Environmental Agency, Dessau, Germany
Corresponding author: Robin Schütz (robin.schuetz@rub.de)
Received: 22 Feb 2021 | Published: 04 Mar 2021
Citation: Macher T-H, Schütz R, Arle J, Beermann A, Koschorreck J, Leese F (2021) Beyond fish eDNA
metabarcoding: Field replicates disproportionately improve the detection of stream-associated vertebrate
species. ARPHA Conference Abstracts 4: e64815. https://doi.org/10.3897/aca.4.e64815
Abstract
Fast, reliable, and comprehensive biodiversity monitoring data are needed for
environmental decision making and management. Recent work on fish environmental DNA
(eDNA) metabarcoding shows that aquatic diversity can be captured fast, reliably, and non-
invasively at moderate costs. Because freshwater ecosystems act as sinks in the
landscape, they also collect traces of terrestrial species via surface runoff or when
specimens come into direct contact with water (e.g., for drinking purposes). Thus, fish
eDNA metabarcoding data can provide information on fish but also on other, even
terrestrial vertebrate species that live in riparian habitats. This data become available and
may offer a much more comprehensive approach for assessing vertebrate diversity at no
additional costs. Studies on how the sampling strategy affects species detection especially
of stream-associated communities, however, are scarce. We therefore performed an
analysis on the effects of biological replication on both fish as well as (semi-)terrestrial
species detection. Along a 2-km stretch of the river Mulde (Germany), we collected 18 1L
water samples and analyzed the relation of detected species richness and quantity of
biological replicates taken. We detected 58 vertebrate species, of which 25 were fish and
lamprey, 18 mammals, and 15 birds, which account for 50%, 24% and 7% of all native
species to the German federal state of Saxony-Anhalt. However, while increasing the
§ §
© Macher T et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY
4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are
credited.
number of biological replicates resulted in only 25 % more detected fish and
lamprey
species, mammal and bird species richness increased disproportionately by 69 % and 84
%, respectively. Contrary, PCR replicates showed little stochasticity. We thus emphasize to
increase the number of biological replicates when the aim is to improve general species
detections. This holds especially true, when the focus is on rare aquatic taxa or on
(semi-)terrestrial species, the so-called ‘bycatch’. As a clear advantage, this information
can be obtained without any additional sampling or laboratory effort when the sampling
strategy regarding biological replication is chosen carefully. With the consideration of
frequent eDNA metabarcoding as part of national biomonitoring programs, the additional
information provided by the bycatch can be used to further investigate the state of the
environment and its biodiversity on a much broader scale.
Keywords
environmental DNA, metabarcoding, vertebrates, biological replication, fish, mammals,
birds, sampling strategies, bycatch
Presenting author
Robin Schütz
Presented at
1st DNAQUA International Conference (March 9-11, 2021)
2Macher T et al
... Replicate samples may be collected or generated at any point in the eDNA workflow, from field sampling to sequencing replicates. Multiple studies have highlighted the benefits of replicates in enhancing the reliability of biological data while also recognizing that additional samples increase the cost of analyses [24][25][26] . Balancing the value of the additional information against budget and time constraints is crucial for researchers and managers. ...
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Environmental DNA (eDNA) is revolutionizing how we investigate biodiversity in aquatic and terrestrial environments. It is increasingly used for detecting rare and invasive species, assessing biodiversity loss and monitoring fish communities, as it is considered a cost-effective and noninvasive approach. Some environments, however, can be challenging for eDNA analyses. Estuarine systems are highly productive, complex environments, but samples collected from these settings may exhibit PCR inhibition and a low fish read recovery. Here we present an approach for detecting fish in turbid, highly productive estuarine systems. The workflow includes bead-based extraction, inhibition removal, high fidelity and specificity DNA polymerase (Platinum SuperFi II) and multiplexing the universal MiFish primers. By applying this hybrid method to a variety of complex estuarine samples with known inhibition, we have more than doubled the number of recovered fish species while removing most of the off-target amplification.
... Replicate samples may be collected or generated at any point in the eDNA work ow, from eld sampling to sequencing replicates. Multiple studies have highlighted the bene ts of replicates in enhancing the reliability of biological data while also recognizing that additional samples increase the cost of analyses [14][15][16] . Balancing the value of the additional information against budget and time constraints is crucial for researchers and managers. ...
Preprint
Full-text available
Environmental DNA (eDNA) is revolutionizing how we investigate biodiversity in aquatic and terrestrial environments. It is increasingly used for detecting rare and invasive species, assessing biodiversity loss and monitoring fish communities, as it is considered a cost-effective and noninvasive approach. Some environments, however, can be challenging for eDNA analyses. Estuarine systems are highly productive, complex environments, but samples collected from these settings may exhibit PCR inhibition and a low fish read recovery. Here we present an approach for detecting fish in turbid, highly productive estuarine systems. The workflow includes bead-based extraction, inhibition removal, high fidelity and specificity DNA polymerase (Platinum SuperFi II) and multiplexing the universal MiFish primers. Applying this hybrid method to a variety of complex estuarine samples with known inhibition we have more than doubled the number of recovered fish species while removing most of the off-target amplification.
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