A novel environmental DNA detection approach for the wading birds Platalea leucorodia, Recurvirostra avosetta and Tringa totanus

Schütz, Robin; Tollrian, Ralph; Schweinsberg, Maximilian

doi:10.1007/s12686-020-01143-x

Cited by 12 publications

(12 citation statements)

References 14 publications

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“…Environmental DNA (eDNA) metabarcoding is a powerful and nowadays frequently applied method to assess and monitor fish biodiversity in streams (Cantera et al 2019), lakes (Muri et al 2020), and the sea . Contrary to conventional methods, such as net trapping or electrofishing, eDNA metabarcoding from In view of global biodiversity loss and the demand for highly resolved spatio-temporal data, eDNA metabarcoding has an additional, so far less explored potential: While fish species are primary targets, eDNA monitoring data can also provide reliable information on many other taxa either living in or in the vicinity of water bodies such as mammals (Andruszkiewicz et al 2017;Closek et al 2019), amphibians (Lacoursière-Roussel et al 2016;Bálint et al 2018;Harper et al 2018), and birds (Ushio et al 2018a;Day et al 2019;Schütz et al 2020). While traditional monitoring of birds is usually conducted by many professional and hobby ornithologists, the monitoring of mammals relies on far more advanced, non-invasive, observational methods such as camera traps or identification of field traces (e.g., hair or feces).…”

Section: Introductionmentioning

confidence: 99%

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

Macher¹,

Schütz²,

Arle³

et al. 2021

MBMG

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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 water in a catchment flows to the lowest point in the landscape, often a stream, it can collect traces of terrestrial species via surface or subsurface runoff along its way or when specimens come into direct contact with water (e.g., when drinking). Thus, fish eDNA metabarcoding data can provide information on fish but also on other vertebrate species that live in riparian habitats. This additional data 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 1-L 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%, 22.2%, and 7.4% of all native species to the German federal state of Saxony-Anhalt. However, while increasing the number of biological replicates resulted in only 24.8% more detected fish and lamprey species, mammal, and bird species richness increased disproportionately by 68.9% and 77.3%, 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 is chosen carefully. With the increased use of eDNA metabarcoding as part of national fish bioassessment and monitoring programs, the complimentary information provided on bycatch can be used for biodiversity monitoring and conservation on a much broader scale.

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Section: Introductionmentioning

confidence: 99%

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

Macher¹,

Schütz²,

Arle³

et al. 2021

MBMG

Self Cite

View full text Add to dashboard Cite

show abstract

“…In view of global biodiversity loss and the demand for spatio-temporally highly resolved data, eDNA metabarcoding has an additional, so far less explored potential: While fish species are primary targets, eDNA monitoring data can also provide reliable information on many other taxa either living in or in the vicinity of water bodies such as mammals (Andruszkiewicz et al 2017; Closek et al 2019), amphibians (Bálint et al 2018; Lacoursière-Roussel et al 2016; Harper et al 2018), and birds (Ushio, Murata, et al 2018; Day et al 2019; Schütz, Tollrian, and Schweinsberg 2020). While traditional monitoring of birds is usually conducted by many hobby and professional ornithologists, the monitoring of mammals relies on far more advanced, non-invasive, observational methods such as camera traps or identification of field traces (e.g., hair or feces).…”

Section: Introductionmentioning

confidence: 99%

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

Macher

Schuetz

Arle

et al. 2021

Preprint

Self Cite

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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 water in a catchment flows to the lowest point in the landscape, often a stream, it can often collect traces of terrestrial species via surface or subsurface runoff along its way 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 vertebrate species that live in riparian habitats. This additional data 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 1-L 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 is chosen carefully. With the increased use of eDNA metabarcoding as part of national fish bioassessment and monitoring programs, the complimentary information provided on bycatch can be used for biodiversity monitoring and conservation on a much broader scale.

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“…The five primers that could cover the highest number of species were as follows: mCOIR2 (n = 767, 88.36%), K_Bird_F1 (n = 761, 87.67%), the redundant set VertebrateR1 and VR1 (n = 718, 82.72% each), AWCintR4 (n = 706, 81.34%), and BirdF1d (n = 688, 79.26%) (Table 1), with the first one designed based on the avian order Dinornithiformes, the third one for vertebrates in general, and the rest for all birds in general (Supplementary Table 1). On the other hand, the five primers that could cover the lowest number of sequences were as follows: AWCintF2 (Patel et al, 2010), L6615(tTyr)_COI (Sorenson et al, 1999), Pel-F2-COI (Nikulina & Schmölcke, 2015), Schutz03F (Schütz et al, 2020), and BC_392F (Ogawa et al, 2015) (n = 1, 0.12% each). There was a positive but not significant relation between the primer's degeneracy level and its coverage ratio (r = 0.11, p = 0.15).…”

Section: Primer Coveragementioning

confidence: 99%

“…Only three primers were capable of binding to at least one species of all 31 bird orders here analyzed, AWCintR4, BirdF1d, and CO1R (Table 1), and these primers were all designed focused on covering the whole avian group (Supplementary Table 1). Seven primers could bind to sequences of a single avian order: COIaRt_F (Tavares & Baker, 2008), PsEmpCOIF (Kerr, 2010), L6615_(tTyr)_ COI (Sorenson et al, 1999), AWCintF2 (Patel et al, 2010), PelF2COI (Nikulina & Schmölcke, 2015), Schutz03F (Schütz et al, 2020), and BC_392F (Ogawa et al, 2015), with only the first two binding to more than one template sequence (Supplementary Table 4).…”

Section: Primer Coveragementioning

confidence: 99%

Same information, new applications: revisiting primers for the avian COI gene and improving DNA barcoding identification

2021

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The process of molecular identification of species known as DNA barcoding consists on discriminating taxa based on cumulative differences of their DNA sequences and is widely used within animals, including birds. Finding the best genomic tools, such as primers, to reach most of the species within the studied groups and evaluating the coverage breadth and physicochemical properties of primers before testing in the laboratory, can save time and financial resources. Therefore, this work aimed to retrieve the available primers for the COI gene currently used on the molecular identification of birds and evaluate them for its coverage range, physicochemical properties, and performance on in silico PCR. Afterwards, we provide the best primer subsets to cover the highest number of avian sequences and the best individual primers for each bird order in terms of coverage breadth. Thirty-one bird orders had at least one COI sequence to serve as template, 152 primers available for assessing the COI gene were evaluated, and 118 could bind to at least one template sequence. No primer subset alone could cover all template sequences; however, when combining two subsets, the complete coverage of avian COI sequences analyzed was achieved. We were able to find optimal primer subsets for more specific taxonomic groups or for analysis involving the complete avian group, in order to guide researchers in the process of choosing the best primer set for each individual barcoding goal.

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A novel environmental DNA detection approach for the wading birds Platalea leucorodia, Recurvirostra avosetta and Tringa totanus

Cited by 12 publications

References 14 publications

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

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

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

Same information, new applications: revisiting primers for the avian COI gene and improving DNA barcoding identification

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