Abstract
The Eurasian otter (Lutra lutra) is a semi-aquatic predator that lives in a wide range of aquatic habitats. Knowledge of the diet of predators is essential for the management and conservation of the species and their habitats. We assessed the diet of otters in fifty-three faecal samples (spraints) by morphological analysis of undigested prey remains and by DNA metabarcoding approaches with two different blocking primers. The blocking primers were shown to be similarly effective in repressing host DNA, improving amplification of non-host taxa. The analyses were conducted to compare the accuracy of the two methods. The prey items were categorized to the highest possible taxonomic resolution, and relative frequency of occurrence was applied in order to compare the morphological and DNA results. The bulk score for difference prey items in the spraints was based on volume estimates in macroscopic observations. The two methods had an overlap of identified prey species ranging from 69.9 to 72.9% (depending on the kind of primers) meaning that a large portion of prey items found by one method was replaced by other prey items in the other method and that most prey items found through DNA-metabarcoding are considered new when compared with the morphological analysis. Therefore, applying both morphological and DNA analysis is crucial in order to determine the diet of otters and, possibly, other predatory species.
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Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410. https://doi.org/10.1016/S0022-2836(05)80360-2
Andersen K, Bird KL, Rasmussen M et al (2012) Meta-barcoding of “dirt” DNA from soil reflects vertebrate biodiversity. Mol Ecol 21:1966–1979. https://doi.org/10.1111/j.1365-294X.2011.05261.x
Andres A, Orme D, Villeger S, Baselga MA (2018) Type package title partitioning Beta diversity into turnover and Nestedness components
Biffi M, Laffaille P, Jabiol J, André A, Gillet F, Lamothe S, Michaux JR, Buisson L (2017) Comparison of diet and prey selectivity of the Pyrenean desman and the Eurasian water shrew using next-generation sequencing methods. Mamm Biol 87:176–184. https://doi.org/10.1016/J.MAMBIO.2017.09.001
Carss DN, Elston DA (1996) Errors associated with otter Lutra lutra faecal analysis. II Estimating prey size distribution from bones recovered in spraints. J Zool 238:319–332. https://doi.org/10.1111/j.1469-7998.1996.tb05397.xs
Casper RM, Jarman SN, Deagle BE, Gales NJ, Hindell MA (2007) Detecting prey from DNA in predator scats: a comparison with morphological analysis, using Arctocephalus seals fed a known diet. J Exp Mar Bio Ecol 347:144–154. https://doi.org/10.1016/J.JEMBE.2007.04.002
Clare EL (2014) Molecular detection of trophic interactions: emerging trends, distinct advantages, significant considerations and conservation applications. Evol Appl 7:1144–1157. https://doi.org/10.1111/eva.12225
Conroy JWH, Watt J, Webb JB, Jones A (1993) A guide to the identification of prey remains in otter spraint. Mammal Society
da Silva LP, Mata VA, Lopes PB et al (2019) Advancing the integration of multi-marker metabarcoding data in dietary analysis of trophic generalists. Mol Ecol Resour 19:1420–1432. https://doi.org/10.1111/1755-0998.13060
Day MG (1966) Identification of hair and feather remains in the gut and faeces of stoats and weasels. J Zool 148:201–217. https://doi.org/10.1111/j.1469-7998.1966.tb02948.x
De Barba M, Miquel C, Boyer F et al (2014) DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet. Mol Ecol Resour 14:306–323. https://doi.org/10.1111/1755-0998.12188
Elmeros M, Mikkelsen DMG, Nørgaard LS, Pertoldi C, Jensen TH, Chriél M (2018) The diet of feral raccoon dog (Nyctereutes procyonoides) and native badger (Meles meles) and red fox (Vulpes vulpes) in Denmark. Mammal Res 63:405–413. https://doi.org/10.1007/s13364-018-0372-2
Gil V, Pinho CJ, Aguiar CAS, Jardim C, Rebelo R, Vasconcelos R (2020) Questioning the proverb ‘more haste, less speed’: classic versus metabarcoding approaches for the diet study of a remote island endemic gecko. PeerJ 8:e8084. https://doi.org/10.7717/peerj.8084
Hill SA, Beard KH, Siers SR, Shiels AB (2019) Invasive coqui frogs are associated with differences in mongoose and rat abundances and diets in Hawaii. Biol Invasions 21:2177–2190. https://doi.org/10.1007/s10530-019-01965-3
Huang K-Y, Lin Y-S, Severinghaus LL (2006) Comparison of three common methods for studying the diet of nestlings in two Accipiter species. Zool Stud 45:234–243
Jacobsen L, Hansen H-M (1996) Analysis of otter (Lutra lutra L.) spraints to estimate prey proportions: a comparison of methods through feeding experiment. J Zool 238:167–180
Klare U, Kamler JF, MacDonald DW (2011) A comparison and critique of different scat-analysis methods for determining carnivore diet. Mamm Rev 41:294–312. https://doi.org/10.1111/j.1365-2907.2011.00183.x
Nielsen JM, Clare EL, Hayden B, Brett MT, Kratina P (2017) Diet tracing in ecology: method comparison and selection. Methods Ecol Evol 9:278–291. https://doi.org/10.1111/2041-210X.12869
Oksanen AJ, Blanchet FG, Friendly M, et al (2017) Package ‘ vegan ’
Pompanon F, Deagle BE, Symondson WOC et al (2012) Who is eating what: diet assessment using next generation sequencing. Mol Ecol 21:1931–1950. https://doi.org/10.1111/j.1365-294X.2011.05403.x
Riaz T, Shehzad W, Viari A, Pompanon F, Taberlet P, Coissac E (2011) EcoPrimers: inference of new DNA barcode markers from whole genome sequence analysis. Nucleic Acids Res 39:1–11. https://doi.org/10.1093/nar/gkr732
Steinmetz B, Müller R (1991) An atlas of fish scales, and other bony structures used for age determination : non-salmonid species found in European fresh waters. Samara Pub
Taastrøm HM, Jacobsen L (1999) The diet of otters (Lutra lutra L.) in Danish freshwater habitats: comparisons of prey fish populations. J Zool 248:1–13. https://doi.org/10.1017/S0952836999005014
Taberlet P, Bonin A, Zinger L, Coissac E (2018) Environmental DNA for biodiversity research and monitoring. Oxford University Press
Thalinger B, Oehm J, Mayr H, Obwexer A, Zeisler C, Traugott M (2016) Molecular prey identification in central European piscivores. Mol Ecol Res 16:123–137. https://doi.org/10.1111/1755-0998.12436
Topgaard M (2011) Sammenhængen mellem findested og fødevalg hos Odder (Lutra lutra), undersøgt vha stabile isotoper (13C/12C og 15N/14N) i collagen og muskler samt vha maveindholdsundersøgelse. Department of Biology, Copenhagen University and Aarhus University, Master thesis
Vestheim H, Jarman SN (2008) Blocking primers to enhance PCR amplification of rare sequences in mixed samples - a case study on prey DNA in Antarctic krill stomachs. Front Zool 5:1–11. https://doi.org/10.1186/1742-9994-5-12
Webb JB (1977) Otter Spraint analysis. Mammal Society
Zinger L, Bonin A, Alsos IG, Bálint M, Bik H, Boyer F, Chariton AA, Creer S, Coissac E, Deagle BE, de Barba M, Dickie IA, Dumbrell AJ, Ficetola GF, Fierer N, Fumagalli L, Gilbert MTP, Jarman S, Jumpponen A, Kauserud H, Orlando L, Pansu J, Pawlowski J, Tedersoo L, Thomsen PF, Willerslev E, Taberlet P (2019) DNA metabarcoding — need for robust experimental designs to draw sound ecological conclusions. Mol Ecol 28:1857–1862
Acknowledgements
We would like to thank Ornithologist Henrik Haaning Nielsen for collecting samples and Erika Yashiro for bioinformatic help. We are also grateful to the Aage V. Jensen Foundation for financial support and to the Aalborg Zoo Conservation Foundation (AZCF, grant number 2017-3) for financial support to Cino Pertoldi.
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Communicated by: Joanna Stojak
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Pertoldi, C., Schmidt, J.B., Thomsen, P.M. et al. Comparing DNA metabarcoding with faecal analysis for diet determination of the Eurasian otter (Lutra lutra) in Vejlerne, Denmark. Mamm Res 66, 115–122 (2021). https://doi.org/10.1007/s13364-020-00552-5
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DOI: https://doi.org/10.1007/s13364-020-00552-5