DNA metabarcoding-based diet survey for the Eurasian otter (Lutra lutra): Development of a Eurasian otter-specific blocking oligonucleotide for 12S rRNA gene sequencing for vertebrates
Autoři:
Priyanka Kumari aff001; Ke Dong aff001; Kyung Yeon Eo aff003; Woo-Shin Lee aff004; Junpei Kimura aff005; Naomichi Yamamoto aff001
Působiště autorů:
Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, South Korea
aff001; Institute of Health and Environment, Graduate School of Public Health, Seoul National University, Seoul, South Korea
aff002; Conservation and Research Center, Seoul Zoo, Gwacheon, South Korea
aff003; Department of Forest Sciences, College of Agriculture and Life Science, Seoul National University, Seoul, South Korea
aff004; College of Veterinary Medicine, Seoul National University, Seoul, South Korea
aff005
Vyšlo v časopise:
PLoS ONE 14(12)
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pone.0226253
Souhrn
The Eurasian otter (Lutra lutra) is an endangered species for which diet analyses are needed as part of its conservation efforts. Eurasian otters feed on vertebrates, such as fishes, and invertebrates, such as crustaceans, but their detailed taxonomies are not fully understood in part due to limited resolving power of traditional morphological identification methods. Here, we used high-throughput sequencing (HTS)-based DNA metabarcoding approaches to analyze diet profiles of Eurasian otters inhabiting a marshy estuary area in Korea. We investigated their diet profiles based on spraint sampling followed by DNA metabarcoding analyses targeting 12S rRNA gene region for vertebrates, 16S rRNA gene region for invertebrates, and cytochrome c oxidase 1 (COI) gene region for fishes. For the vertebrate analysis, a blocking oligonucleotide (OBS1) was designed to suppress amplification of DNA fragments derived from the otters. The 12S rRNA gene sequencing assay detected species belonging to fishes (95%) and amphibians (3.3%). Fishes detected by 12S rRNA gene sequencing included crucian carp (Carassius auratus), mullets (Mugil spp.), bluegill (Lepomis macrochirus), and northern snakehead (Channa argus), which were also detected by COI gene sequencing. Among invertebrates, mud flat crabs (Helicana spp.) and shrimps (Palaemon spp.) were abundant. The designed blocking oligonucleotide OBS1 effectively inhibited amplification of the otter’s DNA, with only up to 0.21% of vertebrate sequence reads assigned to the otter. This study demonstrated that HTS-based DNA metabarcoding methods were useful to provide in-depth information regarding diet profiles of the otters at our sampling site. By using HTS-based DNA metabarcoding approaches, future research will explore detailed taxonomies of their diets across locations and seasons.
Klíčová slova:
DNA – Invertebrates – Vertebrates – Sequence databases – Ribosomal RNA – Otters – Gene sequencing – Oligonucleotides
Zdroje
1. Roos A, Loy A, de Silva P, Hajkova P, Zemanová B. Lutra lutra. The IUCN Red List of Threatened Species 2015. 2015:e.T12419A21935287.
2. Won C, Smith KG. History and current status of mammals of the Korean Peninsula. Mammal Rev. 1999;29(1):3–36.
3. Krawczyk AJ, Bogdziewicz M, Majkowska K, Glazaczow A. Diet composition of the Eurasian otter Lutra lutra in different freshwater habitats of temperate Europe: a review and meta‐analysis. Mammal Rev. 2016;46(2):106–113.
4. Lanszki J, Lehoczky I, Kotze A, Somers MJ. Diet of otters (Lutra lutra) in various habitat types in the Pannonian biogeographical region compared to other regions of Europe. PeerJ. 2016;4:e2266. doi: 10.7717/peerj.2266 27602262
5. Mateo R, Millán J, Rodríguez-Estival J, Camarero PR, Palomares F, Ortiz-Santaliestra ME. Levels of organochlorine pesticides and polychlorinated biphenyls in the critically endangered Iberian lynx and other sympatric carnivores in Spain. Chemosphere. 2012;86(7):691–700. doi: 10.1016/j.chemosphere.2011.10.037 22099537
6. Guillaud E, Bearez P, Denys C, Raimond S. New data on fish diet and bone digestion of the Eurasian otter (Lutra lutra) (Mammalia: Mustelidae) in central France. Eur Zool J. 2017;84(1):226–237.
7. Park H-C, Han T-Y, Kim D-C, Min M-S, Han S-Y, Kim K-S, et al. Individual identification and sex determination of Eurasian otters (Lutra lutra) in Daegu city based on genetic analysis of otter spraint. Genes Genom. 2011;33(6):653–657.
8. Park C-S, Cho G-J. Individual identification of Eurasian otters (Lutra lutra) in South Korea (Sincheon River, Daegu) by microsatellite markers. J Vet Med Sci. 2017;79(6):1064–1067. doi: 10.1292/jvms.16-0563 28428484
9. Carss D. Foraging behaviour and feeding ecology of the otter Lutra lutra: a selective review. Hystrix It J Mamm. 1995;7(1–2):179–194.
10. Hong S, Gim J-S, Kim HG, Cowan P, Joo G-J. A molecular approach to identifying the relationship between resource use and availability in Eurasian otters (Lutra lutra). Can J Zool. 2019;97:797–804.
11. Shehzad W, Riaz T, Nawaz MA, Miquel C, Poillot C, Shah SA, et al. Carnivore diet analysis based on next-generation sequencing: Application to the leopard cat (Prionailurus bengalensis) in Pakistan. Mol Ecol. 2012;21(8):1951–1965. doi: 10.1111/j.1365-294X.2011.05424.x 22250784
12. Farrell LE, Roman J, Sunquist ME. Dietary separation of sympatric carnivores identified by molecular analysis of scats. Mol Ecol. 2000;9(10):1583–1590. doi: 10.1046/j.1365-294x.2000.01037.x 11050553
13. Palomares F, Godoy JA, Piriz A, O'Brien SJ. Faecal genetic analysis to determine the presence and distribution of elusive carnivores: design and feasibility for the Iberian lynx. Mol Ecol. 2002;11(10):2171–2182. doi: 10.1046/j.1365-294x.2002.01608.x 12296958
14. Vesterinen EJ, Ruokolainen L, Wahlberg N, Peña C, Roslin T, Laine VN, et al. What you need is what you eat? Prey selection by the bat Myotis daubentonii. Mol Ecol. 2016;25(7):1581–1594. doi: 10.1111/mec.13564 26841188
15. De Barba M, Miquel C, Boyer F, Mercier C, Rioux D, Coissac E, et al. DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet. Mol Ecol Resour. 2014;14(2):306–323. doi: 10.1111/1755-0998.12188 24128180
16. Vestheim H, Jarman SN. Blocking primers to enhance PCR amplification of rare sequences in mixed samples–a case study on prey DNA in Antarctic krill stomachs. Front Zool. 2008;5(1):12.
17. Riaz T, Shehzad W, Viari A, Pompanon F, Taberlet P, Coissac E. ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis. Nucleic Acids Res. 2011;39(21):e145–e145. doi: 10.1093/nar/gkr732 21930509
18. Ivanova NV, Zemlak TS, Hanner RH, Hebert PDN. Universal primer cocktails for fish DNA barcoding. Mol Ecol Notes. 2007;7(4):544–548.
19. An C, Okamoto Y, Xu S, Eo KY, Kimura J, Yamamoto N. Comparison of fecal microbiota of three captive carnivore species inhabiting Korea. J Vet Med Sci. 2017;79(3):542–546. doi: 10.1292/jvms.16-0472 28049922
20. Hospodsky D, Yamamoto N, Peccia J. Accuracy, precision, and method detection limits of quantitative PCR for airborne bacteria and fungi. Appl Environ Microbiol. 2010;76(21):7004–7012. doi: 10.1128/AEM.01240-10 20817798
21. Bolger AM, Lohse M, Usadel B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–2120. doi: 10.1093/bioinformatics/btu170 24695404
22. Boyer F, Mercier C, Bonin A, Le Bras Y, Taberlet P, Coissac E. obitools: a unix-inspired software package for DNA metabarcoding. Mol Ecol Resour. 2016;16(1):176–182. doi: 10.1111/1755-0998.12428 25959493
23. Ficetola GF, Coissac E, Zundel S, Riaz T, Shehzad W, Bessière J, et al. An in silico approach for the evaluation of DNA barcodes. BMC Genomics. 2010;11(1):434.
24. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75(23):7537–7541. doi: 10.1128/AEM.01541-09 19801464
25. Rognes T, Flouri T, Nichols B, Quince C, Mahé F. VSEARCH: a versatile open source tool for metagenomics. PeerJ. 2016;4:e2584. doi: 10.7717/peerj.2584 27781170
26. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007;73(16):5261–5267. doi: 10.1128/AEM.00062-07 17586664
27. Machida RJ, Leray M, Ho S-L, Knowlton N. Metazoan mitochondrial gene sequence reference datasets for taxonomic assignment of environmental samples. Sci Data. 2017;4:170027. doi: 10.1038/sdata.2017.27 28291235
28. Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, et al. vegan: Community Ecology Package. R package version 2.5–6 [Internet]. 2019 [cited 2019 Sep 9]. Available from: https://CRAN.R-project.org/package=vegan.
29. Deagle BE, Chiaradia A, McInnes J, Jarman SN. Pyrosequencing faecal DNA to determine diet of little penguins: is what goes in what comes out? Conserv Genet. 2010;11(5):2039–2048.
30. Deagle BE, Kirkwood R, Jarman SN. Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces. Mol Ecol. 2009;18(9):2022–2038. doi: 10.1111/j.1365-294X.2009.04158.x 19317847
31. Miya M, Sato Y, Fukunaga T, Sado T, Poulsen JY, Sato K, et al. MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species. Royal Soc Open Sci. 2(7):150088.
32. Stoeckle MY, Soboleva L, Charlop-Powers Z. Aquatic environmental DNA detects seasonal fish abundance and habitat preference in an urban estuary. PLOS ONE. 2017;12(4):e0175186. doi: 10.1371/journal.pone.0175186 28403183
33. Valentini A, Taberlet P, Miaud C, Civade R, Herder J, Thomsen PF, et al. Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Mol Ecol. 2016;25(4):929–942. doi: 10.1111/mec.13428 26479867
34. Yoon J-D, Kim J-H, Byeon M-S, Yang H-J, Park J-Y, Shim J-H, et al. Distribution patterns of fish communities with respect to environmental gradients in Korean streams. Ann Limnol—Int J Lim. 2011;47:S63–S71.
35. Taastrøm H-M, Jacobsen L. The diet of otters (Lutra lutra L.) in Danish freshwater habitats: comparisons of prey fish populations. J Zool. 1999;248(1):1–13.
36. Copp GH, Roche K. Range and diet of Eurasian otters Lutra lutra (L.) in the catchment of the River Lee (south‐east England) since re‐introduction. Aquat Conserv: Mar Freshw Ecosyst. 2003;13(1):65–76.
37. Remonti L, Prigioni C, Balestrieri A, Sgrosso S, Priore G. Trophic flexibility of the otter (Lutra lutra) in southern Italy. Mamm Biol. 2008;73(4):293–302.
38. Jang MH, Kim JG, Park SB, Jeong KS, Cho GI, Joo GJ. The current status of the distribution of introduced fish in large river systems of South Korea. Int Rev Hydrobiol. 2002;87(2–3):319–328.
39. Jang M-H, Joo G-J, Lucas MC. Diet of introduced largemouth bass in Korean rivers and potential interactions with native fishes. Ecol Freshwat Fish. 2006;15(3):315–320.
40. Park SK, Davidson K, Pan M. Economic relationships between aquaculture and capture fisheries in the Republic of Korea. Aquacult Econ Manag. 2012;16(2):102–116.
41. Kawamura K, Yonekura R, Katano O, Taniguchi Y, Saitoh K. Origin and dispersal of bluegill sunfish, Lepomis macrochirus, in Japan and Korea. Mol Ecol. 2006;15(3):613–621. doi: 10.1111/j.1365-294X.2006.02823.x 16499689
42. Miranda R, Copp GH, Williams J, Beyer K, Gozlan RE. Do Eurasian otters Lutra lutra (L.) in the Somerset Levels prey preferentially on non-native fish species? Fundam Appl Limnol. 2008;172(4):339–347.
43. Ju J, Kim JH, Kim SH. Habitat fragmentation by a levee and its Impact on frog population in the civilian control zone. J Wetlands Res. 2016;18(2):113–120.
44. Park J, Song SJ, Ryu J, Kwon B-O, Hong S, Bae H, et al. Macrozoobenthos of Korean tidal flats: A review on species assemblages and distribution. Ocean Coast Manag. 2014;102:483–492.
45. Shih H-T, Suzuki H. Taxonomy, phylogeny, and biogeography of the endemic mudflat crab Helicel Chasmagnathus complex (Crustacea: Brachyura: Varunidae) from East Asia. Zool Stud. 2008;47(1):114–125.
46. Oh C-W, Suh H-L, Park K-Y, Ma C-W, Lim H-S. Growth and reproductive biology of the freshwater shrimp Exopalaemon modestus (Decapoda: Palaemonidae) in a lake of Korea. J Crustacean Biol. 2002;22(2):357–366.
47. Georgiev D, Stoycheva S. Freshwater crabs preyed on by the Eurasian Otter Lutra lutra in a river habitat of southern Bulgaria. Hystrix It J Mamm. 2007;17(2):129–135.
48. Freitas D, Gomes J, Luis TS, Madruga L, Marques C, Baptista G, et al. Otters and fish farms in the Sado estuary: ecological and socio-economic basis of a conflict. Hydrobiologia. 2007;587(1):51–62.
49. Gustafson GT, Miller KB. Systematics and evolution of the whirligig beetle tribe Dineutini (Coleoptera: Gyrinidae: Gyrininae). Zool J Linnean Soc. 2017;181(1):118–150.
50. Bowles E, Schulte PM, Tollit DJ, Deagle BE, Trites AW. Proportion of prey consumed can be determined from faecal DNA using real-time PCR. Mol Ecol Resour. 2011;11(3):530–540. doi: 10.1111/j.1755-0998.2010.02974.x 21481211
51. Elbrecht V, Leese F. Can DNA-based ecosystem assessments quantify species abundance? Testing primer bias and biomass—sequence relationships with an innovative metabarcoding protocol. PLOS ONE. 2015;10(7):e0130324. doi: 10.1371/journal.pone.0130324 26154168
52. Thomas AC, Deagle BE, Eveson JP, Harsch CH, Trites AW. Quantitative DNA metabarcoding: improved estimates of species proportional biomass using correction factors derived from control material. Mol Ecol Resour. 2016;16(3):714–726. doi: 10.1111/1755-0998.12490 26602877
53. Corse E, Meglécz E, Archambaud G, Ardisson M, Martin J-F, Tougard C, et al. A from-benchtop-to-desktop workflow for validating HTS data and for taxonomic identification in diet metabarcoding studies. Mol Ecol Resour. 2017;17(6):e146–e159. doi: 10.1111/1755-0998.12703 28776936
54. Simpson VR, Coxon KE. Intraspecific aggression, cannibalism and suspected infanticide in Otters. Br Wildl. 2000;11(6):423–426.
55. Corse E, Tougard C, Archambaud-Suard G, Agnèse J-F, Messu Mandeng FD, Bilong Bilong CF, et al. One-locus-several-primers: A strategy to improve the taxonomic and haplotypic coverage in diet metabarcoding studies. Ecol Evol. 2019;9(8):4603–4620. doi: 10.1002/ece3.5063 31031930
Článok vyšiel v časopise
PLOS One
2019 Číslo 12
- Metamizol jako analgetikum první volby: kdy, pro koho, jak a proč?
- Nejasný stín na plicích – kazuistika
- Masturbační chování žen v ČR − dotazníková studie
- Úspěšná resuscitativní thorakotomie v přednemocniční neodkladné péči
- Fixní kombinace paracetamol/kodein nabízí synergické analgetické účinky
Najčítanejšie v tomto čísle
- Methylsulfonylmethane increases osteogenesis and regulates the mineralization of the matrix by transglutaminase 2 in SHED cells
- Oregano powder reduces Streptococcus and increases SCFA concentration in a mixed bacterial culture assay
- The characteristic of patulous eustachian tube patients diagnosed by the JOS diagnostic criteria
- Parametric CAD modeling for open source scientific hardware: Comparing OpenSCAD and FreeCAD Python scripts