Abstract
A major focus of ecology is understanding trophic relationships and energy flows in natural systems, associated food web dynamics and changes in food webs due to introduced species. Predator-prey interactions are often assessed by examining stomach contents. However, partially digested remains may be difficult to accurately identify by traditional visual analysis. Here we evaluate the effectiveness of DNA barcoding to identify digested piscine prey remains in invasive Blue Catfish Ictalurus furcatus, non-native, but established Channel Catfish Ictalurus punctatus and native White Catfish Ameiurus catus from Chesapeake Bay, USA. Stomach contents were examined and piscine prey items were scored as lightly digested, moderately digested or severely digested. A 652 base pair region of the cytochrome c oxidase subunit I (COI-5P) mitochondrial DNA gene was sequenced for each prey item. Edited barcode sequences were compared to locally-caught and validated reference sequences in BOLD (Barcode of Life Database). A large majority of prey items were sufficiently digested to limit morphological identification (9.4 % to species and an additional 12.1 % to family). However, overall barcoding success was high (90.3 %) with little difference among the digestion classifications. Combining morphological and genetic identifications, we classified 91.6 % of fish prey items to species. Twenty-three fish species were identified, including species undergoing active restoration efforts (e.g., Alosa spp.) and commercially important species, e.g., Striped Bass Morone saxatilis, White Perch Morone americana, American Eel Anguilla rostrata and Menhaden Brevoortia tyrannus. We found DNA barcoding highly successful at identifying all but the most heavily degraded prey items and to be an efficient and effective method for obtaining diet information to strengthen the resolution of trophic analyses including diet comparisons among sympatric native and non-native predators.
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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
April J, Mayden RL, Hanner RH, Bernatchez L (2011) Genetic calibration of species diversity among North America’s freshwater fishes. Proc Natl Acad Sci U S A 108(26):10602–10607
Arroyave J, Stiassny MLJ (2014) DNA barcoding reveals novel insights into pterygophagy and prey selection in distichodontid fishes (Characiformes: Distichodontidae. Ecol Evol 23(4):4534–4542
Baeza JA, Fuentes MS (2013) Exploring phylogenetic informativeness and nuclear copies of mitochondrial DNA (numts) in three commonly used mitochondrial genes: mitochondrial phylogeny of peppermint, cleaner, and semi-terrestrial shrimps (Caridea: Lysmata, Exhippolysmata, and Merguia). Zoo J Linn Soc-Lond 168:699–722
Baldwin CC, Mounts JH, Smith DG, Weigt LA (2009) Genetic identification and color descriptions of early life-history stages of Belizean Phaeoptyx and Astrapogon (Teleostei: Apogonidae) with comments on identification of adult Phaeoptyx. Zootaxa 2008:1–22
Baldwin CC, Brito BJ, Smith DG, Weigt LA, Escobar-Briones E (2011) Identification of early life-history stages of Caribbean Apogon (Perciformes: Apogonidae) through DNA barcoding. Zootaxa 3133:1–36
Bariche M, Torres M, Smith C, Sayar N, Azzurro E, Baker R, Bernardi G (2015) Red Sea fishes in the Mediterranean Sea: a preliminary investigation of a biological invasion using DNA barcoding. J Biogeogr 42:2363–2373
Barnett A, Redd KS, Frusher SD, Stevens JD, Semmens JM (2010) Non-lethal method to obtain stomach samples from a large marine predator and the use of DNA analysis to improve dietary information. J Exp Mar Biol Ecol 393:188–192
Beauchamp DA, Wahl DH, Johnson BM (2007) Predator-prey interactions. In: Guy CD, Brown ML (eds) Analysis and interpretation of freshwater fisheries data. American Fisheries Society, Bethesda, Maryland, pp. 765–842
Berry O, Bulman C, Bunce M, Coghlan M, Murray DC, Ward RD (2015) Comparison of morphological and DNA metabarcoding analyses of diets in exploited marine fishes. Mar Ecol Prog Ser 540:167–181
Betancur-R R, Broughton RE, Wiley EO, Carpenter K, López JA, Li C, Holcroft NI, Arcila D, Sanciangco M, Cureton II JC, Zhang F, Buser T, Campbell MA, Ballesteros JA, Roa-Varon A, Willis S, Borden WC, Rowley T, Reneau PC, Hough DJ, Lu G, Grande T, Arratia G, Ortí G (2013) The Tree of Life and a New Classification of Bony Fishes. PLoS Curr Tree of Life. Apr 18. Edition 1. doi:10.1371/currents.tol.53ba26640df0ccaee75bb165c8c26288.
Boileau N, Cortesi F, Egger B, Muschick M, Indermaur A, Theis A, Büscher HH, Salzburger W (2015) A complex mode of aggressive mimicry in a scale-eating cichlid fish. Biol Lett 11(9):20150521
BOLD (2015) Barcode of Life Database (BOLD). Available: www. Boldsystems.org/. Accessed 15 December 2015
Braid HE, Deeds J, DeGrasse SL, Wilson JJ, Osborne J, Hanner RH (2012) Preying on commercial fisheries and accumulating paralytic shellfish toxins: a dietary analysis of invasive Dosidicus gigas (Cephalopoda Ommastrephidae) stranded in Pacific Canada. Mar Biol 159:25–31
Carreon-Martinez L, Johnson TB, Ludsin SA, Heath DD (2011) Utilization of stomach content DNA to determine diet diversity in piscivorous fishes. J Fish Biol 78:1170–1182
Chandler L (1998) Trophic ecology of native and introduced catfishes in the tidal James River. Virginia Commonwealth University, Richmond Virginia. Master’s Thesis, 116p
Charles H, Dukes JS (2007) Impacts of invasive species on ecosystems services. In: W. Nentwig (ed.) biological invasions. Ecological Studies 193. Springer, Berlin, Germany. pp. 217–237
Chelsky Budarf A, Burfeind DD, Loh WK, Tibbetts IR (2011) Identification of seagrasses in the gut of a marine herbivorous fish using DNA barcoding and visual inspection. J Fish Biol 79:112–121
Conway KW, Baldwin C, White MD (2014) Cryptic diversity and venom glands in western Atlantic clingfishes of the genus Acyrtus (Teleostei: Gobiesocidae). PLoS One 9(5): e97664
Cote IM, Green SJ, Morris JA, Akins JL, Steinke D (2013) Diet richness of indo-Pacific lionfish revealed by DNA barcoding. Mar Ecol Prog Ser 472:249–256
Dalton DI, Kotze A (2011) DNA barcoding as a tool for species identification in three forensic wildlife cases in South Africa. Forensic Sci Int 207:e51–e254
de Barba M, Miquel C, Boyer F, Mercier C, Rioux D, Coissac E, Taberlet P (2014) DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet. Mol Ecol Resour 14:306–323
Derr RE (2011) Performing exact regression with the SAS system. In: Proceedings of the 25th Annual SAS Users Group International Conference, April 2000, Cary, NC, USA Paper P254–P225
Dunn MR, Szabo A, McVeagh MS, Smith PJ (2010) The diet of deep water sharks and the benefits of using DNA identification of prey. Deep-Sea Res 57:923–930
Eggleton MA, Schramm HL (2004) Feeding ecology and energetic relationships with habitat of blue catfish Ictalurus furcatus and flathead catfish Pylodictis olivaris in the lower Mississippi River, USA. Environ Biol Fish 70:107–121
Ekrem T, Willassen E, Stur E (2007) A comprehensive DNA sequence library is essential for identification with DNA barcodes. Mol Phylogenet Evol 43:530–542
Fritts TH, Rodda GH (1998) The role of introduced species in the degradation of island ecosystems: A case history of Guam. Annu Rev Ecol Syst 29:113–140
Gonçalves PFM, Oliveira-Marques AR, Matsumoto TE, Miyaki CY (2015) DNA Barcoding identifies illegal parrot trade. J Hered 106(S1):560–564
Graham K (1999) A review of the biology and management of blue catfish. In: Irwin ER, Hubert WA, Rabeni CF, Schramm HL, Coon T (ed.) Catfish 2000: Proceedings of the International Ictalurid Symposium Amer Fish Soc Symp 24 Bethesda, MD pp. 37–49
Greenlee RS, Lim CN (2011) Searching for equilibrium: Population parameters and variable recruitment in introduced Blue Catfish populations in four Virginia tidal river systems. In: Michaletz PH, Travnichek VH (ed.) Conservation, Ecology, and Management of Catfish: The Second International Symposium American Fisheries Society, Symposium 77, Bethesda, MD pp. 349–367
Handy SM, Deeds JR, Ivanova NV, Hebert PDN, Hanner RH, Ormos A, Weigt LA, Moore MM, Yancy HF (2011) A single-laboratory validated method for the generation of DNA barcodes for the identification of fish for regulatory compliance. J AOAC Int 94(1):201–210
Hebert PDN, Cywinska A, Ball SL, deWaard JR (2003) Biological identifications through DNA barcodes. P R Soc London 270:313–321
Hebert PDN, Penton EH, Burns JM, Janzen DH, Hallwachs W (2004) Ten species in one: DNA barcoding reveals cryptic species in the neotropical kipper butterfly Astraptes fulgerator. Proc Natl Acad Sci U S A 101(41):14812–14817
Hubert N, Hanner R, Holm E, Mandrak NE Taylor E (2008) Identifying Canadian freshwater fishes through DNA barcodes. PLoS One 3(6): e2490
Hyslop EJ (1980) Stomach contents analysis - a review of methods and their application. J Fish Biol 17:411–429
Ivanova NV, Zemlak TS, Hanner RH, Hebert PDN (2007) Universal primer cocktails for fish DNA barcoding. Mol Ecol Resour 7(4):544–548
Jenkins RE, Burkhead NM (1993) Freshwater fishes of Virginia. American Fisheries Society, Bethesda, Maryland
Jo H, Gim JA, Jeong KS, Kim HS, Joo GJ (2014) Application of DNA barcoding for identification of freshwater carnivorous fish diets: is number of prey items dependent on size class for Micropterus salmoides? Ecol Evol 4:219–229
Joly S, Davies TJ, Bruneau A, Derry A, Kembel SW, Peres-Neto P, Vamosi J, Wheeler TA (2014) Ecology in the age of DNA barcoding: the resource, the promise and the challenges ahead. Mol Ecol Resour 14(2):221–232
Kress WJ, García-Robledo C, Uriarte M, Erickson DL (2015) DNA barcodes for ecology, evolution and conservation. Trends Ecol Evol 30(1):25–35
Legler ND, Johnson TB, Heath DD, Ludsin S (2010) Water temperature and prey size effects on the rate of digestion of larval and early juvenile fish. Trans Am Fish Soc 139:868–875
Leray M, Knowlton N (2015) DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity. Proc Natl Acad Sci U S A 112(7):2076–2081
Leray M, Yang JY, Meyer CP, Mills SC, Agudelo N, Ranwez V, Boehm JT, Machida RJ (2013) A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents. Front Zool 10:34
Leray M, Meyer CP, Mills SC (2015) Metabarcoding dietary analysis of coral dwelling predatory fish demonstrates the minor contribution of coral mutualists to their highly partitioned, generalist diet. PeerJ 3: e1047
MacAvoy SE, Macko SA, McIninch SP, Garman GC (2000) Marine nutrient contributions to freshwater apex predators. Oecologia 122:568–573
MacAvoy SE, Garman GC, Macko SA (2009) Anadromous fish as marine nutrient vectors. Fish B-NOAA 107:165–174
Méheust E, Alfonsi E, Le Ménec P, Hassani S, Jung J (2015) DNA barcoding for the identification of soft remains of prey in the stomach contents of grey seals (Halichoerus grypus) and harbour porpoises (Phocoena phocoena. Mar Biol Res 11(4):385–395
Miya M, Sato Y, Fukunaga T, Sado T, Poulsen JY, Sato K, Minamoto T, Yamamoto S, Yamanaka H, Araki H, Kondoh M, Iwasaki W (2015) MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species. R Soc Open Sci 2: 150088
Moran Z, Orth DJ, Schmitt JD, Hallerman EM, Aguilar R (2015) Effectiveness of DNA barcoding for identifying piscine prey items in stomach contents of piscivorous catfishes. Environ Biol Fish 99(1):161–167
Murdy EO, Birdsong RS, Musick JA (1997) Fishes of Chesapeake Bay. Smithsonian Institution Press, Washington D. C
Nagy ZT, Sonet G, Glaw F, Vences M (2012) First large-scale DNA barcoding assessment of reptiles in the biodiversity hotspot of Madagascar, based on newly designed COI primers. PLoS One 7(3): e34506
Paquin MM, Buckley TW, Hibpshman RE, Canino MF (2014) DNA-based identification methods of prey fish from stomach contents of 12 species of eastern North Pacific groundfish. Deep-Sea Res 85:110–117
Pompanon F, Deagle BE, Symondson WOC, Brown DS, Jarman SN, Taberlet P (2012) Who is eating what: diet assessment using next generation sequencing. Mol Ecol 21:1931–1950
Ratnasingham S, Hebert PDN (2007) BOLD: the barcode of life data system (www.Barcodinglife.Org). Mol Ecol Notes 7: 355–364
Ratnasingham S, Hebert PDN (2013) A DNA-based registry for all animal species: the barcode index number (BIN) system. PLoS One 8(8): e66213
Rocha LA, Rocha CR, Baldwin CC, Weigt LA (2015) Invasive lionfish preying on critically endangered reef fish. Coral Reefs 34:803–806
Ross ST (2001) Inland Fishes of Mississippi. University Press of Mississippi, Jackson, MS. 624 pp.
Schloesser RW, Fabrizio MC, Latour RJ, Garman GC, Greenlee B, Groves M, Gartland J (2011) Ecological role of blue catfish in Chesapeake Bay communities and implications for management. In: Michaletz PH, Travnichek VH (ed.) conservation, ecology, and Management of Catfish: the second international symposium. Am Fish Soc Symp 77, Bethesda, Maryland. pp. 369–382
Schooley JD, Karam AP, Kresner BR, Marsh PC, Pacey CA, Thornbrugh DJ (2008) Detection of larval remains after consumption by fishes. Trans Am Fish Soc 137:1044–1049
Tuckey TD, Fabrizio MC (2010) Estimating relative juvenile abundance of ecologically important finfish in the Virginia portion of Chesapeake Bay. Project #F-104-R-14. Annual Report to Virginia Marine Resources Commission. Virginia Institute of Marine Science, Gloucester Point.
Valdez-Moreno M, Quintal-Lizama C, Gómez-Lozano R, García-Rivas MC (2012) Monitoring an alien invasion: DNA barcoding and the identification of lionfish and their prey on coral reefs of the Mexican Caribbean. PLoS One 7(6):e36636
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 5:12
Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN (2005) DNA barcoding Australia’s fish species. Philos Trans R Soc Lond Ser B Biol Sci 360(1462):1847–1857
Ward RD, Hanner R, Hebert PDN (2009) The campaign to DNA barcode all fishes FISH-BOL. J Fish Biol 74:329–356
Weigt LA, Baldwin CC, Driskell A, Smith DG, Ormos A, Reyier EA (2012a) Using DNA barcoding to assess Caribbean reef fish biodiversity: expanding taxonomic and geographic coverage. PLoS One 7(7): e41059
Weigt LA, Driskell AC, Baldwin CC, Ormos A (2012b) DNA barcoding fishes. In: Lopez Erickson DL (ed) DNA barcodes: Methods and Protocols. Humana Press, New York City, NY, pp. 109–126
Wirta HK, Hebert PDN, Kaartinena R, Prosser SW, Várkonyi G, Roslin T (2014) Complementary molecular information changes our perception of food web structure. Proc Natl Acad Sci U S A 111(5):1885–1890
Worth S (1893) Report on the propagation and distribution of food-fishes. Rep U S Commissioner Fish Fish 1893:78–138
Acknowledgments
This project was conducted with funding support from NOAA’s Chesapeake Bay Office award #NA11NMF4570231, the Smithsonian Institution administered by the Secretariat Office of the Consortium for the Barcode of Life, and the Laboratories of Analytical Biology of the National Museum of Natural History. We gratefully acknowledge Miranda Marvel, Brooke Weigel, Paige Roberts, Angela Owens, Keira Heggie, Mike Goodison, Kim Richie and Midge Kramer for assistance with SERC field collections and sample processing and Timothy Groves, Branson Williams and Ross Williams for MD DNR field collections and sample processing. We would also like to thank Dr. Paul J. Smith (University of Maryland) for his statistical guidance. Internships provided to MM, BW and AO were also funded by NOAA’s Chesapeake Bay Office award #NA11NMF4570231 and MO was partially funded by a Smithsonian Environmental Research Center (SERC) postdoctoral fellowship. This project was reviewed by SERC’s Institutional Animal Care and Use Committee (IACUC) and all applicable international, national, and/or institutional guidelines for humane animal care and use were followed. The manuscript was strengthened by comments from 3 anonymous peer reviewers.
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Aguilar, R., Ogburn, M.B., Driskell, A.C. et al. Gutsy genetics: identification of digested piscine prey items in the stomach contents of sympatric native and introduced warmwater catfishes via DNA barcoding. Environ Biol Fish 100, 325–336 (2017). https://doi.org/10.1007/s10641-016-0523-8
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DOI: https://doi.org/10.1007/s10641-016-0523-8