Skip to main content

Advertisement

SpringerLink
Log in

Sea cucumber (Apostichopus japonicus) eukaryotic food source composition determined by 18s rDNA barcoding

  • Original paper
  • Published:
Marine Biology Aims and scope Submit manuscript

Abstract

Food source determination of deposit-feeding sea cucumbers is difficult because the majority of organic debris in gut cannot be reliably or accurately identified by conventional microscopic examination. Advanced DNA barcoding is an effective and rapid technique to determine dietary composition of such feeders. In this study, the composition of eukaryotic food sources of the sea cucumber, Apostichopus japonicus, harvested in two bays of an offshore island in winter and spring was surveyed by high-throughput DNA sequencing. The 18s rDNA v4 loci sequences were amplified to provide a total of 616,184 optimized reads and 823 operational taxonomic units. Winter group sequences were assigned to 27.20 ± 3.63 and 28.40 ± 2.88 phyla, and those in spring to 25.80 ± 3.90 and 24.20 ± 3.11 phyla. Eukaryote richness was higher in winter than in spring, with Dinoflagellata, Bacillariophyceae, Arthropoda, Cercozoa, and Mollusca the dominant phyla in decreasing order of importance. Our results indicated the guts of A. japonicus contained more organic material sourced from the water column than from within the sediments. The profiling table and cluster analysis revealed winter and spring samples clustered separately, indicating significant seasonal differences in eukaryotic composition. Main winter dietary components were Bacillariophyceae, Dinoflagellata, and Streptophyta, whereas those in spring were Bacillariophyceae, Arthropoda, and Mollusca. In any one season, gut contents did not differ significantly between sampling locations. Our study indicates that DNA sequencing can greatly improve the accuracy of diet studies on sea cucumbers.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • Bachy C, Dolan JR, López-García P, Deschamps P, Moreira D (2013) Accuracy of protist diversity assessments: morphology compared with cloning and direct pyrosequencing of 18S rRNA genes and ITS regions using the conspicuous tintinnid ciliates as a case study. ISME J 7:244–255. doi:10.1038/ismej.2012.106

    Article  CAS  Google Scholar 

  • Backeljau T, De Bruyn L, De Wolf H, Jordaens K, Van Dongen S, Winnepennincks B (1996) Multiple UPGMA and neighbor-joining trees and the performance of some computer packages. Mol Biol Evol 13:309–313. doi:10.1093/oxfordjournals.molbev.a025590

    Article  CAS  Google Scholar 

  • Bade LM, Balakrishnan CN, Pilgrim EM, McRae SB, Luczkovich JJ (2014) A genetic technique to identify the diet of cownose rays, Rhinoptera bonasus: analysis of shellfish prey items from North Carolina and Virginia. Environ Biol Fish 97:999–1012. doi:10.1007/s10641-014-0290-3

    Article  Google Scholar 

  • Bakus GJ (1973) The biology and ecology of tropical holothurians. Biol Geol Coral Reefs 2:326–367. doi:10.1016/B978-0-12-395526-5.50018-3

    Google Scholar 

  • Bengtsson-Palme J, Ryberg M, Hartmann M et al (2013) Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods Ecol Evol 4:914–919. doi:10.1111/2041-210X.12073

    Google Scholar 

  • Bokulich NA, Mills DA (2013) Improved selection of internal transcribed spacer-specific primers enables quantitative, ultra-high-throughput profiling of fungal communities. Appl Environ Microbiol 79:2519–2526. doi:10.1128/AEM.03870-12

    Article  CAS  Google Scholar 

  • Brown DS, Burger R, Cole N, Vencatasamy D, Clare E, Montazam A, Symondson WOC (2014) Dietary competition between the alien Asian Musk Shrew (Suncus murinus) and a re-introduced population of Telfair’s Skink (Leiolopisma telfairii). Mol Ecol 23:3695–3705. doi:10.1111/mec.12445

    Article  CAS  Google Scholar 

  • Caporaso JG, Kuczynski J, Stombaugh J et al (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336. doi:10.1038/nmeth.f.303

    Article  CAS  Google Scholar 

  • Cheung MK, Au CH, Chu KH, Kwan HS, Wong CK (2010) Composition and genetic diversity of picoeukaryotes in subtropical coastal waters as revealed by 454 pyrosequencing. ISME J 4:1053–1059. doi:10.1038/ismej.2010.26

    Article  Google Scholar 

  • Chiang KP, Chou YH, Chang J, Gong GC (2004) Winter distribution of diatom assemblages in the East China Sea. J Oceanogr 60:1053–1062. doi:10.1007/s10872-005-0013-7

    Article  Google Scholar 

  • Dare P, Edwards D (1975) Seasonal changes in flesh weight and biochemical composition of mussels (Mytilus edulis L.) in the Conwy Estuary, North Wales. J Exp Mar Biol Ecol 18:89–97. doi:10.1016/0022-0981(75)90066-0

    Article  CAS  Google Scholar 

  • Dridi S, Romdhane MS, Elcafsi M (2007) Seasonal variation in weight and biochemical composition of the Pacific oyster, Crassostrea gigas in relation to the gametogenic cycle and environmental conditions of the Bizert lagoon, Tunisia. Aquaculture 263:238–248. doi:10.1016/j.aquaculture.2006.10.028

    Article  CAS  Google Scholar 

  • Edgar RC (2013) UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10:996–998. doi:10.1038/nmeth.2604

    Article  CAS  Google Scholar 

  • Elsner M, Jochmann MA, Hofstetter TB, et al (2012) Current challenges in compound-specific stable isotope analysis of environmental organic contaminants. Anal Bioanal Chem 403:2471–2491. doi:10.1007/s00216-011-5683-y

    Article  CAS  Google Scholar 

  • Findley K, Oh J, Yang J et al (2013) Topographic diversity of fungal and bacterial communities in human skin. Nature 498:367–370. doi:10.1038/nature12171

    Article  CAS  Google Scholar 

  • Gao F, Yang H, Xu Q, Wang F, Liu G, German DP (2008) Phenotypic plasticity of gut structure and function during periods of inactivity in Apostichopus japonicus. Comp Biochem Phys B 150:255–262. doi:10.1016/j.cbpb.2008.03.011

    Article  Google Scholar 

  • Gao F, Xu Q, Yang H (2010) Seasonal variations of food sources in Apostichopus japonicus indicated by fatty acid biomarkers analysis. J Fish China 34:760–770. doi:10.3724/SP.J.1231.2010.06768

    Article  Google Scholar 

  • Gao F, Li F, Tan J, Yan J, Sun H (2014) Bacterial community composition in the gut content and ambient sediment of sea cucumber Apostichopus japonicus revealed by 16S rRNA gene pyrosequencing. PLoS ONE 9:e100092. doi:10.1371/journal.pone.0100092

    Article  Google Scholar 

  • Günther B, Rall BC, Ferlian O, Scheu S, Eitzinger B (2014) Variations in prey consumption of centipede predators in forest soils as indicated by molecular gut content analysis. Oikos 123:1192–1198. doi:10.1111/j.1600-0706.2013.00868.x

    Article  Google Scholar 

  • Hauksson E (1979) Feeding biology of Stichopus tremulus, a deposit-feeding holothurian. Sarsia 64:155–160. doi:10.1080/00364827.1979.10411376

    Article  Google Scholar 

  • Huber JA, Welch DBM, Morrison HG, Huse SM, Neal PR, Butterfield DA, Sogin ML (2007) Microbial population structures in the deep marine biosphere. Science 318:97–100. doi:10.1126/science.1146689

    Article  CAS  Google Scholar 

  • Kinoshita T, Tanaka S (1939) Hokkaido san namako no syokuji ni tsuite (a report of the feeding pattern of the sea cucumber Stichopus japonicus in Hokkaido). Suisankenkyushi 34:32–35

    Google Scholar 

  • Leal M, Nejstgaard J, Calado R, Thompson M, Frischer M (2014) Molecular assessment of heterotrophy and prey digestion in zooxanthellate cnidarians. Mol Ecol 23:3838–3848. doi:10.1111/mec.12496

    Article  CAS  Google Scholar 

  • Leray M, Yang JY, Meyer CP et al (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. doi:10.1186/1742-9994-10-34

    Article  Google Scholar 

  • Liao Y (1997) Chinese fauna Echinodermata holothuroidea. Science Press, Beijing

    Google Scholar 

  • Magoč T, Salzberg SL (2011) FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27:2957–2963. doi:10.1093/bioinformatics/btr507

    Article  Google Scholar 

  • Maloy AP, Culloty SC, Slater JW (2009) Use of PCR–DGGE to investigate the trophic ecology of marine suspension feeding bivalves. Mar Ecol Prog Ser 381:109–118

    Article  CAS  Google Scholar 

  • Maloy AP, Nelle P, Culloty SC, Slater JW, Harrod C (2013) Identifying trophic variation in a marine suspension feeder: DNA-and stable isotope-based dietary analysis in Mytilus spp. Mar Biol 160:479–490. doi:10.1007/s00227-012-2105-4

    Article  CAS  Google Scholar 

  • Martin DL, Ross RM, Quetin LB, Murray AE (2006) Molecular approach (PCR–DGGE) to diet analysis in young Antarctic krill Euphausia superba. Mar Ecol Prog Ser 319:155–165. doi:10.3354/meps319155

    Article  CAS  Google Scholar 

  • McShane P (1992) Early life history of abalone: a review. In: Shepherd SA, Tegner MJ, Guzman SA (eds) Abalone of the world: biology, fisheries and culture. Fishing News Books, Oxford, pp 120–138

  • Metfies K, Nicolaus A, Von Harbou L, Bathmann U, Peeken I (2014) Molecular analyses of gut contents: elucidating the feeding of co-occurring salps in the Lazarev Sea from a different perspective. Antarct Sci 26:545–553. doi:10.1017/S0954102014000157

    Article  Google Scholar 

  • Moriarty D (1982) Feeding of Holothuria atra and Stichopus chloronotus on bacteria, organic carbon and organic nitrogen in sediments of the Great Barrier Reef. Mar Freshwater Res 33:255–263. doi:10.1071/MF9820255

    Article  Google Scholar 

  • Mueller RC, Paula FS, Mirza BS, Rodrigues JL, Nüsslein K, Bohannan BJ (2014) Links between plant and fungal communities across a deforestation chronosequence in the Amazon rainforest. ISME J 8:1548–1550. doi:10.1038/ismej.2013.253

    Article  CAS  Google Scholar 

  • O’Rorke R, Lavery S, Chow S et al (2012) Determining the diet of larvae of western rock lobster (Panulirus cygnus) using high-throughput DNA sequencing techniques. PLoS ONE 7:e42757. doi:10.1371/journal.pone.0042757

    Article  Google Scholar 

  • O’Rorke R, Lavery S, Wang M, Nodder S, Jeffs A (2014) Determining the diet of larvae of the red rock lobster (Jasus edwardsii) using high-throughput DNA sequencing techniques. Mar Biol 161:551–563. doi:10.1007/s00227-013-2357-7

    Article  Google Scholar 

  • Oros-Sichler M, Smalla K (2013) Semi-Nested PCR approach to amplify large 18S rRNA gene fragments for PCR–DGGE analysis of soil fungal communities. In: Gupta VK, Tuohy MG, Ayyachamy M, Turner KM (eds) Laboratory protocols in fungal biology. Springer, pp 289–298

  • Pompanon F, Deagle BE, Symondson WO, Brown DS, Jarman SN, Taberlet P (2012) Who is eating what: diet assessment using next generation sequencing. Mol Ecol 21:1931–1950. doi:10.1111/j.1365-294X.2011.05403.x

    Article  CAS  Google Scholar 

  • Riemann L et al (2010) Qualitative assessment of the diet of European eel larvae in the Sargasso Sea resolved by DNA barcoding. Biol Lett 6(6):819–822. doi:10.1098/rsbl.2010.0411

    Article  CAS  Google Scholar 

  • Roberts D, Moore H, Berges J, Patching J, Carton M, Eardly D (2001) Sediment distribution, hydrolytic enzyme profiles and bacterial activities in the guts of Oneirophanta mutabilis, Psychropotes longicauda and Pseudostichopus villosus: what do they tell us about digestive strategies of abyssal holothurians? Prog Oceanogr 50:443–458. doi:10.1016/S0079-6611(01)00065-9

    Article  Google Scholar 

  • Sogin ML, Morrison HG, Huber JA et al (2006) Microbial diversity in the deep sea and the underexplored “rare biosphere”. Proc Natl Acad Sci USA 103:12115–12120. doi:10.1073/pnas.0605127103

    Article  CAS  Google Scholar 

  • Stoeck T et al (2009) Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities. BMC Biol 7:72. doi:10.1186/1741-7007-7-72

    Article  Google Scholar 

  • Sundet J, Vahl O (1981) Seasonal changes in dry weight and biochemical composition of the tissues of sexually mature and immature Iceland scallops, Chlamys islandica. J Mar Biol Assoc UK 61:1001–1010. doi:10.1017/S0025315400023110

    Article  Google Scholar 

  • Suzuki N, Hoshino K, Murakami K, Takeyama H, Chow S (2008) Molecular diet analysis of phyllosoma larvae of the Japanese spiny lobster Panulirus japonicus (Decapoda: Crustacea). Mar Biotechnol 10:49–55. doi:10.1007/s10126-007-9038-9

    Article  CAS  Google Scholar 

  • Tel-Zur N, Abbo S, Myslabodski D, Mizrahi Y (1999) Modified CTAB procedure for DNA isolation from epiphytic cacti of the genera Hylocereus and Selenicereus (Cactaceae). Plant Mol Biol Rep 17:249–254. doi:10.1023/A:1007656315275

    Article  CAS  Google Scholar 

  • Traer K (1980)The consumption of Posidonia oceanica Delile by echinoids at the isle of Ischia. In: Jangoux M (ed) Europ. Colloq. Echinoderms “Echinoderms: present and past. pp 241-242

  • Zhang WJ, Hou HM, Zhang GL, Li QY, Du CM (2011) Study on diversity of intestine cultivable microorganisms from Apostichopus japonicus. Sci Technol Food Ind 32:149–155. doi:10.13386/j.issn1002-0306.2011.09.001

    Google Scholar 

  • Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol (AEM) 73:5261–5267. doi:10.1128/AEM.00062-07

    Article  CAS  Google Scholar 

  • Wang S, Li C, Sun S, Ning X, Zhang W (2009) Spring and autumn reproduction of Calanus sinicus in the Yellow Sea. Mar Ecol Prog Ser 379:123–133. doi:10.3354/meps07902

    Article  Google Scholar 

  • Ward-Rainey N, Rainey FA, Stackebrandt E (1996) A study of the bacterial flora associated with Holothuria atra. J Exp Mar Biol Ecol 203:11–26. doi:10.1016/0022-0981(96)02566-X

    Article  Google Scholar 

  • Whittaker RH (1972) Evolution and measurement of species diversity. Taxon 21:213–251. doi:10.2307/1218190

    Google Scholar 

  • Xia S, Yang H, Li Y, Liu S, Zhou Y, Zhang L (2012) Effects of different seaweed diets on growth, digestibility, and ammonia-nitrogen production of the sea cucumber Apostichopus japonicus(Selenka). Aquaculture 338:304–308. doi:10.1016/j.aquaculture.2012.01.010

    Article  Google Scholar 

  • Xu Q, Gao F, Xu Q, Yang H (2014) Analysis of fatty acid composition of sea cucumber Apostichopus japonicus using multivariate statistics. Chin J Oceanol Limnol 32:1314–1319. doi:10.1007/s00343-015-3328-2

    Article  CAS  Google Scholar 

  • Yingst JY (1976) The utilization of organic matter in shallow marine sediments by an epibenthic deposit-feeding holothurian. J Exp Mar Biol Ecol 23:55–69. doi:10.1016/0022-0981(76)90085-X

    Article  CAS  Google Scholar 

  • Yuan X, Yang H, Zhou Y, Mao Y, Zhang T, Liu Y (2006) The influence of diets containing dried bivalve feces and/or powdered algae on growth and energy distribution in sea cucumber Apostichopus japonicus (Selenka) (Echinodermata: Holothuroidea). Aquaculture 256:457–467. doi:10.1016/j.aquaculture.2006.01.029

    Article  Google Scholar 

  • Zhang B, Sun D, Wu Y (1995) Preliminary analysis on the feeding habit of Apostichopus japonicus in the rocky coast waters off Lingshan Island. Mar Sci 3:11–13

    Google Scholar 

Download references

Acknowledgments

The experimental component of this project was funded by National Key Technology Research and Development Program (No. 2011BAD13B02), Non-Profit Marine Sector (Nos. 201205023, 201305043). We are grateful to Hong Zhang from Nevogene Biotechnology Co. Ltd. for her technical support in raw data processing. Thanks to Steve O’Shea from Edanz Group China for language editing advice for the manuscript. Special thanks to the crew of the Qiansan Islets Aquatic Products Development Co. Ltd. for assistance in sample collection. Experiments were conceived and designed by HZ, QX and HY and performed by HZ, with data analyzed by HZ; HZ, YZ and QX contributed reagents, materials, and/or analysis tools; and the manuscript was written by HZ.

Author information

Authors and Affiliations

  1. Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People’s Republic of China

    Hongye Zhang, Qiang Xu, Ye Zhao & Hongsheng Yang

  2. National Marine Data and Information Service, Tianjin, 300171, People’s Republic of China

    Hongye Zhang

  3. Ocean School, Yantai University, Yantai, 264005, People’s Republic of China

    Ye Zhao

Authors
  1. Hongye Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Qiang Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ye Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Hongsheng Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Qiang Xu or Hongsheng Yang.

Additional information

Responsible Editor: S. Uthicke.

Reviewed by undisclosed experts.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Zhang, H., Xu, Q., Zhao, Y. et al. Sea cucumber (Apostichopus japonicus) eukaryotic food source composition determined by 18s rDNA barcoding. Mar Biol 163, 153 (2016). https://doi.org/10.1007/s00227-016-2931-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00227-016-2931-x

Keywords

Search

Navigation