Abstract
The giant squid, Architeuthis dux, has been reported for centuries, but its distribution and ecology have remained famously mysterious. We investigated the A. dux distribution in the Sea of Japan using the environmental DNA (eDNA) method, which has recently been considered as a useful technique for evaluating the distributions of rare species. To develop the eDNA method to detect A. dux, we first created a species-specific polymerase chain reaction (PCR) primer–probe and tried to detect the eDNA in the western region of the Sea of Japan where A. dux has recently been observed. We successfully collected and amplified the A. dux eDNA in our study area using field water sampling and real-time PCR measurements. A. dux eDNA was detected in winter but not in summer, reflecting the historical record of A. dux observations in the region. The use of eDNA techniques could be a potential method for monitoring "invisible" and rare organisms, even in open ocean habitats.
Code availability
The R code for this study is available from the corresponding author upon reasonable request.
References
Ardura A, Zaiko A, Martinez JL et al (2015) eDNA and specific primers for early detection of invasive species—a case study on the bivalve Rangia cuneata, currently spreading in Europe. Mar Environ Res 112:48–55. https://doi.org/10.1016/j.marenvres.2015.09.013
Bustin SA, Benes V, Garson JA et al (2009) The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 55:611–622. https://doi.org/10.1373/clinchem.2008.112797
Coro G, Magliozzi C, Ellenbroek A, Pagano P (2015) Improving data quality to build a robust distribution model for Architeuthis dux. Ecol Model 30:29–39. https://doi.org/10.1016/j.ecolmodel.2015.03.011
Doi H, Inui R, Akamatsu Y et al (2017) Environmental DNA analysis for estimating the abundance and biomass of stream fish. Freshw Biol 6:30–39. https://doi.org/10.1111/fwb.12846
Doi H, Fukaya K, Oka S et al (2019) Evaluation of detection probabilities at the water-filtering and initial PCR steps in environmental DNA metabarcoding using a multispecies site occupancy model. Sci Rep 9:1–8. https://doi.org/10.1038/s41598-019-40233-1
Ficetola GF et al (2015) Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data. Mol Ecol Res 15:543–556. https://doi.org/10.1111/1755-0998.12338
Forsström T, Vasemägi A (2016) Can environmental DNA (eDNA) be used for detection and monitoring of introduced crab species in the Baltic Sea? Mar Poll Bull 109:350–355. https://doi.org/10.1016/j.marpolbul.2016.05.054
Guerra Á, González ÁF, Pascual S, Dawe EG (2011) The giant squid Architeuthis: an emblematic invertebrate that can represent concern for the conservation of marine biodiversity. Biol Conserv 144:1989–1997. https://doi.org/10.1016/j.biocon.2011.04.021
Jeunen GJ, Knapp M, Spencer HG et al (2019) Environmental DNA (eDNA) metabarcoding reveals strong discrimination among diverse marine habitats connected by water movement. Mol Ecol Res 19:426–438. https://doi.org/10.1111/1755-0998.12982
Katano I, Harada K, Doi H, Souma R, Minamoto T (2017) Environmental DNA method for estimating salamander distribution in headwater streams, and a comparison of water sampling methods. PLoS ONE 12:e0176541. https://doi.org/10.1371/journal.pone.0176541
Kubodera T, Mori K (2005) First-ever observations of a live giant squid in the wild. Proc R Soc B 272:2583–2586. https://doi.org/10.1098/rspb.2005.3158
Kubodera T, Wada T, Higuchi M, Yatabe A (2018) Extraordinary numbers of giant squid, Architeuthis dux, encountered in Japanese coastal waters of the Sea of Japan from January 2014 to March 2015. Mar Biodivers 48:1391–1400. https://doi.org/10.1007/s12526-016-0618-7
Mauvisseau Q et al (2017) On the way for detecting and quantifying elusive species in the sea: the Octopus vulgaris case study. Fish Res 191:41–48. https://doi.org/10.1016/j.fishres.2017.02.023
Minamoto T et al (2020) An illustrated manual for environmental DNA research: water sampling guidelines and experimental protocols. Environ DNA. https://doi.org/10.1002/edn3.121
Okiyama M (1993) Kinds, abundance and distribution of the oceanic squids in the Sea of Japan. In: Okutani T, O’Dor RK, Kubodera T (eds) Recent advances in cephalopod fisheries biology. Tokai University Press, Tokyo, pp 404–451
R Core Team (2019) R: a language and environment for statistical computing
Rees HC, Maddison BC, Middleditch DJ, Patmore JR, Gough KC (2014) Review: the detection of aquatic animal species using environmental DNA—a review of eDNA as a survey tool in ecology. J Appl Ecol 51:1450–1459. https://doi.org/10.1111/1365-2664.12306
Takahara T, Minamoto T, Yamanaka H, Doi H, Kawabata Z (2012) Estimation of fish biomass using environmental DNA. PLoS ONE 7:e35868. https://doi.org/10.1371/journal.pone.0035868
Takahara T, Minamoto T, Doi H (2013) Using environmental DNA to estimate the distribution of an invasive fish species in ponds. PLoS ONE. https://doi.org/10.1371/journal.pone.0056584
Thomsen PF, Kielgast J, Iversen LL, Wiuf C, Rasmussen M, Gilbert MTP, Orlando L, Willerslev E (2012a) Monitoring endangered freshwater biodiversity using environmental DNA. Mol Ecol 21:2565–2573. https://doi.org/10.1002/edn3.21
Thomsen PF et al (2012b) Detection of a diverse marine fish fauna using environmental DNA from seawater samples. PLoS ONE 7:e41732. https://doi.org/10.1371/journal.pone.0041732
Tsuji S, Takahara T, Doi H, Shibata N, Yamanaka H (2019) The detection of aquatic macroorganisms using environmental DNA analysis—a review of methods for collection, extraction, and detection. Environ DNA 1:99–108. https://doi.org/10.1002/edn3.21
Uchii K, Doi H, Minamoto T (2016) A novel environmental DNA approach to quantify the cryptic invasion of non-native genotypes. Mol Ecol Res 16:415–422. https://doi.org/10.1111/1755-0998.12460
Wada T, Kubodera T, Yamada M, Terakado H (2015) First records of small-sized young giant squid Architeuthis dux from the coasts of Kyushu Island and the south-western Sea of Japan. Mar Biodivers Rec 8:e153. https://doi.org/10.1017/S175526721500127X
Weltz K, Lyle JM, Ovenden J et al (2017) Application of environmental DNA to detect an endangered marine skate species in the wild. PLoS ONE 12:e0178124. https://doi.org/10.1371/journal.pone.0178124
Winkelmann I, Campos PF, Strugnell J et al (2013) Mitochondrial genome diversity and population structure of the giant squid Architeuthis: genetics sheds new light on one of the most enigmatic marine species. Proc R Soc B 280:20130273. https://doi.org/10.1098/rspb.2013.0273
Yamamoto S, Masuda R, Sato Y et al (2017) Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea. Sci Rep 7:40368. https://doi.org/10.1038/srep40368
Acknowledgements
We thank Toshifumi Minamoto and Takehisa Yamakita for valuable comments on this study and early manuscript. We thank the captains and crew members of the fisheries research vessel, Tajima, for their cooperation in sampling seawater.
Funding
This study was supported by JST-CREST (JPMJCR13A2) and in part by JSPS KAKENHI (grant numbers 15K00596 and 18K11678) to IK.
Author information
Authors and Affiliations
Contributions
Conception and design of the experiments: TW, HD, KI, HM. Performance of fieldwork: TW, DT, MS, TO. Performance of laboratory work: HD, RK, MN. Analysis of data: HD, RK. Manuscript preparation: HD, DT, RK, MN, IK, HM, MS, TO.
Corresponding author
Ethics declarations
Conflict of interest
We declare no conflicts of interest associated with this manuscript.
Ethics approval
All applicable international, national, and/or institutional guidelines for water sampling were followed.
Additional information
Responsible Editor: A. Zhan.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Reviewed by undisclosed experts.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Wada, T., Doi, H., Togaki, D. et al. Exploring a legendary giant squid: an environmental DNA approach. Mar Biol 167, 160 (2020). https://doi.org/10.1007/s00227-020-03773-z
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s00227-020-03773-z