Exploring a legendary giant squid: an environmental DNA approach

Wada, Takeshi; Doi, Hideyuki; Togaki, Daisuke; Kaida, Ryotaro; Nagano, Mariko; Katano, Izumi; Suzuki, Masami; Ohtani, Tetsuya; Mitsuhashi, Hiromune

doi:10.1007/s00227-020-03773-z

Cited by 11 publications

(9 citation statements)

References 24 publications

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“…eDNA proved to be an efficient and potent technique to establish diversity and distribution of cephalopods in the deep sea, in particular using a vertically stratified approach. We detected 21 of the 83 cephalopod species that have been reported in waters around the Azores to date, plus an additional two new species for the region ( Chiroteuthis mega and Cycloteuthis sirventi ) ( 38 ), as well as giant squid ( Architeuthis ; second eDNA detection worldwide ( 39 )). Moreover, cephalopod distribution patterns were biologically meaningful.…”

Section: Discussionmentioning

confidence: 99%

Deep-sea predator niche segregation revealed by combined cetacean biologging and eDNA analysis of cephalopod prey

et al. 2021

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Fundamental insight on predator-prey dynamics in the deep sea is hampered by a lack of combined data on hunting behavior and prey spectra. Deep-sea niche segregation may evolve when predators target specific prey communities, but this hypothesis remains untested. We combined environmental DNA (eDNA) metabarcoding with biologging to assess cephalopod community composition in the deep-sea foraging habitat of two top predator cetaceans. Risso’s dolphin and Cuvier’s beaked whale selectively targeted distinct epi/meso- and bathypelagic foraging zones, holding eDNA of 39 cephalopod taxa, including 22 known prey. Contrary to expectation, extensive taxonomic overlap in prey spectra between foraging zones indicated that predator niche segregation was not driven by prey community composition alone. Instead, intraspecific prey spectrum differences may drive differentiation for hunting fewer, more calorific, mature cephalopods in deeper waters. The novel combination of methods presented here holds great promise to disclose elusive deep-sea predator-prey systems, aiding in their protection.

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Section: Discussionmentioning

confidence: 99%

Deep-sea predator niche segregation revealed by combined cetacean biologging and eDNA analysis of cephalopod prey

et al. 2021

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“…Even though primer sets for specific cephalopod taxa allow identification of specific elusive species [ 25 ] and might complement a universal cephalopod primer for problematic taxa, it would be difficult to do cephalopod biodiversity assays using only species-specific primers. For example, regional reported species diversity is 32 in the Arctic [ 78 ], 54 in the Antarctic [ 78 ], 68 at the Southwest Indian Ocean Ridge [ 79 ], 70 around the Kermadec Islands [ 80 ], 77 near Bear Seamount [ 81 ], up to 85 around the Canary Islands [ 82 ].…”

Section: Discussionmentioning

confidence: 99%

“…In recent years, there has been a sharp increase in the number of studies that employed eDNA analysis in the deep sea [ 22 , 34 , 35 ], but none to specifically investigate cephalopod diversity. Recently, a species-specific primer has been developed and used to detect the giant squid, Architeuthis dux , in the photic zone of the Sea of Japan [ 25 ].…”

Section: Introductionmentioning

confidence: 99%

“…Sampling eDNA is relatively easy in the marine environment (from water or sediment) and developments in the field of next-generation sequencing have greatly reduced sequencing costs and dramatically increased sequencing output. Therefore, eDNA analysis represents a non-invasive and cost-effective method for biodiversity assessments, especially for rare or elusive species and in remote areas [14,[22][23][24][25].…”

Section: Introductionmentioning

confidence: 99%

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A novel metabarcoding primer pair for environmental DNA analysis of Cephalopoda (Mollusca) targeting the nuclear 18S rRNA region

et al. 2021

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Cephalopods are pivotal components of marine food webs, but biodiversity studies are hampered by challenges to sample these agile marine molluscs. Metabarcoding of environmental DNA (eDNA) is a potentially powerful technique to study oceanic cephalopod biodiversity and distribution but has not been applied thus far. We present a novel universal primer pair for metabarcoding cephalopods from eDNA, Ceph18S (Forward: 5′-CGC GGC GCT ACA TAT TAG AC-3′, Reverse: 5′-GCA CTT AAC CGA CCG TCG AC-3′). The primer pair targets the hypervariable region V2 of the nuclear 18S rRNA gene and amplifies a relatively short target sequence of approximately 200 bp in order to allow the amplification of degraded DNA. In silico tests on a reference database and empirical tests on DNA extracts from cephalopod tissue estimate that 44–66% of cephalopod species, corresponding to about 310–460 species, can be amplified and identified with this primer pair. A multi-marker approach with the novel Ceph18S and two previously published cephalopod mitochondrial 16S rRNA primer sets targeting the same region (Jarman et al . 2006 Mol. Ecol. Notes. 6 , 268–271; Peters et al . 2015 Mar. Ecol. 36 , 1428–1439) is estimated to amplify and identify 89% of all cephalopod species, of which an estimated 19% can only be identified by Ceph18S . All sequences obtained with Ceph18S were submitted to GenBank, resulting in new 18S rRNA sequences for 13 cephalopod taxa.

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“…For cephalopods, eDNA analysis has thus far been used in two field studies. The first study designed a species-specific eDNA primer and was able to detect the giant squid Architeuthis dux in Japanese waters (Wada et al, 2020). The second study used universal cephalopod primers to reconstruct cephalopod community composition in the foraging zones of deep hunting predators off the Azores, detecting 39 cephalopod taxa from 17 families from depths between 50 and 1600 m (Visser et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

An Integrative Assessment Combining Deep-Sea Net Sampling, in situ Observations and Environmental DNA Analysis Identifies Cabo Verde as a Cephalopod Biodiversity Hotspot in the Atlantic Ocean

et al. 2021

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The deep sea is among the largest, most biologically diverse, yet least-explored ecosystems on Earth. Baseline information on deep-sea biodiversity is crucial for understanding ecosystem functioning and for detecting community changes. Here, we established a baseline of cephalopod community composition and distribution off Cabo Verde, an archipelago in the eastern tropical Atlantic. This baseline served to test the hypothesis that Cabo Verde is biogeographically separated from other Macaronesian archipelagos and allowed the identification of cephalopod species which may play a role in the Macaronesian carbon cycle and oceanic food web. To investigate cephalopod community composition, this study used 746 individual cephalopods obtained by nets (0–1000 m) and 52 cephalopod encounters during video surveys with either towed camera (0–2500 m) or manned submersible (0–375 m). Additionally, environmental DNA (eDNA) metabarcoding on 105 seawater samples (50–2500 m), using an 18S rRNA universal cephalopod primer pair, and a species-specific primer pair for Taningia danae resulted in the detection of 32 cephalopod taxa. When combined, the three methods detected a total of 87 taxa, including 47 distinct species. Each method contributed between 7 and 54% of taxa that were not detected by the other methods, indicating that multiple methodological approaches are needed for optimal deep-sea cephalopod biodiversity assessments. This study documents the occurrences of six species and three genera for the first time in waters surrounding Cabo Verde. Video surveys and eDNA analysis detected Taningia danae recurrently (100–2500 m). eDNA metabarcoding proved to be a powerful tool for cephalopod biodiversity monitoring and complementary to traditional sampling methods. When also including literature records, Cabo Verde hosts at least 102 cephalopod taxa including 30 families and 64 benthic and pelagic species. The total number and species composition of Cabo Verde cephalopods is similar to the Canary Islands and Azores, two known cephalopod biodiversity hotspots, but the Cabo Verde octopus fauna seems to differ. Due to a range of life history characteristics, we hypothesize that the squids Taningia danae (Octopoteuthidae) and Sthenoteuthis pteropus (Ommastrephidae) are important in the carbon cycle of Macaronesia. As a cephalopod biodiversity hotspot Cabo Verde could function as a model region to investigate cephalopod biology and ecology in a rapidly changing Atlantic Ocean.

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Exploring a legendary giant squid: an environmental DNA approach

Cited by 11 publications

References 24 publications

Deep-sea predator niche segregation revealed by combined cetacean biologging and eDNA analysis of cephalopod prey

Deep-sea predator niche segregation revealed by combined cetacean biologging and eDNA analysis of cephalopod prey

A novel metabarcoding primer pair for environmental DNA analysis of Cephalopoda (Mollusca) targeting the nuclear 18S rRNA region

An Integrative Assessment Combining Deep-Sea Net Sampling, in situ Observations and Environmental DNA Analysis Identifies Cabo Verde as a Cephalopod Biodiversity Hotspot in the Atlantic Ocean

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