Trapped DNA fragments in marine sponge specimens unveil North Atlantic deep-sea fish diversity

Neave, Erika F.; Cai, Wang; Arias, Maria Belén; Harper, Lynsey R.; Riesgo, Ana; Mariani, Stefano

doi:10.1098/rspb.2023.0771

Cited by 4 publications

(1 citation statement)

References 54 publications

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“…Further exacerbating the time commitment for water filtration is the increased water volume required to be processed in marine eDNA studies compared to freshwater ecosystems (Bowers et al, 2021). To circumvent the need for water filtration, multiple alternative methods have been successfully trialed, including passive filtration (Bessey et al, 2021;Kirtane et al, 2020;Verdier et al, 2021), autonomous sampling (Hansen et al, 2020;Yamahara et al, 2019), and direct sampling of filter-feeding organisms such as marine sponges (Brodnicke et al, 2023;Cai et al, 2022;Harper et al, 2023;Jeunen, Cane, et al, 2023;Mariani et al, 2019;Neave et al, 2023;Turon et al, 2020).…”

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confidence: 99%

Unveiling the hidden diversity of marine eukaryotes in the Ross Sea: A comparative analysis of seawater and sponge eDNA surveys

Jeunen,

Lamare,

Cummings

et al. 2023

Environmental DNA

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The Ross Sea, Antarctica, while largely pristine, is experiencing increased anthropogenic pressures, necessitating enhanced biomonitoring efforts for conservation purposes. Environmental DNA (eDNA) extracted from marine sponges provides a promising approach for biodiversity monitoring in remote areas by circumventing the need for time‐consuming water filtration. Investigations into the efficacy of eDNA signal detection across the tree of life from marine sponges have yet to be fully explored. Here, we conducted a seawater and sponge eDNA metabarcoding survey at seven coastal locations in the Ross Sea to assess spatial eukaryote biodiversity patterns and investigate eDNA signal differences between both substrates. In total, we detected 1450 operational taxonomic units (OTUs) across 30 phyla. Significant differences in water and sponge eDNA signal richness and composition were observed, with a partial overlap in OTU detection between both substrates and, thereby, underscoring the crucial role of substrate selection in eDNA metabarcoding surveys. Furthermore, alpha and beta diversity analyses revealed distinct eDNA signals among sampling locations, which were corroborated by known species distributions. However, only 135 OTUs (9%) could be successfully assigned to species level, and 574 OTUs (40%) were unable to be taxonomically classified, due to limitations in the reference database. Our results provide evidence for the potential of eDNA monitoring in remote areas, demonstrate the need to consider more sophisticated sampling strategies whereby multiple eDNA substrates are incorporated, and highlight the importance of complete reference databases for robust taxonomy assignment of eDNA signals.

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Section: Introductionmentioning

confidence: 99%

Unveiling the hidden diversity of marine eukaryotes in the Ross Sea: A comparative analysis of seawater and sponge eDNA surveys

Jeunen,

Lamare,

Cummings

et al. 2023

Environmental DNA

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North Atlantic deep-sea benthic biodiversity unveiled through sponge natural sampler DNA

Gallego,

Arias,

Corral-Lou

et al. 2024

Commun Biol

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The deep-sea remains the biggest challenge to biodiversity exploration, and anthropogenic disturbances extend well into this realm, calling for urgent management strategies. One of the most diverse, productive, and vulnerable ecosystems in the deep sea are sponge grounds. Currently, environmental DNA (eDNA) metabarcoding is revolutionising the field of biodiversity monitoring, yet complex deep-sea benthic ecosystems remain challenging to assess even with these novel technologies. Here, we evaluate the effectiveness of whole-community metabarcoding to characterise metazoan diversity in sponge grounds across the North Atlantic by leveraging the natural eDNA sampling properties of deep-sea sponges themselves. We sampled 97 sponge tissues from four species across four North-Atlantic biogeographic regions in the deep sea and screened them using the universal COI barcode region. We recovered unprecedented levels of taxonomic diversity per unit effort, especially across the phyla Chordata, Cnidaria, Echinodermata and Porifera, with at least 406 metazoan species found in our study area. These assemblages identify strong spatial patterns in relation to both latitude and depth, and detect emblematic species currently employed as indicators for these vulnerable habitats. The remarkable performance of this approach in different species of sponges, in different biogeographic regions and across the whole animal kingdom, illustrates the vast potential of natural samplers as high-resolution biomonitoring solutions for highly diverse and vulnerable deep-sea ecosystems.

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Utilizing environmental DNA and imaging to study the deep-sea fish community of Takuyo-Daigo Seamount

Iguchi,

Nishijima,

Ikeuchi

et al. 2024

npj biodivers

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The increase in interest of mining at seamounts means there is a critical need to establish baseline inventories through environmental survey, with the aim of promoting the conservation and stewardship of these remote habitats. To efficiently evaluate fish biodiversity around a seamount, we compared environmental DNA (eDNA) methods using seawater and sponge samples against methods using imagery obtained with a remotely operated vehicle (ROV) and a free-fall deep-sea camera lander called the Edokko Mark I on the Takuyo-Daigo Seamount (153.0°E, 23.5°N) in the northwestern Pacific Ocean. We detected a total of 18 fish families by these methods. The fish fauna detected on the seamount included many families commonly found in deep-sea areas and were similar to the fish fauna of other seamounts located at similar latitudes in the northwestern Pacific. Significant differences in the patterns of detection of fish families between the eDNA and imaging methods is attributed to the differing powers of detection of some fish groups between methods (related to primer compatibility and fish size). For deep-sea fish, the difference in fish composition at the family level between seawater and sponge eDNA methods was not significant, but the difference between Edokko Mark I and ROV methods was significant; the latter difference is likely due to whether or not bait is used to attract fish. Although the eDNA workflow implemented here requires improvements, the use of eDNA and imaging methods in combination provided better insight into the biodiversity of deep-sea fishes in the deep-sea around a seamount, where our knowledge of the fish fauna has been extremely limited. Our recovery of eDNA from seawater and sponge samples around the seamount demonstrates the potential of these methods for facilitating environmental baseline surveys and impact assessments of mining activities to obtain results not previously possible with the use of visual methods only.

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Trapped DNA fragments in marine sponge specimens unveil North Atlantic deep-sea fish diversity

Cited by 4 publications

References 54 publications

Unveiling the hidden diversity of marine eukaryotes in the Ross Sea: A comparative analysis of seawater and sponge eDNA surveys

Unveiling the hidden diversity of marine eukaryotes in the Ross Sea: A comparative analysis of seawater and sponge eDNA surveys

North Atlantic deep-sea benthic biodiversity unveiled through sponge natural sampler DNA

Utilizing environmental DNA and imaging to study the deep-sea fish community of Takuyo-Daigo Seamount

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