Dataset Information

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

ABSTRACT: Sponges pump water to filter feed and for diffusive oxygen uptake. In doing so, trace DNA fragments from a multitude of organisms living around them are trapped in their tissues. Here we show that the environmental DNA retrieved from archived marine sponge specimens can reconstruct the fish communities at the place of sampling and discriminate North Atlantic assemblages according to biogeographic region (from Western Greenland to Svalbard), depth habitat (80-1600 m), and even the level of protection in place. Given the cost associated with ocean biodiversity surveys, we argue that targeted and opportunistic sponge samples - as well as the specimens already stored in museums and other research collections - represent an invaluable trove of biodiversity information that can significantly extend the reach of ocean monitoring.

SUBMITTER: Neave EF

PROVIDER: S-EPMC10465980 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature

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

Neave Erika F EF Cai Wang W Arias Maria Belén MB Harper Lynsey R LR Riesgo Ana A Mariani Stefano S

Proceedings. Biological sciences 20230830 2005

Sponges pump water to filter feed and for diffusive oxygen uptake. In doing so, trace DNA fragments from a multitude of organisms living around them are trapped in their tissues. Here we show that the environmental DNA retrieved from archived marine sponge specimens can reconstruct the fish communities at the place of sampling and discriminate North Atlantic assemblages according to biogeographic region (from Western Greenland to Svalbard), depth habitat (80-1600 m), and even the level of protec ...[more]

PMID: 37644836

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Project description:The present study was undertaken to address the recent spate of pasteurellosis outbreaks among sea-farmed Atlantic salmon (Salmo salar) in Norway and Scotland, coinciding with sporadic disease episodes in lumpfish (Cyclopterus lumpus) used for delousing purposes in salmon farms. Genome assemblies from 86 bacterial isolates cultured from diseased salmon or lumpfish confirmed them all as bona fide members of the Pasteurellaceae family, with phylogenetic reconstruction dividing them into two distinct branches sharing <88% average nucleotide identity. These branches therefore constitute two separate species, namely Pasteurella skyensis and the as-yet invalidly named "Pasteurella atlantica". Both species further stratify into multiple discrete genomovars (gv.) and/or lineages, each being nearly or fully exclusive to a particular host, geographic region, and/or time period. Pasteurellosis in lumpfish is, irrespective of spatiotemporal origin, linked almost exclusively to the highly conserved "P. atlantica gv. cyclopteri" (Pac). In contrast, pasteurellosis in Norwegian sea-farmed salmon, dominated since the late-1980s by "P. atlantica gv. salmonicida" (Pas), first saw three specific lineages (Pas-1, -2, and -3) causing separate, geographically restricted, and short-lived outbreaks, before a fourth (Pas-4) emerged recently and became more widely disseminated. A similar situation involving P. skyensis (Ps) has apparently been unfolding in Scottish salmon farming since the mid-1990s, where two historic (Ps-1 and -2) and one contemporary (Ps-3) lineages have been recorded. While the epidemiology underlying all these outbreaks/epizootics remains unclear, repeated detection of 16S rRNA gene amplicons very closely related to P. skyensis and "P. atlantica" from at least five cetacean species worldwide raises the question as to whether marine mammals may play a part, possibly as reservoirs. In fact, the close relationship between the studied isolates and Phocoenobacter uteri associated with harbor porpoise (Phocoena phocoena), and their relatively distant relationship with other members of the genus Pasteurella, suggests that both P. skyensis and "P. atlantica" should be moved to the genus Phocoenobacter.

Project description:Hard-bottom habitats span a range of natural substrates (e.g., boulders, cobble) and artificial habitats (e.g., the base of wind turbines, oil platforms). These hard-bottom habitats can provide a variety of ecosystem services, ranging from the enhancement of fish biomass and production to providing erosion control. Management decisions regarding the construction or fate of hard-bottom habitats require information on the ecological functions of these habitats, particularly for species targeted in ecosystem-based fisheries management. This study provides a systematic review of the relationships of various hard-bottom habitats to individual commercially harvested species that are managed jointly across the Atlantic by the International Council for the Exploration of the Sea (ICES). We systemically reviewed peer-reviewed publications on hard-bottom habitats including both natural and artificial reefs, after applying various exclusion criteria. Most studies were conducted on near-shore hard-bottom habitats, and habitat importance varied according to fish species and region. We quantified the frequency with which studies demonstrate that natural and artificial hard-bottom habitats function as spawning grounds, settlement and nursery areas, and foraging grounds, as well as provide stepping-stones during migration, or new home ranges. Hard-bottom habitats generally support higher fish densities than surrounding habitat types, although not all fish species benefit from hard-bottom habitats. Of the commercially important species, cod (Gadus morhua) was the most frequently studied species, with enhanced biomass, density, feeding, and spawning on hard-bottom habitats compared to unstructured habitats. Moreover, hard-bottom habitats appear to be of particular importance for spawning of herring (Clupea harengus). Collectively, data indicate that loss of hard-bottom habitats may translate into less-favourable conditions for spawning and biomass of diverse commercial species, including cod and herring.

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Dataset Information

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

Publications

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

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