| 1. |
- Dahlgren, Thomas G., 1963, et al.
(author)
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The Use of eDNA to Monitor Pelagic Fish in Offshore Floating Wind Farms
- 2023
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In: Oceanography. - : The Oceanography Society. - 1042-8275. ; 36:Supp 1, s. 94-95
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Journal article (other academic/artistic)abstract
- After nearly 30 years of experience with offshore wind energy (OWE), the industry is moving past the initial learning phase and into large-scale development. One of the strongest motivations for OWE is that projects are large enough to replace fossil-fueled electricity production that we know is a primary contributor to the ongoing climate crisis. Environmental concerns are therefore also at the core of OWE development, and environmental research and impact monitoring have been central parts of the industry since its inception. A large volume of science-based knowledge is available about the environmental impacts of OWE on marine ecosystems, from effects on the seafloor sediment infauna beneath the turbines to those on marine mammals that roam the developed seas.
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| 2. |
- Hestetun Thomassen, Jon, et al.
(author)
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Grab what you can—an evaluation of spatial replication to decrease heterogeneity in sediment eDNA metabarcoding
- 2021
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In: PeerJ. - : PeerJ. - 2376-5992 .- 2167-8359. ; 9, s. 1-21
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Journal article (peer-reviewed)abstract
- Environmental DNA methods such as metabarcoding have been suggested as possible alternatives or complements to the current practice of morphology-based diversity assessment for characterizing benthic communities in marine sediment. However, the source volume used in sediment eDNA studies is several magnitudes lower than that used in morphological identification. Here, we used data from a North Sea benthic sampling station to investigate to what extent metabarcoding data is affected by sampling bias and spatial heterogeneity. Using three grab parallels, we sampled five separate sediment samples from each grab. We then made five DNA extraction replicates from each sediment sample. Each extract was amplified targeting both the 18S SSU rRNA V1–V2 region for total eukaryotic composition, and the cytochrome c oxidase subunit I (COI) gene for metazoans only. In both datasets, extract replicates from the same sediment sample were significantly more similar than different samples from the same grab. Further, samples from different grabs were less similar than those from the same grab for 18S. Interestingly, this was not true for COI metabarcoding, where the differences within the same grab were similar to the differences between grabs. We also investigated how much of the total identified richness could be covered by extract replicates, individual sediment samples and all sediment samples from a single grab, as well as the variability of Shannon diversity and, for COI, macrofaunal biotic indices indicating environmental status. These results were largely consistent with the beta diversity findings, and show that total eukaryotic diversity can be well represented using 18S metabarcoding with a manageable number of biological replicates. Based on these results, we strongly recommend the combination of different parts of the surface of single grabs for eDNA extraction as well as several grab replicates, or alternatively box cores or similar. This will dilute the effects of dominating species and increase the coverage of alpha diversity. COI-based metabarcoding consistency was found to be lower compared to 18S, but COI macrofauna-based indices were more consistent than direct COI alpha diversity measures.
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| 3. |
- Lanzén, Anders, et al.
(author)
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Benthic eDNA metabarcoding provides accurate assessments of impact from oil extraction, and ecological insights
- 2021
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In: Ecological Indicators. - : Elsevier BV. - 1470-160X. ; 130
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Journal article (peer-reviewed)abstract
- Apart from its contribution to climate change, offshore oil and gas extraction is also a potential threat to the diversity and function of marine ecosystems. Routine monitoring of the environmental status of affected areas is therefore critical for effective management. While current morphology-based monitoring is relatively time consuming, costly and prone to identification bias, environmental DNA metabarcoding offers an attractive alternative for assessing the impacts of oil drilling, extraction or spills. However, to be ready for routine monitoring, its performance needs to be demonstrated through agreement with assessments based on physicochemical measurements and current bioindicators. To this end, we applied metabarcoding to sequence the metazoan (COI) and total eukaryotic (18S) benthic components. We targeted a range of sites, with a gradient of low to high level of impact, located near active production installations and reference sites, in the North and Barents Seas. Alpha diversity and community structure of both datasets correlated strongly with a physicochemical pressure index (PI) based on total hydrocarbons (THC), PAH16, Ba and Cu. Calculations of the macroinvertebrate-based Norwegian Sensitivity Index (NSI) based on COI metabarcoding data agreed well with corresponding morpho-taxonomy values and with the PI. Further, we identified a set of bioindicator taxa from both metabarcoding datasets, to develop novel biotic indices and demonstrate their predictive performance using cross-validation. Finally, we compared co-occurrence networks from impacted vs. non-impacted sites, to improve the understanding of the ecological consequences of impacts. Our study demonstrates that metabarcoding can act as a meaningful and relatively accurate complement to the current morpho-taxonomic approach.
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| 4. |
- Taboada, Sergi, et al.
(author)
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Insights into the symbiotic relationship between scale worms and carnivorous sponges (Cladorhizidae, Chondrocladia)
- 2020
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In: Deep Sea Research Part I. - : PERGAMON-ELSEVIER SCIENCE LTD. - 0967-0637 .- 1879-0119. ; 156
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Journal article (peer-reviewed)abstract
- Symbiotic associations between polynoid scale worms and other marine invertebrates are common, but sometimes poorly understood. Compounding this problem is the fact that polynoid systematics is largely unresolved. Here, we transfer the species originally described as Nemidia antillicola chondrocladiae Fauvel (1943), and currently synonymized with Neopolynoe acanellae (Verrill, 1881), to the species Neopolynoe chondrocladiae n. comb. This species is characterized by living in association with the carnivorous sponges Chondrocladia robertballnrdi Cristobo, Rios, Pomponi & Xavier, 2015 and Chondrocladia virgata Thompson, 1873. The existence of specialized chaetae in N. chondrocladiae n. comb. and the occurrence of open galleries in the sponge, derived from a gradual overgrowth of the sponge to accommodate the worm, suggest an obligate symbiotic relationship between worm and sponge. The presence of a gravid female with relatively small oocytes (maximum diameter 56.94 +/- 14.89 mu m) suggests that N. chondrocladiae n. comb. is a gonochoristic broadcaster with a planktotrophic larva, a means of reproduction that would maximize the chances of this species finding new suitable hosts to colonize. We also provide a phylogenetic placement, using four genetic markers (18S, 28S, 16S and COI), for N. chondrocladiae n. comb. and N. acanellae, which confirms they are two different species. In addition, we also report here the occurrence of another deep-water polynoid species in association with the carnivorous sponge Chondrocladia vertical= Topsent, 1920, from the Gulf of Mexico, and place it in a phylogeny.
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| 5. |
- Thomassen Hestetun, Jon, et al.
(author)
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Significant taxon sampling gaps in DNA databases limit the operational use of marine macrofauna metabarcoding
- 2020
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In: Marine Biodiversity. - : Springer Science and Business Media LLC. - 1867-1616 .- 1867-1624. ; 50
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Journal article (peer-reviewed)abstract
- Significant effort is spent on monitoring of benthic ecosystems through government funding or indirectly as a cost of business, and metabarcoding of environmental DNA samples has been suggested as a possible complement or alternative to current morphological methods to assess biodiversity. In metabarcoding, a public sequence database is typically used to match barcodes to species identity, but these databases are naturally incomplete. The North Sea oil and gas industry conducts large-scale environmental monitoring programs in one of the most heavily sampled marine areas worldwide and could therefore be consid- ered a “best-case scenario” for macrofaunal metabarcoding. As a test case, we investigated the database coverage of two common metabarcoding markers, mitochondrial COI and the ribosomal rRNA 18S gene, for a complete list of 1802 macrofauna taxa reported from the North Sea monitoring region IV. For COI, species level barcode coverage was 50.4% in GenBank and 42.4% for public sequences in BOLD. For 18S, species level coverage was 36.4% in GenBank and 27.1% in SILVA. To see whether rare species were underrepresented, we investigated the most commonly reported species as a separate dataset but found only minor coverage increases. We conclude that compared to global figures, barcode coverage is high for this area, but that a significant effort remains to fill barcode databases to levels that would make metabarcoding operational as a taxonomic tool, including for the most common macrofaunal taxa.
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