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opencc-zeroAug 2020View details →

Advances in metabarcoding techniques bring us closer to reliable monitoring of the marine benthos

<p>1. Reliable and accurate biodiversity census methods are essential for monitoring ecosystem health and assessing potential ecological impacts of future development projects. Although metabarcoding is increasingly used to study biodiversity across ecological research, morphology-based identification remains the preferred approach for marine ecological impact assessments. Comparing metabarcoding to morphology-based protocols currently used by ecological surveyors is essential to determine whether this DNA-based approach is suitable for the long-term monitoring of marine ecosystems. 2. We compared metabarcoding and morphology-based approaches for the analysis of invertebrates in low diversity intertidal marine sediment samples. We used a recently developed bioinformatics pipeline and two taxonomic assignment methods to resolve and assign amplicon sequence variants (ASVs) from Illumina amplicon data. We analysed the community composition recovered by both methods and tested the effects, on the levels of diversity detected by the metabarcoding method, of sieving samples prior to DNA extraction. 3. Metabarcoding of the mitochondrial marker cytochrome c oxidase I (COI) gene recovers the presence of more taxonomic groups than the morphological approach. We found that sieving samples results in lower alpha diversity detected and suggests a community composition that differs significantly from that suggested by un-sieved samples in our metabarcoding analysis. We found that whilst metabarcoding and morphological approaches detected similar numbers of species, they are unable to identify the same set of species across samples. 4. Synthesis and Applications We show that metabarcoding using the COI marker provides a more holistic, community-based, analysis of benthic invertebrate diversity than a traditional morphological approach. We also highlight current gaps in reference databases and bioinformatic pipelines for the identification of intertidal benthic invertebrates that need to be addressed before metabarcoding can replace traditional methods. Ultimately, with these limitations taken into consideration, resolving community-wide diversity patterns with metabarcoding could improve the management of non-protected marine habitats in the U.K.14-Jul-2020</p>

opencc-zeroDec 2016View details →

Data from: Trophic mechanisms underlying bentho-demersal community recovery in the north-east Atlantic

1. Bottom trawling is considered one of the greatest and most widespread causes of anthropogenic change in shelf seas, with major and prolonged impacts in areas with a long history of exploitation by fisheries such as the North-Atlantic. Here, signs of recovery following the put into force of regulations are increasingly being reported. 2. We examined the extent to which biological diversity and functionality are restored when fishing pressure is reduced by evaluating changes in species biomass and that of the main functional groups present in the continental platform, as obtained from systematic survey (IBTS) results. Moreover, we examined how this recovery is mirrored in the trophic organization of the affected communities by assessing variations in link density and strength of the main consumer species and investigating whether variations in species richness were paralleled by changes in network properties. Finally, we investigated whether reductions in fishing pressure (fishing mortality) were correlated with the abovementioned variations in community and trophic structure of the bentho-demersal assemblages. 3. Our results corroborate the apparent recovery of North Atlantic fishing stocks and further substantiate the improved welfare of the bentho-demersal assemblages of the Southern Bay of Biscay. Specifically, we found an increase in species richness and in the abundance of most functional groups, especially those more closely related to the benthos with the over time reduction in fishing mortality. Increases in overall species richness were paralleled by an augment in the number of links and a reduction in mean interaction strength connecting the main consumer species with their prey items. This is in accordance with ecological theory and could explain the mechanism by which bentho-demersal assemblages restructure their trophic network towards more stable organizations. 4. 4. Synthesis and applications. Detecting patterns of recovery or change to alternative stable states following stress release is essential to unravel the effects of perturbations and to design effective management strategies. Our study shows that trophic network properties provide a convincing tool to evaluate and perceive recovery patterns. The trends shown in our study appear to be related with the decline in fishing mortality resulting from the enforcement of fisheries regulations in the area. They substantiate the efficiency of these regulations as a guarantee for an ecosystem approach to fisheries management and advocate their enforcement at a wider level as a convincing measure to preserve the sustainability of marine resources and their welfare.17-Jan-2017

FIGURES 21–26 in Cotylegaleatidae, a new family of Ploima (Rotifera: Monogononta), for Cotylegaleata perplexa gen. et sp. nov., from freshwater benthos of Belgium

FIGURES 21–26. Lepadellidae, SEM photographs of trophi. 21, 22. Colurella adriatica Ehrenberg, 1831. 21. Incus, dorsal view; manubria, inner view. 22. Incus, ventral view; unci and manubria, outer view. 23, 24. Lepadella patella (Müller, 1786). 23. Incus dorsal view; unci and manubria, inner view. 24. Incus, ventral view; unci and manubria, outer view. 25, 26. Squatinella bifurca (Hudson, 1886). 25. Incus, dorsal view; manubria, outer view; unci, inner view. 26. Incus, ventral view; unci, outer view; manubria, inner view. Scale bars: 10 µm.

FIGURES 13–14 in Cotylegaleatidae, a new family of Ploima (Rotifera: Monogononta), for Cotylegaleata perplexa gen. et sp. nov., from freshwater benthos of Belgium

FIGURES 13–14. Cotylegaleata perplexa gen. nov., sp. nov., trophi. 13. Ventral view. 14. Dorsal view. Scale bar: 10 µm.

FIGURES 15–20 in Cotylegaleatidae, a new family of Ploima (Rotifera: Monogononta), for Cotylegaleata perplexa gen. et sp. nov., from freshwater benthos of Belgium

FIGURES 15–20. Cotylegaleata perplexa gen. nov., sp. nov., SEM photographs of trophi. 15. Ventral view. 16. Dorsal view. 17. Lateral view. 18. Detail, dorso-frontal view. 19. Same as 15, detail of incus. 20. Detail, ventro-frontal view. Scale bars: 15–19: 10 µm; 20: 1 µm. m: membrane, e: epipharyngeal element.

FIGURES 3–12 in Cotylegaleatidae, a new family of Ploima (Rotifera: Monogononta), for Cotylegaleata perplexa gen. et sp. nov., from freshwater benthos of Belgium

FIGURES 3–12. Cotylegaleata perplexa gen. nov., sp. nov. 3. Adult female, ventral view. 4. Same as 3, lateral view. 5. Cross-section of trunk. 6. Distal foot pseudosegment and toes, ventral view. 7. Same as 6, lateral view. 8. Head, ventral view. 9. Head, dorsal view. 10. Head, lateral view. 11. Juvenile female, dorsal view. 12. Same as 11, lateral view. Scale bars: 3–5, 11, 12: 50 µm; 6–10: 10 µm.

FIGURES 1–2 in Cotylegaleatidae, a new family of Ploima (Rotifera: Monogononta), for Cotylegaleata perplexa gen. et sp. nov., from freshwater benthos of Belgium

FIGURES 1–2. Cotylegaleata perplexa gen. nov., sp. nov. 1. Adult female, lateral view. 2. Same as 1, dorsal view. Scale bar: 50 µm.

publicAug 2020View details →

Advances in metabarcoding techniques bring us closer to reliable monitoring of the marine benthos

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publicJan 2018View details →

Data from: Trophic mechanisms underlying bentho-demersal community recovery in the north-east Atlantic

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Fig. 17. A–B in Aglaopheniid hydroids (Cnidaria: Hydrozoa: Aglaopheniidae) from off New Caledonia collected during KANACONO and KANADEEP expeditions of the French Tropical Deep-Sea Benthos Program

Fig. 17. A–B. Lytocarpia cf. spiralis (Totton, 1930), portion of stem (A) and hydrotheca (B), from sample MNHN-IK-2015-546. — C–J. Lytocarpia subtilis sp. nov. C. Portion of stem. D–I. Lateral view of a hydrotheca (D), with details of its basal (E) and distal (F) parts; hydrotheca seen apically (G), and variation in the shape of its margin seen frontally (H) and laterally (I). J. Portion of corbula rachis with costa and gonotheca. From samples MNHN-IK-2015-525 (C, E–G) and MNHN-IK-2015-526 (D, H–J). Scale bars: A = 300 µm; B, D–F, J = 200 µm; C = 1 mm; G–I = 100 µm.

Fig. 19 in Aglaopheniid hydroids (Cnidaria: Hydrozoa: Aglaopheniidae) from off New Caledonia collected during KANACONO and KANADEEP expeditions of the French Tropical Deep-Sea Benthos Program

Fig. 19. Macrorhynchia spiralis sp. nov., from sample MNHN-IK-2015-519. A– B. Portion of stem (A) and detail of the nematothecae from the vicinity of a cladial apophysis (B). C. Pseudophylactocarp. D–E. Hydrotheca (D) and one of its lateral nematothecae (E), both in lateral view. F–H. Same phylactocarp with empty gonotheca in two different views (F–G), and phylactocarp with two gonothecae, one of which bears a female medusoid gonophore (H). Scale bars: A, D = 200 µm; B, E = 100 µm, C, F–H = 500 µm.

Fig. 13 in Aglaopheniid hydroids (Cnidaria: Hydrozoa: Aglaopheniidae) from off New Caledonia collected during KANACONO and KANADEEP expeditions of the French Tropical Deep-Sea Benthos Program

Fig. 13. Lytocarpia nigra (Nutting, 1905), from sample MNHN-IK-2015-509. A–B. Two stem internodes, to show variation in the shape of the frontal nematothecae. C–E. Hydrotheca in lateral (C), frontal (D) and apical (E) views. F–H. Rachis of corbula in frontal (F) and dorsal (G) aspects, and costa (H). Scale bars: A–H = 200 µm.

Fig. 3. Aglaophenia sinuosa Bale, 1888 in Aglaopheniid hydroids (Cnidaria: Hydrozoa: Aglaopheniidae) from off New Caledonia collected during KANACONO and KANADEEP expeditions of the French Tropical Deep-Sea Benthos Program

Fig. 3. Aglaophenia sinuosa Bale, 1888, from sample MNHN-IK-2015-545. A–B. Same portion of a stem in frontal (A) and dorsal (B) aspects. C–E. Same hydrotheca in lateral (C), frontal (D) and apical (E) views. Scale bars: A–E = 200 µm.

Fig. 6. A–B in Aglaopheniid hydroids (Cnidaria: Hydrozoa: Aglaopheniidae) from off New Caledonia collected during KANACONO and KANADEEP expeditions of the French Tropical Deep-Sea Benthos Program

Fig. 6. A–B. Cladocarpus partitus sp. nov., fertile cormoid (A) and phylactocarp (B) from sample MNHN-IK-2015-529 (holotype). — C–E. Cladocarpus pennatus sp. nov., fertile colony (C) and phylactocarp with male gonothecae (D) from sample MNHN-IK-2015-534 (holotype); phylactocarp with female gonothecae from sample MNHN-IK-2015-537 (one paratype). Scale bars: A, C–E = 1 cm; B = 1 mm.