scholarly journals A reliable DNA barcode reference library for the identification of benthic invertebrates: essential for biomonitoring of the North Sea

2021 ◽  
Vol 4 ◽  
Author(s):  
Magdalini Christodoulou ◽  
Berry van der Hoorn ◽  
Laure Van den Bulcke ◽  
Sofie Derycke ◽  
Annelies De Backer ◽  
...  
Keyword(s):  
North Sea ◽  
High Throughput Sequencing ◽  
Dna Barcode ◽  
Morphological Identification ◽  
Indigenous Species ◽  
Reference Library ◽  
The North ◽  
Sampling Campaign ◽  
The North Sea ◽  
Cost Efficient

Benthic macroinvertebrates are key components in environmental impact assessments. Nevertheless, their use as bioindicators can be constrained by the time- and cost-consuming processes needed for their morphological identification. The recent advances in high-throughput sequencing, particularly DNA metabarcoding can provide an alternative to morphology-based approaches. The main limitation for DNA-based tools to be implemented in biomonitoring projects is the considerable investment needed to build high-quality and curated taxonomic reference DNA sequence libraries for species identification. To begin addressing this shortage, Interreg NSR project GEANS aim in developing a curated DNA reference library based on mitochondrial cytochrome c oxidase subunit I (COI) for the North Sea macrobenthos that will serve as the backbone of all the molecular protocols. For the collection of the macroinvertebrates, a targeted sampling campaign is underway across the North Sea Region, while existing collections are being scanned. Macrobenthic specimens are being processed following a series of standardised work flows covering sampling, morphological identifications, molecular lab processing and data handling. GEANS' reference library, currently holds DNA barcodes for 3443 specimens collected from various areas of the North Sea. In total 11 phyla, 28 classes, 80 orders, 280 families, 428 genera and 586 species (37 non-indigenous species) are represented within the library. Species-level identification is taxonomically verified for over 90 % of the species, while genus-level identifications are verified for almost 100 % of the genera. GEANS reference library covers so far over 30 % of North Sea species and its constantly enriched. All specimens are photographed and together with the accompanying sequences, collection and taxonomic data are archived in a dedicate BOLD project. Voucher specimens and DNA extracts are archived at three different institutes in Germany (Senckenberg am Meer), the Netherlands (Naturalis) and Belgium (ILVO). Once available, this DNA-library will be based on taxonomically well-curated specimens and it will support the implementation of fast, cost-efficient and reliable DNA-based identifications and subsequently environmental health assessments in the North Sea.

scholarly journals Effects of anthropogenic pressures on diatom communities using morphological and molecular approaches

2021 ◽  
Vol 4 ◽  
Author(s):  
Marco Teixeira ◽  
Salomé Almeida ◽  
Maria Feio ◽  
Andreia Mortágua ◽  
Manuela Sales
Keyword(s):  
Environmental Variables ◽  
High Throughput Sequencing ◽  
Dna Barcode ◽  
Ecological Indicator ◽  
Morphological Identification ◽  
Anthropogenic Pressure ◽  
Reference Library ◽  
Promising Alternative ◽  
The North ◽  
Diatom Communities

The relevance of molecular composition of diatom assemblages to detect river impairment caused by different intensive land uses (industrial, agricultural, and urbanization) was tested in this study with data from two rivers (Ferreira and Sousa rivers) and 21 sampling sites located in the north of Portugal. The Water Framework Directive (WFD) gives the legal basis for the use of this ecological indicator for water quality assessment (Vasselon et al. 2017 ). However, the morphological identification and count of diatoms using the light microscope requires a high level of expertise, is time-consuming and costly (Valentin et al. 2019). DNA metabarcoding combined with high-throughput sequencing techniques (HTS), offers a promising alternative to classic methodologies, reducing time and costs (Mortágua et al. 2019 ). Thus, here we compared the response of the two approaches in terms of ecological assessments (IPS Ecological Quality Ratios) to the different types of pressures felt in the 21 sites. Diatoms were sampled at 21 sites located in the North of Portugal in autumn of 2019 (Fig. 1). Samples were submitted in parallel to the molecular and morphological analyses. The eDNA was extracted, PCR amplified (312 bp rbcL DNA barcode), and finally sequenced (Illumina MiSeq). The Mothur software was used to obtain the Operational Taxonomic Units (OTUs), which were then taxonomically assigned to the species through the R-Syst::diatom version 7.1 (Rimet et al. 2018) reference library. EQR values indicated a good correlation between morphological and molecular methods (Fig. 2). PCA analysis (Fig. 3 ) revealed that in urban, agricultural, and industrial areas there is a greater concentration of nutrients (phosphorus and nitrogen), organic matter, and heavy metals due to the discharge of urban/industrial effluents, while in places considered natural (without any type of anthropogenic pressure) we find low levels of these pollutants and high concentrations of dissolved oxygen (DO). The BEST (BIO-ENV) analysis (Tables 1, 2) shows in the case of the morphological approach, the combination of 4 environmental variables (NO₃⁻, Li, K, and Cu) is highly correlated with the biological patterns, and in the molecular approach the combination of only 2 of the environmental variables (Li and K), explains the distribution of diatom communities composition and has a slightly higher correlation. The morphological methodology seems to demonstrate a better response to urban pressures, mainly to effluent discharges, while the molecular one demonstrates a more diffuse response with special emphasis on good correlation with variables such as zinc and nitrate, which may also be related to effluent discharges and use of fertilizers in agriculture. However, it is necessary to improve the reference library so that there is a better response of the molecular methodology to the existing pressures.

scholarly journals Ecological implications of removing a concrete gas platform in the North Sea

2020 ◽  
Author(s):  
Joop W.P. Coolen ◽  
Oliver Bittner ◽  
Floor M.F. Driessen ◽  
Udo van Dongen ◽  
Midas S. Siahaya ◽  
...  
Keyword(s):  
North Sea ◽  
Local Community ◽  
Rocky Reef ◽  
Taxonomic Structure ◽  
Indigenous Species ◽  
Feeding Mode ◽  
Artificial Structures ◽  
The North ◽  
Species Invasions ◽  
The North Sea

ABSTRACTArtificial structures such as offshore oil and gas platforms can significantly alter local species communities. It has been argued that this effect should be considered during decisions over their removal during decommissioning. In the North Sea, leaving such structures in place is prohibited but derogations are allowed for large concrete installations. To assess removal options for one such installation, the Halfweg GBS (gravity-based structure) a concrete platform foundation off the Dutch coast, we studied the resident fouling macrofauna community. The faunal structure, biomass and trophic composition of the Halfweg was then compared with those from the surrounding seabed sediments, other local artificial structures and a natural rocky reef.In total, 65 macrofaunal species were observed on the concrete (52 species), steel legs (32) and surrounding rock dump (44) of Halfweg. Mean Simpson diversity per sample was highest on the rock dump (0.71) but concrete (0.54) and steel (0.60) of the GBS were lower than seabed (0.69). Ten of the species observed on the concrete were not reported on other substrates while 10 of the species were also observed in the surrounding seabed. The GBS structure was numerically dominated by Arthropoda which comprised 98% of the total abundance. Mean ash free dry weight (AFDW) was significantly higher (p<0.001) on the Halfweg substrates (204 g AFDW per m2) than in the surrounding seabed (65 g AFDW per m2). Over 94% of the biomass on Halfweg consisted of the plumose anemone Metridium senile. While common on other reefs, this species was absent from the surrounding seabed. Macrofaunal feeding mechanisms of the concrete and rock dump communities on the GBS were similar to those of nearby sediments, although these differed from those on the Halfweg steel legs. Therefore, the presence of Halfweg alters the local community feeding modes. Multivariate analysis revealed that taxonomic structure of the GBS and other artificial structures significantly differed from that of the sedimentary habitats. Low numbers of non-indigenous species on Halfweg indicated that the structure does not act as a stepping stone for species invasions.Our data show that the Halfweg structures significantly increase local biodiversity and biomass. Removal of the concrete and steel legs of the GBS (leaving the rock dump) will significantly reduce local macrofauna biodiversity. The long-term impact on macrofaunal biomass is low. Leaving the complete Halfweg structure in place will result in an enriched local macrofaunal biodiversity and feeding mode diversity.

scholarly journals Contrasting morphological and DNA barcode-suggested species boundaries among shallow-water amphipod fauna from the southern European Atlantic coast

Genome ◽  
2017 ◽  
Vol 60 (2) ◽  
pp. 147-157 ◽  
Author(s):  
Jorge Lobo ◽  
Maria S. Ferreira ◽  
Ilisa C. Antunes ◽  
Marcos A.L. Teixeira ◽  
Luisa M.S. Borges ◽  
...  
Keyword(s):  
North Sea ◽  
Dna Sequences ◽  
Atlantic Coast ◽  
Dna Barcode ◽  
Species Boundaries ◽  
Amphipod Species ◽  
The North ◽  
Sampling Locations ◽  
The North Sea ◽  
Corophium Multisetosum

In this study we compared DNA barcode-suggested species boundaries with morphology-based species identifications in the amphipod fauna of the southern European Atlantic coast. DNA sequences of the cytochrome c oxidase subunit I barcode region (COI-5P) were generated for 43 morphospecies (178 specimens) collected along the Portuguese coast which, together with publicly available COI-5P sequences, produced a final dataset comprising 68 morphospecies and 295 sequences. Seventy-five BINs (Barcode Index Numbers) were assigned to these morphospecies, of which 48 were concordant (i.e., 1 BIN = 1 species), 8 were taxonomically discordant, and 19 were singletons. Twelve species had matching sequences (<2% distance) with conspecifics from distant locations (e.g., North Sea). Seven morphospecies were assigned to multiple, and highly divergent, BINs, including specimens of Corophium multisetosum (18% divergence) and Dexamine spiniventris (16% divergence), which originated from sampling locations on the west coast of Portugal (only about 36 and 250 km apart, respectively). We also found deep divergence (4%–22%) among specimens of seven species from Portugal compared to those from the North Sea and Italy. The detection of evolutionarily meaningful divergence among populations of several amphipod species from southern Europe reinforces the need for a comprehensive re-assessment of the diversity of this faunal group.

Direct multiplex PCR-NALFIA to inform marine conservation: Use of an innovative diagnostic tool for the detection of Ostrea edulis larvae

2021 ◽  
Vol 34 ◽  
pp. 23
Author(s):  
Andreas Benkens ◽  
Claudia Buchholz ◽  
Bernadette Pogoda ◽  
Carsten Georg Harms
Keyword(s):  
North Sea ◽  
Marine Conservation ◽  
Lateral Flow ◽  
Ecosystem Functions ◽  
Morphological Identification ◽  
Ostrea Edulis ◽  
Marine Research ◽  
The North ◽  
Mitochondrial Cytochrome B ◽  
The North Sea

The European oyster Ostrea edulis played a key role in the North Sea by providing several ecosystem functions and services. Today, O. edulis is classified as severely degraded or functionally extinct in Europe. Marine conservation is focusing on biogenic reef restoration, namely the restoration of O. edulis in Natura 2000 sites of the North Sea. The identification of oyster larvae related to natural spatfalls of restored reefs and monitoring of larval drift is a key aspect of marine protected area management. Morphological identification and distinction from other abundant bivalve larvae using microscopy is difficult. Existing molecular biological methods are expensive and bound to stationary laboratory equipment, or are inadequate in the visualization. In this study, we identified nucleic acid lateral flow immunoassay (NALFIA), a well-established tool in human pathogen diagnostics, as an efficient approach for point-of-care (POC) testing in marine monitoring. Based on the genetic sequence of the mitochondrial cytochrome b of O. edulis, forward and reverse primers were developed. The reverse primer was labelled with fluorescent dye FITC, forward primer with biotin. Reaction on the lateral flow stripe could be realized with a single O. edulis larva in direct PCR with multiplex primers in a portable PCR-cycler. The established NALFIA system can distinguish O. edulis larvae from Crassostrea gigas and Mytilus edulis larvae, respectively. This method offers new approaches in POC testing in marine research and monitoring. It gives quick and clear results, is inexpensive, and could be easily adapted to other species of interest.

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