scholarly journals Accurate long-read eDNA metabarcoding of North Sea fish using Oxford Nanopore sequencing

2021 ◽  
Vol 4 ◽  
Author(s):  
Karlijn Doorenspleet ◽  
Lara Jansen ◽  
Saskia Oosterbroek ◽  
Reindert Nijland
Keyword(s):  
Species Composition ◽  
North Sea ◽  
Taxonomic Resolution ◽  
Reference Database ◽  
Test Accuracy ◽  
Nanopore Sequencing ◽  
The North ◽  
Field Samples ◽  
Long Read ◽  
The North Sea

To halt North Sea ecosystem degradation, accurate and intensive monitoring of the North Sea ecosystem and its fish is vital to correctly inform management decisions. DNA based techniques and especially the use of environmental (e)DNA from seawater can become a powerful monitoring tool. However, current eDNA based metabarcoding approaches are based on genetic target regions of <500 nucleotides which offers only limited taxonomic resolution. We tested sensitivity and applicability for field samples of newly designed universal fish primer targeting a 2kb region covering mitochondrial 12S and 16S genes in eDNA samples. Samples were processed using long read nanopore sequencing in combination with the consensus builder Decona and retrieved accurate read identities of up to 99.9%. To test accuracy of the primer, eDNA was analyzed from a tropical aquarium with a known species composition of bony fish and elasmobranchs. This showed that over 50% of species present can be identified. The majority of remaining reads are identified as -in aquarium present- genera and can be explained by an incomplete reference database for the fish present in the aquarium. Primers were also applied in North sea eDNA field samples. Distinct species compositions between different locations could be observed and consisted of ecological relevant species and shows the applicability for long-read eDNA metabarcoding in field studies. Incomplete reference databases currently form the main bottleneck to further develop high resolution nanopore based long read sequencing as metabarcoding strategy. Nevertheless, this study shows that long read nanopore sequencing of eDNA can be used to obtain accurate information on the fish and elasmobranch species composition in the North Sea and beyond.

scholarly journals High resolution species detection: accurate long read eDNA metabarcoding of North Sea fish using Oxford Nanopore sequencing

2021 ◽  
Author(s):  
Karlijn Doorenspleet ◽  
Lara Jansen ◽  
Saskia Oosterbroek ◽  
Oscar Bos ◽  
Pauline Kamermans ◽  
...  
Keyword(s):  
High Resolution ◽  
North Sea ◽  
Fish Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Nanopore Sequencing ◽  
Nature Restoration ◽  
Oxford Nanopore ◽  
Field Samples ◽  
Long Read

To monitor the effect of nature restoration projects in North Sea ecosystems, accurate and intensive biodiversity assessments are vital. DNA based techniques and especially environmental DNA (eDNA) metabarcoding from seawater is becoming a powerful monitoring tool. However, current approaches are based on genetic target regions of <500 nucleotides, which offer limited taxonomic resolution. This study aims to develop and validate a long read nanopore sequencing method for eDNA that enables improved identification of fish species. We designed a universal primer pair targeting a 2kb region covering the 12S and 16S rRNA genes of fish mitochondria. eDNA was amplified and sequenced using the Oxford Nanopore MiniON. Sequence data was processed using the new pipeline Decona, and accurate consensus identities of above 99.9% were retrieved. The primer set efficiency was tested with eDNA from a 3.000.000 L zoo aquarium with 31 species of bony fish and elasmobranchs. Over 55% of the species present were identified on species level and over 75% on genus level. Next, our long read eDNA metabarcoding approach was applied to North Sea eDNA field samples collected at ship wreck sites, the Gemini Offshore Wind Farm, the Borkum Reef Grounds and a bare sand bottom. Here, location specific fish and vertebrate communities were obtained. Incomplete reference databases still form a major bottleneck in further developing high resolution long read metabarcoding. Yet, the method has great potential for rapid and accurate fish species monitoring in marine field studies.

Coincident changes in four components of the North Sea ecosystem

1999 ◽  
Vol 79 (1) ◽  
pp. 183-185 ◽  
Author(s):  
K.F. Pearce ◽  
C.L.J. Frid
Keyword(s):  
Time Series ◽  
Species Composition ◽  
North Sea ◽  
Food Chain ◽  
Demersal Fish ◽  
North West ◽  
The North ◽  
The North Sea ◽  
Chain Links ◽  
Single Set

An analysis of species composition of the zooplankton, macrobenthos (two stations) and demersal fish from Northumberland (north-west North Sea) are reported. The four time-series show synchronous changes in species composition. While some of these changes coincide with changes in climateological variables, others do not. The degree of synchrony implies that either all the time-series are responding to a single set of extraneous forcing factors, or that food chain links, rapidly translate the signal through all ecosystem components.

scholarly journals High resolution species detection: accurate long read eDNA metabarcoding of North Sea fish using Oxford Nanopore sequencing

2021 ◽  
Author(s):  
Karlijn Doorenspleet ◽  
Lara Jansen ◽  
Saskia Oosterbroek ◽  
Oscar Bos ◽  
Pauline Kamermans ◽  
...  
Keyword(s):  
High Resolution ◽  
North Sea ◽  
Fish Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Nanopore Sequencing ◽  
Nature Restoration ◽  
Oxford Nanopore ◽  
Field Samples ◽  
Long Read

To monitor the effect of nature restoration projects in North Sea ecosystems, accurate and intensive biodiversity assessments are vital. DNA based techniques and especially environmental DNA (eDNA) metabarcoding from seawater is becoming a powerful monitoring tool. However, current approaches are based on genetic target regions of <500 nucleotides, which offer limited taxonomic resolution. This study aims to develop and validate a long read nanopore sequencing method for eDNA that enables improved identification of fish species. We designed a universal primer pair targeting a 2kb region covering the 12S and 16S rRNA genes of fish mitochondria. eDNA was amplified and sequenced using the Oxford Nanopore MiniON. Sequence data was processed using the new pipeline Decona, and accurate consensus identities of above 99.9% were retrieved. The primer set efficiency was tested with eDNA from a 3.000.000 L zoo aquarium with 31 species of bony fish and elasmobranchs. Over 55% of the species present were identified on species level and over 75% on genus level. Next, our long read eDNA metabarcoding approach was applied to North Sea eDNA field samples collected at ship wreck sites, the Gemini Offshore Wind Farm, the Borkum Reef Grounds and a bare sand bottom. Here, location specific fish and vertebrate communities were obtained. Incomplete reference databases still form a major bottleneck in further developing high resolution long read metabarcoding. Yet, the method has great potential for rapid and accurate fish species monitoring in marine field studies.

scholarly journals To blend or not to blend? The role of morphological traits for the detection of marine macrobenthos in bulk DNA and eDNA from the ethanol preservative

2021 ◽  
Vol 4 ◽  
Author(s):  
Sofie Derycke ◽  
Sara Maes ◽  
Laure Van den Bulcke ◽  
Joran Vanhollebeke ◽  
Jan Wittoeck ◽  
...  
Keyword(s):  
North Sea ◽  
Beta Diversity ◽  
Coi Gene ◽  
Reference Database ◽  
Successful Implementation ◽  
Diversity Patterns ◽  
The North ◽  
Dna Metabarcoding ◽  
The North Sea ◽  
The Impact

The impact of methodological choices on the reliability and reproducibility of DNA metabarcoding need to be well understood to allow successful implementation in routine monitoring frameworks. For macrobenthos communities, the metabarcoding protocol focuses on a fragment of the mitochondrial COI gene and depending on the primer set used for amplification of COI, different taxa can be detected. To identify the primer set that allows the best diversity estimates for macrobenthos in the North Sea region, we sampled four distinct and well characterised communities and identified macrobenthos using traditional morpho-taxonomy before molecular processing. Of the five primer sets tested, the Leray primer set yielded the highest number of non-chimeric reads, detected the highest number of macrobenthos species and best recovered beta diversity patterns. Despite the availability of a nearly complete reference database, 19 out of the 59 morphological species were not picked up with DNA metabarcoding. Next to primer choice, the DNA source used in metabarcoding studies can affect whether or not a species is detected. DNA can be extracted from bulk specimens or from the ethanol preservative in which the macrobenthos sample was preserved. The latter DNA source would greatly speed up processing time of samples in the laboratory. We therefore compared species detection in bulk DNA and eDNA from the ethanol preservative from the four macrobenthos communities in the North Sea. Our results show that community composition differed significantly between bulk DNA and eDNA samples, but both sample types are able to differentiate the four macrobenthos communities from the North Sea. Of the 49 species that are detected in both sample types, 27 are also found in the morphological dataset. The 14 species that are exclusively detected in the ethanol preservative are mainly pelagic species. In view of the low read numbers allocated to these species (at most 153 reads) they most likely represent “contaminant” DNA molecules that are attached to the specimens or the organic debris. To better understand the different results between bulk DNA and eDNA from the ethanol preservative, we investigated the importance of four categorical traits in explaining the probability of detecting a species in the two sample types: body, larval stage (benthic or pelagic), longevity and body skeleton (chitin, CaCO3 or soft tissue). A generalized linear mixed effects model approach shows that the probability of detecting a species in the eDNA from the ethanol preservative is significantly lower than for bulk DNA for macrobenthos species having small to medium body size and for species having chitine or CaCO3 in their skeleton. In contrast, detection in the bulk DNA samples is not affected by the investigated traits. Although the ethanol preservative can be used to characterize beta diversity patterns, our results show that monitoring of macrobenthos species will be most robust when using bulk DNA as template for metabarcoding.

The Ship Canal between the North Sea and the Baltic

1891 ◽  
Vol 32 (828supp) ◽  
pp. 13224-13224
Keyword(s):  
North Sea ◽  
The North ◽  
The North Sea ◽  
The Baltic

Long Term Changes in Wind and Wave Climate on the North Sea

1991 ◽  
Author(s):  
Frank M. J. Hoozemans
Keyword(s):  
North Sea ◽  
Wave Climate ◽  
The North ◽  
Long Term Changes ◽  
The North Sea

Detecting plankton shifts in the North Sea: a new abrupt ecosystem shift between 1996 and 2003

2014 ◽  
Vol 502 ◽  
pp. 85-104 ◽  
Author(s):  
G Beaugrand ◽  
X Harlay ◽  
M Edwards
Keyword(s):  
North Sea ◽  
The North ◽  
Ecosystem Shift ◽  
The North Sea
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