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.

scholarly journals Detection of Macrobenthos Species With Metabarcoding Is Consistent in Bulk DNA but Dependent on Body Size and Sclerotization in eDNA From the Ethanol Preservative

2021 ◽  
Vol 8 ◽  
Author(s):  
Sofie Derycke ◽  
Sara Maes ◽  
Laure Van den Bulcke ◽  
Joran Vanhollebeke ◽  
Jan Wittoeck ◽  
...  
Keyword(s):  
Body Size ◽  
Reference Database ◽  
Biodiversity Monitoring ◽  
Marine Monitoring ◽  
Diversity Patterns ◽  
The North ◽  
Dna Metabarcoding ◽  
The North Sea ◽  
Primer Sets ◽  
Marine Macrobenthos

DNA metabarcoding is a promising method to increase cost and time efficiency of marine monitoring. While substantial evidence exists that bulk DNA samples adequately reflect diversity patterns of marine macrobenthos, the potential of eDNA in the ethanol preservative of benthic samples for biodiversity monitoring remains largely unexplored. We investigated species detection in bulk DNA and eDNA from the ethanol preservative in samples from four distinct macrobenthic communities in the North Sea. Bulk DNA and eDNA were extracted with different extraction kits and five COI primer sets were tested. Despite the availability of a nearly complete reference database, at most 22% of the amplicon sequence variants (ASVs) were assigned taxonomy at the phylum level. However, the unassigned ASVs represented only a small fraction of the total reads (13%). The Leray primer set outperformed the four other primer sets in the number of non-chimeric reads and species detected, and in the recovery of beta diversity patterns. Community composition differed significantly between bulk DNA and eDNA samples, but both sample types were able to differentiate the four communities. The probability of detecting a species in the eDNA from the ethanol preservative was significantly lower than for bulk DNA for macrobenthos species having small to medium body size and for species having chitine or CaCO3 in their cuticula. Detection in the bulk DNA samples was not affected by the investigated morphological traits, indicating that monitoring of macrobenthos species will be most robust when using bulk DNA as template for metabarcoding.

Ten Demi-Culverins for Aldeburgh: Whitehall, the Dunkirkers, and a Suffolk Fishing Community, 1625–1630

2019 ◽  
Vol 58 (2) ◽  
pp. 315-337 ◽  
Author(s):  
Thomas Cogswell
Keyword(s):  
North Sea ◽  
East Coast ◽  
Central Government ◽  
Fishing Community ◽  
Close Attention ◽  
The North ◽  
The North Sea ◽  
The Impact

AbstractHistorians have not paid close attention to the activities of freebooters operating out of Dunkirk in the late 1620s. This essay corrects that omission by first studying the threat from Dunkirk to England's east coast and then addressing how the central government, counties, and coastal towns responded. A surprisingly rich vein of manuscript material from Great Yarmouth and particularly from the Suffolk fishing community of Aldeburgh informs this case study of the impact of this conflict around the North Sea.

scholarly journals The impact of sedimentary alkalinity release on the water column CO<sub>2</sub> system in the North Sea

2016 ◽  
Vol 13 (3) ◽  
pp. 841-863 ◽  
Author(s):  
H. Brenner ◽  
U. Braeckman ◽  
M. Le Guitton ◽  
F. J. R. Meysman
Keyword(s):  
Coastal Zone ◽  
North Sea ◽  
Dissolved Inorganic Carbon ◽  
Co2 Uptake ◽  
Overlying Water ◽  
Southern North Sea ◽  
The North ◽  
Alkalinity Generation ◽  
The North Sea ◽  
The Impact

Abstract. It has been previously proposed that alkalinity release from sediments can play an important role in the carbonate dynamics on continental shelves, lowering the pCO2 of seawater and hence increasing the CO2 uptake from the atmosphere. To test this hypothesis, sedimentary alkalinity generation was quantified within cohesive and permeable sediments across the North Sea during two cruises in September 2011 (basin-wide) and June 2012 (Dutch coastal zone). Benthic fluxes of oxygen (O2), alkalinity (AT) and dissolved inorganic carbon (DIC) were determined using shipboard closed sediment incubations. Our results show that sediments can form an important source of alkalinity for the overlying water, particularly in the shallow southern North Sea, where high AT and DIC fluxes were recorded in near-shore sediments of the Belgian, Dutch and German coastal zone. In contrast, fluxes of AT and DIC are substantially lower in the deeper, seasonally stratified, northern part of the North Sea. Based on the data collected, we performed a model analysis to constrain the main pathways of alkalinity generation in the sediment, and to quantify how sedimentary alkalinity drives atmospheric CO2 uptake in the southern North Sea. Overall, our results show that sedimentary alkalinity generation should be regarded as a key component in the CO2 dynamics of shallow coastal systems.

Detecting drought conditions related to vegetation at west continental Europe based on variations from the North and Caspian Seas

2021 ◽  
Author(s):  
Bolin Xu ◽  
Qing He ◽  
Kwok Pan Chun ◽  
Julian Klaus ◽  
Rémy Schoppach ◽  
...  
Keyword(s):  
North Sea ◽  
Vegetation Index ◽  
Lower Troposphere ◽  
Principal Component ◽  
Positive Phase ◽  
Vegetation Patterns ◽  
Limited Region ◽  
The North ◽  
The North Sea ◽  
The Impact

&lt;p&gt;Teleconnections relate regional pressure patterns to local climate anomalies, influencing the variation of vegetation patterns. Over west continental Europe, droughts have been widely investigated with persistent low-frequency atmospheric circulation patterns (e.g. the North Atlantic Oscillation, NAO) with the centers over the Atlantic based on the 500mb height anomalies of the Northern Hemisphere. However, the effects of teleconnection patterns with the centers of active variability over the North and Caspian Seas is largely unexplored for droughts related to vegetation patterns. In this study, we explored the impact of the North Sea-Caspian Pattern (NCP) on regional ecohydrologic conditions in the Greater Region of Luxembourg in Western Europe. Using a Principal Component Analysis (PCA), we first decomposed the annual Normalized Difference Vegetation Index (NDVI) from the Global Inventory Monitoring and Modeling System (GIMMS) between 1981 and 2015. In the first PCA component, a distinctive greening trend of NDVI is detected since the late 1980s. However, the corresponding station observations and the ERA5 reanalysis data show that the region in west continental Europe became increasingly drier based on the difference between precipitation and evaporation. We explain the above paradoxical greening but drying patterns by the mechanism of NCP over the region. During the positive phase of NCP, the high pressure over the North Sea weakens circulation over the region and leads to warmer conditions in west continental Europe. These conditions are good for vegetation growth because the region was mainly energy-limited during the observed period at the annual scale based on a Budyko analysis. However, the positive phase of NCP also promotes divergent conditions at the lower troposphere and it reduces moisture flux over the region. In the Budyko space, the persistent positive phase of NCP would lead the energy-limited region to be water-limited. As the positive phase of NCP is expected to be more frequent along with the increasing global temperatures, the region may start to experience increasing water stress on vegetation. These results suggest that unforeseen droughts related to vegetation may be emerging in the region. New drought monitoring and management measures related to vegetation should be developed at west continental Europe, especially during the positive phase of NCP.&lt;/p&gt;

scholarly journals Looking beyond stratification: a model-based analysis of the biological drivers of oxygen deficiency in the North Sea

2016 ◽  
Vol 13 (8) ◽  
pp. 2511-2535 ◽  
Author(s):  
Fabian Große ◽  
Naomi Greenwood ◽  
Markus Kreus ◽  
Hermann-Josef Lenhart ◽  
Detlev Machoczek ◽  
...  
Keyword(s):  
North Sea ◽  
Oxygen Deficiency ◽  
Low Oxygen ◽  
The North ◽  
Oxygen Conditions ◽  
Southern Central ◽  
The North Sea ◽  
Central North Sea ◽  
The Impact ◽  
Oxygen Dynamics

Abstract. Low oxygen conditions, often referred to as oxygen deficiency, occur regularly in the North Sea, a temperate European shelf sea. Stratification represents a major process regulating the seasonal dynamics of bottom oxygen, yet, lowest oxygen conditions in the North Sea do not occur in the regions of strongest stratification. This suggests that stratification is an important prerequisite for oxygen deficiency, but that the complex interaction between hydrodynamics and the biological processes drives its evolution. In this study we use the ecosystem model HAMSOM-ECOHAM to provide a general characterisation of the different zones of the North Sea with respect to oxygen, and to quantify the impact of the different physical and biological factors driving the oxygen dynamics inside the entire sub-thermocline volume and directly above the bottom. With respect to oxygen dynamics, the North Sea can be subdivided into three different zones: (1) a highly productive, non-stratified coastal zone, (2) a productive, seasonally stratified zone with a small sub-thermocline volume, and (3) a productive, seasonally stratified zone with a large sub-thermocline volume. Type 2 reveals the highest susceptibility to oxygen deficiency due to sufficiently long stratification periods (>  60 days) accompanied by high surface productivity resulting in high biological consumption, and a small sub-thermocline volume implying both a small initial oxygen inventory and a strong influence of the biological consumption on the oxygen concentration. Year-to-year variations in the oxygen conditions are caused by variations in primary production, while spatial differences can be attributed to differences in stratification and water depth. The large sub-thermocline volume dominates the oxygen dynamics in the northern central and northern North Sea and makes this region insusceptible to oxygen deficiency. In the southern North Sea the strong tidal mixing inhibits the development of seasonal stratification which protects this area from the evolution of low oxygen conditions. In contrast, the southern central North Sea is highly susceptible to low oxygen conditions (type 2). We furthermore show that benthic diagenetic processes represent the main oxygen consumers in the bottom layer, consistently accounting for more than 50 % of the overall consumption. Thus, primary production followed by remineralisation of organic matter under stratified conditions constitutes the main driver for the evolution of oxygen deficiency in the southern central North Sea. By providing these valuable insights, we show that ecosystem models can be a useful tool for the interpretation of observations and the estimation of the impact of anthropogenic drivers on the North Sea oxygen conditions.

scholarly journals Different bottom trawl fisheries have a differential impact on the status of the North Sea seafloor habitats

2020 ◽  
Vol 77 (5) ◽  
pp. 1772-1786 ◽  
Author(s):  
A D Rijnsdorp ◽  
J G Hiddink ◽  
P D van Denderen ◽  
N T Hintzen ◽  
O R Eigaard ◽  
...  
Keyword(s):  
North Sea ◽  
Management Strategies ◽  
Demersal Fish ◽  
Time Interval ◽  
The North ◽  
The Status ◽  
Fisheries Conservation ◽  
The North Sea ◽  
The Impact ◽  
Trawl Fisheries

Abstract Fisheries using bottom trawls are the most widespread source of anthropogenic physical disturbance to seafloor habitats. To mitigate such disturbances, the development of fisheries-, conservation-, and ecosystem-based management strategies requires the assessment of the impact of bottom trawling on the state of benthic biota. We explore a quantitative and mechanistic framework to assess trawling impact. Pressure and impact indicators that provide a continuous pressure–response curve are estimated at a spatial resolution of 1 × 1 min latitude and longitude (∼2 km2) using three methods: L1 estimates the proportion of the community with a life span exceeding the time interval between trawling events; L2 estimates the decrease in median longevity in response to trawling; and population dynamic (PD) estimates the decrease in biomass in response to trawling and the recovery time. Although impact scores are correlated, PD has the best performance over a broad range of trawling intensities. Using the framework in a trawling impact assessment of ten métiers in the North Sea shows that muddy habitats are impacted the most and coarse habitats are impacted the least. Otter trawling for crustaceans has the highest impact, followed by otter trawling for demersal fish and beam trawling for flatfish and flyshooting. Beam trawling for brown shrimps, otter trawling for industrial fish, and dredging for molluscs have the lowest impact. Trawling is highly aggregated in core fishing grounds where the status of the seafloor is low but the catch per unit of effort (CPUE) per unit of impact is high, in contrast to peripheral grounds, where CPUE per unit of impact is low.

scholarly journals The significance of coastal bathymetry representation for modelling the tidal response to mean sea level rise in the German Bight

Ocean Science ◽  
2020 ◽  
Vol 16 (1) ◽  
pp. 31-44 ◽  
Author(s):  
Caroline Rasquin ◽  
Rita Seiffert ◽  
Benno Wachler ◽  
Norbert Winkel
Keyword(s):  
Sea Level Rise ◽  
Sea Level ◽  
North Sea ◽  
German Bight ◽  
Coastal Areas ◽  
Tidal Dynamics ◽  
Mean Sea Level ◽  
The North ◽  
The North Sea ◽  
The Impact

Abstract. Due to climate change an accelerated mean sea level rise is expected. One key question for the development of adaptation measures is how mean sea level rise affects tidal dynamics in shelf seas such as the North Sea. Owing to its low-lying coastal areas, the German Bight (located in the southeast of the North Sea) will be especially affected. Numerical hydrodynamic models help to understand how mean sea level rise changes tidal dynamics. Models cannot adequately represent all processes in overall detail. One limiting factor is the resolution of the model grid. In this study we investigate which role the representation of the coastal bathymetry plays when analysing the response of tidal dynamics to mean sea level rise. Using a shelf model including the whole North Sea and a high-resolution hydrodynamic model of the German Bight we investigate the changes in M2 amplitude due to a mean sea level rise of 0.8 and 10 m. The shelf model and the German Bight Model react in different ways. In the simulations with a mean sea level rise of 0.8 m the M2 amplitude in the shelf model generally increases in the region of the German Bight. In contrast, the M2 amplitude in the German Bight Model increases only in some coastal areas and decreases in the northern part of the German Bight. In the simulations with a mean sea level rise of 10 m the M2 amplitude increases in both models with largely similar spatial patterns. In two case studies we adjust the German Bight Model in order to more closely resemble the shelf model. We find that a different resolution of the bathymetry results in different energy dissipation changes in response to mean sea level rise. Our results show that the resolution of the bathymetry especially in flat intertidal areas plays a crucial role for modelling the impact of mean sea level rise.

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