Currently available genome assemblies for Atlantic cod (Gadus morhua) have been constructed from fish belonging to the Northeast Arctic Cod (NEAC) population; a migratory population feeding in the Barents Sea. These assemblies have been crucial for the development of genetic markers which have been used to study population differentiation and adaptive evolution in Atlantic cod, pinpointing four discrete islands of genomic divergence located on linkage groups 1, 2, 7 and 12. In this paper, we present a high-quality reference genome from a male Atlantic cod representing a southern population inhabiting the Celtic sea. The genome assembly (gadMor_Celtic) was produced from long-read nanopore data and has a combined contig length of 686 Mb with an N50 of 10 Mb. Integrating contigs with genetic linkage mapping information enabled us to construct 23 chromosome sequences which mapped with high confidence to the latest NEAC population assembly (gadMor3) and allowed us to characterize, to an extent not previously reported large chromosomal inversions on linkage groups 1, 2, 7 and 12. In most cases, inversion breakpoints could be located within single nanopore contigs. Our results suggest the presence of inversions in Celtic cod on linkage groups 6, 11 and 21, although these remain to be confirmed. Further, we identified a specific repetitive element that is relatively enriched at predicted centromeric regions. Our gadMor_Celtic assembly provides a resource representing a 9southern9 cod population which is complementary to the existing 9northern9 population based genome assemblies and represents the first step towards developing pan-genomic resources for Atlantic cod.

A Nanopore Based Chromosome-Level Assembly Representing Atlantic Cod from the Celtic Sea

Decapod crustaceans, such as those from the Homarus genus, are key benthic representatives supporting very valuable fishing and aquaculture industries. Those commercially caught, such as the European lobster (H. gammarus) can be stored in live facilities for short (few days) to long periods (up to 6 months) before being traded. Conditions in captivity are not standardized, including holding temperatures or feeding regimes. Herein, the physiological condition during long-term starvation (24 weeks) in H. gammarus was assessed at three temperatures (4, 8 and 12°C). Our results indicate that, H. gammarus have the capacity to endure long-term starvation. Principal component analysis (PCA) of measured parameters showed two main components (Eigen value>1). Fasted animals kept at 12°C separated from all others experimental groups due to higher total phenoloxidase (PO) activity in the hemolymph and water content in the muscle, suggesting that keeping H. gammarus un-fed at this higher temperature is physiologically more demanding and detrimental. This was later confirmed by significant changes particularly in this group in histology and lipid class composition of the hepatopancreas. These data call into question the suitability of current accepted in-vivo condition markers (e.g. hemolymph protein concentration) for determining the physiological condition and welfare of decapods such as H. gammarus.

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The Effect of Temperature on the Physiological Condition and Immune-Capacity of European Lobsters (Homarus gammarus) During Long-Term Starvation

. Fishing – especially trawling – is one of the most
ubiquitous anthropogenic pressures on marine ecosystems worldwide, yet very
few long-term, spatially explicit datasets on trawling effort exist; this
greatly hampers our understanding of the medium- to long-term impact of
trawling. This important gap is addressed here for the North Sea, a highly
productive shelf sea which is also subject to many anthropogenic pressures.
For a 31-year time span (1985–2015), we provide a gridded dataset of the
spatial distribution of total international otter and beam trawling effort,
with a resolution of 0.5 ∘ latitude by 1 ∘ longitude, over
the North Sea. The dataset was largely reconstructed using compiled effort
data from seven fishing effort time series, each covering shorter time spans and
only some of the countries fishing the North Sea. For the years where effort
data for particular countries were missing, the series was complemented using
estimated (modelled) effort data. This new, long-term and large-scale
trawling dataset may serve the wider scientific community, as well as those
involved with policy and management, as a valuable information source on
fishing pressure in a large marine ecosystem which is heavily impacted but
which simultaneously provides a wealth of ecosystem services to society. The
dataset is available on the Cefas Data Hub at: https://doi.org/10.14466/CefasDataHub.61 , version 2 (Couce et al., 2019).

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Reconstructing three decades of total international trawling effort in the North Sea

An accurate description of trophic interactions is crucial to understand ecosystem functioning and sustainably manage marine ecosystems exploitation. Carbon and nitrogen stable isotopes were coupled with stomach content analyses to investigate whiting (Merlangius merlangus, Linnaeus, 1758) feeding behavior in the Eastern English Channel and Southern North Sea. Whiting juveniles and adults were sampled in autumn and winter to investigate both ontogenetic and seasonal changes. In addition, queen scallops (Aequipecten opercularis) samples were collected along with fish to be used as isotopic benthic baseline. Results indicated an ontogenetic diet change from crustaceans to fish and cephalopods. In autumn, δ15N values generally increased with fish size while in winter, a decrease of δ15N values with fish size was observed, as a potential result of spatial variation in baseline δ15N values. In winter, a nutrient-poor period, an increase in feeding intensity was observed, especially on the copepod Temora longicornis. This study provides further insights into whiting trophic ecology in relation to ontogenetic and seasonal variations, and it confirms the importance of combining several trophic analysis methods to understand ecosystem functioning.

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Seasonal and ontogenetic variation of whiting diet in the Eastern English Channel and the Southern North Sea.

The fecal indicator organism (FIO) Escherichia coli is frequently used as a general indicator of sewage contamination and for evaluating the success of shellfish cleaning (depuration) processes. To evaluate the robustness of this approach, the accumulation, retention, and depuration of non-pathogenic E. coli, pathogenic E. coli O157:H7 and norovirus GII (NoV GII) RNA were evaluated using a combination of culture-based (E. coli) and molecular methods (E. coli, NoV GII) after exposure of mussels (Mytilus edulis) to water contaminated with human feces. We simulated water contamination after a point-source release from a combined sewer overflow (CSO) where untreated wastewater is released directly into the coastal zone. All three microbiological indicators accumulated rapidly in the mussels, reaching close to maximum concentration within 3 h of exposure, demonstrating that short CSO discharges pose an immediate threat to shellfish harvesting areas. Depuration (72 h) in clean water proved partially successful at removing both pathogenic and non-pathogenic E. coli from shellfish tissue, but failed to eradicate NoV GII RNA. We conclude that current EU standards for evaluating microbiological risk in shellfish are inadequate for protecting consumers against exposure to human norovirus GII found in polluted marine waters.

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E. coli Is a Poor End-Product Criterion for Assessing the General Microbial Risk Posed From Consuming Norovirus Contaminated Shellfish.

. The datasets described here bring together quality-controlled seawater temperature measurements from over 130 years of departmental government-funded marine science investigations in the UK (United Kingdom). Since before the foundation of a Marine Biological Association fisheries laboratory in 1902 and through subsequent evolutions as the Directorate of Fisheries Research and the current Centre for Environment Fisheries & Aquaculture Science, UK government marine scientists and observers have been collecting seawater temperature data as part of oceanographic, chemical, biological, radiological, and other policy-driven research and observation programmes in UK waters. These datasets start with a few tens of records per year, rise to hundreds from the early 1900s, thousands by 1959, and hundreds of thousands by the 1980s, peaking with  >  1 million for some years from 2000 onwards. The data source systems vary from time series at coastal monitoring stations or offshore platforms (buoys), through repeated research cruises or opportunistic sampling from ferry routes, to temperature extracts from CTD (conductivity, temperature, depth) profiles, oceanographic, fishery and plankton tows, and data collected from recreational scuba divers or electronic devices attached to marine animals. The datasets described have not been included in previous seawater temperature collation exercises (e.g. International Comprehensive Ocean–Atmosphere Data Set, Met Office Hadley Centre sea surface temperature data set, the centennial in situ observation-based estimates of sea surface temperatures), although some summary data reside in the British Oceanographic Data Centre (BODC) archive, the Marine Environment Monitoring and Assessment National (MERMAN) database and the International Council for the Exploration of the Sea (ICES) data centre. We envisage the data primarily providing a biologically and ecosystem-relevant context for regional assessments of changing hydrological conditions around the British Isles, although cross-matching with satellite-derived data for surface temperatures at specific times and in specific areas is another area in which the data could be of value (see e.g. Smit et al., 2013). Maps are provided indicating geographical coverage, which is generally within and around the UK Continental Shelf area, but occasionally extends north from Labrador and Greenland to east of Svalbard and southward to the Bay of Biscay. Example potential uses of the data are described using plots of data in four selected groups of four ICES rectangles covering areas of particular fisheries interest. The full dataset enables extensive data synthesis, for example in the southern North Sea where issues of spatial and numerical bias from a data source are explored. The full dataset also facilitates the construction of long-term temperature time series and an examination of changes in the phenology (seasonal timing) of ecosystem processes. This is done for a wide geographic area with an exploration of the limitations of data coverage over long periods. Throughout, we highlight and explore potential issues around the simple combination of data from the diverse and disparate sources collated here. The datasets are available on the Cefas Data Hub ( https://www.cefas.co.uk/cefas-data-hub/ ). The referenced data sources are listed in Sect. 5.

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Over 10 million seawater temperature records for the United Kingdom Continental Shelf between 1880 and 2014 from 17 Cefas (United Kingdom government) marine data systems

Stephen Flatman

Papers

Over 10 million seawater temperature records for the United Kingdom Continental Shelf between 1880 and 2014 from 17 Cefas (United Kingdom government) marine data systems