scholarly journals Switching on the light: using metagenomic shotgun sequencing to characterize the intestinal microbiome of Atlantic cod

2019 ◽  
Author(s):  
Even Sannes Riiser ◽  
Thomas H.A. Haverkamp ◽  
Srinidhi Varadharajan ◽  
Ørnulf Borgan ◽  
Kjetill S. Jakobsen ◽  
...  
Keyword(s):  
Gadus Morhua ◽  
Atlantic Cod ◽  
North Atlantic Ocean ◽  
Bacterial Species ◽  
Abundant Species ◽  
Shotgun Sequencing ◽  
Intestinal Microbiome ◽  
Geographical Differences ◽  
Important Species ◽  
The North

AbstractThe biological roles of the intestinal microbiome and how it is impacted by environmental factors are yet to be determined in wild marine fish species. Atlantic cod (Gadus morhua) is an ecologically important species with a wide-spread distribution in the North Atlantic Ocean. 16S rRNA-based amplicon analyses found no geographical differentiation between the intestinal microbiome of Atlantic cod from different locations. Nevertheless, it is unclear if this lack of differentiation results from an insufficient resolution of this method to resolve fine-scaled biological complexity. Here, we take advantage of the increased resolution provided by metagenomic shotgun sequencing to investigate the intestinal microbiome of 19 adult Atlantic cod individuals from two coastal populations in Norway – located 470 km apart. Our results show that the intestinal microbiome is dominated by theVibrionalesorder, consisting of varying abundances ofPhotobacterium, AliivibrioandVibriospecies. Moreover, resolving the species community to unprecedented resolution, we identify two abundant species,P. iliopiscariumandP. kishitanii,which comprise over 50% of the classified reads. Interestingly, genomic data shows that the intestinalP. kishitaniistrains have functionally intactluxgenes, and its high abundance suggests that fish intestines form an important part of its ecological niche. These observations support a hypothesis that bioluminescence plays an ecological role in the marine food web. Despite our improved taxonomical resolution, we identify no geographical differences in bacterial community structure, indicating that the intestinal microbiome of these coastal cod is colonized by a limited number of closely related bacterial species with a broad geographical distribution that are well suited to thrive in this host-associated environment.

scholarly journals Metagenomic Shotgun Analyses Reveal Complex Patterns of Intra- and Interspecific Variation in the Intestinal Microbiomes of Codfishes

2020 ◽  
Vol 86 (6) ◽  
Author(s):  
Even Sannes Riiser ◽  
Thomas H. A. Haverkamp ◽  
Srinidhi Varadharajan ◽  
Ørnulf Borgan ◽  
Kjetill S. Jakobsen ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Interspecific Variation ◽  
Shotgun Sequencing ◽  
Intestinal Microbiome ◽  
Ecological Niches ◽  
Content Type ◽  
Evolutionary Trajectories ◽  
Species Specific

ABSTRACT The relative importance of host-specific selection or environmental factors in determining the composition of the intestinal microbiome in wild vertebrates remains poorly understood. Here, we used metagenomic shotgun sequencing of individual specimens to compare the levels of intra- and interspecific variation of intestinal microbiome communities in two ecotypes (NEAC and NCC) of Atlantic cod (Gadus morhua) that have distinct behavior and habitats and three Gadidae species that occupy a range of ecological niches. Interestingly, we found significantly diverged microbiomes among the two Atlantic cod ecotypes. Interspecific patterns of variation are more variable, with significantly diverged communities for most species’ comparisons, apart from the comparison between coastal cod (NCC) and Norway pout (Trisopterus esmarkii), whose community compositions are not significantly diverged. The absence of consistent species-specific microbiomes suggests that external environmental factors, such as temperature, diet, or a combination thereof, comprise major drivers of the intestinal community composition of codfishes. IMPORTANCE The composition of the intestinal microbial community associated with teleost fish is influenced by a diversity of factors, ranging from internal factors (such as host-specific selection) to external factors (such as niche occupation). These factors are often difficult to separate, as differences in niche occupation (e.g., diet, temperature, or salinity) may correlate with distinct evolutionary trajectories. Here, we investigate four gadoid species with contrasting levels of evolutionary separation and niche occupation. Using metagenomic shotgun sequencing, we observed distinct microbiomes among two Atlantic cod (Gadus morhua) ecotypes (NEAC and NCC) with distinct behavior and habitats. In contrast, interspecific patterns of variation were more variable. For instance, we did not observe interspecific differentiation between the microbiomes of coastal cod (NCC) and Norway pout (Trisopterus esmarkii), whose lineages underwent evolutionary separation over 20 million years ago. The observed pattern of microbiome variation in these gadoid species is therefore most parsimoniously explained by differences in niche occupation.

scholarly journals Barents Sea cod (Gadus morhua) diet composition: long-term interannual, seasonal, and ontogenetic patterns

2019 ◽  
Vol 76 (6) ◽  
pp. 1641-1652 ◽  
Author(s):  
Rebecca E Holt ◽  
Bjarte Bogstad ◽  
Joël M Durant ◽  
Andrey V Dolgov ◽  
Geir Ottersen
Keyword(s):  
Gadus Morhua ◽  
Trophic Ecology ◽  
Barents Sea ◽  
Atlantic Cod ◽  
Prey Size ◽  
Ecosystem Dynamics ◽  
Polar Cod ◽  
Important Species ◽  
Predator Prey ◽  
The North

Abstract Atlantic cod (Gadus morhua) is an ecologically and commercially important species in the North-Atlantic region. Cod is a top predator and information on its trophic ecology is integral for understanding predator–prey relationships and food-web dynamics. We present an analysis of the trophic patterns of Barents Sea (BS) cod using a unique 33-year time-series of stomach-content data from 1984 to 2016. We assessed patterns in diet (prey) composition across years, between seasons, as well as ontogenetic trends in diet, including predator–prey size relationships. Ontogenetic shifts in diet were observed, with fish becoming more important prey with increasing cod size. A very early onset of piscivory was found in <20 cm cod. Cannibalism was found in cod > 20 cm and increased with size. Juvenile cod exhibit a tendency towards consuming prey up to 33% of their body length, whereas larger cod feed on all prey sizes, resulting in asymmetric predator–prey size distributions. Diet varied significantly during 1984–2016, consistent with changes in both prey, cod abundance, and distribution. Seasonal differences were observed; capelin dominated the winter diet, whereas cod, polar cod, and other fish species were prevalent in summer/autumn months. This work represents an important step towards understanding trophic linkages that determine BS ecosystem dynamics.

scholarly journals Metagenomic shotgun analyses reveal complex patterns of intra- and interspecific variation in the intestinal microbiomes of codfishes

2019 ◽  
Author(s):  
Even Sannes Riiser ◽  
Thomas H.A. Haverkamp ◽  
Srinidhi Varadharajan ◽  
Ørnulf Borgan ◽  
Kjetill S. Jakobsen ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Interspecific Variation ◽  
Shotgun Sequencing ◽  
Intestinal Microbiome ◽  
Ecological Niches ◽  
Evolutionary Trajectories ◽  
Species Comparisons ◽  
Species Specific

AbstractThe relative importance of host-specific selection or environmental factors in determining the composition of the intestinal microbiome in wild vertebrates remains poorly understood. Here, we use metagenomic shotgun sequencing of individual specimens to compare the intra- and interspecific variation of intestinal microbiome communities in two ecotypes (NEAC and NCC) of Atlantic cod (Gadus morhua) – that have distinct behavior and habitats– and three Gadidae species that occupy a range of ecological niches. Interestingly, we find significantly diverged microbiomes amongst the two Atlantic cod ecotypes. Interspecific patterns of variation are more variable, with significantly diverged communities for most species’ comparisons, apart from the comparison between coastal cod (NCC) and Norway pout (Trisopterus esmarkii), whose community compositions are not significantly diverged. The absence of consistent species-specific microbiomes suggests that external environmental factors, such as temperature, diet or a combination there-off comprise major drivers of the intestinal community composition of codfishes.ImportanceThe composition of the intestinal microbial community associated with teleost fish is influenced by a diversity of factors, ranging from internal factors (such as host-specific selection) to external factors (such as niche occupation). These factors are often difficult to separate, as differences in niche occupation (e.g. diet, temperature or salinity) may correlate with distinct evolutionary trajectories. Here, we investigate four gadoid species with contrasting levels of evolutionary separation and niche occupation. Using metagenomic shotgun sequencing, we observe distinct microbiomes amongst two Atlantic cod (Gadus morhua) ecotypes (NEAC and NCC) with distinct behavior and habitats. In contrast, interspecific patterns of variation are more variable. For instance, we do not observe interspecific differentiation between the microbiomes of coastal cod (NCC) and Norway pout (Trisopterus esmarkii) whose lineages have evolutionary separated over 20 million years ago. The observed pattern of microbiome variation in these gadoid species is therefore most parsimoniously explained by differences in niche occupation.

High-resolution melting analysis of common and recombinant genotypes of the Atlantic cod (Gadus morhua) hemoglobin β1 gene in transatlantic populations

2012 ◽  
Vol 69 (3) ◽  
pp. 525-531 ◽  
Author(s):  
Ola Frang Wetten ◽  
Robert C. Wilson ◽  
Øivind Andersen
Keyword(s):  
High Resolution ◽  
Atlantic Ocean ◽  
Gadus Morhua ◽  
Elevated Temperatures ◽  
High Resolution Melting ◽  
Atlantic Cod ◽  
North Atlantic Ocean ◽  
Low Cost ◽  
Northeast Atlantic ◽  
The North

High-resolution melting (HRM) analysis was applied to haplotype the Met55Val–Lys62Ala mutations of the Atlantic cod ( Gadus morhua ) Hb-β1 gene responsible for the important hemoglobin polymorphisms. The Val55–Ala62 haplotype predominated in cod populations throughout the Northwest Atlantic Ocean and the northern Norwegian and Baltic seas, while the Met55–Lys62 variant was mostly found in the North Sea, Kattegat, and along the southern part of the Norwegian coast. Whereas the distribution of the two main haplotypes show a temperature-related north–south gradient in Northeast Atlantic populations, this study provided no evidence for such a cline on the western side of the North Atlantic Ocean. Coupling and repulsion double heterozygotes were readily distinguished by the HRM assay, but no repulsion heterozygote specimens were found on either side of the Atlantic Ocean. The recombinant haplotype Val55–Lys62 was detected in variable numbers in both Northwest and Northeast Atlantic populations, with the highest frequencies in the Canadian populations. The reciprocal Met55–Ala62 recombination was almost absent in the populations examined and probably represents a disadvantage, particularly at elevated temperatures. Our HRM assay affords low-cost, precise, and efficient Hb-β1 polymorphism haplotyping in large numbers of DNA samples in small, moderately equipped laboratories.

An "experiment" on effort allocation of fishing vessels: the role of interference competition and area specialization

2007 ◽  
Vol 64 (2) ◽  
pp. 304-313 ◽  
Author(s):  
Jan-Jaap Poos ◽  
Adriaan D Rijnsdorp
Keyword(s):  
North Sea ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Seasonal Pattern ◽  
Interference Competition ◽  
Catch Rate ◽  
The North ◽  
Closed Area ◽  
Fishing Vessels ◽  
The North Sea

A temporarily closed area established to protect spawning Atlantic cod (Gadus morhua) in the North Sea allowed us to study the response of the Dutch beam trawl fleet exploiting common sole (Solea solea) and plaice (Pleuronectes platessa). A number of vessels left the North Sea 1 month earlier than the normal seasonal pattern. The vessels that continued fishing in the North Sea were concentrated in the remaining open areas. In the first week after the closure, the catch rate decreased by 14%, coinciding with an increase in crowding of 28%. Area specialisation affected the response of individual vessels because vessels without prior experience in the open areas showed a larger decline in catch rate compared with vessels that previously fished in these open areas and were more likely to stop fishing during the closed period. The decrease in catch rate in response to the increase in competitor density allowed us to estimate the strength of the interference competition.

Influence of climatic changes on the parasites of Atlantic cod Gadus morhua off coastal Labrador, Canada

2006 ◽  
Vol 80 (2) ◽  
pp. 193-197 ◽  
Author(s):  
R.A. Khan ◽  
C.V. Chandra
Keyword(s):  
North Atlantic ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Age Groups ◽  
Climatic Conditions ◽  
Otter Trawl ◽  
Commercial Fishery ◽  
Metazoan Parasites ◽  
Mean Values ◽  
The North

AbstractA study was conducted in 2000 and 2003, following the collapse of the commercial fishery in 1990, to compare metazoan parasites of Atlantic cod Gadus morhua, captured off coastal Labrador, with samples taken in 1980 and 1986. Fish were captured by otter trawl offshore in the North Atlantic Fish Organisation subarea 2J. Parasites were removed from the digestive tract, stained, identified and compared between the different groups. Both the prevalence and mean abundance of trematodes, larval nematodes and E. gadi were significantly lower in fish taken in 2000 and 2003 than in 1980. While mean values of trematodes and nematodes declined in 1986, those of Echinorhynchus gadi remained unchanged in 1986 and 1990. Four-year-old cod sampled in 1990 harboured significantly fewer E. gadi than older age groups. The most commonly occurring trematodes included Podocotylereflexa, Lepidapedon elongatum, Derogenes varicus and Hemiurus levinseni while the larval nematode, Anisakis sp. was predominant. Comparison of offshore samples taken in 2000 and 2003 with others taken in previous years suggests an overall decline of parasites coincident with a change in climatic conditions, the absence of a major food source, namely capelin Mallotus villosus, of cod and ultimately the decline of the Labrador population.

scholarly journals Haemoglobin polymorphisms affect the oxygen-binding properties in Atlantic cod populations

2008 ◽  
Vol 276 (1658) ◽  
pp. 833-841 ◽  
Author(s):  
Øivind Andersen ◽  
Ola Frang Wetten ◽  
Maria Cristina De Rosa ◽  
Carl Andre ◽  
Cristiana Carelli Alinovi ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
Quaternary Structure ◽  
Atlantic Cod ◽  
Three Dimensional ◽  
Oxygen Affinity ◽  
Oxygen Binding ◽  
Low Oxygen ◽  
Binding Properties ◽  
Important Species ◽  
The North

A major challenge in evolutionary biology is to identify the genes underlying adaptation. The oxygen-transporting haemoglobins directly link external conditions with metabolic needs and therefore represent a unique system for studying environmental effects on molecular evolution. We have discovered two haemoglobin polymorphisms in Atlantic cod populations inhabiting varying temperature and oxygen regimes in the North Atlantic. Three-dimensional modelling of the tetrameric haemoglobin structure demonstrated that the two amino acid replacements Met55β 1 Val and Lys62β 1 Ala are located at crucial positions of the α 1 β 1 subunit interface and haem pocket, respectively. The replacements are proposed to affect the oxygen-binding properties by modifying the haemoglobin quaternary structure and electrostatic feature. Intriguingly, the same molecular mechanism for facilitating oxygen binding is found in avian species adapted to high altitudes, illustrating convergent evolution in water- and air-breathing vertebrates to reduction in environmental oxygen availability. Cod populations inhabiting the cold Arctic waters and the low-oxygen Baltic Sea seem well adapted to these conditions by possessing the high oxygen affinity Val55–Ala62 haplotype, while the temperature-insensitive Met55–Lys62 haplotype predominates in the southern populations. The distinct distributions of the functionally different haemoglobin variants indicate that the present biogeography of this ecologically and economically important species might be seriously affected by global warming.

scholarly journals Local cod (Gadus morhua) revealed by egg surveys and population genetic analysis after longstanding depletion on the Swedish Skagerrak coast

2018 ◽  
Vol 76 (2) ◽  
pp. 418-429 ◽  
Author(s):  
Henrik Svedäng ◽  
Julia M I Barth ◽  
Anders Svenson ◽  
Patrik Jonsson ◽  
Sissel Jentoft ◽  
...  
Keyword(s):  
North Sea ◽  
West Coast ◽  
Population Genetic ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Early Stage ◽  
Population Genetic Analysis ◽  
Swedish West Coast ◽  
The North ◽  
Spawning Areas

Abstract Dramatic and persistent reductions in Atlantic cod (Gadus morhua) are common in many coastal areas. While offshore cod stocks still were abundant and productive, the Swedish west coast showed signs of diminishing adult cod abundance at the beginning of the 1980s, where the local cod component was considered to be extirpated. To survey the present cod spawning activity and stock composition, we initiated egg trawling over two consecutive years (203 hauls in total) in combination with population genetic analyses (425 individually genotyped eggs). Here, we provide evidence of cod spawning at the Swedish Skagerrak coast, suggesting recolonization or that local cod has recovered from a nearly depleted state. Early stage eggs were found inside fjords too far to have been transported by oceanic drift from offshore spawning areas. The cod eggs were genetically similar in early to late life-stages and cluster mainly with the local adult cod, indicating that eggs and adults belong to the same genetic unit. The cod eggs were genetically differentiated from adult North Sea cod, and, to a lesser degree, also from the Kattegat and Öresund cod, i.e. indicating a possible recovery of local coastal stock. The patterns of the genetic structure in the inshore areas are, however, difficult to fully disentangle, as Atlantic cod in the North Sea-Skagerrak area seem to be a mixture of co-existing forms: local cod completing their entire life cycle in fjords and sheltered areas, and oceanic populations showing homing behaviours. The egg abundances are considerably lower compared with what is found in similar studies along the Norwegian Skagerrak coast. Nevertheless, the discovery of locally spawning cod along the Swedish west coast—although at low biomasses—is an encouraging finding that highlights the needs for endurance in protective measures and of detailed surveys to secure intraspecific biodiversity and ecosystem services.

Movements and distribution of cod (Gadus morhua) in the southern North Sea and English Channel: results from conventional and electronic tagging experiments

2007 ◽  
Vol 87 (2) ◽  
pp. 599-613 ◽  
Author(s):  
David Righton ◽  
Victoria Anne Quayle ◽  
Stuart Hetherington ◽  
Gary Burt
Keyword(s):  
North Sea ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
English Channel ◽  
Seasonal Movement ◽  
Southern North Sea ◽  
The North ◽  
Fisheries Policy ◽  
The Uk ◽  
Electronic Tags

The sub-structure of Atlantic cod (Gadus morhua) stocks in the North Sea has important consequences for fisheries management as the Common Fisheries Policy moves towards a more regional approach. We investigated the movements, distribution and behaviour of cod in the southern North Sea (ICES IVc) and English Channel (ICES VIId) by re-analysing historic data from conventional tagging experiments, and by conducting new experiments with electronic tags. Cod tagged and released in IVc showed a northwards shift in distribution during the feeding season consistent with a homing migration away from spawning grounds along the coasts of the UK and the Netherlands. In contrast, cod tagged and released in VIId did not exhibit a consistent pattern of seasonal movement. Many cod released in VIId were subsequently recaptured close to their release position, although some moved out of the Channel and into the southern North Sea. Overlap between the recapture areas of cod released in the different management areas was no more than 25% in either the spawning or feeding season. Behavioural data from electronic tags suggest that cod in IVc make use of tidal streams to migrate northwards and eastwards in spring, whereas selective tidal stream transport was rarely exhibited by cod tagged and released in VIId. Overall, the evidence suggests that there are behavioural differences between cod in IVc and VIId that limit the mixing of cod from these two areas during the feeding and spawning seasons.

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