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.

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 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 Environmentally mediated trends in otolith composition of juvenile Atlantic cod (Gadus morhua)

2015 ◽  
Vol 72 (8) ◽  
pp. 2350-2363 ◽  
Author(s):  
Ryan R. E. Stanley ◽  
Ian R. Bradbury ◽  
Claudio DiBacco ◽  
Paul V. R. Snelgrove ◽  
Simon R. Thorrold ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Inductively Coupled Plasma ◽  
Life Histories ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Environmental Influence ◽  
Inductively Coupled ◽  
Baseline Information ◽  
Significant Temperature ◽  
Species Specific

Abstract We evaluated the influence of environmental exposure of juvenile Atlantic cod (Gadus morhua) to inform interpretations of natal origins and movement patterns using otolith geochemistry. Laboratory rearing experiments were conducted with a variety of temperature (∼5, 8.5, and 12°C) and salinity (∼25, 28.5, and 32 PSU) combinations. We measured magnesium (Mg), manganese (Mn), strontium (Sr), and barium (Ba), expressed as a ratio to calcium (Ca), using laser ablation inductively coupled plasma mass spectrometry (ICP-MS), and stable carbon (δ13C) and oxygen (δ18O) isotopes using isotope ratio monitoring mass spectrometry. Temperature and salinity significantly affected all elements and isotopes measured, except salinity on Mg:Ca. We detected significant interactions among temperature and salinity for Mn:Ca and Ba:Ca partition coefficients (ratio of otolith chemistry to water chemistry), with significant temperature effects only detected in the 32 and 28.5 PSU salinity treatments. Similarly, we detected a significant interaction between temperature and salinity in incorporation of δ13C, with a significant temperature effect except at intermediate salinity. These results support the contention that environmental mediation of otolith composition varies among species, thus limiting the ability of generalized models to infer life history patterns from chemistry. Our results provide essential baseline information detailing environmental influence on juvenile Atlantic cod otolith composition, punctuating the importance of laboratory validations to translate species-specific otolith composition when inferring in situ life histories and movements.

scholarly journals The use of species-specific TaqMan probes for identifying early stage gadoid eggs following formaldehyde fixation

2008 ◽  
Vol 65 (9) ◽  
pp. 1573-1577 ◽  
Author(s):  
Freya Goodsir ◽  
Michael J. Armstrong ◽  
Peter R. Witthames ◽  
David L. Maxwell ◽  
Clive J. Fox
Keyword(s):  
Gadus Morhua ◽  
Atlantic Cod ◽  
Early Stage ◽  
Melanogrammus Aeglefinus ◽  
Fish Eggs ◽  
Important Species ◽  
Taqman Probes ◽  
Positive Rate ◽  
Identification Technique ◽  
Species Specific

Abstract Goodsir, F., Armstrong, M. J., Witthames, P. R., Maxwell, D. L., and Fox, C. J. 2008. The use of species-specific TaqMan probes for identifying early stage gadoid eggs following formaldehyde fixation. – ICES Journal of Marine Science, 65: 1573–1577. Surveys of fish eggs are increasingly being used to monitor the spawning areas and stock status of commercially important species such as Atlantic cod (Gadus morhua), but early stage cod eggs are visually indistinguishable from those of several other common co-occurring species, including haddock (Melanogrammus aeglefinus) and whiting (Merlangius merlangus). In recent surveys in the Irish and North Seas, a molecular identification technique (TaqMan multiplex real-time polymerase chain-reaction) assay has been used to overcome this problem. The method needs high-quality DNA, so the current protocol requires that individual “cod-like” eggs are “presorted” from plankton hauls on board ship and immediately preserved in ethanol. This increases seagoing staff costs, can be a difficult process at sea, and means that plankton sampling cannot be undertaken from non-specialized vessels such as fishing boats. Successful application of TaqMan probes to DNA from eggs preserved in formalin would overcome these problems, but previous attempts have resulted in poor success. In this study, batches of hatchery-sourced cod, haddock, and whiting eggs were fixed in 4% buffered formalin for up to 3 weeks, then transferred to a formaldehyde-free solution for 1, 2, or 3 months. After these periods they were assessed visually for fixation quality and analysed using species-specific TaqMan probes. Eggs, which had been fixed for up to 3 weeks in formalin, were identified successfully, although the positive rate (84–96%) was slightly lower than samples preserved throughout in ethanol (92–99%). There was no increase in the percentage of eggs misidentified comparing formalin-fixed and ethanol-preserved material. These results suggest that TaqMan probes can be applied successfully to fish eggs fixed in 4% buffered formalin for up to 3 weeks.

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

2019 ◽  
Vol 21 (7) ◽  
pp. 2576-2594 ◽  
Author(s):  
Even Sannes Riiser ◽  
Thomas H.A. Haverkamp ◽  
Srinidhi Varadharajan ◽  
Ørnulf Borgan ◽  
Kjetill S. Jakobsen ◽  
...  
Keyword(s):  
Atlantic Cod ◽  
Shotgun Sequencing ◽  
Intestinal Microbiome

Discarding practices for commercial gadoids in the North Sea

1998 ◽  
Vol 55 (7) ◽  
pp. 1632-1644 ◽  
Author(s):  
Yorgos Stratoudakis ◽  
Robert J Fryer ◽  
Robin M Cook
Keyword(s):  
North Sea ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Melanogrammus Aeglefinus ◽  
The North ◽  
The North Sea ◽  
Merlangius Merlangus ◽  
Using Data ◽  
Species Specific ◽  
Catch Composition

Understanding fishers' discarding behaviour, and anticipating their reactions to changes in the biological or regulatory characteristics of a fishery, are important for dealing with the problem of discarding. In this paper, we investigate the discarding of haddock (Melanogrammus aeglefinus), whiting (Merlangius merlangus), and Atlantic cod (Gadus morhua) in the North Sea, using data collected by scientific observers onboard Scottish demersal vessels. We describe discarding on each trip by species-specific discard curves and explore how these curves depend on biological and regulatory variables. There are large differences in the size of discarded fish between inshore and offshore areas, with offshore-operating vessels discarding larger fish (high-grading). Increases in legal landing size correspond to immediate increases in the size of discarded fish, particularly for haddock and cod in inshore areas. In general, discarding practices for haddock and cod are similar over time and consistent across gears, whereas decisions for the lesser valued whiting are more variable and can be affected by the catch composition.

Species-specific residence times in the aft part of a pelagic survey trawl: implications for inference of pre-capture spatial distribution using the Deep Vision system

2018 ◽  
Vol 75 (4) ◽  
pp. 1393-1404 ◽  
Author(s):  
Melanie J Underwood ◽  
Shale Rosen ◽  
Arill Engås ◽  
Terje Jørgensen ◽  
Anders Fernö
Keyword(s):  
Spatial Distribution ◽  
Residence Time ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Vision System ◽  
Ground Truth ◽  
Clupea Harengus ◽  
Melanogrammus Aeglefinus ◽  
Camera System ◽  
Species Specific

Abstract In-trawl camera systems promise to improve the resolution of trawl sampling used to ground-truth the interpretation of acoustic survey data. In this study, the residence time of fish in front of the Deep Vision camera system, used to identify, measure and count fish inside the trawl, was analysed to determine the reliability of spatial distribution recorded by the system. Although Atlantic herring (Clupea harengus), haddock (Melanogrammus aeglefinus), and most Atlantic cod (Gadus morhua) moved quickly back through the aft part of the pelagic trawl, saithe (Pollachius virens) spent up to 4 min in front of the system. The residence time increased for saithe and cod when other individuals were present, and cod swimming in the low water flow close to the trawl netting spent longer there than cod at the centre of the trawl. Surprisingly, residence time was not related to the size of the fish, which may be explained by the collective behaviour of shoaling fish. Our findings suggest that while in-trawl images can be used to identify, measure and count most species, when sampling fast-swimming species such as saithe the position inferred from when they were imaged may not reflect the actual spatial distribution prior to capture.

Predicting Recruitment Variation from Year Class Specific Vertebral Counts: An Analysis of the Potential and a Plan for Verification

1991 ◽  
Vol 48 (8) ◽  
pp. 1350-1357 ◽  
Author(s):  
Kenneth T. Frank
Keyword(s):  
Environmental Factors ◽  
North Sea ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Negative Relationship ◽  
Early Life History ◽  
Clupea Harengus ◽  
Melanogrammus Aeglefinus ◽  
Southern Limit ◽  
Stock Discrimination

Recruitment prediction has been an elusive and seemingly unobtainable goal with no entirely satisfactory general approach yet available. I propose the use of meristic variation, traditionally applied to problems associated with stock discrimination studies, as a new method to predict recruitment variation. The approach is evaluated using literature data on year class strength (YCS) and year class specific average vertebral counts (VS), two apparently interrelated variables that are affected by environmental factors operating during the early life history. Three marine stocks at the southern limit of their species geographic range (Georges Bank haddock (Melanogrammus aeglefinus), North Sea Atlantic cod (Gadus morhua), and North Sea Atlantic herring (Clupea harengus hargenus)) and one stock at its northern limit (Pacific herring (Clupea harengus pallasi)) generally conformed to the prediction of a positive relationship between YCS and VS for southern stocks and a negative relationship for northern stocks. Exceptions to these patterns were found among stocks showing low temporal variability in recruitment or for stocks whose year class formation is not linked to environmental factors that establish the vertebral count of a year class. The approach adopted is consistent with the growing initiative of focusing on characteristics of the survivors of a population to provide insight into recruitment mechanisms.

Stock Discrimination Using Otolith Shape Analysis

1993 ◽  
Vol 50 (5) ◽  
pp. 1062-1083 ◽  
Author(s):  
Steven E. Campana ◽  
John M. Casselman
Keyword(s):  
Growth Rate ◽  
Shape Analysis ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Otolith Shape ◽  
Otolith Shape Analysis ◽  
Stock Discrimination ◽  
The Difference ◽  
Highly Correlated ◽  
Species Specific

Otolith shape has long been known to be species specific, but recent reports have pointed to its value as an indicator of stock identity. To test this hypothesis, all three pairs of otoliths were sampled from 2349 Atlantic cod (Gadus morhua) collected on spawning grounds throughout the northwest Atlantic. Otolith shape was determined with Fourier analysis and combined with measures of otolith area and perimeter. There were highly significant differences in otolith shape among most of the cod samples, but shape also differed among ages, sexes, and year-classes. The sagittal otoliths (largest pair) provided slightly better stock discrimination than did the lapillar or asteriscal otoliths. The first discriminant function was highly correlated with both fish and otolith growth rate, indicating that stock discrimination improved as the difference in stock-specific growth rate increased. Reevaluation of published studies on other species indicated that growth rate contributes more variation to regional differences in otolith shape than does stock origin. Differences in otolith shape among ages, sexes, and year-classes were also attributable to growth rate differences. To the extent that growth rates vary more between than within stocks, otolith shape analysis can provide an easily determined measure of stock identity.

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