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Background

The bacteriology during storage of the North Atlantic cod has been investigated for the past decades using conventional cultivation strategies which have generated large amount of information. This paper presents a study where both conventional cultivation and cultivation independent approaches were used to investigate the bacterial succession during storage of cod loins at chilled and superchilled temperatures.

Results

Unbrined (0.4% NaCl) and brined (2.5% NaCl) cod loins were stored at chilled (0 ° C) and superchilled (-2 and -3.6 ° C) temperatures in air or modified atmosphere (MA, % CO₂/ O₂/ N₂: 49.0 ± 0.6 / 7.4 ± 0.2 / 43.7 ± 0.4). Discrepancy was observed between cultivation enumeration and culture independent methods where the former showed a general dominance of Pseudomonas spp. (up to 59%) while the latter showed a dominance of Photobacterium phosphoreum (up to 100%).

Gas chromatography-mass spectrophotometry (GC-MC) showed that trimethylamine was the most abundantly volatile in mid- and late storage periods. Terminal restriction polymorphism (t-RFLP) analysis showed that the relative abundance of P. phosphoreum increased with storage time.

Conclusion

The present study shows the bacteriological developments on lightly salted or non-salted cod loins during storage at superchilled temperatures. It furthermore confirms the importance of P. phosphoreum as a spoilage organism during storage of cod loins at low temperatures using molecular techniques. The methods used compensate each other, giving more detailed data on bacterial population developments during spoilage.

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Atlantic herring (Clupea harengus) is an important commercial fish and shows to be more and more demanded for human consumption. Therefore, it is very important to find good methods for monitoring the freshness of the fish in order to keep it in the best quality for human consumption. In this study, the fish was stored in ice up to 2 weeks. Quality changes during storage were assessed by the Quality Index Method (QIM), quantitative descriptive analysis (QDA) and Torry scheme, by texture measurements: puncture tests and Texture Profile Analysis (TPA) tests on texture analyzer TA.XT2i, and by electronic nose (e-nose) measurements using FreshSense instrument. Storage time of herring in ice could be estimated by QIM with ± 2 days using 5 herring per lot. No correlation between instrumental texture parameters and storage time or between sensory and instrumental texture variables was found. E-nose measurements could be used to detect the onset of spoilage.

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In 2006, we sampled the anoxic bottom waters of a volcanic lake beneath the Vatnajökull ice cap (Iceland). The sample contained 5 × 10⁵ cells per ml, and whole-cell fluorescent in situ hybridization (FISH) and PCR with domain-specific probes showed these to be essentially all bacteria, with no detectable archaea. Pyrosequencing of the V6 hypervariable region of the 16S ribosomal RNA gene, Sanger sequencing of a clone library and FISH-based enumeration of four major phylotypes revealed that the assembly was dominated by a few groups of putative chemotrophic bacteria whose closest cultivated relatives use sulfide, sulfur or hydrogen as electron donors, and oxygen, sulfate or CO₂ as electron acceptors. Hundreds of other phylotypes are present at lower abundance in our V6 tag libraries and a rarefaction analysis indicates that sampling did not reach saturation, but FISH data limit the remaining biome to <10–20% of all cells. The composition of this oligarchy can be understood in the context of the chemical disequilibrium created by the mixing of sulfidic lake water and oxygenated glacial meltwater.

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Volatile compounds in cold smoked salmon products were identified by gas chromatography to study their suitability for rapid detection as indicators to predict sensory quality evaluated by quantitative descriptive analysis. Smoked salmon odor contributed by guaiacol, boiled potato- and mushroom-like odors characteristic of fish lipid degradation and sweet odors associated with the microbial metabolites 3-methyl-butanal and 3-hydroxybutanone were the most intense odors. Other key volatiles were present in high levels but contributed less to the odors. These included furan-like compounds originating from the smoking, spoilage compounds like ethanol, 3-methyl-1-butanol, 2-butanone, and acetic acid along with oxidatively derived compounds like 1-penten-3-ol, hexanal, nonanal and decanal . Partial least square regression models based on data from storage studies of cold smoked salmon from Iceland and Norway verified that selected key volatile compounds performed better as predictors to explain variation in sensory attributes (smoked, sweet / sour rancid and off odor and flavor) than traditional chemical and microbial variables.

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During the past decade, genetic markers have been used increasingly to improve stock discrimination and to aid fisheries management. Today, the Icelandic and Faroese Plateau cod (Gadus morhua) are managed as separate units, belonging to ICES Subareas Va and Vb1, respectively. There is little information on the genetic connectivity of the two units, however, except in terms of tagging experiments which revealed limited adult migration between the two areas, and few genetic studies describing genetic differentiation among Faroese and East Icelandic cod. Here, previously published data on the genetic structure of Icelandic cod were combined with new data from the Faroe Plateau to assess the level and the source of genetic variability of Atlantic cod around the Iceland – Faroe Ridge and the potential sources of genetic variation. In all, 771 cod were genotyped at nine microsatellite loci and at the Pantophysin locus (Pan I). The genetic markers employed were congruent and showed that South Icelandic and East Icelandic – Faroese Plateau populations have limited genetic connectivity. Diversifying selection associated with restricted gene flow is likely to explain the observed pattern with the Pan I locus. Further analyzes detected historical imprints in the microsatellite data, suggesting that the divergence could be due to isolation of different cod populations during the last glacial maximum.

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Most studies of the genetic structure of Atlantic cod have focused on small geographical scales. In the present study, the genetic structure of cod sampled on spawning grounds in the North Atlantic was examined using eight microsatellite loci and the Pan I locus. A total of 954 cod was collected from nine different regions: the Baltic Sea, the North Sea, the Celtic Sea, the Irish Sea and Icelandic waters during spring 2002 and spring 2003, from Norwegian waters and the Faroe Islands (North and West spawning grounds ) in spring 2003, and from Canadian waters in 1998. Temporal stability among spawning grounds was observed in Icelandic waters and the Celtic Sea, and no significant difference was observed between the samples from the Baltic Sea and between the samples from Faroese waters. F-statistics showed significant differences between most populations and a pattern of isolation-by-distance was described with microsatellite loci. The Pan I locus revealed the presence of two genetically distinguishable basins, the North-west Atlantic composed of the Icelandic and Canadian samples and the North-east Atlantic composed of all other samples. Permutation of allele sizes at each microsatellite locus among allelic states supported a mutational component to the genetic differentiation, indicating a historical origin of the observed variation. Estimation of the time of divergence was approximately 3000 generations, which places the origin of current genetic pattern of cod in the North Atlantic in the late Weichselian (Wisconsinian period), at last glacial maximum.

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The identification of North Atlantic redfish has been controversial and remains a difficult task due to overlapping of meristic and morphological characters. Here we used nine microsatellite loci to assess the level of genetic differentiation among these species and assess the resolution power of these microsatellite loci for individual assignment-based analyzes. Conventional analyzes as well as individual Bayesian assignment methods clearly separated the four species of North Atlantic redfish as well as the giant form of Sebastes marinus and the so-called “oceanic” and “deep-sea” types of Sebastes mentella. Locus-by-locus analyzes revealed that only five microsatellite loci out of nine used could discriminate the species concerned. The advantage of the Bayesian methods relies in the individual information retrieved. It therefore gave additional information on the interrelationship among species. Indeed, we provide evidence of potential hybridization among species as well as individual misclassification based on morphological identification. We provide a powerful tool to discriminate North Atlantic redfish species, which might be useful for legal issues such as poaching, unintentional harvesting and control label.

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The deepwater redfish Sebastes mentella has a wide distribution in the North Atlantic Ocean. In the Irminger Sea, there is evidence for two phenotypes (deep-sea and oceanic) of deepwater redfish. The two phenotypes have overlapping geographic distributions but differ in depth preferences. There are two hypotheses on deepwater redfish stock structure in the Irminger Sea. One suggests that mature individuals of a single stock segregate according to size and age and therefore that the phenotypes represent different life stages of the same stock. The other hypothesis suggests that there are two different stocks and that these stocks segregate mainly according to depth. Additionally, it is not clear whether the fish of the deep-sea phenotype in the Irminger Sea and those on the Icelandic continental shelf represent one stock. Analysis of genetic variability at eight allozyme markers in 1,763 deepwater redfish from 26 samples collected at different depths in the Irminger Sea and the Icelandic continental slope showed a significant difference between deep-sea and oceanic samples, suggesting the presence of two distinguishable stocks. This is supported by (1) significant heterozygous deficiency at most loci in pooled samples, (2) extensive allele frequency differences between samples classified as belonging to deep-sea and oceanic phenotypes, and (3) clustering of deepwater redfish samples of the same phenotype in a neighbor-joining dendrogram and in Bayesian analyzes (STRUCTURE and the ΔK procedure for determining the number of clusters). The results indicate that deepwater redfish stock structure should be taken into account for sustainable fisheries management in the Irminger Sea and adjacent waters.

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In many cases marine organisms and especially their diverse developmental stages are difficult to identify by morphological characters. DNA-based identification methods offer an analytically powerful addition or even
an alternative. In this study, a DNA microarray has been developed to be able to investigate its potential as a tool for the identification of fish species from European seas based on mitochondrial 16S rDNA sequences. Eleven commercially important fish species were selected for a first prototype. Oligonucleotide probes were designed based on the 16S rDNA sequences obtained from 230 individuals of 27 fish species. In addition, more than 1200 sequences of 380 species served as sequence background against which the specificity of the probes was tested in silico. Single target
hybridizations with Cy5-labeled, PCR-amplified 16S rDNA fragments from each of the 11 species on microarrays containing the complete set of probes confirmed their suitability. True-positive, fluorescence signals obtained were at least one order of magnitude stronger than false-positive
cross-hybridizations. Single nontarget hybridizations resulted in cross-hybridization signals at approximately 27% of the cases tested, but all of them were at least one order of magnitude lower than true-positive signals. This study demonstrates that the 16S rDNA gene is suitable for designing oligonucleotide probes, which can be used to differentiate 11 fish species. These data are a solid basis for the second step to create a “Fish Chip” for approximately 50 fish species relevant in marine environmental and fisheries research, as well as control of fisheries products.

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