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Deep investigation of the microbiome of food-production and food-processing environments through whole-metagenome sequencing (WMS) can provide detailed information on the taxonomic composition and functional potential of the microbial communities that inhabit them, with huge potential benefits for environmental monitoring programs. However, certain technical challenges jeopardize the application of WMS technologies with this aim, with the most relevant one being the recovery of a sufficient amount of DNA from the frequently low-biomass samples collected from the equipment, tools and surfaces of food-processing plants.

Here, we present the first complete workflow, with optimized DNA-purification methodology, to obtain high-quality WMS sequencing results from samples taken from food-production and food-processing environments and reconstruct metagenome assembled genomes (MAGs). The protocol can yield DNA loads >10 ng in >98% of samples and >500 ng in 57.1% of samples and allows the collection of, on average, 12.2 MAGs per sample (with up to 62 MAGs in a single sample) in ~1 week, including both laboratory and computational work. This markedly improves on results previously obtained in studies performing WMS of processing environments and using other protocols not specifically developed to sequence these types of sample, in which <2 MAGs per sample were obtained. The full protocol has been developed and applied in the framework of the European Union project MASTER (Microbiome applications for sustainable food systems through technologies and enterprise) in 114 food-processing facilities from different production sectors.

The muscle structure and composition may vary along the different portions of fish fillets, which can complicate the quality and storage stability of products. Loins and tails from Atlantic cod (Gadus morhua) and redfish (Sebastes marinus) fillets were therefore stored at −25 °C up to 16 months and 20 months, respectively, to investigate the quality changes influenced by the duration of frozen storage within the fillet portions. Throughout the storage period, the loss of total sulfhydryl groups correlates with increased disulfide bonds, indicating partial oxidative protein degradation. This may be linked with protein denaturation as evidenced by the decrease of soluble proteins, as well as decreased water holding capacity and increased thawing drip loss and cooking loss. The results from the cod samples reveal that stronger degradation changes occur in the tail. The loin, therefore, had more storage stability as well as higher nutritional value. However, other quality attributes were similar between the two portions in the redfish fillets. Higher free fatty acid (FFA) values, lower soluble protein contents, and higher disulfide bond contents were obtained in the cod samples compared to the redfish samples at the same storage time, indicating that lipid hydrolysis and protein degradation effects were stronger in the cod ( lean fish) compared to redfish (medium fat species).

Link to article.

Contact

Jónas Rúnar Viðarsson

Sviðsstjóri rannsókna

jonas@matis.is

A prototype for a Responsive Fisheries Management System (RFMS) was developed in the context of the European FP7 project EcoFishMan and tested on the Portuguese crustacean trawl fishery. Building on Results Based Management principles, RFMS involves the definition of specific and measurable objectives for a fishery by the relevant authorities but allows resource users the freedom to find ways to achieve the objectives and to provide adequate documentation. Taking into account the main goals of the new Common Fisheries Policy, such as sustainable utilization of the resources, end of discards and unwanted catches, a management plan for the Portuguese crustacean trawl fishery was developed in cooperation with the fishing industry, following the process and design laid out in the RFMS concept. The plan considers biological, social and economic goals and assigns a responsibility for increased data collection to the resource users. The performance of the plan with regard to selected indicators was evaluated through simulations. In this paper the process towards a RFMS is described and the lessons learned from the interaction with stakeholders in the development of an alternative management plan are discussed.

Contact

Jónas Rúnar Viðarsson

Sviðsstjóri rannsókna

jonas@matis.is

The reformed Common Fisheries Policy (CFP), adopted by the European Union in 2013, aims to achieve sustainable exploitation of marine resources. Beyond the mainstream of stakeholders' engagement, the literature increasingly calls for shared accountability in fisheries management. In such scenarios, identifying stakeholders' insights becomes critical for a successful design of innovative management approaches. This paper analyzes how the stakeholders perceive a results-based management system for four fisheries in different European sea-basins as well as at a pan-European level. The results indicate a need for adaptive spirit participatory management approaches, building on regional adaptations within transparent and plural frameworks for fisheries. To succeed, the system should explicitly address its associated public and private costs; neither participation nor accountability comes for free.

Contact

Sæmundur Sveinsson

Research Group Leader

saemundurs@matis.is

Objective

Sidalcea is a genus of flowering plants restricted to the west coast of North America, commonly known as checkermallows. Remarkably, of the ~ 30 recognized species, 16 are of conservation concern (vulnerable, imperiled or critically imperiled). To facilitate biological studies in this genus, and in the wider Malvaceae, we have sequenced the whole plastid genome of Sidalcea hendersonii. This will allow us both to check those regions already developed as general Malvaceae markers in a previous study, and to search for new regions.

Results

By comparing the Sidalcea genome to that of Althaea, we have identified a hypervariable approximately 1 kb region in the short single copy region. This region shows promise for examining phylogeographic patterns, hybridization and haplotype diversity. Remarkably, considering the conservation of plastome architecture between Sidalcea and Althaea, the former has a 237 bp deletion in the otherwise highly conserved inverted repeat region. Newly designed primers provide a PCR assay to determine the presence of this indel across the Malvaceae. Screening of previously designed chloroplast microsatellite markers indicates two markers with variation within S. hendersonii that would be useful in future population conservation genetics.

Capelin (Mallotus villosus) is both an important commercial and ecological resource of the North Atlantic subpolar region. Two decades ago, the stock distribution around Iceland drastically changed. During autumn, which corresponds to the main feeding period, the capelin stock was previously located between the North of Iceland and the Jan Mayen area. Since the beginning of 2000s, the feeding aggregation has been located at the east coast of Greenland, inducing slight changes in the timing and route of the capelin spawning migration along the Icelandic shelf, and therefore in the catches. Changes in the distribution of capelin around Iceland made it both more difficult and expensive to assess the distribution of the stock with current survey methods. Here, we compare environmental DNA (eDNA) data to the acoustic data collected during the autumn monitoring survey, which leads to a preliminary estimate of the stock size. eDNA samples were collected at five different depths and were analyzed both horizontally across latitudes and longitudes and vertically across depth profiles. We detected eDNA in most of the locations where acoustic data detected capelin. Generalized linear models suggested that eDNA concentrations can be used as a proxy for the detection and quantification of capelin. The horizontal distribution of eDNA observed during both years corresponds with the horizontal distribution of capelin registered with the acoustic approach, while the vertical distribution indicates both effects of oceanic currents and diel vertical migration on eDNA detection and quantification.

Contact

Sophie Jensen

Project Manager

sophie.jensen@matis.is

Shark is a unique traditional Icelandic product and is obtained by fermenting and drying Greenland shark (Somniosus microcephalus). However, little is known about the chemical and microbial changes occurring during the process. In this small-scale industrial study, fresh and frozen shark meat was fermented for eight and seven weeks, respectively, and then dried for five weeks. During the fermentation, trimethylamine N-oxide levels decreased to below the limit of detection within five weeks and pH increased from about 6 to 9. Simultaneously, trimethylamine and dimethylamine levels increased significantly. Totally viable plate counts, and specific spoilage organisms increased during the first weeks of the fermentation period but decreased during drying. Culture-independent analyzes (16S rRNA) revealed gradual shifts in the bacterial community structure as fermentation progressed, dividing the fermentation process into three distinct phases but stayed rather similar throughout the drying process. During the first three weeks of fermentation, Photobacterium was dominant in the fresh group, compared to Pseudoalteromonas in the frozen group. However, as the fermentation progressed, the groups became more alike Atopotypes, Pseudomonas and Tissierella being dominant. The PCA analysis done on the chemical variables and 16S rRNA analysis variables confirmed the correlation between high concentrations of TMAO and Pseudoalteromonas, and Photobacterium at the initial fermentation phase. During the final fermentation phase, correlation was detected between high concentrations of TMA/DMA and Atopotypes, Pseudomonas and Tissierella. The results indicate the possibility of shortening the fermentation period and it is suggested that the microbial community can potentially be standardized with starter cultures to gain an optimal fermentation procedure.

Genetic mixing with farmed salmon can change the genetic composition of wild populations, lead to changes in life history parameters and even cause population decline. In Iceland, aquaculture of salmon of Norwegian origin is a growing industry. The production of farmed salmon has gone from almost nothing in 2010 to 43,000 tons in 2022. According to the current advice of the Norwegian Marine Research Institute (risk assessment of genetic mixing), it is estimated that it is possible to raise 106,500 tons of fertile salmon without causing a negative impact on useful wild populations. salmon

In a genetic study from 2017, where 15 microsatellites were used, signs of genetic admixture were found in rivers close to seagull farming in the Westfjords. In this study, salmon samples were taken in rivers around the country and the number of samples was almost ten times higher. A total of 6,348 salmon fry from 89 rivers were studied and emphasis was placed on areas in the vicinity of sea pig farming.

Most samples belonged to the spawning cohorts of 2014-2018, when the production of farmed salmon was around 6,900 tons on average. Samples were genetically analyzed with 60,250 alleles (SNP genetic boundaries) and the genetic information of 250 farmed salmon was used for comparison. The coefficient of genetic difference (FST) between Icelandic salmon and farmed salmon was 0.14 on average (based on 34,700 SNPs) and 0.62 for the genetic boundaries that showed the greatest separation between the two groups (196 SNPs). Genetic admixture was analyzed by multivariate analysis (PCA) and in the models of the programs ADMIXTURE, STRUCTURE and NewHybrids.

A total of 133 first-generation hybrids (offspring of farmed and wild salmon) were detected in 17 rivers (2.1% samples, within 18% rivers). Older admixture (second generation or older) was detected in 141 juveniles in 26 rivers (2.2% samples, within 29% rivers). First-generation hybrids were more common in the Westfjords than in the Eastfjords, which is consistent with the fact that the fire in the Eastfjords started later and has been less extensive.

Hybridization was usually detected less than 50 km away from breeding areas, but some hybrids were found up to 250 km away. On the other hand, older genetic admixture was more frequent in the Eastfjords than in the Westfjords and is most likely related to the fire that operated there at the beginning of this century. Older genetic admixture was most evident in Breiðdalsá and was detected in 32% (72 out of 228) of the juveniles. More research is needed on the intergenerational distribution of hybrids, the extent and causes of the spread of older admixtures.

As mentioned above, the study analyzed the effects from the early years of the current farming, when production volumes were low, and older experiments in sea pig farming. The results in this report show that genetic mixing has occurred at relatively low breeding rates.

In book: The World of Sea Cucumbers, Challenges, Advances, and Innovations. 1st Edition, pp. Editors: Annie Mercier, Jean-Francois Hamel, Andrew Suhrbier, Christopher Pearce. ISBN: 9780323953771.