Flokkur: Greinar

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 correlated 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 occurred 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).

Hlekkur að grein.

Tengiliður

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 learnt from the interaction with stakeholders in the development of an alternative management plan are discussed.

Tengiliður

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 analyses 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 and 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.

Tengiliður

Sæmundur Sveinsson

Fagstjóri

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, imperilled or critically imperilled). 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 circa 1 kb region in the short single copy region. This region shows promise for examining phylogeographic pattern, 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 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 estimation 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 indicated both effects of oceanic currents and diel vertical migration on eDNA detection and quantification.

Tengiliður

Sophie Jensen

Verkefnastjóri

sophie.jensen@matis.is

Hákarl 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. Total viable plate counts, and specific spoilage organisms increased during the first weeks of the fermentation period but decreased during drying. Culture-independent analyses (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 with Atopostipes, 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 Atopostipes, Pseudomonas and Tissierella. The results indicate the possibility to 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.

Erfðablöndun við eldislax getur breytt erfðasamsetningu villtra stofna, leitt af sér breytingum í lífsögulegum þáttum og jafnvel valdið hnignun stofna. Á Íslandi er sjókvíaeldi á laxi af norskum uppruna vaxandi atvinnugrein. Framleiðsla á eldislaxi hefur farið úr því að vera nánast engin árið 2010 upp í 43.000 tonn árið 2022. Samkvæmt núgildandi ráðgjöf Hafrannsóknastofnunar (áhættumat erfðablöndunar) er talið að hægt sé að ala 106.500 tonn af frjóum laxi án þess að það valdi neikvæðum áhrifum á nytjastofna villtra laxa.

Í erfðarannsókn frá 2017, þar sem notast var við 15 örtungl (e. microsatellites), fundust merki um erfðablöndun í ám í nálægð við sjókvíaeldi á Vestfjörðum. Í þessari rannsókn voru laxasýni tekin í ám hringinn í kringum landið og sýnafjöldi var tæplega tíu sinnum meiri. Alls voru 6.348 laxaseiði úr 89 ám rannsökuð og áhersla lögð á svæði í nálægð við sjókvíaeldi.

Flest sýni tilheyrðu hrygningarárgöngum 2014-2018 þegar framleiðsla á eldislaxi var um 6.900 tonn að meðaltali. Sýni voru erfðagreind með 60.250 samsætum (SNP-erfðamörkum) og erfðaupplýsingar 250 eldislaxa nýttar til samanburðar. Stuðull erfðamunar (FST) milli íslenskra laxa og eldislaxa var 0,14 að meðaltali (miðað við 34.700 SNP) og 0,62 fyrir þau erfðamörk sem sýndu mestan aðskilnað milli hópanna tveggja (196 SNP). Erfðablöndun var greind með fjölþáttagreiningu (PCA) og í líkönum forritanna ADMIXTURE, STRUCTURE og NewHybrids.

Alls greindust 133 fyrstu kynslóðar blendingar (afkvæmi eldislaxa og villtra laxa) í 17 ám (2,1% sýna, innan 18% áa). Eldri blöndun (önnur kynslóð eða eldri) greindist í 141 seiðum í 26 ám (2,2% sýna, innan 29% áa). Fyrstu kynslóðar blendingar voru algengari á Vestfjörðum en Austfjörðum sem er í samræmi við að eldið á Austfjörðum hófst síðar og hefur verið umfangsminna.

Erfðablöndun greindist yfirleitt í minna en 50 km fjarlægð frá eldissvæðum en nokkrir blendingar fundust í allt að 250 km fjarlægð. Aftur á móti var eldri erfðablöndun tíðari á Austfjörðum en Vestfjörðum og tengist líklegast eldinu sem þar var starfrækt í byrjun þessarar aldar. Eldri erfðablöndun var mest áberandi í Breiðdalsá og greindist í 32% (72 af 228) seiðanna. Þörf er á frekari rannsóknum á kynslóðaskiptingu blendinga, umfangi og orsökum dreifingar eldri blöndunar.

Rannsóknin greindi sem fyrr segir áhrif frá upphafsárum núverandi eldis, meðan framleiðslumagn var lítið, og eldri tilrauna í sjókvíaeldi. Niðurstöðurnar í þessari skýrslu sýna að erfðablöndun hefur orðið við hlutfallslega lítið eldismagn.

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.