Category: Reports

Reports

Optimized Chilling Protocols for Fresh Fish

Published:

01/12/2010

Authors:

Björn Margeirsson, Hélène L. Lauzon, Lárus Þorvaldsson, Sveinn Víkingur Árnason, Sigurjón Arason, Kristín Líf Valtýsdóttir, Emilía Martinsdóttir

Supported by:

AVS R&D Fund of Ministry of Fisheries in Iceland, the Technology Development Fund at the Icelandic Center for Research, University of Iceland Research Fund and EU (contract FP6-016333-2)

Contact

Sigurjón Arason

Chief Engineer

sigurjon.arason@matis.is

Optimized Chilling Protocols for Fresh Fish

Guidelines for cooling fresh fish describe the most effective cooling methods at all stages of the cooling chain, with an emphasis on white fish. It describes how to best cool and maintain temperatures in order to maximize product quality and safety and reduce costs and energy consumption. The report contains background information for instructions in the information source Kæligátt on Matís' website, which is presented in a user-friendly way in Icelandic www.kaeligatt.is and English www.chillfish.net. The guidelines are intended for fishermen, manufacturers, carriers and other members of the value chain. The guidelines are based on research that has been carried out within research projects such as Chill ‐ on, Simulation of cooling processes and Cooling improvement. The main chapters deal with refrigeration on board, during processing, during packing, transport and storage of fish.

The overall aim of the optimized chilling protocols is to describe the most effective chilling methods for any stage in the food supply chain with emphasis on whitefish. This comprises optimization of the whole chain for lowering and maintaining low temperature with the aim of maximizing quality and safety of the products and minimizing costs and energy use. This report is the background for the protocols and guidelines published with open access at Matís website in Icelandic and English in a user ‐ friendly way: www.chillfish.net. These are protocols to follow aimed at the use of fishermen, manufacturers, transporters and other stakeholders in the fisheries chain. The information is divided into subchapters of different links in the chain. How to chill fish on ‐ board, during processing, packaging, transport and storage are the main chapters.

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Reports

Guidelines for precooling of fresh fish during processing and choice of packaging with respect to temperature control in cold chains

Published:

01/12/2010

Authors:

Kristín Líf Valtýsdóttir, Björn Margeirsson, Sigurjón Arason, Hélène L. Lauzon, Emilía Martinsdóttir

Supported by:

AVS Fund of Ministry of Fisheries in Iceland (R-037 08), Technology Development Fund at the Icelandic Center for Research (081304508), University of Iceland Research Fund and EU (contract FP6-016333-2)

Contact

Sigurjón Arason

Chief Engineer

sigurjon.arason@matis.is

Guidelines for precooling of fresh fish during processing and choice of packaging with respect to temperature control in cold chains

The purpose of the guidelines is to assist in the choice between different methods of pre-cooling fresh fish products as well as to assist in the selection of packages with regard to the heat load that the product experiences on its way from producer to buyer. The following pre-cooling methods are discussed: liquid cooling, sludge cooling and skin cooling (CBC, touch and blow cooling). The treatment of products during processing and the effect of different refrigerants on temperature control, quality and shelf life of fillets before packaging the product are also discussed. The guidelines take into account the processing of lean whitefish, such as cod and haddock. The results of research show that a well-designed pre-cooling before packing can result in a shelf life of 3 - 5 days longer due to no pre-cooling before packing. Inadequate fluid exchange during hydraulic cooling with associated cross-contamination can, however, negate the positive effect of pre-cooling. Icelandic fresh fish producers mainly use expanded polystyrene (EPS) and corrugated plastic (CP) boxes for the export of fresh fillets and fillet pieces. Therefore, only the aforementioned packaging types are discussed here. The conclusion is that if the temperature control is inadequate and the temperature fluctuations are high, it is desirable to use foam plastic boxes that provide better thermal insulation than corrugated plastic boxes.

The aim of the guidelines is to provide and assist with choice of different precooling techniques for fresh fish fillets as well as assist with choice of packaging with respect to thermal abuse, which the product experiences during transport and storage from processor to customer. The following precooling techniques are discussed; liquid cooling (LC), slurry ice cooling (SIC) and combined blast and contact cooling (CBCC). In addition, the following is discussed; handling during processing and the effect of applying different cooling media before packaging on temperature control, quality and shelf life of fresh fillets. The guidelines are designed with lean white fish muscle in mind, such as cod and haddock. The results reveal that efficient precooling before packaging can prolong shelf life up to 3 to 5 days compared to no precooling before packaging. If the liquid exchange in the liquid cooler's circulation system is insufficient, cross-contamination can diminish the positive effects of precooling. Icelandic fresh fish processors mainly use expanded polystyrene (EPS) and corrugated plastic (CP) boxes for export of fresh fish fillets. The guidelines are therefore only focused on the above-mentioned packaging types. The conclusion is that if temperature control is unsatisfactory and temperature fluctuations are great, then expanded polystyrene boxes are the preferred alternative because they provide better insulation.

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Reports

North Cage 2

Published:

01/12/2010

Authors:

Ólafur Ögmundarson, Róbert Hafsteinsson, Þorleifur Eiríksson, Böðvar Þórisson, Kristján G. Jóakimsson, Egil Lien, Jón Árnason

Supported by:

AVS and the Technology Development Fund

North Cage 2

The Norðurkví project was set up to:

  • Design a technical solution for a fish farm to enable farmers to sink it and lift it in Icelandic conditions.
  • Maximize the usefulness of submersible pens with regard to working conditions.
  • In addition, find a new solution for handling net bags in aquaculture to repel baits.

The focus of this part of the project, called Norðurkví 2, is to design a technical solution for a fish farm that can be sunk and lifted again to prevent damage due to drift. In addition, several new types of treatments on net bags were tested to see which of the tested treatments worked best.

North Cage was established to:

  • Develop sea cage technique to sink cages fit for Icelandic conditions.
  • Optimize functionality of sinkable sea cages considering working conditions.
  • In addition different types of netting and impregnation were tested in order to minimize the necessity of frequent change of nets in the cages.

This part, North Cage 2 of the North cage project is concentrated on the development of a cage that can be temporarily submerged and re ‐ lifted to the surface to avoid the damage on the installation during the occurrence of drifting ice. In addition different types of netting and impregnation were tested in order to minimize the necessity of frequent change of nets in the cages.

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Reports

Biodiversity in hot springs in high-temperature areas in Iceland. Overall summary prepared for the Framework Program. Final report

Published:

01/12/2010

Authors:

Sólveig K. Pétursdóttir, Snædís H. Björnsdóttir, Guðmundur Óli Hreggviðsson, Sólveig Ólafsdóttir

Contact

Guðmundur Óli Hreggviðsson

Strategic Scientist

gudmundo@matis.is

Biodiversity in hot springs in high-temperature areas in Iceland. Overall summary prepared for the Framework Program. Final report

Research was carried out on the ecosystem in hot springs in five high-temperature areas in Iceland under the framework of the Framework Program in the years 2004-2009. The aim was to answer questions about the extent and nature of the variability in microbial flora between high-temperature areas in Iceland, which were studied mainly in terms of diversity and rare groups. This report summarizes the results obtained from the above studies. The areas that were examined were the Hengill area, Torfajökull area, Krafla / Námafjall, Krísuvík and Vonarskarð. Furthermore, the results of a similar study carried out for the environmental assessment of the geothermal areas at Þeistareykir and Gjástykki were included in this summary. A total of 115 samples were taken in the six areas and a species composition in 80 of them was analyzed. Species-identifying bacterial and archaeal bacteria in the DNA from the samples were amplified and sequenced. The sequences were classified by affinity and classified by species or genus by comparison with comparable sequences in Genbank. A total of 4424 bacterial sequences and 1006 ancient bacterial sequences were detected from the samples. The distribution of bacteria and ancient bacteria in the samples was examined and it was found that 16 bacterial assemblages were found in most areas and species of the Aquificae array were most common, as they are often primary producers in hot springs. Species of the β- and γ-proteobacterial and Deinococcus-Thermus factions were also found to a significant extent in all areas except Krísuvík. In addition, several other factions were found in individual areas. Within the ancient bacteria, Crenarcheota species were found in all areas, Euryarchaeota species were found in Vonarskarð and Þeistareykir, Thaumarchaeota was found in Vonarskarð and in Krafla / Námafjall and Nanoarchaeota in the Torfajökull area. Calculations of biodiversity (H) microorganisms in the six areas showed that the Krafla area was the most diverse, then Torfajökull, then Vonarskarð, Þeistareykir, Hengill and finally Krísuvík. The assessment of biodiversity by calculating the collection curves largely supported this conclusion. Biological specificity was assessed on the basis of rare species by ≤96% corresponding to close relatives in Genbank. A total of 74 rare species or genera were found in the samples and they seemed for the most part regional and it is not unlikely that some of them are endemic. Most new species or genera were found in the Torfajökull area. Vonarskarð, Krafla / Námafjall and Þeistareykir had slightly fewer rare species or genera. New tribes were also found in the Hengill area, but not to the same extent as in the former.

Culture independent methods were used to study the microbial composition of hot springs in five geothermal areas in Iceland in 2004-2009. The aim was to answer questions on the degree of biodiversity and to what extend the species found were unique to the sites investigated. In this report the site specific research results were combined and compared. The geothermal sites investigated were the Hengill area, the Torfajökull area, the Krafla / Námafjall area, Krísuvík and Vonarskarð. Results from a similar research from an environmental assessment of the geothermal areas of Þeistareykir and Gjástykki were also used. A total of 115 samples were collected from the six geothermal areas and the microbial species composition was estimated in 80 of them. The 16S rRNA genes were amplified from DNA from the samples and partially sequenced. The obtained sequences were classified and identified to the species or genus level by comparison to similar sequences in Genbank. The total of 4424 bacterial sequences and 1006 archaeal sequences were analyzed. The distribution of bacterial and archaeal phyla of the samples was investigated and revealed that 16 bacterial phyla were represented in all areas. Also, that the phylum of the primary producers of hot springs - Aquificae - was dominating. Species belonging to β‐ and γ ‐ proteobacteraa and Deinococcus - Thermus were also found in considerable amounts in all areas except Krísuvík. Several bacterial phyla were only found at one or two geothermal areas. Species belonging to Crenarchaeota were found in all six areas, Euryarchaeota were found in Vonarskarð and Þeistareykir, Thaumarchaeota was found in Vonarskarð as well as in the Krafla / Námafjall area and Nanoarchaeota in the Torfajökull area. Calculation of the biodiversity index (H) of microbial species of the six geothermal areas revealed that the index for the Krafla / Námafjall area was highest, then Torfajökull, Vonarskarð, Þeistareykir, Hengill and finally Krísuvík. The estimate of biodiversity based on Rarefaction curves confirmed the results. The estimation of uniqueness of the areas was based on the number of novel species found using ≤96% similarity to closest relative in Genbank as the cutoff value. The total of 74 novel species or genera were found in the samples most of which were only found in one or at most two areas. Most of these were from the Torfajökull area. A considerable number of novel species were also found in Vonarskarð, Námafjall and Þeistareykir. Novel species or genera were also found in the Hengill geothermal area.

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Reports

Shortening the growing time of mussels - FINAL REPORT / Shortening the growing time of blue mussels on long lines

Published:

01/12/2010

Authors:

Helga Gunnlaugsdóttir, Guðrún G. Þórarinsdóttir, Jón Benedikt Gíslason, Hreiðar Þór Valtýsson, Björn Theodórsson, Hrönn Jörundsdóttir

Supported by:

Increased value of seafood (AVS), Marine Research Institute, Matís, Fisheries Center at the University of Akureyri

Shortening the growing time of mussels - FINAL REPORT / Shortening the growing time of blue mussels on long lines

The main objective of the project was to develop and evaluate a method for the cultivation of mussel shells on seaweeds that yields at least a year earlier than the traditional cultivation method. The sub-goals were to assess the stock size and recruitment capacity in the experimental small shellfish fishing areas in Hvalfjörður and the uptake of cadmium in mussels after transport and in further cultivation.

The summary conclusions of the project are as follows:

a) The stock size assessment of mussels in Hvalfjörður revealed a fairly large fishing stock and based on a 10% fishing quota of stock size, it would be possible to fish 1,500 tonnes annually in the fjord. The mainstay of the population in most areas are large shells that are not suitable for cultivation.

b) The collection of wild small shells (approximately 20-30 mm) for soaking and rearing of hangers (rotating) in the sea yields a harvest at least a year earlier than the traditional cultivation method.

c) Small shells can be fished, transported, socked and released in cultivation areas away from fishing grounds. However, the size of the shells has a lot to say about the possibilities for further cultivation, as their mobility seems to decrease from 25 mm shell length. In the study, a crop of lines of caught and plucked shell was about 5 kilograms of marketable shell per meter of length.

d) This cultivation method can be useful in addition to conventional cultivation. Being able to pick up wild mussels can be very important, especially if traditional larval collection has been destroyed for some reason. The results of the current project will potentially be useful for more than shortening the growing season and can play a key role in the development of mussel farming around the country.

e) Uptake of cadmium in mussels can be a problem after transport and in further cultivation and it is important to monitor the concentration of cadmium in mussels before it is placed on the market.

This report presents results from a research project funded by AVS year 2009. The main aim of the project was to evaluate whether it would be possible to shorten the growing time of blue mussels so that they reach market size more rapidly. The following technique was tested; harvesting of natural stocks of blue mussel in two fjords in West Iceland where small individuals were sorted out from the catch (<40 mm) and put into socks to grow to market size in hanging culture. > <40 mm) and put into socks to grow to market size in hanging culture. Using this technique, small mussels between ca 20-30 mm in shell length reach market size (45mm +) in hanging culture in one year, while using traditional methods (spat collection and growth) this takes 2-3 years. This technique thus offers possibilities to utilize an unexploited natural stock of mussels and shorten considerably the growing time to market size.

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Reports

Sókn á ný mið / Thawing processes

Published:

01/12/2010

Authors:

Róbert Hafsteinsson, Albert Högnason, Sigurjón Arason

Supported by:

Technology Development Fund

Contact

Sigurjón Arason

Chief Engineer

sigurjon.arason@matis.is

Sókn á ný mið / Thawing processes

This project is a joint project of Brims hf, Matís ohf and 3X Technology ehf and aims to develop new equipment and processes for thawing gutted catfish for processing. The project was for two years and was funded by the Technology Development Fund. The project contains several experimental reports that were made by the participants of the project and were carried out in Brims' premises in Akureyri. The experiments were largely based on examining the heat distribution of cod at different thawing temperatures on the lake. Thermal inserts were placed in the core and redness of the cod to monitor the temperature in the fillet. The aim was to try to find out the best thawing method in terms of the quality of the raw material after thawing and storage in the refrigerator overnight. The main variables in these experiments were time and temperature. The thawing was tested in a so-called auger made by 3X Technology in Ísafjörður. By using snails in thawing, it will be very easy to control the thawing time and also ensure that the raw material that enters first comes out first. The main results of the project were that the best result from the thawing in terms of color and loss of the fillet in the processing was to thaw the cod in the shortest possible time and have the temperature of the water (thawing temperature) even throughout the thawing process. Then after storage in the refrigerator overnight, the temperature of the fish is about zero to -1 ° C. This will give the best result in terms of the quality of the raw material.

This project is a collaboration work between Brim hf, Matis ohf and 3X Technology ehf. The project objectives is to develop a new equipment and processing for thawing fish. This project is for two years and is supported by Icelandic Center for Research (Rannis). This project contains several experiment reports and their payoff which was executed by the members of this project. All these experiments were done within Brims accommodation. Their main object was to investigate the temperature gradient of codfish with various thawing temperature. Thawing experiments were executed in so called screw tank, manufactured by the company 3X Technology. By using these tanks you will ensure that the fish whos goes first in the tank will go first out when thawing is over. And thereby all control of time and temperature will be much easier. The primary conclusion from this project is that the best outcome from the thawing experiment, when taking into account the color and looseness of the fish fillet, is to have the thawing time as short as possible and the temperature of the water as even as possible throughout the thawing process.

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Reports

Food safety and added value of Icelandic fishmeal - Determination of toxic and non ‐ toxic arsenic species in fish meal / Verðmæti og tryggi íslensks fiskimjöls - Kaupthing

Published:

01/12/2010

Authors:

Ásta Heiðrún E. Pétursdóttir, Hrönn Ólína Jörundsdóttir, Helga Gunnlaugsdóttir

Supported by:

AVS Fisheries Research Fund

Contact

Ásta Heiðrún E. Pétursdóttir

Project Manager

asta.h.petursdottir@matis.is

Food safety and added value of Icelandic fishmeal - Determination of toxic and non ‐ toxic arsenic species in fish meal / Verðmæti og tryggi íslensks fiskimjöls - Kaupthing

There is a lot of arsenic in the ecosystem in organic compounds as well as in inorganic form and more than 50 natural chemical forms of arsenic have been found. Seafood naturally contains a high concentration of the total arsenic compared to, for example, agricultural products. However, most arsenic in seafood is bound in an organic form called arsenobetanide, which is considered safe. Other forms of arsenic in marine products are generally present in lower concentrations, including inorganic arsenic (arsenite and arsenate) which is toxic and rarely exceeds 3% of the total concentration of arsenic in fish and crustaceans. The morphology of arsenic in seafood is important because the bioavailability and toxicity of arsenic depend on its chemical form. Recently, the EFSA (European Food Safety Authority) called for information on inorganic and organic forms of arsenic in food and for chemical analysis methods to detect inorganic arsenic. This dissertation presents the results and evaluation of measurements of the total concentration in over 100 samples of Icelandic fishmeal. Among other things, it was examined whether there was a seasonal difference in the total concentration of arsenic. The samples were first decomposed by microwave and then measured on an ICP mass spectrometry (ICP-MS). To evaluate the chemical forms of arsenic present in the flour, a three-part distribution method was first developed. Emphasis was then placed on the analysis of toxic inorganic arsenic. The previously published alkali-alcohol extraction method, for the detection of inorganic arsenic, was adapted and the samples were measured by HPLC equipment connected to ICP-MS. Arsenobetanide was found to be the predominant form of arsenic in all cases. Inorganic arsenic was found to be less than four percent of the total concentration in twelve measured fishmeal samples. On the other hand, when another chemical analysis technique (HPLC-HGAFS) was applied to a sample of certified reference material, the concentration of inorganic arsenic was three times lower. The alkali-alcohol distribution method proved to give a convincing upper limit on the concentration of inorganic arsenic. The results also show that it is not enough to rely on one method when analyzing and quantifying arsenic forms. In addition, they demonstrate the need for a certified concentration of inorganic arsenic in standard materials to test the reliability of chemical analysis methods. The need for further development of chemical analysis methods in this field is urgent.

Arsenic is found in the biosphere in both organic and inorganic forms, and there have been recognized more than 50 naturally occurring arsenic species. Seafood products have naturally high concentration of total arsenic compared to eg agricultural produce. Arsenic is toxic to humans and animals and is known to be carcinogenic. The toxicity of the arsenic species varies severely and a large portion of the arsenic in seafood is present in the form of the organic compound arsenobetaine, which is considered non ‐ toxic. Other arsenic species are generally present in lower concentrations, including the most toxic inorganic arsenic species, arsenite, As (III) and arsenate, As (V), which usually do not exceed 3% of the total arsenic in fish and crustaceans. Existent European regulations on limits of arsenic in foodstuff and feed only take into account total arsenic concentration, not the toxic arsenic species. Recently the EFSA (European Food Safety Authority) stressed the need for more data on levels of organic and inorganic arsenic in different foodstuffs and the need for robust validated analytical methods for the determination of inorganic arsenic. In this thesis results from total arsenic concentration from over 100 samples of Icelandic fish meal are presented and evaluated. The samples were microwave digested and measured with inductively coupled plasma mass spectrometry (ICP ‐ MS). The samples were screened for a seasonal difference in the total arsenic concentration. To evaluate the arsenic species present in the meal a sequential method of extraction was developed. In addition, a special focus was on the determination of inorganic arsenic and a previously published method for an alkaline ‐ alcoholic extraction of the inorganic arsenic was modified and applied. For determination of arsenic species high pressure liquid chromatography (HPLC) was coupled to the ICP ‐ MS. The predominant arsenic species found in all samples was the non ‐ toxic arsenobetaine. Inorganic arsenic was not found to exceed 4% of total arsenic concentration in 12 samples of fish meal. However, a suspicion of co ‐ elution arose, and when another analytical instrument technique (Hydride generation atomic fluorescence spectroscopy (HPLC ‐ HG ‐ AFS)) was applied, concentration of inorganic arsenic was approximately three times lower in a certified reference material, TORT‐ 2. The alkaline ‐ alcoholic extraction method was found to give convincing upper limits of the inorganic arsenic concentration in fish meal samples. These results show the necessity of further method development and separate methods when identifying and quantifying species. This further stresses the need for a certified value of inorganic arsenic in a certified material to check the robustness of developed methods.

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Reports

Production of salted fish in the Nordic countries. Variation in quality and characteristics of the salted products

Published:

01/12/2010

Authors:

Kristín Anna Þórarinsdóttir, Ingebrigt Bjørkevoll, Sigurjón Arason

Supported by:

NORA (Journal No. 510-036)

Contact

Sigurjón Arason

Chief Engineer

sigurjon.arason@matis.is

Production of salted fish in the Nordic countries. Variation in quality and characteristics of the salted products

The Nordic countries are the largest exporters of salted gadoid products, whereas countries in South ‐ Europe and Latin America are the biggest importers. In Norway, Iceland and Faroe Islands, cod is primarily used for the production. The characteristics of the salted fish, such as commercial quality and weight yield vary between the countries and between producers. These attributes are influenced by differences in catching methods, handling and salting methods. This report summarizes the variation in these procedures, and in addition, the market segmentation of salted products, from the different countries.

The majority of the world's salted fish production takes place within the Nordic countries, but the largest group of consumers is in Southern Europe and South America. Cod is the main raw material, but salted fish is also produced from other related species, such as saithe, ling, haddock and saithe. Properties of salted fish products, such as quality and utilization, vary between countries of production and producers. These variables depend on fishing methods, raw material handling and salting methods. The report is a summary of the variability in these factors between producing countries, as well as an assessment of their share in the salted fish markets.

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Reports

Functionality testing of selected Chill ‐ on technologies during a transport ‐ simulation study of palletized cod boxes: qPCR for fish spoilage bacteria, SLP model and QMRA to evaluate pathogen growth in spiked cod

Published:

01/11/2010

Authors:

Hélène L. Lauzon, Björn Margeirsson, Kolbrún Sveinsdóttir, Eyjólfur Reynisson, María Guðjónsdóttir, Emilia Martinsdóttir (Matís); Radovan Gospavic, Nasimul Haque, Viktor Popov (WIT); Guðrún Ólafsdóttir, Tómas Hafliðason, Einir Guðlaugsson, Sigurður Bogason (UoI)

Supported by:

EU IP Chill ‐ on (contract FP6‐016333‐2)

Contact

Kolbrún Sveinsdóttir

Project Manager

kolbrun.sveinsdottir@matis.is

Functionality testing of selected Chill ‐ on technologies during a transport ‐ simulation study of palletized cod boxes: qPCR for fish spoilage bacteria, SLP model and QMRA to evaluate pathogen growth in spiked cod

In this study, tests were carried out on technical solutions developed in the EU project Chill ‐ on, where a simulation experiment was set up to simulate the actual transport of fish from Iceland to Europe. The temperature fluctuations experienced by the fish were aimed at mimicking transport from Iceland to France by ship. Pallets of cod fillets in foam plastic boxes were transported to the Westman Islands by ship and back to Matís in Reykjavík. Samples from these pallets were then compared with control samples that had been stored in Matís' refrigerated conditions. Cod nuggets were also packed in consumer packs (trays) immediately after processing and then after 6 days and were stored in subcooled or refrigerated conditions. Microbial growth experiments were also performed in which Listeria monocytogenes, Escherichia coli and Salmonella Dublin were added to cod necks stored in foam boxes in conditions similar to the storage and transport processes during export. Temperature measurements, sensory evaluation, microbial and chemical measurements were used to present data to test and verify the QMRA / SLP models and quantification of Pseudomonas bacteria using qPCR technology.

The aim of the cod wet trials and the corresponding shelf life study was to include scenarios to test and demonstrate the functionality of some Chill ‐ on technologies in a simulated cod supply chain. Temperature fluctuations were induced according to the actual scenario in the supply chain of cod from Iceland to France via sea freight. The study included sample groups created at the point of processing after packaging in EPS boxes. The reference group was stored at Matís under superchilled conditions. Simulation trials for downward distribution were performed at Matís upon receipt of the pallets shipped to the Westman Isles from Reykjavik (Iceland ‐ Europe freight simulation) and compared with the reference group. Repackaging of loins in retail trays was performed on days 0 and 6 with storage under superchilled and chilled conditions, respectively. In addition, a pathogen challenge trial was performed by spiking loins (5 kg) with Listeria monocytogenes, Escherichia coli and Salmonella Dublin, followed by storage in EPS boxes under temperature conditions simulating export and distribution. Temperature recordings along with microbial, chemical and sensory analyzes from the groups evaluated provided necessary data to test and validate the QMRA / SLP models and the quantitative molecular (qPCR) method to estimate counts of pseudomonads.

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Reports

Optimization of sample preparation - filtration and DNA extraction - for the analysis of sea water samples

Published:

01/11/2010

Authors:

Eyjólfur Reynisson, Árni Rafn Rúnarsson, Sveinn Haukur Magnússon, Desiree Seehafer, Viggó Þór Marteinsson

Supported by:

Fisheries Project Fund, Ministry of Fisheries and Agriculture

Contact

Viggó Marteinsson

Research Group Leader

viggo@matis.is

Optimization of sample preparation - filtration and DNA extraction - for the analysis of sea water samples

Little is known about microorganisms or the diversity of microbial communities in Icelandic waters, but they play an important role in the marine ecosystem. It is necessary to study the microbiology of the ocean around Iceland with new and powerful methods based on molecular biology. In such work, the quality of the samples and sample preparation are very important. In this study, a preliminary survey of sea samples, sampling and sample handling was performed before large quantities of samples are taken. First, samples were taken from the marina in Reykjavík for preliminary study and then we continued with samples from the open sea. Yields were examined for DNA levels and how well the microorganisms' genes were amplified by PCR. The results showed that the best method was a purchased DNA isolation kit that isolated most of the DNA and was quantifiable by PCR. A cheaper and faster method with an automatic isolator and home-made substrates also proved to be very successful, as comparable results were obtained from PCR amplification, although lower DNA recovery was obtained. Based on these results, it is possible to set up procedures based on automatic DNA isolation of samples but the use of purchased isolation kits on more difficult samples. It is planned to use these results for sea samples from the Marine Research Institute's spring survey.

The knowledge on microbial diversity and community structure in Icelandic seawater is scarce at present despite their important role in ocean ecology. The agenda is to increase our knowledge in this field by applying recent and powerful analytical tools. In order to do that it is essential to have access to high quality samples and sample preparation procedures. In the present study sea sample preparation was studied with aim of comparing different methods and optimizes the workflow. Samples from a harbor in Reykjavík and open sea samples were used for this purpose. The results showed that an extraction method based on an Epicenter kit gave the best results regarding DNA recovery from the samples and suitability in a PCR amplification. However, a method based on semi ‐ automatic protocol and in house reagents proved to be more cost effective and showed comparable performance with PCR suitability of the samples although a lower DNA recovery was obtained. From these results it is now possible to establish an efficient work flow for microbial diversity analysis of sea samples using an automated method as a first choice with the option of more costly method for more challenging samples.

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