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.th.marteinsson@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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Reports

The value and safety of Icelandic seafood. Food safety and added ranking / Food safety and added value of Icelandic seafood. Risk profiling and risk ranking

Published:

01/05/2007

Authors:

Eva Yngvadóttir, Birna Guðbjörnsdóttir

Supported by:

AVS Fisheries Research Fund and IFL / Matís ohf

The value and safety of Icelandic seafood. Food safety and added ranking / Food safety and added value of Icelandic seafood. Risk profiling and risk ranking

In this project, basic work was carried out on risk assessment for cod, shrimp, redfish, haddock, halibut, herring, saithe and kúfisk. These species were mapped for risk and their risk composition was obtained and a semi-quantitative risk assessment was performed on them. This risk assessment used a calculation model that has been developed in Australia and is called Risk Ranger. The risk assessment used data on consumption habits (dosages, frequency, etc.), frequency and causes of foodborne illness. Thus, the risk associated with the consumption of these marine products was calculated, based on certain assumptions. The reliability of a risk assessment is entirely dependent on the data and information used in its implementation. According to the available measurement data and given assumptions, the above-mentioned seafood products are classified in the lowest risk category (level <32) - low risk, compared to healthy individuals. In international food markets, Icelandic seafood has a good reputation for health and safety. Concerns about food safety, however, are growing in many places, so it is a great challenge for Icelanders to maintain this good reputation in the future.

This report contains the preliminary results of a risk profiling and risk ranking study for the following species: cod (Gadus moruha), shrimp (Pandalus borealis), ocean perch (Sebastes marinus), haddock (Melanogrammus aeglefinus), Greenland halibut (Reinhardtius hippoglossoides) , saithe (Pollachius virens) and Iceland cyprine (Cyprina islandica). These species were surveyed with regard to terms of undesirable substances (Risk profiling and risk ranking, as well as semiquantitative risk assessment). An Australian software, Risk ranger, was used to compute the risk assessment. Various data, eg consumer behavior (daily intake, frequency etc.), and incidence and origin of food-borne diseases, were used. Thus, the risk of consuming these species was determined. The reliability of a risk assessment is dependent on the quality of the data which are used to carry it out. Based on the existing data and given prerequisites, it can be stated that the aforementioned species come under the lowest risk group (degree <32) - small risk, considering healthy individuals. Icelandic seafood products are renowned on the international food markets as being quality and safe food. However, in light of growing concern worldwide for food safety, it is a challenge for Icelandic seafood producers to maintain that good reputation.

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