I'm a beginner and would like to ask you some questions about identifying nematodes in soil: How do I preserve soil samples? 4°C or -20°C? What are the steps to identify nematodes with a DNA barcode? If I give the sample to a sequencing company, do I still need to complete the isolation of the nematode myself? Or just give the soil sample to the sequencing company? I very much hope that there will be kind people who can solve these doubts, thank you!
Hey there,
I'll try to answer some of your questions. Firstly, soil samples are most commonly stored at 4 Celsius degrees prior to biological analyses. It is critical to reduce the refrigeration period to less than a given period (e.g., less than 2 weeks). This is because the moment you have collected your samples, you have disturbed the soil ecosystem. Therefore, the longer you refrigerate your soil samples, the higher the probability that your soil's biological parameters will change. This might lead to unrealistic or even biased results.
DNA barcoding requires that DNA be extracted and purified before it is sequenced. Most companies need you to send them purified samples of extracted DNA. However, this may differ among companies. You should contact your laboratory to ask for sample preparation instructions.
Moreover, you could study recent and relevant articles to become familiar with the standards methodologies.
Check out: Article Profiling Nematode Communities in Unmanaged Flowerbed and Ag...
A comparison of molecular methods for monitoring soil nematode...
Good luck!
To preserve soil samples for the identification of nematodes, the best method is freezing. Here are the steps to follow:
1. Collect the soil samples needed for nematode identification and bring them to the laboratory as quickly as possible. If you need to store them for a short period, keep the soil samples refrigerated at 4°C.
2. Once you are ready to preserve the samples, measure out about 500 grams of soil sample and place it in a plastic bag with a zip-lock closure.
3. Add enough water to the soil to make it moist but not saturated. Aim for a consistency similar to that of a damp sponge.
4. Seal the bag and label it with the sample ID, date, and any other relevant information.
5. Place the bag in a freezer at -20°C or lower.
6. Leave the samples in the freezer for at least 24 hours. This will kill the living nematodes in the soil sample.
7. After freezing, the soil samples can then be sent to a nematology laboratory for nematode identification.
It is essential to note that the freezing and thawing process may make the nematode extraction process more challenging in some situations. Therefore, it is best to process samples as soon as possible once they are obtained to best preserve soil nematodes.
@ Ziqing, It is generally recommended to store soil samples at cool temperatures of 5 or 10°C (Hooper, 1986; Hunt and De Ley, 1996; Oba and Okada, 2008) or room temperature (Mizukubo, 2004) until nematode extraction.
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