I will co-extract RNA and DNA from soil (andosols). Taking into account the difficulty of extracting good yields of nucleic acids in these particular soils, is it okay to sieve them before freezing in liquid nitrogen? Will it not lead to greater loss of RNA and DNA?
Your question can be answered at least two ways. First, if you keep all of the soil and simply extract in fractionated batches, the total RNA and DNA in the SOM should not differ much, so long as the freezing stops all chemical reactions and you do not wait long after size separation to freeze. The degradation rates will vary by particle size (smaller particles have greater surface size, increasing geometrically with decreasing size), so I would suspect the "bins" of different sized particles will each have different degradation rates. The clay content, SOM and other characteristics of the soil will also change the reaction rates of genetic material and other biomolecules.
The second way to answer your question is whether you will keep all of the soil. If not, the answer to your question is likely to be "no," since you will change the overall degradation rate. However, if your research is only for a certain size fraction, perhaps you could report the genetic makeup of the SOM for size separated andosol particles between x and y diameters. This would require a justificaiton (e.g. detection limits would not be reached, such as the justification for concentrating environmental samples of air or water after collection).
DAV
To my understanding, for DNA/RNA extraction you'll remove the gravels and roots from the soil anyways because they'll hinder the extraction from real soil. Therefore, the soil should be sieved before the freezing.
2nd, for DNA/RNA extraction you need minute amount of soil (gram, half gram) so sieving would not take much time to cause degradation of the target nucleotides.
That is a very good point, Dr. Nazir. So, we also need to decide what we mean by "soil," since in the O and A horizons, will contain living biota. In this case, you will need to clarify that the soil contains some biota (e.g. microbes), but not others (e.g. macrophytic, such as roots). The same goes for texture, i.e. only soil particles and aggregates < x diameter.
Thank you both for your contributions. The aim of this study is to analyze the biodiversity of the microbial communities in soil, so it makes sense sieving it in order to discard some roots and other larger organisms. My question would be whether sieving will increase the release of RNases and thus diminish the possibility of obtaining Rna. The volcanic soils in question have high concentration of organic matter and clays, which are authentic sponges to any genetic material that eventually isolated.. Any of you have experience with volcanic soils?
When we perform this kind of abalysis in our laboratory we use to sieved the soil at 2mm in order to perform all the physico-chemicla standard analysys (pH. EC, C/N, OM, texture and granulometry, respirometry, etc) in this way we can correlated all the results and copared all samples. These studies are focused on soil remediation (applying biiorremediatio) and for soil helath / quality evaluation. In specific cases, depending on your objetive or hyothesis, you can only remosve gravel, stones and roots.
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