By using these methods, DNA extraction, PCR amplification and bioinformatics assay are core steps to process the sequence analysis. After process the data, we have a abundant information regarding microbes phylogenetic classification, community level. etc. However, we are not quiet sure about our effective soil sampling, How can we ensure that our soil samples are efficiently collected represent the viable microbs. How can we detect the alive and dead microorganism.
Hi Ahmad,
One way to make sure you have sampled enough is to look at rarefaction curves of you sequenced samples. Basically, on y-axis you plot the number of OTUs and on x-axis number of reads (sequencing depth). If the curves flatten, that means you have covered majority of the diversity, if not, you would need to sample/sequence more.
For detecting "alive" (I would call it active) or "dead" (I would call it not active) members of microbial community via sequencing approach I would go for sequencing of 16S rRNA gene based on DNA and RNA extracts from your samples. Fundamentally, 16S rRNA copies from the isolated DNA would provide a glimpse into total community (active or non-active), while 16S rRNA sequences obtained from isolated RNA would provide insights only into active members of the community, since RNA is actively transcribed.
Hope this helps,
Deni
Hi Ahmad,
I believe your second answer is actually a complete different question which needs to be it's own thread. Hence, you should post it as a new inquiry.
FYI, if my original answer to your question was of any help to you, you can recommend it by hitting the recommend button. This is one of the ways how we make progress here on ResearchGate.
Regards,
Deni
Hi Ahmad,
I have no expertise in taxonomy of fungi whatsoever, so I am not able to answer you this question.
That is precisely why I have encouraged you to make a new thread on this. There is a high chance someone is an expert in that field on ResearchGate and will be able to provide some answer to your question.
Regards,
Deni
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