What’s the Answer? (soil fungi)

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of thecommunity and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

Today’s featured question:

Which database and primer sets are the best for NGS (Ilumina) study of Fungal Soil Metapopulation study?

I choice ITS1F/ITS4, but now, I got some doubts. Is it the good choice? Which region is better – ITS or LSU? or better is to use both of them? and what about curated fungal database?

Which primers are less preferable to amplify some fungal genus? We are looking for the best all fungi specific primers (without matching plant DNA and without preference to some groups of fungi.

We want to answer the question about in time variation of soil fungal population after addition Trichoderma`s biocontrol strains.

Thanks a lot and Best regards

michal

This week’s question hasn’t generated much discussion in the answers section but the answer that was offered was terrific–yay Josh Herr. It was a great example of the right person to take on the question, offering information that is helpful but not yet published, and provided information that was new to me about some public resources–and the Taylor lab resources and guidance is very nice. Check it out in the answer.

EDIT: coincidentally, there was a video put out today about soil sampling that might give you some more information on this process if you aren’t familiar with it:

Chris Packham helps test cutting-edge soil sampling