What do you think about use of Denaturing Gradient Gel Electrophoresis (DGGE) for evaluation of structure of fungal communities? I think that technic is a good tool for understanding of structuration of communities in natural environments. How many researchers are using this method too?
Thank you for your contribution!
FJSC.
Hi Francisco,
I totally agree with Katherine in her answer. I would add that if your specific experimental questions are related with the study of diversity (understood as the number of species or taxonomic units), probably it is better to use a massive sequencing approach. If what you are looking for is ecological patterns/community responses, the fingerprint of communities is usually fine to detect these trends. By other hand, for specific microbial groups in which the taxonomic diversity is low (for example arbuscular mycorrhizal fungi with ca. 300 described species) I think that a cloning-sequencing approach mediated by a screening of clones using a fingerprint approach works fine and save costs in sequencing (i.e. it is not necessary to sequence every clone but a subset of those having the same fingerprint patterns).
Álvaro
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