Seeking for advice / suggestions. Currently working on project - Influence of Mycorrhiza colonization on soil bacterial community in two wheat lines which had different colonization efficiency. Its pot experiment, so all the soils from pot has considered as Rhizospher. Further, I am interested to study root associated community too. So my question is that is it good to study all root associated community or just root endophytes? Any suggestions are highly appreciated. Thanks
Hi Shamina,
here you have two options:
1) you just wash the roots with water and you extract the DNA from these roots. You will then characterize the microbes that are associated with the roots.
2) you wash the roots + root surface sterilization. In this case you get only the endophytes.
I prefer the first options as I want to characterize the microorganisms that are also able to colonize or are present in the root surface, in order to compare the microbial community between soil-plant compartments (rhizosphere vs. roots)
I feel both are good to study , microbial diversity within rhizosphere and endosphete , coupled with metagenomics. .
With roots, the distinction between rhizosphere and root is often fuzzy. Endomycorrhizae extend from the root into the soil; cells from the root cap can detach and remain associated with mucigel; some fungi have complicated transitions from rhizosphere-dwellers to pathogens. It may be an artificial distinction that isn't useful to you.
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