I need to sample soil around 2 m high shrubs - so no 'pullup the plant and shake of the soil' will work. These plants have taproot systems of 2m deep. My idea is to compare the microbes in the rhizosphere in nature and in cultivation. I also want to have a look at the endohphytes.
Anélia Marais _ Its sad that people answering here before, neither have read your question carefully nor have read the articles they are just suggesting you, of course with the help of google.
Nevertheless, for your question, I could suggest that you have to design your experiment in a way that you could cover the maximum diversity without much struggle. And as far as I know, maximum diversity is associate with in the top few inches of soil. So, it would not be too hard to collect that kind of sample.
Nevertheless, to confirm that, you can do a pre study in which you can study the diversity across different strata of root zones and decide at what length its the threshold.
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