Community profiling of the bacteria and fungi to determine the extent to which soil microbes contribute to phenotypic differences in crop growth has been appreciably studies. There are several commercialized consortium based microbes are available for use in crops. Different reviews conclude that evolutionary history contributes little to understanding plant–soil feedbacks in agricultural fields; however, microbial legacies can be predicted by species identity and relatedness.

Subhradip Bhattacharjee

Sometimes it is very hard to understand why people on RG act like imbecilic and answer even though they don't understanding what has been asked. More funny, when such answers gets recommendations from even more fatuous people. Similar is the case in above post.

Anyway, your question is referring to two things and they need not be related. First you mentioned what you want to analyse and another thing is the environment. These two are not dependent on each other. So the first thing, which is method can be used in any environment of interest whether it is manure amended soil or gut environment. There are several method which can be used to estimate the diversity and relative abundance, but when you ask which is the most straight forward method, you need to present a reference frame on which your question is based. "most straight forward, competent and more insightful" these all the different things and not single method can be used for the purpose. In experimental science, there is nothing most/best/perfect rather it is relative and hugely depends on purpose, monetary resources and availability of all experimental components.

It would be better if you come up with something which focuses on any particular query. It will increase chances of getting good answers and not spam like Suresh K Malhotra .