I think rhizospheric study would be better, it included all biological phenomena in the soil. Depth, expansion and proliferation of roots and enzymatic activity and microbial biomass are of some parameters that would be taken for study, even layer wise moisture and fertilizer extration can also be helpful. You can also study carbon auditing as it is under CA practices. Regards
The choice of the method must consider the question that the research intends to answer. To study the ecology and functionality of microbial communities in the roots and rhizosphere, you can follow two holistic approaches: i) classical microbiology: isolation of microorganisms from the roots and rhizosphere, followed by the selection of microbial strains [fungi and bacteria] beneficial to the plant. In addition to biochemical tests (basal soil respiration, metabolic coefficient [qCO2], carbon and nitrogen from the microbial biomass and Biolog test that will inform about the functioning of soil biology in this region (root soils and rhizosphere). Ii) based approach in molecular biology: sequencing of 16S rRNA and ITS genes, metagenomics, quantification of functional genes (nifH, PhosD, AmoA, AmoB, etc.)