What a wonderful question! Plants used for phyto extraction (also called phyto remediation) extract some metals from the soil through their roots but the metals tend to travel through the plant and concentrate into the plant stems, shoots, and leaves. These are places easily harvested for testing. When the plants are collected for testing they are usually cut and burned and the metal ore is collected and measured from the ash.

As for the amount in the soil, I would suspect that soil samples are taken from a few different areas before and after the plants are grown and the amounts of metals is compared.

There is a lot of new research going on in this field as using plants could be a more beneficial way of saving some of our contaminated environment. There is a lot of work looking into how the plants are able to uptake metals and the specificity for different kinds of metals. Unfortunately right now many of the phytoextractors are weed-like plants that uptake metals rather slowly. Hopefully new research will find other similar plants that can make this process happen a little faster.