Secondary metabolites are results of specific biosynthesis through a specific pathway. The pollutant assimilation in plants parts in form of specific products generally in modified form of main pollutants accumulated in plants. The traces of same can be identified through any spectral mass spectroscopy. HPLC etc. 

My Dear Dr. Rushdi Sabah Abdulqader,

The process for used the secondary metabolites in measurement of pollution was depended on the pollutes agents types. The most used was with microbial pollutes more than others. Such as of used the detect of protein concentration to measure the microbial content pollution in the medium.  The pollutes effects was a different story from the pollutes assays. May use the chemo-physical or chemical assay to pollutants detect, while must use the physiological assay to detect of pollutes effects.

Dear

Generation of secondary metabolites is a result of different factors. Nevertheless they produced from few biosynthesis pathways but they are very varied both in type and quantity from living organisms to another. However the environmental effect is a considerable factor in the synthesis of these secondary metabolites e.g. microbial infection, UV, levels of compounds in air or soil..etc. The living organisms produce high amounts of compounds to decrease the effect of these factors or to adapt. For case study I suggest you can use different plants samples and to study the amounts of secondary metabolites in the different types of environmental factors.

i see the concentrations of one or more from secondary products such as alkaloids or phenol differ from stress to rest phase of plants depend on the factors effects as pollutant, but how i sure that differ in the one or more compound depend pollutant on anther factor?

Dear Doctor,

I think to conduct experimental used the more pollutant factors  at different concentrations that you suggested to effects on plant growths to get there clear results. There if were not have the previous studies.