The best way should be the use of molecular tools (sequencing, qPCR,...) if they are available to you.

Sequencing is the best method.... though not so easy and cost effective. MPN is just to know the presence or absence of coliform bacteria. 

You can go for total soil or sludge DNA isolation, DGGE/TGGE, pyrosequencing and other sequencing methods.

Suggest you also validate coliform recovery by MPN with the mateirla being tested.

Best method is MPN for isolation of coliforms from sewage but you have to go for its all three test (Presumptive, Completed and Confirmed) and for isolation of microbes from rhizosphere you may go to 16SrRNA sequencing