@ Ranjan, I think standard plate count agar method is the best to count microorganisms in the compost. A marker can be used pointing each counted colony on the back of the Petri dish or you can use colony counter, if you have , to count the colonies. The microbial load was quantified using the following formula: microbial load (CFU/g) = (number of CFUs on plate ×103) / dilution.

For autotrophic count you can prepare agar plates using mineral salt medium, while for hetertrophic count prepare nutrient agar, rose bengal agar and actinomycetes agar. Count the colony as mentioned by Dr J C Tarafdar

I do agree with J. C. Tarafdar.

Thank you Dr. Tarafdar and Dr Vyas for your guidance