Well there are common methods available for microfaunal assessment. But before that let me understand why do you consider that AFS microfauna would be different?
Yes Dr Jha pointed why AFS microfauna? at microlevel AFS microfauna is might have seperated from other forest ot or agriculture soil microfauna to asses the diffrence but mehodology to asses in all landuse will be same. Microfunal population include diverse groups from arthopods to fungi but micribial will have bacteria nd fungi mainly. Please find attached merial and methods used by one our Ph.D students in AFS for abcteria and fungi studies.
PLFA analysis can provide a real-time snapshot of the soil microbial community (soil microbiota) structure. PLFA analysis is a widely-used technique for estimation of the total biomass and to observe broad changes in the soil microbiota composition. Have a look in the following articles....
http://www.midi-inc.com/pages/plfa.html
Article Extraction and Analysis of Microbial Phospholipid Fatty Acids in Soils
Article High throughput fatty acid analysis of soils