Soil communities are so diverse it is difficult to find one method to describe all that we find in soil. On a very basic level, size can be a useful measurement although one has to recognise the presence of juveniles or larval stages which may be very different from the parent form and be in different habitats.
More information can be gained by comparing morphology against standard or type species. This can be done at an initially gross level to describe families and later to describe genera and eventually species as more information is obtained. This level of information requires great specialist technical knowledge and a familiarity with the organisms. Many of the methods used are not transferable to other groups. For example the description of microbial species is mainly based on biochemical and physiological information rather than gross anatomy where as for arthropods, for example, the emphasis is placed on morphology and life history of the organism.
The ease at which DNA can be sequenced is making the task of assessing biodiversity easier although this is itself not without its own problems not least in defining what actually is a species.