There have been several past threads about using beneficial bacteria for decomposing bottom muck and organics.
Read through this thread for some basic information.
http://forums.pondboss.com/ubbthreads.php?ubb=showflat&Number=461031#Post461031

A couple of pond owners were going to run a some bacterial test comparisons. But i do not remember seeing any of the results.
Here is another long thread about pond bacteria and discussion
http://forums.pondboss.com/ubbthreads.php?ubb=showflat&Number=420651&page=1