The general successful trend in decomposing bottom muck is keeping or infusing oxygen into the offending zone. The problem with aeration is it moves water over top the sediments and does not mix or infuse oxygen down into the sediments. Oxygenating or regular mixing at the mud water interface results in rapid decay of the top sediment / muck layer. Now all we have to do is figure out a way to practically mix or till the pond bottom muck - sediment. Common carp, koi, gizzard shad or other bottom activity will cause natural sediment mixing but their constant activity almost always results in too much muddy turbid water that deters the sport fishery by inhibiting the plankton populations.
See May-June 2016 Pond Boss Mag for: POND ENVIRONMENT: FOOD REQUIREMENTS AND DIRTY WATER. West reviews current research about protein (amino acid taurine) needs of pond fish and how suspended sediment significantly impacts pond fish and a majority of the ecosystem.
Advanced Readings
Photosynthesis Production. From
http://www.fondriest.com/environmen...ty-total-suspended-solids-water-clarity/Turbidity can also inhibit photosynthesis by blocking sunlight. Halted or reduced photosynthesis means a decrease in plant survival and decreased dissolved oxygen output. The higher the turbidity levels, the less light that can reach the lower levels of water. This reduces plant productivity at the bottom of an ocean, lake or river. Without the needed sunlight, seaweed and bay grasses below the water�s surface will not be able to continue photosynthesis and may die.
Underwater vegetation die-off has two main effects. First, as photosynthetic processes decrease, less dissolved oxygen is produced, thus further reducing DO levels in a body of water. The subsequent decomposition of the organic material can drop dissolved oxygen levels even lower. Second, seaweed and underwater plants are necessary food sources for many aquatic organisms. As they die off, the amount of vegetation available for other aquatic life to feed on is reduced. This can cause population declines up the food chain
https://www.fws.gov/northeast/virgi...cumseh/EffectsofSediment_Henley_2000.pdfhttp://link.springer.com/chapter/10.1007%2F978-1-4757-1674-0_15https://www.jstor.org/stable/1940593?seq=1#page_scan_tab_contents
http://onlinelibrary.wiley.com/doi/10.2307/1937582/full 
