From the point of view of community ecology, soft bottoms are not as well understood as rocky shores.
Most experiments using cages tend to alter the sedimentary regime.
Further, we do not have a complete understanding of the food base of soft bottoms, particularly for deposit feeders. We cannot say with assurance how much of the non-living organic matter in muddy sediments is used as food. The three- dimensional nature of burrowing also makes it difficult to even see what is going on within the sediment, although many interesting techniques allow us to get around this. We do, however, have much elegant physiological and natural history information about the soft bottom intertidal habitat. Unlike rocky shores, mud flats are far less observable without disturbing the habitat, because many species are infaunal.