Oysters eat microscopic phytoplankton, including algae, which the bay generally has overabundance of thanks to excess fertilizer runoff. Oysters are not just a tasty economic resource they make Chesapeake Bay cleaner. The missing shells are a direct loss to oyster restoration, because oyster larvae are choosy about where they glue themselves down and start building their shells. They prefer other oyster shells as anchorage.
But in addition to providing habitat for future generations, oyster reefs appear to alter their local water chemistry. Like slow dissolving Tums in the belly of the estuary, disintegrating oyster shells are slow release capsules of calcium carbonate, an alkaline salt and a buffer against acidity. Seawater mixing in on the tide has a relatively high capacity to absorb acid inputs without a large change in pH. Fresh water flowing out to sea generally has a low buffering capacity, and is sensitive to acid sources, whether from human made point sources like coal plants or natural processes like the oysters' own respiration. Coastal estuaries, where the waters meet, are also where oysters tend to cluster.
Ecosystem effects of shell aggregations and cycling in coastal waters: An example of Chesapeake Bay oyster reefs. (2013) George G. Waldbusser, Eric N. Powell, and Roger Mann. Ecology 94(4): 895-903 (Currently in authors'
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Ecological Society of America