Shell Bottom: Building Reefs and Cleaning Water

March 18, 2021
The North Carolina Coastal Habitat Protection Plan (2016)
North Carolina Coastal Federation

Oyster reefs are critical for North Carolina's seafood industry and for a healthy habitat

Shell bottom is unique because it is the only coastal fish habitat that is also a fishery species (oysters). Shell bottom is estuarine intertidal or subtidal bottom composed of surface shell concentrations of living or dead oysters, hard clams, and other shellfish. Oysters, the primary shell-building orngaism in North Carolina estuaries, are found throughout the coast, from southeast Albemarle Sound to the South Carolina border. The protection and restoration of living oyster beds is critical to the restoration of numerous fishery species, as well as to the proper functioning and protection of surrounding coastal fish habitats. historically ,restoration was managed for osyter fishery enhancement. Current efforts mix fishery and ecosystem enhancement with sanctuary development.

Restored and protected oyster reefs provide up to $40,200 per acre per year

Over 40 species of fish using oyster reefs as nursery habitat or foraging, including red drum southern flounder, and black sea bass

Shell bottom is widely recognized as essential fish habitat (EFH) for oysters  and other reef-forming mollusks and provides critical fish habitat for ecologically and economically important finfish, mollusks, and crustaceans. In North Carolina, over 40 species of fish and crustaceans have been documented to use natural and restored oysters reefs, including American eel, Atlantic croaker, Atlantic menhaden, black sea bass, sheepshead, spotted seatrout, red drum, and southern flounder. Oysters are ecosystem engineers that alter current and flows, protect shorelines, and trap and stabilize large quantities of suspended solids, reducing turbidity by building high relief structures. The interstitial spaces between and within the shell matrix of oyster reefs are critical refuges for the survival of recruiting oysters and other small, slow-moving macrofauna, such as worms, crabs and clams. Shell bottom is also valuable nursery habitat for juveniles of commercially and recreationally important finfish, such as black sea bass, sheepshead, gag grouper, and snappers. Additionally, shell bottom is important foraging ground for many economically and ecologically important species. The proximity and connectvitiy of oyster beds enhances the fish utilization of nearby habitats, especially SAV. Shell bottom contributes primary production indirectly from plants on and around it, but it is more important for its high secondary productivity contribution from the biomass of oysters and other macroinvertebrates living among the shell structure. this in turn supports a high density of mobile finfish and invertebrates, which was found to be more than two times greater than in marshes, soft bottom and SAV.

Oyster  populations  in  North  Carolina  have  declined  by  as  much  as  90% from  historic  levels, but populations are increasing

Oyster  populations  in  North  Carolina  have  declined  by  as  much  as  90%  from  historic  levels due to poor harvesting practices. After  1991,  oyster  stocks  and  harvests began  to  collapse  from  disease  mortalities  and  low  spawning  stock  biomass.  Harvests began  to  rise  again  around  2002,  and  the  trend  has  continued.  Between  2000  and  2013, oyster dredging trips and hand harvest trips have risen substantially, with increasing larval availability,
connectivity,  and  recruitment  potential  for  restored  and  existing  reefs.  As  of  January  2015, there were 13 established oyster sanctuaries, with an additional two proposed.

Oyster populations are threatened by overharvesting, damaging fishing gear, navigational dredging, poor water quality, sedimentation and low dissolved oxygen

Shell bottom  habitat  can  be  damaged  by  overharvesting, mechanical harvest  fishing  gear,  navigational dredging, marinas  and  boating  activity.  Water  quality  degradation,  especially  toxin  contamination,  sedimentation,  and hypoxia, can cause lethal or sublethal impacts.  Shell bottom is occasionally susceptible to diseases and microbial stressors.  The  protozoan  pathogen  Perkinsus  marinus,  also  called “dermo”  has  been  responsible  for  major  oyster  mortalities  in  North Carolina. Monitoring of dermo disease by DMF shows a declining trend in prevalence, with an increasing trend in overall infection.

Boring sponges create holes in oyster shells and can dramatically reduce oyster populations

Boring  sponge,  sponges  belonging  to  the  genus  Cliona,  are  found  in North  Carolina  shell  bottom  habitats.  Boring  sponges  compromise  the integrity  of  shells  and  are  linked  to  reduced  reproductive  viability  and possibly  increased  oyster  mortality  rates.  Two  North  Carolina  oyster sanctuaries  experienced  dramatic  population  declines  since  2012, coinciding with increasing percent cover of marine boring sponge.  Cliona is  endemic  to  North  Carolina  but  has  recently  become  more  pervasive,  especially  on  limestone  marl  rocks.  To improve  reef  design  in  high  salinity  waters,  DMF  is  conducting  research  on  alternative  substrates  to  identify materials  that  maximize  oyster  recruitment,  growth,  and  survival,  while  offering  high  resistance  to  environmental stressors, such as Cliona boring sponge.

Shell bottom is considered to be one of the most threatened habitats because of its greatly reduced extent

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