Estuarine nekton community shows minimal response following large-scale oyster reef habitat loss in Apalachicola Bay, Florida

Structural habitats support high biodiversity by providing refuge, forage resources, and recruitment habitat that upwardly influence the broader faunal community structure. However, there are few system-wide studies that empirically measure communities before and after major shifts in habitat structure or availability, limiting our ability to predict the consequences of changes in structural habitat above local scales. We used the collapse of the Apalachicola Bay, Florida oyster population as a natural experiment to assess the impacts of estuary-wide structural habitat loss on the nekton community through long-term faunal monitoring data. Habitat losses of this magnitude are expected to decrease diversity and alter composition, so we expected to observe these changes in Apalachicola Bay after the oyster population collapse. We assessed changes in Gini-Simpson diversity and composition over a 21-year period encompassing the 2012 oyster collapse using generalized linear mixed models to account for confounding drivers. We surprisingly found no evidence that Gini-Simpson diversity or composition differed immediately before or following the collapse, which may be explained if estuarine fauna were able to effectively use other habitats. This suggests that proportional changes in diversity or composition from loss or gain of structural habitats cannot be assumed at the system-wide scale.