Benthic habitat mapping and assessment using organism-sediment relationships

The study of organism-sediment relationships involves characterizing a suite of biological and geological features that control the spatial and temporal patterns of the benthic landscape and the response of these ecosystems to natural and anthropogenic disturbance. Acknowledging this variability is essential for effective monitoring and management of all marine ecosystems, but especially coastal environments where anthropogenic stresses tend to dominate. This dissertation examines organism-sediment relationships to support habitat mapping and assessment in Greenwich Bay, a shallow sub-embayment within Narragansett Bay, Rhode Island, USA. Sediment profile imagery (SPI) played a prominent role in linking sediments, organisms and water quality in these studies. In the first chapter, we found that burrow structures and the apparent redox potential discontinuity (aRPD), or oxidized layer of surface sediment visible in SPI were the strongest surrogates for water quality over multiple assessment windows and dissolved oxygen thresholds. Therefore, the use of SPI widens the spatial extent of water quality monitoring efforts by reflecting the near-term water quality of sites where it is impractical to deploy multiple probes. In the second chapter, SPI is used in combination with traditional grab samples and acoustics to integrate biotic (benthic biological communities) and abiotic (sediment types, depositional environments) data to create accurate and useful habitat maps. Relationships between the biology and geology were preserved when maps were created using a linkage tree based on significant associations between macrofauna abundance and percent sand, backscatter standard deviation and bathymetry. In the third chapter, water quality and biological habitat data were combined to characterize the effects of a major change in wind-driven circulation on hypoxia prevalence and benthic communities. Persistent hypoxia and weak exchange with Narragansett Bay promoted the dominance of opportunistic species in enclosed parts of the study area. Periodic hypoxia and intermittent exchange followed by normoxia and increased flushing allowed tube-building amphipods (Ampelisca abdita) to reach mat densities at the mouth of the bay. The horizontal and vertical transport of water was important to the structure of benthic communities by influencing water column structure, nutrient and organic matter transport and deposition, and larval delivery