Molecular assessment of benthic diatom assemblages in Delaware’s Inland Bays

Lee, Katherine
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University of Delaware
The investigation of biological indicators in marine systems is an important conservation tool. In this study, denaturing gradient gel electrophoresis (DGGE) and terminal-restriction fragment length polymorphism (T-RFLP) methods were developed to analyze diatom community structure in sediment cores taken from several sites in the Delaware Inland Bays. Statistical analyses were used to evaluate differences in diatom assemblages between site type (creek, dead end canal and open water), year of collection (2009, 2010 and 2011), location (Rehoboth Bay, Indian River Bay, and Little Assawoman Bay) and month of collection. Differences in assemblages and diversity were also correlated with other environmental parameters including nutrient concentration, percent total organic carbon, and sediment chlorophyll concentration. My results show that diatom assemblages in the Delaware Inland Bays are diverse and that populations are significantly different between site type and year of collection. Some environmental variables including dissolved oxygen, total organic carbon and sediment chlorophyll were found to be linked to diatom community composition. Changes in diatom diversity were also correlated with water column phosphate and dissolved N:P ratios. Several laboratory incubation experiments were conducted to evaluate the effects of light attenuation and elevated N:P on diatom assemblages. Light attenuation resulted in decreased diversity, with a species 98% similar to Skeletonema japonicum dominating the community under low light conditions. Finally, I developed quantitative real-time PCR (qPCR) assays for Skeletonema japonicum along with several previously identified diatom indicatorsand analyzed their abundance relative to the whole diatom community in laboratory incubation experiments and environmental samples. Navicula gregaria and Skeletonema sp. 1 were evaluated as indicators of high N:P. Thalassiosira pseudonana was evaluated as an indicator of low N:P. Indicator Value (IndVal) indices were calculated quantifying the predictive capability of Skeletonema japonicum as an indicator of turbid conditions, Skeletonema sp. 1 as an indicator of high N:P, and Thalassiosira pseudonana as an indicator of low N:P. Navicula gregaria results deviated from previous research and it proved instead to be a good indicator of low N:P.