Molecular microbial ecology of ammonia oxidation in coastal sediments

This thesis focuses on the processes of nitrification in three coastal bays, specifically, aerobic ammonia oxidation which is the rate limiting step of nitrification and is mediated by ammonia oxidising bacteria and/or archaea (AOB/AOA). Rusheen, Clew and Kinvarra bay are located on the Atlantic coast of Ireland. The aim of this project is to combine in situ field data with experimental approaches, addressing temporal and spatial changes in ammonia oxidiser (AO) activity, abundance and diversity across environmental gradients in coastal bay ecosystems, in order to elucidate the key AO and environmental drivers within dynamic intertidal sediment ecosystems. Using this approach we report for the first time transcriptionally active AOB and AOA were present within Rusheen bay intertidal sediments, bringing us a step closer to confirming actively nitrifying co-occurring AOB and AOA in intertidal sediments. In chapter three we observe the huge diversity that can be found in coastal sediments. We show that using 16S rRNA transcripts enables us to identify low abundant or rare OTUs that were not picked up by sequencing DNA alone. Finally in chapter four through the use of experimental sediment microcosm incubations combined with SIP, we were able to demonstrate the growth and activity of Nitrosoarchaeum like AOAs in a low salinity habitat originating from intertidal coastal sediment. In addition throughout all three chapters we saw the impact environmental conditions such as nutrient concentrations, salinity, pH and temperature have on driving the distribution of communities within intertidal sediments