| Summary: | Coastal sediments are major sites for microbially-mediated nitrate reduction, In particular denitrification. Estuarine sediments are prime locations for this process due to anthropogenic ally generated nitrate pollution from agricultural sources and wastewater treatment plants. The Colne estuary (UK) is one such hypernutrified estuary, receiving significant inputs of nitrate and ammonium. Rates of denitrification have been previously characterised along the estuary and found to be highest at the estuary head and lowest at the mouth. The aim of this current study was to investigate spatial and temporal variation in microbial community structure along nutrient and salinity gradients of the estuary, as well as assess the bacterial and archaeal community composition and denitrification potential of the sediments located at the mouth of the estuary and via the use of slurry microcosm experiments to examine the responses of bacterial communities to changes in levels of nitrate and organic carbon. Molecular techniques based on both the microbial taxonomic marker gene (16S rRNA) and denitrification (nirS, nirK) genes were employed to investigate these changes in community structure and composition. Distinct sediment bacterial communities were present at the low salinity and marine sites of the estuary with seasonal variability observed at the lowest salinity site (Hythe) and monthto- month variation at the brackish and marine sites (Alresford and Brightlingsea). The marine bacterial community was dominated by proteobacteria, with Crenarchaeota the dominant archaeal phylum. The potential for denitrification was investigated in the marine sediments, with denitrifying populations distinct from those previously described in low salinity sediments of the Colne. In microcosm experiments, bacterial communities in sediments amended with only nitrate, or nitrate and acetate showed major shifts in community composition relative to those in unamended sediments. This research has revealed a diverse microbial community structure exists along the Colne estuary and demonstrates considerable capacity for nitrate removal at the mouth of the estuary and that changes in nitrate and organic carbon can result in major changes in sediment microbial community composition.
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