<i>amoA</i> Gene Abundances and Nitrification Potential Rates Suggest that Benthic Ammonia-Oxidizing Bacteria and Not Archaea Dominate N Cycling in the Colne Estuary, United Kingdom

<jats:title>ABSTRACT</jats:title> <jats:p> Nitrification, mediated by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), is important in global nitrogen cycling. In estuaries where gradients of salinity and ammonia concentrations occur, there may be differential selections for ammonia-oxidizer populations. The aim of this study was to examine the activity, abundance, and diversity of AOA and AOB in surface oxic sediments of a highly nutrified estuary that exhibits gradients of salinity and ammonium. AOB and AOA communities were investigated by measuring ammonia monooxygenase ( <jats:italic>amoA</jats:italic> ) gene abundance and nitrification potentials both spatially and temporally. Nitrification potentials differed along the estuary and over time, with the greatest nitrification potentials occurring mid-estuary (8.2 μmol N grams dry weight [gdw] <jats:sup>−1</jats:sup> day <jats:sup>−1</jats:sup> in June, increasing to 37.4 μmol N gdw <jats:sup>−1</jats:sup> day <jats:sup>−1</jats:sup> in January). At the estuary head, the nitrification potential was 4.3 μmol N gdw <jats:sup>−1</jats:sup> day <jats:sup>−1</jats:sup> in June, increasing to 11.7 μmol N gdw <jats:sup>−1</jats:sup> day <jats:sup>−1</jats:sup> in January. At the estuary head and mouth, nitrification potentials fluctuated throughout the year. AOB <jats:italic>amoA</jats:italic> gene abundances were significantly greater (by 100-fold) than those of AOA both spatially and temporally. <jats:named-content content-type="genus-species">Nitrosomonas</jats:named-content> spp. were detected along the estuary by denaturing gradient gel electrophoresis (DGGE) band sequence analysis. In conclusion, AOB dominated over AOA in the estuarine sediments, with the ratio of AOB/AOA <jats:italic>amoA</jats:italic> gene abundance increasing from the upper (freshwater) to lower (marine) regions of the Colne estuary. These findings suggest that in this nutrified estuary, AOB (possibly <jats:named-content content-type="genus-species">Nitrosomonas</jats:named-content> spp.) were of major significance in nitrification. </jats:p>