Geochemistry of sediment cores from the Colne estuary

Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are important processes occurring simultaneously under oxygen-limited or anaerobic conditions both competing for nitrate and organic carbon. Despite their ecological importance, there has been little investigation of how denitrification and DNRA potentials and related key functional genes vary vertically with sediment depth. Nitrate reduction potentials measured in sediment depth profiles along the Colne estuary were in the upper range of nitrate reduction rates reported from other sediments and showed the existence of strong decreasing trends both with increasing depth and from the head to the estuary mouth. Denitrification potential decreased along the estuary, decreasing more rapidly with depth towards the estuary mouth; in contrast, DNRA potential increased along the estuary. Significant decreases in 16S rRNA and nitrate reducing genes copy numbers were observed along the estuary and from surface to deeper sediments. Both metabolic potentials and functional genes persisted at sediment depths where porewater nitrate was absent. Transport of nitrate by bioturbation could only account for the upper 10 cm depth of sediment based on macrofauna distribution. A several fold higher combined freeze-lysable KCl-extractable nitrate pool compared to porewater nitrate was detected. We hypothesised that his could be attributed to intracellular nitrate pools from nitrate accumulating microorganisms like Thioploca or Beggiatoa. However, pyrosequencing analysis did not detect any such organisms, leaving other bacteria, microbenthic algae or foraminiferans which have also been shown to accumulate nitrate, as possible candidates. The importance and bioavailability of a KCl-extractable nitrate sediment pool remains to be tested. The significant variation in the vertical pattern and abundance of the various nitrate reducing genes phylotypes reasonably suggests differences in their activity throughout the sediment column, raising interesting questions as to what could the alternative metabolic roles for the various nitrate reductases be , as previously found for nitrite reductases.