Abstract
Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are processes occurring simultaneously under oxygen-limited or anaerobic conditions, where both compete for nitrate and organic carbon. Despite their ecological importance, there has been little investigation of how denitrification and DNRA potentials and related 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 along the estuary. 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 copy numbers of 16S rRNA and nitrate reducing genes 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, based on macrofauna distributions, could only account for the upper 10 cm depth of sediment. 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. This raises interesting questions as to what the alternative metabolic roles for the various nitrate reductases could be, analogous to the alternative metabolic roles found for nitrite reductases.
Highlights
Increased anthropogenic inputs of nitrogen (N) from fertiliser run-off, sewage discharges and aquaculture into coastal systems, like estuaries, stimulate primary production, occasionally leading to anoxia in the water column and mass mortality of fish stocks and other macrofauna [1]
Anaerobic ammonium oxidation (Anammox) may remove significant amounts of nitrite and ammonium as N2 at some marine and estuarine sites [4,5]. Another process, dissimilatory nitrate reduction to ammonium (DNRA) converts nitrate to biologically available ammonium, which can be retained within the system
The step in the two processes is distinct and for denitrification involves the enzyme nitrite reductase (NIR) converting nitrite to nitric oxide, and for DNRA the nitrite reductase (NRF) enzyme which converts nitrite to ammonium
Summary
Increased anthropogenic inputs of nitrogen (N) from fertiliser run-off, sewage discharges and aquaculture into coastal systems, like estuaries, stimulate primary production (eutrophication), occasionally leading to anoxia in the water column and mass mortality of fish stocks and other macrofauna [1]. We investigated the relationship between potential rates from the slurry experiments with in situ functional gene abundance, Corg availability and C:N ratio by performing distance based multiple regression [39], after removing environmental variables with correlation .0.9, using the best selection procedure and the AIC criterion.
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