School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, United Kingdom.
PLoS One. 2014 Apr 11;9(4):e94111. doi: 10.1371/journal.pone.0094111. eCollection 2014.
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.
反硝化和异化硝酸盐还原为铵（DNRA）是在缺氧或厌氧条件下同时发生的过程，两者都竞争硝酸盐和有机碳。尽管它们具有重要的生态意义，但对于反硝化和 DNRA 潜力以及相关功能基因如何随沉积物深度垂直变化的研究甚少。在科尔尼河口的沉积物深度剖面中测量的硝酸盐还原潜力处于其他沉积物报道的硝酸盐还原率的上限范围内，并且显示出随着深度的增加和沿河口的增加而存在强烈的递减趋势。反硝化潜力随河口而降低，向河口口部的深度减小更快。相比之下，DNRA 潜力沿河口增加。在河口和从表层到更深的沉积物中，16S rRNA 和硝酸盐还原基因的拷贝数都显著下降。在没有底水硝酸盐的情况下，代谢潜力和功能基因仍然存在于沉积物深度。基于大型动物分布的硝酸盐生物扰动运输只能解释沉积物上层 10 厘米的深度。与底水硝酸盐相比，检测到结合可冻结的 KCl 可提取硝酸盐库高出几个数量级。我们假设这可能归因于硝酸盐积累微生物（如硫细菌或贝氏硫菌）的细胞内硝酸盐库。然而，焦磷酸测序分析未检测到任何此类生物体，留下其他细菌、微型底栖藻类或已显示出积累硝酸盐的有孔虫作为可能的候选物。KCl 可提取硝酸盐沉积物库的重要性和生物利用度仍有待测试。各种硝酸盐还原基因的垂直模式和丰度的显著变化合理地表明它们在整个沉积物柱中的活性存在差异。这就提出了一个有趣的问题，即各种硝酸盐还原酶的替代代谢作用可能是什么，类似于发现的亚硝酸盐还原酶的替代代谢作用。
