Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA.
Environ Microbiol. 2010 Jul;12(7):1989-2006. doi: 10.1111/j.1462-2920.2010.02205.x. Epub 2010 Mar 23.
A combination of stable isotope and molecular biological approaches was used to determine the activity, abundance and diversity of nitrifying organisms in the central California Current. Using (15)NH(4)(+) incubations, nitrification was detectable in the upper water column down to 500 m; maximal rates were observed just below the euphotic zone. Crenarchaeal and betaproteobacterial ammonia monooxygenase subunit A genes (amoA), and 16S ribosomal RNA (rRNA) genes of Marine Group I Crenarchaeota and a putative nitrite-oxidizing genus, Nitrospina, were quantified using quantitative PCR. Crenarchaeal amoA abundance ranged from three to six genes ml(-1) in oligotrophic surface waters to > 8.7 x 10(4) genes ml(-1) just below the core of the California Current at 200 m depth. Bacterial amoA abundance was lower than archaeal amoA and ranged from below detection levels to 400 genes ml(-1). Nitrification rates were not directly correlated to bacterial or archaeal amoA abundance. Archaeal amoA and Marine Group I crenarchaeal 16S rRNA gene abundances were correlated with Nitrospina 16S rRNA gene abundance at all stations, indicating that similar factors may control the distribution of these two groups. Putatively shallow water-associated archaeal amoA types ('Cluster A') decreased in relative abundance with depth, while a deep water-associated amoA type ('Cluster B') increased with depth. Although some Cluster B amoA sequences were found in surface waters, expressed amoA gene sequences were predominantly from Cluster A. Cluster B amoA transcripts were detected between 100 and 500 m depths, suggesting an active role in ammonia oxidation in the mesopelagic. Expression of marine Nitrosospira-like bacterial amoA genes was detected throughout the euphotic zone down to 200 m. Natural abundance stable isotope ratios (delta(15)N and delta(18)O) in nitrate (NO(3)(-)) and nitrous oxide (N(2)O) were used to evaluate the importance of nitrification over longer time scales. Using an isotope mass balance model, we calculate that nitrification could produce between 0.45 and 2.93 micromol m(-2) day(-1) N(2)O in the central California Current, or approximately 1.5-4 times the local N(2)O flux from deep water.
采用稳定同位素和分子生物学方法的组合，确定了加利福尼亚中部洋流中硝化生物的活性、丰度和多样性。通过（15）NH（4）（+）培养，在 500 米以下的上层水柱中可检测到硝化作用；最适速率出现在透光带以下。古菌和β变形菌氨单加氧酶亚基 A 基因（amoA）以及海洋 I 群古菌的 16S 核糖体 RNA（rRNA）基因和假定的亚硝酸盐氧化属 Nitrospina ，使用定量 PCR 进行定量。古菌 amoA 的丰度范围从贫营养表层水中的 3 到 6 个基因 ml（-1）到 200 米深处加利福尼亚洋流核心以下的> 8.7 x 10（4）个基因 ml（-1）。细菌 amoA 的丰度低于古菌 amoA，范围从检测下限到 400 个基因 ml（-1）。硝化速率与细菌或古菌 amoA 的丰度没有直接相关性。在所有站位，古菌 amoA 和海洋 I 群古菌 16S rRNA 基因丰度与 Nitrospina 16S rRNA 基因丰度相关，表明可能有相似的因素控制这两个群体的分布。与浅水相关的古菌 amoA 型（“Cluster A”）的相对丰度随深度降低，而与深水相关的 amoA 型（“Cluster B”）的丰度随深度增加。虽然在表层水中发现了一些 Cluster B amoA 序列，但表达的 amoA 基因序列主要来自 Cluster A。在 100 至 500 米深度检测到 Cluster B amoA 转录本，表明在中层水层中氨氧化具有活性作用。海洋 Nitrosospira 样细菌 amoA 基因的表达在透光带一直检测到 200 米以下。硝酸盐（NO（3）（-））和氧化亚氮（N（2）O）的天然丰度稳定同位素比值（δ（15）N 和 δ（18）O）用于评估硝化作用在较长时间尺度上的重要性。通过同位素质量平衡模型，我们计算出在加利福尼亚中部洋流中，硝化作用每平方米每天可产生 0.45 至 2.93 微摩尔 N（2）O，或大约是来自深层水的本地 N（2）O通量的 1.5-4 倍。
