Molecular and biogeochemical evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of California
Molecular and biogeochemical evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of California
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DOI：
10.1038/ismej.2008.33
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发表时间：
2008
期刊：
影响因子：
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通讯作者：
J. Beman;B. Popp;C. A. Francis
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文献类型：
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作者：
J. Beman;B. Popp;C. A. Francis
硝化作用在海洋生物地球化学中发挥着重要作用，但将该过程与介导该过程的微生物联系起来的努力却非常有限。特别是，氨氧化是硝化的第一步，也是硝化作用的限速步骤，但氨氧化速率和氨氧化细菌（AOB）的丰度很少同时测量。氨氧化率尚未与氨氧化古菌（AOA）一起直接量化，尽管越来越多的证据表明海洋泉古菌能够氧化氨，并且它们是海洋中最丰富的微生物群之一。在这里，我们通过 15 N 标记直接量化氨氧化率，并通过对加利福尼亚湾氨单加氧酶亚基 A (amoA) 基因进行定量 PCR 分析来量化 AOA 和 AOB 丰度。基于上部水柱 (60米) 和最低氧区 (OMZ; 450米) 中明显不同的古细菌序列类型，novamoAPCR 引物被设计用于专门针对和量化“浅层”（A 组）和“深层”（B 组）进化枝。这些引物恢复了随深度的广泛变化。在 OMZ 内，硝化作用可能与反硝化作用耦合的地方，AOA 最丰富。在上部水体中，A 组跟踪氮生物地球化学随深度和盆地之间的变化，而 AOB 的数量相对较低或无法检测到。总体而言，15NH4+氧化率与AOA组AamoAgene拷贝数（r2=0.90，P<0.001）以及海洋Crenarchaeota的16S rRNA基因拷贝数显着相关（r2=0.85，P<0.005）。这些发现为古细菌在海洋硝化作用中的作用提供了令人信服的证据。
Nitrification plays an important role in marine biogeochemistry, yet efforts to link this process to the microorganisms that mediate it are surprisingly limited. In particular, ammonia oxidation is the first and rate-limiting step of nitrification, yet ammonia oxidation rates and the abundance of ammonia-oxidizing bacteria (AOB) have rarely been measured in tandem. Ammonia oxidation rates have not been directly quantified in conjunction with ammonia-oxidizing archaea (AOA), although mounting evidence indicates that marine Crenarchaeota are capable of ammonia oxidation, and they are among the most abundant microbial groups in the ocean. Here, we have directly quantified ammonia oxidation rates by15N labeling, and AOA and AOB abundances by quantitative PCR analysis of ammonia monooxygenase subunit A (amoA) genes, in the Gulf of California. Based on markedly different archaealamoAsequence types in the upper water column (60 m) and oxygen minimum zone (OMZ; 450 m), novelamoAPCR primers were designed to specifically target and quantify ‘shallow’ (group A) and ‘deep’ (group B) clades. These primers recovered extensive variability with depth. Within the OMZ, AOA were most abundant where nitrification may be coupled to denitrification. In the upper water column, group A tracked variations in nitrogen biogeochemistry with depth and between basins, whereas AOB were present in relatively low numbers or undetectable. Overall,15NH4+oxidation rates were remarkably well correlated with AOA group AamoAgene copies (r2=0.90,P<0.001), and with 16S rRNA gene copies from marine Crenarchaeota (r2=0.85,P<0.005). These findings represent compelling evidence for an archaeal role in oceanic nitrification.