A comparison of primer sets for detecting 16S rRNA and hydrazine oxidoreductase genes of anaerobic ammonium-oxidizing bacteria in marine sediments
A comparison of primer sets for detecting 16S rRNA and hydrazine oxidoreductase genes of anaerobic ammonium-oxidizing bacteria in marine sediments
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海洋沉积物中厌氧氨氧化菌16S rRNA和肼氧化还原酶基因检测引物组比较
DOI：
10.1007/s00253-009-2361-5
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发表时间：
2010-03-01
影响因子：
5
通讯作者：
Gu, Ji-Dong
中科院分区：
文献类型：
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作者：
Li, Meng;Hong, Yiguo;Gu, Ji-Dong
利用相同的沿海海洋沉积物样本，对已发表的用于检测厌氧氨氧化细菌中编码16S rRNA基因和肼氧化还原酶（hzo）基因的聚合酶链反应引物组进行了比较。虽然之前报道的用于检测16S rRNA基因的四组引物显示出12% - 77%不同的特异性，但一种优化的引物组合特异性高达98%，并且所获得的厌氧氨氧化16S rRNA基因序列与来自暂定分类单元“Scalindua”组的厌氧氨氧化细菌已发表序列的相似度>95%。此外，用于检测厌氧氨氧化细菌hzo基因的四组引物具有高度特异性（高达92%）且高效，本研究中新设计的引物组可扩增出更长的适用于系统发育分析的hzo基因片段。针对16S rRNA基因的优化引物组和针对hzo基因的新设计引物组成功应用于从水产养殖区、沿海湿地和深海的海洋沉积物中鉴定厌氧氨氧化细菌，这三个生态系统形成了人为影响的梯度。结果表明，厌氧氨氧化细菌在每个海洋生态系统内广泛分布，且具有高度的生态位特异性群落结构。
Published polymerase chain reaction primer sets for detecting the genes encoding 16S rRNA gene and hydrazine oxidoreductase (hzo) in anammox bacteria were compared by using the same coastal marine sediment samples. While four previously reported primer sets developed to detect the 16S rRNA gene showed varying specificities between 12% and 77%, an optimized primer combination resulted in up to 98% specificity, and the recovered anammox 16S rRNA gene sequences were >95% sequence identical to published sequences from anammox bacteria in theCandidatus“Scalindua” group. Furthermore, four primer sets used in detecting thehzogene of anammox bacteria were highly specific (up to 92%) and efficient, and the newly designed primer set in this study amplified longerhzogene segments suitable for phylogenetic analysis. The optimized primer set for the 16S rRNA gene and the newly designed primer set for thehzogene were successfully applied to identify anammox bacteria from marine sediments of aquaculture zone, coastal wetland, and deep ocean where the three ecosystems form a gradient of anthropogenic impact. Results indicated a broad distribution of anammox bacteria with high niche-specific community structure within each marine ecosystem.