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Community Structure of Ammonia-Oxidizing Bacteria within Anoxic Marine Sediments

机译：缺氧海洋沉积物中氨氧化细菌的群落结构

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The potential for oxidation of ammonia in anoxic marine sediments exists through anaerobic oxidation by Nitrosomonas-like organisms, utilizing nitrogen dioxide, coupling of nitrification, manganese reduction, and anaerobic oxidation of ammonium by planctomycetes (the Anammox process). Here we describe the presence of microbial communities with the potential to carry out these processes in a natural marine sediment system (Loch Duich, Scotland). Natural microbial communities of Planctomycetales-Verrucomicrobia and β- and γ-proteobacterial ammonia-oxidizing bacteria were characterized by analysis of 16S rRNA genes amplified using group-specific primers by PCR- and reverse transcription-PCR amplification of 16S rDNA and RNA, respectively. Amplification products were analyzed by sequencing of clones and by denaturant gradient gel electrophoresis (DGGE). Amplification of primers specific for Planctomycetales-Verrucomicrobia and β-proteobacterial ammonia-oxidizing bacteria generated products at all sampling sites and depths, but no product was generated using primers specific for γ-proteobacterial ammonia-oxidizing bacteria. 16S rDNA DGGE banding patterns indicated complex communities of β-proteobacterial ammonia-oxidizing bacteria in anoxic marine sediments. Phylogenetic analysis of sequences from clones and those excised from DGGE gels suggests dominance of Nitrosospira cluster 1-like organisms and of strains belonging to a novel cluster represented in dominant bands in 16S rRNA DGGE banding patterns. Their presence indicates a group of organisms closely related to recognized β-proteobacterial ammonia-oxidizing bacteria that may be selected in anoxic environments and may be capable of anoxic ammonia oxidation. Sequence analysis of planctomycete clone libraries and sequences excised from DGGE gels also demonstrated a diverse microbial community and suggested the presence of new subdivisions, but no sequence related to recognized Anammox organisms was detected.
机译：缺氧海洋沉积物中氨的氧化潜力是通过亚硝化单胞菌样生物的厌氧氧化，利用二氧化氮，偶合的硝化作用，锰还原以及通过扁平菌对铵的厌氧氧化而存在的（厌氧氨氧化法）。在这里，我们描述了微生物群落的存在，这些微生物群落有可能在天然海洋沉积物系统中（苏格兰洛奇·杜伊奇）进行这些过程。通过对16S rRNA基因的分析，分别使用16S rDNA和RNA的PCR和逆转录PCR扩增，对16S rRNA基因进行了分析，从而表征了浮游细菌-疣状微生物和β-和γ-变形杆菌氨氧化细菌的天然微生物群落。通过克隆测序和变性梯度凝胶电泳（DGGE）分析扩增产物。浮游细菌-疣状微生物和β-变形杆菌氨氧化细菌特异性引物的扩增在所有采样位点和深度均产生产物，但使用γ-变形杆菌氨氧化细菌特异性引物没有产生产物。 16S rDNA DGGE谱带图谱表明缺氧海洋沉积物中复杂的β-变形细菌氨氧化细菌群落。从克隆序列和从DGGE凝胶中切除的序列的系统进化分析表明，硝化螺菌簇1类生物体以及属于以16S rRNA DGGE显性带中的优势带表示的新型簇的菌株的优势。它们的存在表明一组与公认的β-变形杆菌氨氧化细菌密切相关的生物，这些细菌可以在缺氧环境中进行选择并可能发生缺氧氨氧化。浮游菌克隆文库的序列分析和从DGGE凝胶中切除的序列还显示了不同的微生物群落，并提示存在新的细分，但未检测到与公认的Anammox生物有关的序列。

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