Biogeography of Rhizobium radiobacter and distribution of associated temperate phages in deep subseafloor sediments
Biogeography of Rhizobium radiobacter and distribution of associated temperate phages in deep subseafloor sediments
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DOI：
10.1038/ismej.2012.92
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发表时间：
2013-01-01
期刊：
影响因子：
11
通讯作者：
Engelen, Bert
中科院分区：
文献类型：
--
作者：
Engelhardt, Tim;Sahlberg, Monika;Engelen, Bert
噬菌体可能是海洋深层海底的主要捕食者，并可能对本土微生物群落产生重大影响。为了确定它们在这个栖息地内的功能，我们确定了它们的丰度和分布，沿着在大洋钻探计划第201阶段期间恢复的两个大陆边缘和两个开阔海洋地点的沉积物柱。对于所有调查地点，病毒丰度遵循细胞总数，病毒与细胞的比率在100Mbsf以上(海底以下几米)介于1至10之间。更深层约20%的比例增加表明，在长达11 Ma的古老沉积物中，病毒正在产生。我们使用放射型根瘤菌作为最常见的从深层地下分离的生物，具有很高的原位丰度来鉴定相关的根瘤菌体的频率。在本研究中，定量聚合酶链式反应检测到放射杆菌16S rRNA基因拷贝数占细菌16S rRNA基因拷贝数的5.6%，平均为0.75%。根据遗传相似群体的特定位置排列，确定了放射状杆菌的独特分布。利用根瘤菌噬菌体RR1-A的全基因组信息，建立了针对温带噬菌体抗阻遏子基因的定量聚合酶链式反应的引物体系。不同沉积层中该基因的定量结果显示，温带噬菌体对病毒总丰度的贡献率高达14.3%。因此，沉积物中和所调查的所有分离物中都有大量的温带噬菌体，这表明溶原性是深层地下种群中病毒的主要增殖方式。《ISME期刊》(2013年)7期，1999.209期；doi：10.1038/ismej.2012.92；2012年8月2日在线出版
Bacteriophages might be the main 'predators' in the marine deep subsurface and probably have a major impact on indigenous microbial communities. To identify their function within this habitat, we have determined their abundance and distribution along the sediment columns of two continental margin and two open ocean sites that were recovered during Leg 201 of the Ocean Drilling Program. For all investigated sites, viral abundance followed the total cell numbers with a virus-to-cell ratio between 1 and 10 in the upper 100 mbsf (meters below seafloor). An increasing ratio of about 20 in deeper layers indicated an ongoing viral production in up to 11 Ma old sediments. We have used Rhizobium radiobacter as the most frequently isolated organism from the deep subsurface with a high in situ abundance to identify the frequency of associated rhizobiophages. In this study, 16S rRNA gene copies of R. radiobacter accounted for up to 5.6% of total bacterial 16S rRNA genes (average: 0.75%) as detected by quantitative PCR. A distinctive distribution was identified for R. radiobacter as indicated by a site-specific arrangement of genetically similar populations. Whole genome information of rhizobiophage RR1-A was used to generate a primer system for quantitative PCR specifically targeting the prophage antirepressor gene, indicative for temperate phages. The quantification of this gene within various sediment horizons showed a contribution of temperate phages of up to 14.3% to the total viral abundance. Thus, the high amount of temperate phages within the sediments and among all investigated isolates indicates that lysogeny is the main viral proliferation mode in deep subsurface populations. The ISME Journal (2013) 7, 199-209; doi: 10.1038/ismej.2012.92; published online 2 August 2012