Quantification, base composition, and fate of extracellular DNA in marine sediments
Quantification, base composition, and fate of extracellular DNA in marine sediments
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DOI：
10.4319/lo.2002.47.3.0899
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发表时间：
2002-05-01
影响因子：
4.5
通讯作者：
Danovaro, R
中科院分区：
文献类型：
--
作者：
Dell'Anno, A;Bompadre, S;Danovaro, R
海洋沉积物中高浓度DNA的发现表明存在大部分胞外DNA，这可能在通过自然转化的基因转移以及磷的生物地球化学循环中发挥重要作用。但目前还没有一种普遍接受的细胞外DNA提取方法。在这项研究中，我们开发了一种新的基于核酸酶的程序，从海洋沉积物中提取细胞外DNA。收集了沿海沙子和深海泥浆样品，以测试从不同类型的沉积物中去除细胞外DNA的效率。在六个沉积物深度的细胞外DNA浓度进行了定量，并在基地组成的变化进行了调查，以收集有关细胞外DNA命运的信息。提取过程是高度特异性的，只有胞外DNA被水解后的核酸酶处理。可水解DNA占总DNA池的70%，表明胞外DNA只能部分降解。随着沉积物深度的增加，脱氧胞苷含量增加，脱氧腺苷含量下降，垂直基组成发生变化。整合我们的研究结果的顶部15厘米的沉积物，我们计算出，超过50%的细胞外DNA的酶促降解。这一发现可能解释了DNA在表层沉积物中的积累，并表明DNA在磷地球化学循环中可能起着不可忽视的作用。
The discovery of high concentrations of DNA in marine sediments unaccounted for by living biomass suggests the presence of a large fraction of extracellular DNA, which might play an important role in gene transfer via natural transformation as well as in phosphorous biogeochemical cycling. But a universally accepted procedure for extracellular DNA extraction is not available yet. In this study, we developed a new nuclease-based procedure to extract extracellular DNA from marine sediments. Coastal sand and deep-sea mud samples were collected to test the efficiency of extracellular DNA removal from different sediment types. Extracellular DNA concentrations were quantified at six sediment depths, and changes in base composition were investigated to gather information on extracellular DNA fate. The extraction procedure was highly specific and only extracellular DNA was hydrolyzed after nuclease treatment. Hydrolyzable DNA accounted for 70% of the total DNA pool, suggesting that extracellular DNA can only be partially degraded. Base composition changed vertically with depth in the sediment as deoxycytidine content increased and deoxyadenosine decreased with increasing depth. Integrating our results for the top 15 cm of the sediment, we calculate that more than 50% of extracellular DNA was recalcitrant to enzymatic degradation. This finding might explain why DNA accumulates in surface sediments and suggests that DNA, might play a nonnegligible role in P biogeochemical cycle.