An Evaluation of Postdepositional Controls on the Preservation of DNA in Marine Sediments

最近的研究表明，可以从缺氧的湖泊和海洋沉积物中恢复保存下来的适合分子生物学分析的浮游植物来源的DNA。这是一个非常令人兴奋的发现，因为它开辟了在物种甚至菌株水平上重建过去水柱微生物群落结构的可能性。“沉积古基因组学”这个新领域可能为研究海洋初级生产力的过去变化及其与其他因素（尤其是气候）的联系提供了一个前所未有的窗口。它还提供了一个重要的手段来验证和帮助解释更传统的基于脂质生物标志物的古代用物。然而，DNA在不同海洋环境下的保存程度、影响DNA保存的因素、由此产生的沉积记录的保真度以及与基于脂质的分子地层学记录的关系，在很大程度上仍然未知。在古dna记录能够广泛应用于古生态和古环境研究之前，这些问题必须得到解决，这是本提案的核心。在这个项目中，伍兹霍尔海洋研究所的研究人员将(i)分析来自各种具有古海洋学兴趣的缺氧海洋环境的沉积物中关键浮游植物成员的DNA的早期沉积后命运及其相应的脂质生物标志物。（二）确定有利于海洋沉积物中浮游植物DNA长期保存的主要沉积条件。具体来说，他们将：(a)对来自同一前体生物的脂质和DNA进行定量的下核比对，作为在原位沉积条件下保存水平的衡量标准；(b)进行实验室降解实验，研究沉积硫酸盐还原条件下浮游植物DNA对脂质的早期命运；(c)研究DNA在海洋沉积物基质上的吸附动力学，并比较不同浮游植物类被吸附DNA的保存潜力。更广泛的影响。该项目将为一名研究生和一名本科生暑期学生（SSF）提供支持。这个跨学科项目将向研究生和科学基金介绍最先进的微生物和有机地球化学方法。WHOI SSF项目极大地扩大了代表性不足的群体（妇女、少数民族、国际学生）对研究的参与。由于沉积古基因组学和更广泛的古基因组学是相对较新的学科，研究人员将通过已建立的MBL/NASA天体生物学网站（http://www.mbl.edu/microscope）向中学科学教师提供有关DNA在古生态学和古气候学中的应用的一般信息。这个网站是对天体生物学和微生物多样性感兴趣的学生和教师的中央教育储存库。

Recent studies have demonstrated that preserved phytoplankton-derived DNA suitable for molecular biological analysis can be recovered from anoxic lacustrine and marine sediments. This is an extremely exciting finding because it opens up the possibility for the reconstruction of past water column microbial community structure at the species and even strain level. This new field of "sedimentary paleogenomics" may offer an unprecedented window into past changes in the ocean primary productivity and its link to other factors, notably climate. It also provides an important means to validate and aid in the interpretation of the more traditional lipid biomarker-based paleo-proxies. However, the extent to which DNA is preserved under different marine settings, the factors that influence the survival of DNA, the fidelity of the resulting sedimentary records, and relationships to lipid-based molecular stratigraphic records, remain largely unknown. These issues, which must be resolved before paleo-DNA records can be broadly applied in paleoecological and paleoenvironmental studies, lie at the heart of this proposal. In this project, researchers at the Woods Hole Oceanographic Institution will (i) analyze the early post-depositional fate of DNA from key phytoplankton members together with their corresponding lipid biomarkers within sediments from various anoxic marine settings of great paleoceanographic interest. (ii) Determine the main sedimentary conditions that are conducive to the long-term preservation of the phytoplankton DNA in marine sediments. Specifically, they will: (a) perform a quantitative down-core intercomparison between lipids and DNA derived from the same precursor organisms as a measure for the level of preservation under in situ depositional conditions; (b) perform laboratory degradation experiments to study the early fate of phytoplankton DNA vs. lipids under sedimentary sulfate-reducing conditions; and ( c) investigate the sorption kinetics of DNA on marine sediment matrices and compare the preservation potential of sorbed DNA of different phytoplankton classes.Broader impacts. The project will provide support for a graduate student and an undergraduate Summer Student Fellow (SSF). This cross-disciplinary project will introduce the graduate student and the SSF to state-of-the-art microbiological and organic geochemical methods. The WHOI SSF program has significantly broadened participation of underrepresented groups (women, minorities, international students) in research. Since sedimentary paleogenomics, and more broadly paleogenomics are relatively new subjects, the researchers will make general information about the employment of DNA in paleoecology and paleoclimatology available to secondary science teachers through the established MBL/NASA Astrobiology website, (http://www.mbl.edu/microscope). This website is a central educational repository for students and teachers interested in astrobiology and microbial diversity.