Experimentally linking identification and function of marine bacteria

海洋细菌在海水中极其丰富，是全球生物地球化学循环的主要驱动力。分子生物学技术使我们能够开始识别存在于海洋不同部分的不同种类的细菌，但在了解生物的身份和谁在生物地球化学或生态意义上做什么之间仍然存在严重的脱节。然而，这些信息对于理解系统的工作原理并准确地对其进行建模非常重要。这在理解全球变化方面可能变得尤为关键。到目前为止，这个问题已经通过联合放射自显影和荧光原位杂交、稳定同位素探测、大型元基因组计划和现场数据统计分析等技术来解决，每种技术都有其优点和缺点。虽然没有单一的方法提供完整的答案，但每个新的结果都为不同的微生物成分如何对系统功能做出贡献这一谜题提供了有用的片断。这个项目将使用一种实验方法，通过各种方式操纵田间样本，然后使用分子技术来观察微生物群落的各个成员的生长反应(通过DNA和RNA分析)。这种方法已经被成功地以有限的方式使用，新的信息允许我们改进它，并将生物体鉴定中的歧义降至最低。福尔曼博士建议将这种方法广泛应用于在不同地点、深度和季节收集的一系列野外样本。具体的操作将涉及光、pH、无机营养物质和有机物质的变化。预计实验计划将受益于新的结果，包括即将公布的大量元基因组数据，以及来自海洋细菌的全基因组序列。实验将主要在洛杉矶到南加州大学瑞格利海洋实验室圣卡塔利纳岛之间的一个研究充分的站点收集样本进行，我们经常免费进入这个站点，他有几年关于海洋学参数和微生物学的大量背景数据(作为圣佩德罗海洋时间序列和南加州大学微生物观测站的一部分)。他还预计，机会号邮轮以及加州和其他地方的其他邮轮上会有更多的样本。所有的实验都将对容器和其他可能的人工制品的影响进行控制，他将努力通过大容量和使用产生效果的最短孵化时间将人工制品降至最低。拟议的研究的优点是将系统发育信息与生物体功能联系起来，而拟议的项目的更广泛的影响包括通过COSEE West计划、本科教学和研究以及包括一个网站的面向普通公众的部分的推广，与K-12教学有重要的联系。

Marine bacteria are tremendously abundant in seawater and are major driving forces in global biogeochemical cycles. Molecular biological techniques have permitted us to start to identify the different kinds of bacteria present in various parts of the sea, but there is still a major disconnect between knowing the identity of the organisms and who does what in a biogeochemical or ecological sense. Yet such information is important to understand the workings of the system and to model it accurately. This may become particularly critical in understanding global change. This question has been addressed to date with techniques like combined autoradiography & fluorescence in situ hybridization, stable isotope probing, large metagenomic projects, and statistical analysis of field data, each with its strengths and weaknesses. While no single approach provides the whole answer, each new result provides useful pieces to the puzzle of how the different microbial components contribute to system functions. This project will use an experimental approach, by manipulating field samples various ways and then using molecular techniques to observe the growth reactions of various members of the microbial community (by DNA and RNA analysis). This approach has been used successfully in a limited way, and new information permits us to refine it and minimize ambiguity in organism identification. Dr. Fuhrman proposes to apply this approach broadly to an array of field samples collected at various locations, depths, and seasons. Specific manipulations will involve changes in light, pH, inorganic nutrients, and organic substances. The experimental plans are expected to benefit from new results including large amounts of metagenomic data soon to be released and also whole genome sequences from marine bacteria. Experiments will be done with samples collected primarily at a well-studied station between Los Angeles to the USC Wrigley Marine Laboratory Santa Catalina Island, to which we have frequent free access and for which he has several years of substantial background data on oceanographic parameters and microbiology (as part of the San Pedro Ocean Time Series and USC Microbial Observatory). He also anticipates additional samples on cruises of opportunity and other cruises along California and elsewhere. All experiments will employ controls for effects of containment and other possible artifacts, and he will endeavor to minimize artifacts through large volumes and use of the shortest incubations that yield an effect. The merit of the proposed research is the linking of phylogenetic information to organism function while the broader impacts of the proposed project include a significant connection to K-12 teaching, through the COSEE West program, undergraduate teaching and research, and outreach that will include a website with sections for the general public.