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中不同部位的不同种类的细菌，但在生物地球化学或生态学意义上，知道生物的身份和谁在做什么之间仍然存在着重大的脱节。然而，这些信息对于理解系统的工作原理和准确建模是很重要的。这在理解全球变化方面可能变得尤为关键。到目前为止，这个问题已经通过结合放射自显影和荧光原位杂交、稳定同位素探测、大型宏基因组项目和现场数据统计分析等技术得到解决，每种技术都有其优缺点。虽然没有一种方法能提供完整的答案，但每一项新结果都为解开不同微生物成分如何促进系统功能的谜团提供了有用的线索。该项目将采用实验方法，通过各种方式操作现场样品，然后使用分子技术观察微生物群落不同成员的生长反应（通过DNA和RNA分析）。这种方法在有限的情况下已经成功地使用了，新的信息使我们能够改进它并最大限度地减少生物识别中的歧义。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。具体操作将涉及光，pH值，无机营养物质和有机物质的变化。实验计划预计将受益于新的结果，包括即将发布的大量宏基因组数据和海洋细菌的全基因组序列。实验将主要在洛杉矶和南加州大学瑞格利海洋实验室圣卡塔利娜岛之间的一个研究充分的站点收集样本，我们经常免费访问该站点，他有几年的海洋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）。他还预计在机遇号和其他沿着加州和其他地方的游轮上还会有更多的样本。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，他将努力通过大量的人工制品和使用产生效果的最短孵育时间来最小化人工制品。拟议研究的优点是将系统发育信息与生物体功能联系起来，而拟议项目的更广泛影响包括通过COSEE West计划与K-12教学，本科教学和研究以及将包括面向公众的网站的推广。

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.