SGER: Profile of Signal Molecules in a Soil Microbial Community

这是一项探索研究小额赠款(SGER)奖，旨在识别和测序来自阿拉斯加土壤的元基因组克隆，这些克隆产生具有生物活性的小分子。这个探索性的项目受到最近两个事件的刺激：第一，开发了一种快速的细胞内分析来鉴定产生信号分子的克隆；第二，最近发表的分别对马尾藻海和酸性矿山排水群落的元基因组的研究，说明了从元基因组来源获得大量序列数据的力量。对复杂的微生物群落进行许多方法的切片是构建它们的全面肖像所必需的。获得微生物群落切片的一些最有效的方法包括：培养、16S rRNA序列的PCR扩增、鉴定元基因组克隆上的系统发育锚以及分析元基因组克隆的随机末端序列。系统发育锚定方法涉及对包含特定系统发育标记的所有克隆进行测序。包含16S rRNA系统发育信息的克隆的收集为从核苷酸序列推断元基因组DNA片段起源的生物体所执行的功能提供了基础。相比之下，这个项目将引入功能锚的使用--与系统发育锚方法相反。功能锚方法将被用来识别文库中表达某一特定功能的所有克隆，然后对它们进行测序，以获得关于它们起源的系统发育信息。如果成功，这将成为元基因组文库分析的新标准，将提供对新基因的访问，这些基因的功能可能通过检查其序列和对这些功能的起源进行系统发育推断而不被怀疑。本科生也将参与这个项目，研究人员利用和评估两种不同的方法来吸引和纳入科学领域中代表性不足的群体的成员。

This is a Small Grant for Exploratory Research (SGER) award to identify and sequence metagenomic clones derived from Alaskan soil that produce biologically active small molecules. This exploratory project was stimulated by two recent events: first, the development of a rapid intracellular assay to identify clones that produce signaling molecules; and second, recently published studies of the metagenomes of the Sargasso Sea and an acid mine drainage community, respectively, that illustrate the power of obtaining vast amounts of sequence data from metagenomic sources.Slicing complex microbial communities many ways is necessary to construct a comprehensive portrait of them. Some of the most fruitful approaches to obtain slices of microbial communities include: culturing, PCR amplification of 16S rRNA sequences, identification of phylogenetic anchors on metagenomic clones, and analysis of random end sequences of metagenomic clones. The phylogenetic anchor approach involves sequencing all clones that contain a certain phylogenetic marker. The collection of clones containing 16S rRNA phylogenetic information provides the basis for inferences from nucleotide sequence about functions performed by the organisms from which the fragments of metagenomic DNA originated. By contrast, this project will introduce the use of a functional anchor - the converse of the phylogenetic anchor approach. The function anchor approach will be used to identify all clones in a library that express a certain function and then sequence them to obtain phylogenetic information about their origins. If successful, this will become a new standard of analysis of metagenomic libraries that will provide access to new genes whose functions might not have been suspected by inspection of their sequences and phylogenetic inference about the origins of those functions. Undergraduate students will also be involved in the project, with the investigators utilizing and evaluating two different approaches to attracting and incorporating members of underrepresented groups in science.