SGER: Profile of Signal Molecules in a Soil Microbial Community

这是一项探索性研究（SGER）小额赠款，用于鉴定和测序来自阿拉斯加土壤的产生生物活性小分子的宏基因组克隆。这个探索性项目是由最近的两个事件刺激的：首先，细胞内快速测定的发展，以识别产生信号分子的克隆；其次，最近发表的关于马尾藻海和酸性矿井排水群落宏基因组的研究，分别说明了从宏基因组来源获得大量序列数据的力量。通过多种方式对复杂的微生物群落进行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，鉴定宏基因组克隆的系统发育锚点，以及分析宏基因组克隆的随机末端序列。系统发育锚点方法包括对所有包含某种系统发育标记的克隆进行测序。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产生宏基因组DNA片段的生物体所执行的功能提供了基础。相比之下，本项目将介绍功能锚的使用-与系统发育锚方法相反。功能锚点方法将用于识别文库中表达某种功能的所有克隆，然后对它们进行测序，以获得有关其起源的系统发育信息。如果成功，这将成为宏基因组文库分析的新标准，将提供对新基因的访问，这些新基因的功能可能不会通过检查其序列和对这些功能起源的系统发育推断而被怀疑。本科生也将参与该项目，研究人员将利用和评估两种不同的方法来吸引和吸收科学界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.