Microbial Genome Sequencing: Complete Genome Sequences of Green Bacteria

光合细菌将光转化为化学能，随后将大气中的二氧化碳固定为生物质。这些生物占所有光合作用的50%，因此它们确保了地球上生命的继续存在。在这项研究中，15个光合细菌的基因组序列将被完成、注释和比较。绿色硫磺细菌(GSB)是缺氧环境中的主要初级生产者，对地球上碳、氮和硫的生物地球化学循环有重要贡献。直到最近，基因组信息只有Chlorobium tepidum才有，这是一种可能来自富含硫化物的温泉的非典型生物。联合基因组研究所(JGI-DOE)已经完成了八个GSB的序列草图，第九个GSB基因组将于2005年测序。JGI-DOE还将为Chloroflei的七个成员产生高质量的序列草案，其中六个是丝状厌氧光营养细菌(FAPs；以前是绿色滑动/非硫细菌)。目前只有一种FAP的不完整的草案序列可用。最近的研究表明，FAP在生理上是多样化的，在自然界中分布广泛。新描述的菌株可以通过不同的途径固定碳，固定氮，并氧化硫化物，可能还有亚铁和其他金属。FAP是陆地、淡水和盐碱环境中重要但特征不佳的组成部分，全基因组分析将为了解它们的特性提供许多新的见解。目前，许多科学家正在研究光自养代谢、光合作用的机制和起源，以及光自养生物之间的进化关系。这些问题将在这项研究中通过全基因组测序和随后的数据比较生物信息学分析直接解决。由于它将是有史以来为GSB和FAP收集的最大和最全面的数据库，本研究中获得的数据将产生非常广泛的影响。完成的序列将存放在公共数据库中，这些数据以及自动和手动注释数据也将通过一个可公开访问的网站提供。两名博士后科学家和四名本科生研究人员将在这项研究计划的执行期间接受培训。PI和Co-PI将为高级本科生和研究生组织一门课程，提供微生物基因组学和生物信息学方面的被动和主动学习经验。这门课程将填补宾夕法尼亚州立大学微生物学和生物信息学课程的现有空白。

Photosynthetic bacteria convert light into chemical energy for the subsequent fixation of carbon dioxide from the atmosphere into biomass. These organisms account for 50% of all photosynthesis, and thus they insure the continued existence of life on Earth. In this study, the genome sequences of 15 photosynthetic bacteria will be completed, annotated and compared. Green Sulfur Bacteria (GSB) are major primary producers in anoxic environments, where they contribute significantly to the biogeochemical cycling of carbon, nitrogen, and sulfur on Earth. Until recently, genome information was only available for Chlorobium tepidum, a possibly atypical organism from a sulfide-rich hot spring. The Joint Genome Institute (JGI-DOE) has completed draft sequences for eight GSB, and a ninth GSB genome will be sequenced in 2005. JGI-DOE will also produce high-quality draft sequences for seven members of the Chloroflexi, six of which are Filamentous Anoxygenic Phototrophs (FAPs; formerly, green gliding/non-sulfur bacteria). Only an incomplete draft sequence for one FAP, Chloroflexus aurantiacus is currently available. Recent studies suggest that FAPs are physiologically diverse and widely distributed in nature. Newly described isolates can fix carbon using different pathways, fix nitrogen, and oxidize sulfide and possibly ferrous iron and other metals. FAPs are important but poorly characterized components of terrestrial, freshwater and saline environments, and whole-genome analyses will provide many new insights into their properties. Many scientists are currently studying photoautotrophic metabolism, the mechanisms and origins of photosynthesis, and the evolutionary relationships among photoautotrophs. These issues will be directly addressed in this study through whole-genome sequencing and subsequent comparative bioinformatic analyses of the data. Since it will be the largest and most comprehensive database ever assembled for both GSB and FAPs, the data obtained in this study will have very broad impact. The finished sequences will be deposited in public databases, and these data, as well as the automatic and manual annotation data, will also be made available via a publicly accessible website. Two postdoctoral scientists and four undergraduate researchers will be trained during the execution of this research program. The PI and Co-PI will organize a course for advanced undergraduates and graduate students that will provide both passive and active learning experiences in Microbial Genomics and Bioinformatics. This course will fill an existing void in the microbiology and bioinformatics curriculum at The Pennsylvania State University.