Environmental Genome Shotgun Sequencing: Ocean Microbial Populations off The Coast of Nova Scotia, Canada

环境基因组霰弹枪测序：加拿大新斯科舍省海岸附近的海洋微生物种群

• 批准号: 0412119
• 负责人: John Heidelberg
• 金额: --
• 依托单位: J. Craig Venter Institute, Inc.
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2005
• 资助国家: 美国
• 起止时间: 2005-10-01 至 2009-03-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0412119&HistoricalAwards=false
• 关键词: Environmental; Genome; Shotgun; Sequencing; Ocean

To assess the extent of microbial genomic diversity in the ocean, the J. Craig Venter Institute has so far collected samples from over 70 oceanic sites between Halifax, Nova Scotia and Australia as part of the Sorcerer II Global Ocean Sampling Expedition (GOS). A"metagenome" analysis of the plankton community will be performed on samples from the seven northernmost sites, constituting surface waters of the Western North Atlantic Ocean near Halifax, Nova Scotia for this NSF-funded project. A metagenome is the combined genetic information of an entire microbial community. The significance of a metagenomic analysis is that most bacteria cannot be cultured, thus we currently know very little about the identities and properties of natural microbial populations. In contrast with some other regions of the ocean, nutrient gradients (e.g., nitrogen and phosphorus) in the Western North Atlantic are typically moderate except during periods of deep vertical mixing. Marine microbial community biodiversity will be quantitatively characterized using high throughput DNA sequencing and whole genome shotgun assembly techniques. Through this "whole environment" shotgun genomics approach, microorganisms will be inventoried to determine overall species diversity, discover and characterize new prokaryotic species and genes, and evaluate the ecological roles that microbes play in the Western North Atlantic biome. Results will be compared to those from previous metagenomic work at the Bermuda Atlantic Time-Series (BATS) site as well as to other sites along the GOS. Very preliminary analysis of sequences from each of the seven Western North Atlantic sites has indicated that they are distinct from all other samples collected thus far on the GOS expedition. This underscores the importance of obtaining far deeper sequence data since genes and organisms detected in these samples do not seem to be similar to those at other locations on the GOS. Genomics is a rapidly developing field that is creating changes in medicine, business, and agriculture on a scale analogous to the industrial revolution, but it's impact in environmental microbiology will likely be even greater than in these other areas. By having deeper DNA sequence coverage of the Western North Atlantic samples, a comparative genomic analysis of uncultured organisms will be undertaken at an unprecedented level of interrogation. All results of the genomic analysis will be made rapidly and readily available to the global scientific community. Students and teachers who have an understanding of genomics can appreciate the impact it is making on society and make informed decisions about the issues it raises. Therefore, a critical step in this project is to include training and outreach for K - 12 students, through mobile laboratories, as well as to graduate students, post-doctoral fellows, and established faculty members through a two-day workshop on the analysis and availability of the Western North Atlantic metagenomic data.

为了评估海洋中微生物基因组多样性的程度，J. Craig Venter研究所迄今已收集了哈利法克斯，新斯科舍省和澳大利亚之间70多个海洋地点的样品，这是巫师II Global II Global Ocean Sampling Expedition（GOS）的一部分。 对浮游生物社区的“元基因组”分析将对来自最北端的七个地点的样品进行，这是新斯科舍省哈利法克斯附近北大西洋西部的地表水，用于该NSF资助的项目。 元基因组是整个微生物群落的组合遗传信息。 宏基因组分析的重要性是大多数细菌无法培养，因此我们目前对天然微生物种群的身份和特性知之甚少。 与海洋的其他一些区域相反，北大西洋西部的营养梯度（例如氮和磷）通常是温和的，除非在深垂直混合期间。 海洋微生物群落生物多样性将通过高吞吐量DNA测序和整个基因组shot弹枪装配技术进行定量表征。 通过这种“整个环境” shot弹枪基因组学方法，将库存微生物，以确定整体物种的多样性，发现和表征新的原核生物物种和基因，并评估微生物在北大西洋生物群落中的生态作用。 结果将与Bermuda大西洋时间序列（BAT）站点以及GOS沿线的其他地点的宏基因组工作的结果进行比较。 对来自北大西洋七个西部七个西部七个地点的序列的非常初步的分析表明，它们与迄今为止在GOS探险中收集的所有其他样品不同。 这强调了获得更深层序列数据的重要性，因为这些样品中检测到的基因和生物似乎与GOS上其他位置的基因和生物都不相似。 基因组学是一个迅速发展的领域，它正在以类似于工业革命的规模来创造医学，商业和农业的变化，但是它对环境微生物学的影响可能会比其他这些领域更大。通过具有北大西洋西部样品的更深的DNA序列覆盖范围，将在前所未有的审讯水平进行对未培养生物的比较基因组分析。 基因组分析的所有结果都将迅速且容易为全球科学界提供。了解基因组学的学生和老师可以欣赏它对社会产生的影响，并就提出的问题做出明智的决定。 因此，该项目的关键一步是通过移动实验室以及研究生，博士后研究员以及通过为期两天的北大西洋巨大核心数据的分析和可用性来包括针对K-12名学生的培训和宣传。