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.

为了评估海洋微生物基因组多样性的程度，克雷格·文特尔研究所迄今在哈利法克斯、新斯科舍省和澳大利亚之间的70多个海洋站点收集了样本，作为魔术师II全球海洋采样考察的一部分。对浮游生物群落的“元基因组”分析将对七个最北端的地点的样本进行，这些地点是新斯科舍省哈利法克斯附近的西北大西洋表层水域，是这个由NSF资助的项目的组成部分。元基因组是整个微生物群落的组合遗传信息。元基因组分析的意义在于，大多数细菌不能培养，因此我们目前对自然微生物种群的身份和性质知之甚少。与海洋的一些其他区域不同，北大西洋西部的营养梯度(例如氮和磷)通常是中等的，但在深度垂直混合期间除外。海洋微生物群落生物多样性将使用高通量DNA测序和全基因组鸟枪组装技术进行定量表征。通过这种“全环境”的鸟枪式基因组学方法，将对微生物进行清点，以确定总体物种多样性，发现和鉴定新的原核生物物种和基因，并评估微生物在北大西洋西部生物群中所起的生态作用。结果将与百慕大大西洋时间序列(BATS)站点以及GOS沿线其他站点先前的元基因组学工作进行比较。对北大西洋西部七个地点的每一个地点的非常初步的序列分析表明，它们与迄今为止在GOS探险中收集的所有其他样本不同。这突显了获得更深层次序列数据的重要性，因为在这些样本中检测到的基因和生物体似乎与GOS上其他位置的基因和生物体并不相似。基因组学是一个快速发展的领域，它正在给医学、商业和农业带来类似工业革命的规模的变化，但它对环境微生物学的影响可能会比这些其他领域更大。通过对北大西洋西部样本进行更深层次的DNA序列覆盖，将在前所未有的审问水平上对未培养生物进行比较基因组分析。基因组分析的所有结果将迅速和容易地提供给全球科学界。对基因组学有一定了解的学生和教师可以意识到它对社会产生的影响，并对它提出的问题做出明智的决定。因此，该项目的一个关键步骤是通过流动实验室对K-12学生进行培训和推广，以及通过为期两天的关于分析和获得北大西洋西部元基因组数据的讲习班向研究生、博士后研究员和常设教员提供培训和外联服务。