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

为了评估海洋中微生物基因组多样性的程度，J.克雷格文特尔研究所迄今已从哈利法克斯、新斯科舍省和澳大利亚之间的70多个海洋地点收集了样本，这是魔法师II全球海洋采样探险（GOS）的一部分。在这个nsf资助的项目中，浮游生物群落的“宏基因组”分析将在新斯科舍省哈利法克斯附近北大西洋西部表层水域的七个最北端地点的样本上进行。宏基因组是整个微生物群落的综合遗传信息。宏基因组分析的意义在于大多数细菌无法培养，因此我们目前对天然微生物种群的特性和特性知之甚少。与海洋的其他一些区域相比，北大西洋西部的营养物梯度（例如氮和磷）通常是温和的，除了在深度垂直混合期间。利用高通量DNA测序和全基因组霰弹枪组装技术定量表征海洋微生物群落的生物多样性。通过这种“全环境”霰弹枪基因组学方法，微生物将被盘点以确定总体物种多样性，发现和描述新的原核物种和基因，并评估微生物在北大西洋西部生物群系中的生态作用。结果将与先前在百慕大大西洋时间序列（BATS）站点以及GOS沿线其他站点进行的宏基因组工作进行比较。对北大西洋西部七个地点的序列进行的非常初步的分析表明，它们与GOS考察队迄今为止收集的所有其他样本都不同。这强调了获得更深层序列数据的重要性，因为在这些样本中检测到的基因和生物体似乎与GOS其他位置的基因和生物体不相似。基因组学是一个快速发展的领域，正在以类似于工业革命的规模给医学、商业和农业带来变化，但它对环境微生物学的影响可能比这些其他领域更大。通过对北大西洋西部样本进行更深入的DNA序列覆盖，将在前所未有的审问水平上对未培养生物体进行比较基因组分析。基因组分析的所有结果将迅速和方便地提供给全球科学界。了解基因组学的学生和教师可以理解它对社会的影响，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，并通过为期两天的关于北大西洋西部宏基因组数据分析和可用性的研讨会对研究生、博士后研究员和现有教员进行培训和推广。

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.