Coordinated Shotgun Metagenomic Sequencing and Proteomics: A Double-Barreled Approach to Cyanobacterial Community Analysis

协调鸟枪法宏基因组测序和蛋白质组学：蓝藻群落分析的双管方法

• 批准号: 0731771
• 负责人: Brian Palenik
• 金额: $ 50.84万
• 依托单位: University of California-San Diego Scripps Inst of Oceanography
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-10-01 至 2011-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0731771&HistoricalAwards=false
• 关键词: Coordinated; Shotgun; Metagenomic; Sequencing; Proteomics

Marine cyanobacteria contribute perhaps 25% of global primary productivity and are thus of major importance in the global carbon and other element cycles. Multiple whole genomes are now available for model isolated strains of these organisms. These have been invaluable for understanding some of the different ecological strategies of these organisms and their ability to thrive in diverse environments from the coast to the open ocean. An important issue however is to what extent does the whole genome of a model organism isolated as a single cell from an environment really reflect the total repertoire of that species (referred to as its pan-genome). Some microbes seem to be able to access a larger pool of genes through horizontal transfer of DNA from other organisms. The types of genes they are obtaining and the mechanisms by which they are obtaining them is largely unknown, but could be very important to their ability to fix carbon and compete in an ecosystem. On the other hand, some microbes seem less able to gain genes through horizontal gene transfer. This research seeks to address these issues by performing metagenomic sequencing (DNA sequencing on a pool of environmental DNA) using 454 sequencing technology. Coastal marine cyanobacteria are sorted out of the sample before sequencing, greatly increasing the information available to understand the genetic diversity of these microbes. In this way the pan-genome of two major marine cyanobacteria (Synechococcus) species will be investigated and likely lead to the discovery of novel genes in these microorganisms. Understanding the genetic diversity of these important microbes will help us understand how they fix carbon and compete in the constantly changing marine environment. It will provide a window into how genes can move between microbes in aquatic environments, a topic of great interest because of its similarity to horizontal gene transfer and associated antibiotic resistance in human health and agriculture. The metagenomic analyses used here are in their infancy in the aquatic sciences and training scientists in this cross-disciplinary area will spur its development. The broader impact of this research thus includes the interdisciplinary research training of an undergraduate, a graduate student, and a post-doctoral fellow. Mentoring undergraduates in an environmental microbiology lab course at UCSD will also further broaden the outreach of the work.

海洋蓝藻可能贡献了全球初级生产力的25%，因此在全球碳循环和其他元素循环中具有重要意义。多个全基因组现在可用于这些有机体的模式分离菌株。这些对于了解这些生物的一些不同的生态策略以及它们在从海岸到开阔海洋的不同环境中茁壮成长的能力是非常宝贵的。然而，一个重要的问题是，从环境中分离出来的作为单个细胞的模式生物的整个基因组在多大程度上真正反映了该物种的全部基因组(称为泛基因组)。一些微生物似乎能够通过水平转移其他生物体的DNA来获得更大的基因库。他们正在获得的基因类型和获得这些基因的机制在很大程度上是未知的，但对他们固定碳和在生态系统中竞争的能力可能非常重要。另一方面，一些微生物似乎不太能通过水平基因转移获得基因。这项研究试图通过使用454测序技术进行元基因组测序(对环境DNA池进行DNA测序)来解决这些问题。沿海海洋蓝藻在测序前从样本中分离出来，极大地增加了可用于了解这些微生物的遗传多样性的信息。通过这种方式，将对两个主要海洋蓝藻(聚球藻)物种的泛基因组进行调查，并可能在这些微生物中发现新的基因。了解这些重要微生物的遗传多样性将有助于我们了解它们如何固定碳并在不断变化的海洋环境中竞争。它将提供一个窗口，了解基因如何在水环境中的微生物之间移动，这是一个非常有兴趣的话题，因为它与水平基因转移以及与人类健康和农业相关的抗生素耐药性相似。这里使用的元基因组分析在水产科学中还处于初级阶段，培训这一跨学科领域的科学家将促进其发展。因此，这项研究的更广泛影响包括本科生、研究生和博士后研究员的跨学科研究培训。在加州大学圣迭戈分校的环境微生物学实验室课程中指导本科生也将进一步扩大这项工作的范围。