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

海洋蓝藻可能贡献了全球初级生产力的25%，因此在全球碳和其他元素循环中具有重要意义。这些生物的模型分离菌株现在有多个全基因组可用。这些对于了解这些生物的不同生态策略以及它们在从海岸到开阔海洋的各种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，从环境中分离出的作为单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曲目（称为其泛基因组）。一些微生物似乎能够通过水平转移其他生物体的DNA来获取更大的基因库。它们获得的基因类型和它们获得基因的机制在很大程度上是未知的，但对于它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够通过水平基因转移获得基因。本研究试图通过使用454测序技术进行宏基因组测序（在环境DNA池上进行DNA测序）来解决这些问题。沿海海洋蓝藻在测序前从样本中被分类，大大增加了了解这些微生物遗传多样性的可用信息。通过这种方式，两种主要的海洋蓝藻（聚藻球菌）物种的泛基因组将被研究，并可能导致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。它将为了解基因如何在水生环境中的微生物之间移动提供一个窗口，这是一个非常有趣的话题，因为它与人类健康和农业中的水平基因转移和相关的抗生素耐药性相似。这里使用的宏基因组分析在水生科学中尚处于起步阶段，在这一跨学科领域培训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、研究生和博士后的跨学科研究训练。在加州大学圣地亚哥分校指导本科生的环境微生物实验室课程也将进一步拓宽工作的范围。

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.