EAGER: Harnessing the Power of Short-read Technology to Investigate Unexplored Microbial Communities in the Deep Euphotic Zone

基因组测序的最新进展改变了海洋微生物生态。元基因组数据集导致了新的蛋白质家族的发现，强调了稀有生物圈的重要性，甚至允许研究群落中主要成员的种群内多样性，如原氯球菌。尽管已多次证明，在系统发育多样性和生物地球化学功能方面，公海微生物群落随深度变化很大，但公共数据库中现有的绝大多数序列都来自地表水。人们对海洋表面下的微生物群落知之甚少，即使是那些50-200米的微生物也是如此。与桑格甚至焦磷酸测序方法相比，下一代测序技术提供了大幅降低每个碱基的成本。来自这些平台的极短的阅读长度尚未成功地应用于混合社区。该项目是使用ABI Solid Platform对南大西洋环流整个水柱中的微生物群落进行的元基因组研究，目标如下：-使用ABI Solid技术从南大西洋环流的表层、叶绿素最大值、深层真光带和黄昏带构建成对的末端元基因组文库。-应用基于信息论的软件方法组装短阅读序列，并重建这些群落的系统发育多样性和代谢潜力。-将重建的序列与来自世界其他海洋部分的现有元基因组数据以及来自同一地点的元蛋白质组数据进行比较，以便为拟议的全球分子海洋调查(BiogeoTRACE)提供抽样战略和方法选择。该项目适合作为一个迫切的项目，因为深层真光带和黄昏带群落的基因组潜力将与表层水域的基因组潜力截然不同。因此，这个数据集将重塑我们对寡营养群落功能的理解。其次，短读测序平台以低成本产生的数据的巨大进步，通过允许在假设驱动的实验中常规使用元基因组分析，有可能改变微生物海洋学。然而，需要新的跨学科工具来汇编和解释这些数据。在这些下一代生物信息学方法建立之前，利用这些技术突破的提议仍然存在高风险。广泛影响：在南大西洋符合GEOTRACES标准的邮轮上收集的微生物群落的元基因组分析将提供一个试点数据集，展示短读测序技术在未来分段分子调查计划中的潜力。一名博士后研究人员和一名研究生将接受跨学科视角的培训，以分析这些序列数据，并在生物地球化学背景下对其进行解释。

Recent advances in genome sequencing have transformed marine microbial ecology. Metagenomic datasets have led to the discovery of new protein families, underscored the importance of the rare biosphere and even allowed the study of intra-population diversity of dominant members of the community such as Prochlorococcus. Although open ocean microbial communities have been repeatedly demonstrated to vary significantly with depth, in terms of both phylogenetic diversity and biogeochemical function, the vast majority of sequence available in public databases is from surface waters. Much less is known about microbial communities below the surface of the ocean, even those at 50-200m. Next generation sequencing technologies offer a dramatic reduction in cost per base compared to Sanger or even pyrosequencing approaches. The very short read lengths from these platforms have not yet been successfully applied to mixed communities. This project is a metagenomic study of the microbial communities throughout the water column in the South Atlantic gyre using the ABI SOLiD platform with the following objectives:- Construct and sequence paired-end metagenomic libraries from the surface, chlorophyll maximum, deep euphotic zone and twilight zone in the South Atlantic gyre using ABI SOLiD technology.- Apply information theory based software methods to assemble the short read sequences and reconstruct the phylogenetic diversity and metabolic potential of these communities. - Compare reconstructed sequences to existing metagenomic data from other parts of the world's oceans and to metaproteomic data from the the same location to inform sampling strategies and methodological choices for a proposed global molecular oceanic survey (Biogeotraces)This project is appropriate as an EAGER because the genomic potential of deep euphotic zone and twilight zone communities will be very different from those in surface waters. Thus, this dataset will reshape our understanding of oligotrophic community function. Second, the massive advance in data generated at a low cost by short-read sequencing platforms has the potential to transform microbial oceanography by allowing metagenomic analyses to be routinely employed in hypothesis-driven experiments. However, new interdisciplinary tools are required to assemble and interpret this data. Until these next generation bioinformatic methods are established, proposals that take advantage of these technological breakthroughs remain high risk.Broader Impacts: Metagenomic analyses of microbial communities collected on a GEOTRACES compliant cruise in the South Atlantic will provide a pilot dataset demonstrating the potential of short-read sequencing technologies for a future sectional molecular survey program. A post-doctoral researcher and a graduate student will be trained in the interdisciplinary perspectives required to analyze this sequence data and interpret it in a biogeochemical context.