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

EAGER：利用短读长技术的力量来研究深光层中未经探索的微生物群落

• 批准号: 1138368
• 负责人: Gabrielle Rocap
• 金额: $ 29.94万
• 依托单位: University of Washington
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-07-15 至 2015-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1138368&HistoricalAwards=false
• 关键词: EAGER; Harnessing; Power; Short; read

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.

基因组测序的最新进展改变了海洋微生物生态学。宏基因组数据集导致了新蛋白质家族的发现，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（如原绿球藻）的种群内多样性。尽管已多次证明开阔海洋微生物群落在系统发育多样性和生物地球化学功能方面随深度而显著变化，但公共数据库中的绝大多数序列来自表面沃茨。对海洋表面以下的微生物群落知之甚少，即使是50- 200米的微生物群落也是如此。与桑格或甚至焦磷酸测序方法相比，下一代测序技术提供了每碱基成本的显著降低。来自这些平台的非常短的读取长度尚未成功应用于混合社区。该项目是使用ABI SOLiD平台对整个南大西洋环流水柱中的微生物群落进行宏基因组研究，其目标如下：-使用ABI SOLiD技术从南大西洋环流的表面，叶绿素最大值，深真光区和黄昏区构建和测序配对末端宏基因组文库。应用基于信息论的软件方法组装短读段序列，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海洋其他地区的现有宏基因组数据和来自同一地点的元蛋白组数据进行比较，为拟议的全球分子海洋调查（Biogeotraces）提供采样策略和方法选择。因此，这个数据集将重塑我们对贫营养群落功能的理解。其次，通过短读测序平台以低成本生成的数据的巨大进步有可能通过允许宏基因组分析在假设驱动的实验中常规使用来改变微生物海洋学。然而，需要新的跨学科工具来收集和解释这些数据。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建议仍然具有很高的风险。更广泛的影响：在南大西洋的GEOTRACES合规巡航中收集的微生物群落的宏基因组分析将提供一个试点数据集，展示未来部分分子调查计划的短读测序技术的潜力。一名博士后研究员和一名研究生将接受跨学科观点的培训，以分析该序列数据并在生物地球化学背景下对其进行解释。