GE:GenEn: Solar Saltern Extremophage: Genomics and Population Modeling

GE：GenEn：太阳盐沼极端噬菌体：基因组学和群体建模

• 批准号: 0421955
• 负责人: Forest Rohwer
• 金额: $ 165.26万
• 依托单位: San Diego State University Foundation
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2004
• 资助国家: 美国
• 起止时间: 2004-10-01 至 2008-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0421955&HistoricalAwards=false
• 关键词: GE; GenEn; Solar; Saltern; Extremophage

Bacteriophage are viruses of bacteria, and recent evidence is that they are hugely abundant and diverse in nature. This biocomplexity project is studying the composition and diversity of bacteriophage communities in solar salterns by high throughput DNA sequencing. The sequencing includes the complete genomes of cultured phage and partial shotgun sequencing of entire phage communities. Since phage genomes are ~50X smaller than those of prokaryotes, similar coverage of the phage community genome is being obtained with much less sequencing. Additionally, by focusing on lower diversity saltern systems, this project is obtaining high genomic coverage of the phage community from numerous samples. This approach will allow the research team to measure bacterial and phage diversity on a community level and determine if diversity changes as phage and host concentrations increase. The sequencing efforts are being combined with microarray methods, microbial ecology measurements (e.g., production and decay rates), and microscopy to investigate the types, concentration, distribution, and colonization of particles that contribute to spatial and temporal heterogeneity.The resulting data on diversity, dynamics, and environmental parameters are being used to model phage-host dynamics across other ecosystems. Bioinformatic analyses of the data are also being used to address questions in phage taxonomy and genomics. Tools for analyzing and disseminating sequence data, as well as for mathematically modeling populations based on shotgun sequencing data are being developed. This project is producing robust bioinformatic, genomic, and mathematical tools that are applicable for assessing uncultured phage diversity in any ecosystem. This work is being made accessible to the public through several outreach programs and will also contribute to the education of K-12, undergraduate, and graduate students.

噬菌体是细菌的病毒，最近的证据表明它们在自然界中非常丰富和多样。 这个生物复杂性项目是通过高通量DNA测序来研究太阳盐藻中噬菌体群落的组成和多样性。测序包括培养的噬菌体的完整基因组和整个噬菌体群落的部分鸟枪测序。由于噬菌体基因组比原核生物的基因组小约50倍，因此可以用少得多的测序获得噬菌体群落基因组的相似覆盖率。此外，通过关注低多样性盐场系统，该项目正在从众多样品中获得噬菌体群落的高基因组覆盖率。 这种方法将使研究小组能够在群落水平上测量细菌和噬菌体的多样性，并确定多样性是否随着噬菌体和宿主浓度的增加而变化。 测序工作正在与微阵列方法、微生物生态学测量（例如，产生和衰减率），以及显微镜研究的类型，浓度，分布，并有助于空间和时间异质性粒子的定植。由此产生的多样性，动态和环境参数的数据正在被用来模拟噬菌体宿主动态在其他生态系统。 数据的生物信息学分析也被用于解决噬菌体分类学和基因组学中的问题。 用于分析和传播序列数据以及基于鸟枪测序数据对群体进行数学建模的工具正在开发中。 该项目正在产生强大的生物信息学，基因组学和数学工具，适用于评估任何生态系统中未培养的噬菌体多样性。这项工作正在通过几个外展计划向公众开放，也将有助于K-12，本科生和研究生的教育。