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

噬菌体是细菌的病毒，最近的证据表明，它们在自然界中数量巨大，种类繁多。这个生物复杂性项目是通过高通量DNA测序研究太阳盐碱地噬菌体群落的组成和多样性。测序包括培养噬菌体的全基因组和整个噬菌体群落的部分散弹枪测序。由于噬菌体基因组比原核生物的基因组小约50倍，因此可以用更少的测序获得类似的噬菌体群落基因组覆盖率。此外，通过关注低多样性的盐碱地系统，该项目正在从众多样本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，生产和衰减率）和显微镜相结合，以调查导致时空异质性的颗粒的类型、浓度、分布和定植。所得到的关于多样性、动力学和环境参数的数据正被用于模拟其他生态系统中噬菌体-宿主动力学。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方面的问题。目前正在开发分析和传播序列数据的工具，以及根据鸟枪测序数据对种群进行数学建模的工具。该项目正在开发强大的生物信息学、基因组学和数学工具，可用于评估任何生态系统中未培养噬菌体的多样性。这项工作正在通过几个外展项目向公众开放，也将为K-12、本科生和研究生的教育做出贡献。

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.