Dissertation Research: Intra-population genomic and metabolic diversity among understudied archaea in methane-cycling wetlands

论文研究：甲烷循环湿地中待研究古细菌的种群内基因组和代谢多样性

• 批准号: 1701970
• 负责人: Christopher Miller
• 金额: $ 2.02万
• 依托单位: University of Colorado at Denver-Downtown Campus
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-06-01 至 2018-05-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1701970&HistoricalAwards=false
• 关键词: Dissertation; Research; Intra; population; genomic

Archaea are microorganisms that are known to play critical roles in carbon and nitrogen cycling, but little is known about the diversity and evolution of the group. Woesearchaeota, is a poorly known group of Archaea that is commonly found in freshwater wetlands but can also be found in diverse ecosystems globally. As with most members of Archaea, there are no cultured representatives to study in the laboratory, and few available genomes sequences to help infer function. This research will employ environmental DNA sequencing methods and associated computational approaches to generate multiple novel Woesearchaeota genomes from a freshwater wetland. Analysis of these genomes will advance knowledge of the functional potential of this group globally. This work will provide new insights into the role of Archaea in regulating biogeochemical processes. One graduate student will be trained in molecular systematics and undergraduates will receive hands-on research experience on the fundamentals of scientific computing and bioinformatics. This research will produce novel whole-genome sequences and inferences about the metabolic potential for the recently described archaeal group, Woesearchaeota. To-date only a handful of Woesearchaeota genomes and partial genomes have been reconstructed. A high-resolution census of Archaea in a freshwater wetland has revealed that Woesearchaeota at this site are phylogenetically diverse, and comprise two ecologically differentiated ecotypes with niches defined by site geochemistry. The hypothesis that observed niche preferences can be explained by genomic variation will be tested by targeted reconstruction of multiple Woesearchaeota genomes. Researchers will also test the hypotheses that local evolutionary diversifications have resulted in a small core genome, and that the high phylogenetic diversity observed within this phylum is mirrored by high levels of inferred functional diversity.

古细菌是微生物，已知在碳和氮循环中起关键作用，但对该群体的多样性和演变知之甚少。 Woesearchaeota是一群众所周知的古细菌，通常在淡水湿地中发现，但也可以在全球各种生态系统中找到。与古细菌的大多数成员一样，没有文化的代表可以在实验室中研究，也没有很少有可用的基因组序列来帮助推断功能。这项研究将采用环境DNA测序方法和相关的计算方法，从而从淡水湿地产生多种新型的Woesearchaeota基因组。对这些基因组的分析将提高全球该组功能潜力的知识。这项工作将为古细菌在调节生物地球化学过程中的作用提供新的见解。一名研究生将接受分子系统学培训，本科生将获得有关科学计算和生物信息学基础知识的动手研究经验。这项研究将产生有关最近描述的古细菌群Woesearchaeota的代谢潜力的新型全基因组序列和推断。迄今为止仅重建了少数WoesearchAeota基因组和部分基因组。淡水湿地中古细菌的高分辨率人口普查表明，该地点的Woesearchaeota在系统发育上是多种多样的，并且包含两个生态分化的生态型，其壁nikes由现场地球化学定义。可以通过基因组变异来解释观察到的利基偏好的假设将通过针对多个WoesearchAeota基因组的靶向重建来检验。研究人员还将测试局部进化多样性导致核心基因组的假设，并且在该门中观察到的高系统发育多样性与高水平的推断功能多样性相吻合。