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

古生菌是已知在碳和氮循环中起关键作用的微生物，但对该群体的多样性和进化知之甚少。Woesearchaeota是一种鲜为人知的古菌群，通常在淡水湿地中发现，但也可以在全球各种生态系统中发现。与古生菌的大多数成员一样，没有培养的代表可以在实验室研究，也没有可用的基因组序列来帮助推断功能。本研究将采用环境DNA测序方法和相关的计算方法从淡水湿地中生成多个新的Woesearchaeota基因组。对这些基因组的分析将在全球范围内促进对这一群体功能潜力的了解。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，本科生将获得科学计算和生物信息学基础的实践研究经验。这项研究将产生新的全基因组序列，并推断最近描述的古菌群Woesearchaeota的代谢潜力。迄今为止，仅重建了少量的毛藻基因组和部分基因组。对淡水湿地古细菌的高分辨率普查表明，该遗址的古细菌具有系统发育多样性，包括两种生态分化的生态类型，其生态位由遗址地球化学定义。基因组变异可以解释观察到的生态位偏好的假设，将通过多个Woesearchaeota基因组的靶向重建来验证。研究人员还将验证一些假设，即局部进化多样性导致了一个小的核心基因组，以及在这个门中观察到的高系统发育多样性反映了推断出的高水平功能多样性。

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.