DeepH: Horizontal evolution of uncultivated archaea in the deep biosphere

地球深层地下容纳了大约70%的原核生物，但关于其生态系统中主要的原核生物进化模式的信息很少，这些模式的主要特征是缺乏阳光，几乎没有氧气可用，几乎没有营养物质。最近的研究表明，来自不同地下地点的一些基因组可以具有极高的相似性，这表明深层地下微生物的进化过程很低。然而，这些分析只使用了保守的核心基因。与此同时，以前从深层地下古菌中解析基因组的尝试表明，转座子繁殖可以导致菌株的多样化。因此，关于大陆次表层基因组进化的范围和动态的结论性分析是缺失的。在DeepH项目中，我们建议通过进行长时间阅读的基因组分辨元基因组学，结合邻近连接(Hi-C)元基因组学和甲基化碱基呼吁从全球不同的亚表层生态系统重建(近)完整的高山假丝酵母基因组，来解决转座元件(TES)如何影响大陆亚表层的古生物基因组进化和基因组可塑性的问题。这些古菌被选为模式生物，因为它们在其生态系统中可以丰富(相对丰度高达70%)，表现出非常严格的生物地理学，并且除了我们最近证明的保守的核心基因组外，还具有许多细菌起源的基因。在解析完完整基因组后(现有基因组极其零散)，我们将通过关注支撑其起源的宿主基因组中的TE(一些由病毒携带)和调查TE在采样点(从美国、欧洲到日本)的分布来研究基因转移的模式。我们还将研究这些微生物的基因组重排、转座和一般基因组结构。最后，加州TES的存在和多样性。阿尔蒂古菌菌株将使用单分子荧光显微镜在单细胞水平上进行检测。我们预计在TES上检测到细菌货运基因，以及在不破坏核心基因组的情况下驱动这些古菌的短期进化的位点特异性TES。总体而言，我们认为DeepH项目将大大有助于更好地了解古生菌的基因组进化和基因组(重新)组织，特别是钙。阿尔蒂古生菌，位于生物圈深处，揭示了这些生态系统的一种主要进化模式。

The deep subsurface houses approximately 70% of Earth’s Prokaryotes, yet there is little information on major modes of prokaryotic evolution in its ecosystems that are mainly characterized by the absence of sunlight, little to no oxygen availability, and little amounts of nutrients. Recent investigations demonstrated that some genomes from different subsurface sites can be of extremely high similarity, suggesting low evolutionary processes of deep subsurface microbes. However, only conserved core genes were used for these analyses. At the same time, previous attempts at resolving genomes from deep subsurface archaea showed that transposon propagation can result in diversification of strains. Consequently, a conclusive analysis on the extent and dynamics of genome evolution in the continental subsurface is missing. In the project DeepH, we propose to tackle the question of how transposable elements (TEs) impact archaeal genome evolution and genome plasticity in the continental subsurface by performing long-read genome-resolved metagenomics, coupled to proximity-ligation (Hi-C) metagenomics and methylation base calling to reconstruct (near) complete genomes of Candidatus Altiarchaea from various subsurface ecosystems across the globe. These archaea have been selected as model organisms since they can be abundant in their ecosystem (up to ~70% in relative abundance), show a very strict biogeography, and have many genes of bacterial origin besides their conserved core genomes as we recently demonstrated. After resolving complete genomes (existing genomes are extremely fragmented), we will investigate the mode of gene transfer by focusing on TEs in the host genome underpinning their origin (some are carried by viruses) and investigating TE distribution across sampling sites (from US over Europe to Japan). We will also investigate genome rearrangements, transposition, and the general genome architecture of these microbes. Finally, presence and diversity of TEs in Ca. Altiarchaea strains will be detected at single cell level using single molecule fluorescence microscopy. We anticipate the detection of bacterial cargo genes on TEs as well as site-specific TEs that drive the short-term evolution of these archaea without spoilage of the core genome. Overall, we propose that the DeepH project will substantially contribute to a better understanding of genome evolution and genome (re)organization of archaea, particularly Ca. Altiarchaea, in the deep biosphere and reveal a major mode of evolution in these ecosystems.