DeepH: Horizontal evolution of uncultivated archaea in the deep biosphere

地球上大约70%的原核生物居住在地下深处，但关于其生态系统中原核生物进化的主要模式的信息很少，其主要特征是缺乏阳光，几乎没有氧气可用性，以及少量的营养物质。最近的研究表明，来自不同地下位置的一些基因组可能具有极高的相似性，这表明深层地下微生物的进化过程较低。然而，这些分析只使用了保守的核心基因。与此同时，先前从深层地下古细菌中分离基因组的尝试表明，转座子的繁殖可以导致菌株的多样化。因此，缺乏对大陆地下基因组进化的范围和动态的结论性分析。在DeepH项目中，我们建议通过执行长读基因组解析宏基因组学，结合近端连接宏基因组学（Hi-C）宏基因组学和甲基化碱基来重建来自全球各种地下生态系统的Candidatus Altiarchaea（近）完整基因组，来解决转座因子（TEs）如何影响大陆地下古菌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是因为它们在生态系统中丰富（相对丰度高达70%），表现出非常严格的生物地理特征，并且正如我们最近证明的那样，除了它们保守的核心基因组外，还有许多细菌起源的基因。在解决完整基因组（现有基因组非常碎片化）之后，我们将通过关注宿主基因组中支持其起源的TE（一些由病毒携带）和调查TE在采样点（从美国到欧洲到日本）的分布来研究基因转移模式。我们还将研究这些微生物的基因组重排、转位和一般基因组结构。最后，利用单分子荧光显微镜在单细胞水平检测Ca. Altiarchaea菌株中TEs的存在和多样性。我们期望在TEs上检测到细菌货物基因，以及在不破坏核心基因组的情况下驱动这些古菌短期进化的位点特异性te。总的来说，我们认为DeepH项目将大大有助于更好地理解古细菌，特别是Ca. Altiarchaea，在深层生物圈中的基因组进化和基因组（再）组织，并揭示这些生态系统的主要进化模式。

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.