BACKGROUND The newly defined superphylum Patescibacteria such as Parcubacteria (OD1) and Microgenomates (OP11) has been found to be prevalent in groundwater, sediment, lake, and other aquifer environments. Recently increasing attention has been paid to this diverse superphylum including > 20 candidate phyla (a large part of the candidate phylum radiation, CPR) because it refreshed our view of the tree of life. However, adaptive traits contributing to its prevalence are still not well known. RESULTS Here, we investigated the genomic features and metabolic pathways of Patescibacteria in groundwater through genome-resolved metagenomics analysis of > 600 Gbp sequence data. We observed that, while the members of Patescibacteria have reduced genomes (~ 1 Mbp) exclusively, functions essential to growth and reproduction such as genetic information processing were retained. Surprisingly, they have sharply reduced redundant and nonessential functions, including specific metabolic activities and stress response systems. The Patescibacteria have ultra-small cells and simplified membrane structures, including flagellar assembly, transporters, and two-component systems. Despite the lack of CRISPR viral defense, the bacteria may evade predation through deletion of common membrane phage receptors and other alternative strategies, which may explain the low representation of prophage proteins in their genomes and lack of CRISPR. By establishing the linkages between bacterial features and the groundwater environmental conditions, our results provide important insights into the functions and evolution of this CPR group. CONCLUSIONS We found that Patescibacteria has streamlined many functions while acquiring advantages such as avoiding phage invasion, to adapt to the groundwater environment. The unique features of small genome size, ultra-small cell size, and lacking CRISPR of this large lineage are bringing new understandings on life of Bacteria. Our results provide important insights into the mechanisms for adaptation of the superphylum in the groundwater environments, and demonstrate a case where less is more, and small is mighty.

中文翻译：

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小而强大：Patescibacteria总门对地下水环境的适应促使其基因组变得简单。


背景技术新定义的Patescibacteria总门例如Parcubacteria (OD1)和Microgenomates (OP11)被发现在地下水、沉积物、湖泊和其他含水层环境中普遍存在。最近，人们越来越关注这个多样化的超门，包括超过 20 个候选门（候选辐射门的很大一部分，CPR），因为它刷新了我们对生命树的看法。然而，导致其流行的适应性特征仍不清楚。结果在这里，我们通过对 > 600 Gbp 序列数据进行基因组解析宏基因组分析，研究了地下水中 Patescibacteria 的基因组特征和代谢途径。我们观察到，虽然 Patescibacteria 的成员仅减少了基因组 (~ 1 Mbp)，但保留了生长和繁殖所必需的功能，例如遗传信息处理。令人惊讶的是，它们急剧减少了多余和非必要的功能，包括特定的代谢活动和应激反应系统。 Patescibacteria 具有超小细胞和简化的膜结构，包括鞭毛组装、转运蛋白和双组分系统。尽管缺乏 CRISPR 病毒防御，细菌可能通过删除常见的膜噬菌体受体和其他替代策略来逃避捕食，这可能解释了原噬菌体蛋白在其基因组中的代表性较低和缺乏 CRISPR 的原因。通过建立细菌特征和地下水环境条件之间的联系，我们的结果为该 CPR 群体的功能和进化提供了重要的见解。结论我们发现Patescibacteria简化了许多功能，同时获得了避免噬菌体入侵等优势，以适应地下水环境。 这种大谱系的小基因组大小、超小细胞大小以及缺乏 CRISPR 的独特特征正在为细菌的生命带来新的认识。我们的研究结果为了解超门在地下水环境中的适应机制提供了重要的见解，并证明了少即是多、小即是强大的情况。