The candidate phyla radiation (CPR) comprises a large monophyletic group of bacterial lineages known almost exclusively based on genomes obtained using cultivation-independent methods. Within the CPR, Gracilibacteria (BD1-5) are particularly poorly understood due to undersampling and the inherent fragmented nature of available genomes. Here, we report the first closed, curated genome of a gracilibacterium from an enrichment experiment inoculated from the Gulf of Mexico and designed to investigate hydrocarbon degradation. The gracilibacterium rose in abundance after the community switched to dominance by Colwellia Notably, we predict that this gracilibacterium completely lacks glycolysis, the pentose phosphate and Entner-Doudoroff pathways. It appears to acquire pyruvate, acetyl coenzyme A (acetyl-CoA), and oxaloacetate via degradation of externally derived citrate, malate, and amino acids and may use compound interconversion and oxidoreductases to generate and recycle reductive power. The initial genome assembly was fragmented in an unusual gene that is hypervariable within a repeat region. Such extreme local variation is rare but characteristic of genes that confer traits under pressure to diversify within a population. Notably, the four major repeated 9-mer nucleotide sequences all generate a proline-threonine-aspartic acid (PTD) repeat. The genome of an abundant Colwellia psychrerythraea population has a large extracellular protein that also contains the repeated PTD motif. Although we do not know the host for the BD1-5 cell, the high relative abundance of the C. psychrerythraea population and the shared surface protein repeat may indicate an association between these bacteria.IMPORTANCE CPR bacteria are generally predicted to be symbionts due to their extensive biosynthetic deficits. Although monophyletic, they are not monolithic in terms of their lifestyles. The organism described here appears to have evolved an unusual metabolic platform not reliant on glucose or pentose sugars. Its biology appears to be centered around bacterial host-derived compounds and/or cell detritus. Amino acids likely provide building blocks for nucleic acids, peptidoglycan, and protein synthesis. We resolved an unusual repeat region that would be invisible without genome curation. The nucleotide sequence is apparently under strong diversifying selection, but the amino acid sequence is under stabilizing selection. The amino acid repeat also occurs in a surface protein of a coexisting bacterium, suggesting colocation and possibly interdependence.

中文翻译：

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来自降解石油社区的十字杆菌（BD1-5）基因组中的异常代谢和高变。

候选门放射（CPR）包含一大类细菌谱系，几乎完全基于使用独立于培养的方法获得的基因组而已知。在CPR中，由于采样不足和可用基因组固有的片段化性质，人们对Gracilibacteria（BD1-5）的了解特别少。在这里，我们报道了来自墨西哥湾接种的富集实验的第一个封闭的，根瘤菌的基因组，该基因组设计用于调查烃的降解。在社区由Colwellia转变为优势之后，杆菌变得大量上升。值得注意的是，我们预测该杆菌完全缺乏糖酵解，磷酸戊糖和Entner-Doudoroff途径。它似乎获得了丙酮酸，乙酰辅酶A（乙酰-CoA），草酰乙酸和草酰乙酸通过降解外部来源的柠檬酸，苹果酸和氨基酸而分解，并可能使用化合物相互转化和氧化还原酶来产生和再循环还原能力。最初的基因组组装被片段化为一个在重复区域内高变的不寻常基因。这种极端的局部变异很少见，但具有赋予性状以使种群内多样化的基因特征。值得注意的是，四个主要的重复的9-mer核苷酸序列均产生脯氨酸-苏氨酸-天冬氨酸（PTD）重复序列。丰富的Collwellia psychrerythraea种群的基因组具有较大的细胞外蛋白，该蛋白还包含重复的PTD基序。尽管我们不知道BD1-5细胞的宿主，但C的相对丰度很高。精神性红斑人群和共享的表面蛋白重复序列​​可能表明这些细菌之间存在关联。重要提示CPR细菌由于其广泛的生物合成缺陷而通常被认为是共生细菌。尽管是单一的，但就生活方式而言，它们并不是单一的。这里描述的生物似乎已经进化出不依赖葡萄糖或戊糖的异常代谢平台。它的生物学似乎集中在细菌宿主衍生的化合物和/或细胞碎屑周围。氨基酸可能提供核酸，肽聚糖和蛋白质合成的基础。我们解决了一个不寻常的重复区域，如果没有基因组管理，该区域将是不可见的。核苷酸序列显然处于强烈的多样化选择下，​​但氨基酸序列处于稳定的选择下。