Community structure and metabolism through reconstruction of microbial genomes from the environment
Community structure and metabolism through reconstruction of microbial genomes from the environment
复制标题
DOI：
10.1038/nature02340
复制
发表时间：
2004-03-04
期刊：
影响因子：
64.8
通讯作者：
Banfield, JF
中科院分区：
文献类型：
--
作者：
Tyson, GW;Chapman, J;Banfield, JF
微生物群落对于所有生态系统的运作至关重要；然而，大多数微生物未经培养，它们在自然系统中的作用尚不清楚。在这里，我们使用来自天然嗜酸生物膜的 DNA 进行随机鸟枪测序，报告了 II 型钩端螺旋菌和 II 型铁原体近乎完整的基因组重建，以及其他三个基因组的部分恢复。这是可能的，因为生物膜主要由少数物种种群主导，并且基因组重排和基因插入或缺失的频率相对较低。因为每个序列读数都来自不同的个体，所以我们可以确定单核苷酸多态性是菌株水平异质性的主要形式。尽管存在低丰度变异体，但 II 类钩端螺旋菌基因组的核苷酸多态性却非常少。 II 型铁原体基因组似乎是三个祖先菌株的复合体，这些菌株经过同源重组形成大量嵌合基因组。对每种生物体的基因互补体的分析揭示了碳和氮的固定以及能量产生的途径，并为极端环境中的生存策略提供了见解。
Microbial communities are vital in the functioning of all ecosystems; however, most microorganisms are uncultivated, and their roles in natural systems are unclear. Here, using random shotgun sequencing of DNA from a natural acidophilic biofilm, we report reconstruction of near-complete genomes of Leptospirillum group II and Ferroplasma type II, and partial recovery of three other genomes. This was possible because the biofilm was dominated by a small number of species populations and the frequency of genomic rearrangements and gene insertions or deletions was relatively low. Because each sequence read came from a different individual, we could determine that single-nucleotide polymorphisms are the predominant form of heterogeneity at the strain level. The Leptospirillum group II genome had remarkably few nucleotide polymorphisms, despite the existence of low-abundance variants. The Ferroplasma type II genome seems to be a composite from three ancestral strains that have undergone homologous recombination to form a large population of mosaic genomes. Analysis of the gene complement for each organism revealed the pathways for carbon and nitrogen fixation and energy generation, and provided insights into survival strategies in an extreme environment.