Toward quantifying the adaptive role of bacterial pangenomes during environmental perturbations
Toward quantifying the adaptive role of bacterial pangenomes during environmental perturbations
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DOI：
10.1038/s41396-021-01149-9
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发表时间：
2021-12-09
期刊：
影响因子：
11
通讯作者：
Konstantinidis, Konstantinos T.
中科院分区：
文献类型：
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作者：
Conrad, Roth E.;Viver, Tomeu;Konstantinidis, Konstantinos T.
宏基因组调查显示，天然微生物群落主要由序列离散的类物种种群组成，但维持这些种群的遗传和/或生态过程仍然是推测性的，限制了我们对种群物种形成和对扰动的适应的理解。为了解决这一知识差距，我们对来自西班牙马略卡岛4个邻近盐渍池塘的112株橡胶盐杆菌和12个伴生宏基因组进行了测序，并通过实验操作显著改变了该生态系统的两个主要驱动因素盐度和光照强度。我们的分析表明，当地的全基因组的萨尔。橡胶种群是开放的，在大小上与随机抽样的大肠杆菌基因组相似（类似15000个基因）。虽然大多数附属（非核心）基因是分离特异性的，并且与核心基因相比，基于宏基因组显示出较低的原位丰度，表明它们在功能上不重要和/或短暂，但3.5%的附属基因在盐度（而不是光照）条件改变时变得丰富，并编码与渗透调节相关的功能。尽管如此，这些基因的生态优势虽然显著，但显然不足以消除种群内的多样性。总的来说，我们的研究结果解释了这种巨大的种群内基因多样性是如何维持的，这对原核物种概念具有启示意义。
Metagenomic surveys have revealed that natural microbial communities are predominantly composed of sequence-discrete, species-like populations but the genetic and/or ecological processes that maintain such populations remain speculative, limiting our understanding of population speciation and adaptation to perturbations. To address this knowledge gap, we sequenced 112 Salinibacter ruber isolates and 12 companion metagenomes from four adjacent saltern ponds in Mallorca, Spain that were experimentally manipulated to dramatically alter salinity and light intensity, the two major drivers of this ecosystem. Our analyses showed that the pangenome of the local Sal. ruber population is open and similar in size (similar to 15,000 genes) to that of randomly sampled Escherichia coli genomes. While most of the accessory (noncore) genes were isolate-specific and showed low in situ abundances based on the metagenomes compared to the core genes, indicating that they were functionally unimportant and/or transient, 3.5% of them became abundant when salinity (but not light) conditions changed and encoded for functions related to osmoregulation. Nonetheless, the ecological advantage of these genes, while significant, was apparently not strong enough to purge diversity within the population. Collectively, our results provide an explanation for how this immense intrapopulation gene diversity is maintained, which has implications for the prokaryotic species concept.