Center for Microbial Ecology and Technology (CMET), Ghent University, Ghent, Belgium.
Belgian Nuclear Research Centre (SCK•CEN), Mol, Belgium.
mSphere. 2019 Feb 6;4(1):e00011-19. doi: 10.1128/mSphereDirect.00011-19.
We examined the genomic adaptations of prevalent bacterial taxa in a highly nutrient- and ion-depleted freshwater environment located in the secondary cooling water system of a nuclear research reactor. Using genome-centric metagenomics, we found that none of the prevalent bacterial taxa were related to typical freshwater bacterial lineages. We also did not identify strong signatures of genome streamlining, which has been shown to be one of the ecoevolutionary forces shaping the genome characteristics of bacterial taxa in nutrient-depleted environments. Instead, focusing on the dominant taxon, a novel sp. which we propose to name , we detected extensive positive selection on genes involved in phosphorus and carbon scavenging pathways. These genes were involved in the high-affinity phosphate uptake and storage into polyphosphate granules, metabolism of nitrogen-rich organic matter, and carbon/energy storage into polyhydroxyalkanoate. In parallel, comparative genomics revealed a high number of paralogs and an accessory genome significantly enriched in environmental sensing pathways (i.e., chemotaxis and motility), suggesting extensive gene expansions in The type strain of (LMG 30558) displayed optimal growth kinetics and productivity at low nutrient concentrations, as well as substantial cell size plasticity. Our findings with LMG 30558 demonstrate that positive selection and gene expansions may represent successful adaptive strategies to oligotrophic environments that preserve high growth rates and cellular productivity. By combining a genome-centric metagenomic approach with a culture-based approach, we investigated the genomic adaptations of prevalent populations in an engineered oligotrophic freshwater system. We found evidence for widespread positive selection on genes involved in phosphorus and carbon scavenging pathways and for gene expansions in motility and environmental sensing to be important genomic adaptations of the abundant taxon in this system. In addition, microscopic and flow cytometric analysis of the first freshwater representative of this population ( LMG 30558) demonstrated phenotypic plasticity, possibly due to the metabolic versatility granted by its larger genome, to be a strategy to cope with nutrient limitation. Our study clearly demonstrates the need for the use of a broad set of genomic tools combined with culture-based physiological characterization assays to investigate and validate genomic adaptations.
我们研究了位于核研究反应堆二级冷却水中的高度营养和离子贫化淡水环境中流行细菌分类群的基因组适应性。使用基于基因组的宏基因组学，我们发现没有一个流行的细菌分类群与典型的淡水细菌谱系有关。我们也没有发现基因组简化的强烈特征，这已经被证明是塑造营养贫乏环境中细菌分类群基因组特征的生态进化力量之一。相反，我们专注于优势分类群，一种新的 sp. ，我们提议将其命名为 ，我们检测到广泛的正选择作用于涉及磷和碳摄取途径的基因。这些基因参与高亲和力磷酸盐吸收和储存到多磷酸盐颗粒中、富含氮有机物的代谢以及将碳/能量储存到聚羟基烷酸酯中。与此同时，比较基因组学揭示了大量的基因重复和一个显著富含环境感应途径（即趋化性和运动性）的辅助基因组，这表明在 中广泛的基因扩张。 （LMG 30558）的模式株在低营养浓度下表现出最佳的生长动力学和生产力，以及显著的细胞大小可塑性。我们对 LMG 30558 的研究结果表明，正选择和基因扩张可能代表了在保留高生长速率和细胞生产力的情况下适应贫营养环境的成功策略。通过将基于基因组的宏基因组学方法与基于培养的方法相结合，我们研究了工程贫营养淡水系统中流行种群的基因组适应性。我们发现，参与磷和碳摄取途径的基因广泛受到正选择，运动和环境感应的基因扩张是该系统中丰富分类群的重要基因组适应性的证据。此外，对该种群的第一个淡水代表（LMG 30558）的显微镜和流式细胞术分析表明，表型可塑性，可能是由于其较大基因组赋予的代谢多功能性，是应对营养限制的一种策略。我们的研究清楚地表明，需要使用广泛的基因组工具结合基于培养的生理特征分析来研究和验证基因组适应性。
