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Experimental evolution at ecological scales allows linking of viral genotypes to specific host strains
The ISME Journal ( IF 10.8 ) Pub Date : 2024-11-23 , DOI: 10.1093/ismejo/wrae208 María Dolores Ramos-Barbero, Borja Aldeguer-Riquelme, Tomeu Viver, Judith Villamor, Miryam Carrillo-Bautista, Cristina López-Pascual, Konstantinos T Konstantinidis, Manuel Martínez-García, Fernando Santos, Ramon Rossello-Mora, Josefa Antón
The ISME Journal ( IF 10.8 ) Pub Date : 2024-11-23 , DOI: 10.1093/ismejo/wrae208 María Dolores Ramos-Barbero, Borja Aldeguer-Riquelme, Tomeu Viver, Judith Villamor, Miryam Carrillo-Bautista, Cristina López-Pascual, Konstantinos T Konstantinidis, Manuel Martínez-García, Fernando Santos, Ramon Rossello-Mora, Josefa Antón
Viruses shape microbial community structure and activity through the control of population diversity and cell abundances. Identifying and monitoring the dynamics of specific virus-host pairs in nature is hampered by the limitations of culture-independent approaches such as metagenomics, which do not always provide strain-level resolution, and culture-based analyses, which eliminate the ecological background and in-situ interactions. Here, we have explored the interaction of a specific “autochthonous” host strain and its viruses within a natural community. Bacterium Salinibacter ruber strain M8 was spiked into its environment of isolation, a crystallizer pond from a coastal saltern, and the viral and cellular communities were monitored for one month using culture, metagenomics, and microscopy. Metagenome sequencing indicated that the M8 abundance decreased sharply after being added to the pond, likely due to forces other than viral predation. However, the presence of M8 selected for two species of a new viral genus, Phoenicisalinivirus, for which 120 strains were isolated. During this experiment, an assemblage of closely related viral genomic variants was replaced by a single population with the ability to infect M8, a scenario which was compatible with the selection of a genomic variant from the rare biosphere. Further analysis implicated a viral genomic region putatively coding for a tail fiber protein to be responsible for M8 specificity. Our results indicate that low abundance viral genotypes provide a viral seed bank that allows for a highly specialized virus-host response within a complex ecological background.
中文翻译:
生态尺度的实验进化允许将病毒基因型与特定宿主菌株联系起来
病毒通过控制种群多样性和细胞丰度来塑造微生物群落的结构和活性。识别和监测自然界中特定病毒-宿主对的动力学受到不依赖培养的方法的局限性,例如宏基因组学,它并不总是提供菌株水平的分辨率,以及基于培养的分析,它消除了生态背景和原位相互作用。在这里,我们探讨了特定的 “本土 ”宿主菌株及其病毒在自然群落中的相互作用。将细菌 Salinibacter ruber 菌株 M8 加标到其分离环境中,即沿海盐田的结晶池,并使用培养、宏基因组学和显微镜监测病毒和细胞群落一个月。宏基因组测序表明,M8 丰度在加入池塘后急剧下降,可能是由于病毒捕食以外的力量。然而,M8 的存在被选择用于新病毒属 Phoenicisalinivirus 的两个物种,该病毒分离了 120 个菌株。在这个实验中,密切相关的病毒基因组变异的集合被具有感染 M8 能力的单个群体所取代,这种情况与从稀有生物圈中选择基因组变异是兼容的。进一步的分析表明,推测编码尾纤维蛋白的病毒基因组区域是 M8 特异性的原因。我们的结果表明,低丰度病毒基因型提供了一个病毒种子库,允许在复杂的生态背景下进行高度专业化的病毒-宿主反应。
更新日期:2024-11-23
中文翻译:
生态尺度的实验进化允许将病毒基因型与特定宿主菌株联系起来
病毒通过控制种群多样性和细胞丰度来塑造微生物群落的结构和活性。识别和监测自然界中特定病毒-宿主对的动力学受到不依赖培养的方法的局限性,例如宏基因组学,它并不总是提供菌株水平的分辨率,以及基于培养的分析,它消除了生态背景和原位相互作用。在这里,我们探讨了特定的 “本土 ”宿主菌株及其病毒在自然群落中的相互作用。将细菌 Salinibacter ruber 菌株 M8 加标到其分离环境中,即沿海盐田的结晶池,并使用培养、宏基因组学和显微镜监测病毒和细胞群落一个月。宏基因组测序表明,M8 丰度在加入池塘后急剧下降,可能是由于病毒捕食以外的力量。然而,M8 的存在被选择用于新病毒属 Phoenicisalinivirus 的两个物种,该病毒分离了 120 个菌株。在这个实验中,密切相关的病毒基因组变异的集合被具有感染 M8 能力的单个群体所取代,这种情况与从稀有生物圈中选择基因组变异是兼容的。进一步的分析表明,推测编码尾纤维蛋白的病毒基因组区域是 M8 特异性的原因。我们的结果表明,低丰度病毒基因型提供了一个病毒种子库,允许在复杂的生态背景下进行高度专业化的病毒-宿主反应。