Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr Héctor N. Torres" (INGEBI-CONICET), Vuelta de Obligado 2490, C1428ADN, Buenos Aires, Argentina.
Agua y Saneamientos Argentinos S.A., Tucumán 752, C1049APP, Buenos Aires, Argentina.
ISME J. 2021 Mar;15(3):636-648. doi: 10.1038/s41396-020-00802-z. Epub 2020 Oct 16.
Bacterial viruses are widespread and abundant across natural and engineered habitats. They influence ecosystem functioning through interactions with their hosts. Laboratory studies of phage-host pairs have advanced our understanding of phenotypic and genetic diversification in bacteria and phages. However, the dynamics of phage-host interactions have been seldom recorded in complex natural environments. We conducted an observational metagenomic study of the dynamics of interaction between Gordonia and their phages using a three-year data series of samples collected from a full-scale wastewater treatment plant. The aim was to obtain a comprehensive picture of the coevolution dynamics in naturally evolving populations at relatively high time resolution. Coevolution was followed by monitoring changes over time in the CRISPR loci of Gordonia metagenome-assembled genome, and reciprocal changes in the viral genome. Genome-wide analysis indicated low strain variability of Gordonia, and almost clonal conservation of the trailer end of the CRISPR loci. Incorporation of newer spacers gave rise to multiple coexisting bacterial populations. The host population carrying a shorter CRISPR locus that contain only ancestral spacers, which has not acquired newer spacers against the coexisting phages, accounted for more than half of the total host abundance in the majority of samples. Phages genome co-evolved by introducing directional changes, with no preference for mutations within the protospacer and PAM regions. Metagenomic reconstruction of time-resolved variants of host and viral genomes revealed how the complexity at the population level has important consequences for bacteria-phage coexistence.
细菌病毒广泛存在于自然和工程环境中。它们通过与宿主的相互作用影响生态系统功能。噬菌体-宿主对的实验室研究促进了我们对细菌和噬菌体表型和遗传多样化的理解。然而，噬菌体-宿主相互作用的动态在复杂的自然环境中很少被记录。我们使用从一个全规模废水处理厂收集的三年样本数据集，对 Gordonia 及其噬菌体之间相互作用的动态进行了观察性宏基因组研究。目的是在相对较高的时间分辨率下，获得自然进化种群中协同进化动态的全面图景。通过监测 Gordonia 宏基因组组装基因组中 CRISPR 基因座随时间的变化以及病毒基因组的相应变化来跟踪协同进化。全基因组分析表明 Gordonia 的菌株变异性低，CRISPR 基因座的尾部几乎克隆保守。新间隔子的加入导致了多个共存的细菌种群。携带较短 CRISPR 基因座的宿主种群仅包含祖先间隔子，而没有针对共存噬菌体获得新间隔子，在大多数样本中，该种群占总宿主丰度的一半以上。噬菌体通过引入定向变化共同进化，对原间隔子和 PAM 区域内的突变没有偏好。宿主和病毒基因组的时间分辨变体的宏基因组重建揭示了种群水平的复杂性如何对细菌-噬菌体共存产生重要影响。
