Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA.
Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA.
Appl Environ Microbiol. 2023 Jul 26;89(7):e0017723. doi: 10.1128/aem.00177-23. Epub 2023 Jul 5.
Bacteriophages (phages), which are viruses that infect bacteria, are the most abundant components of microbial communities and play roles in community dynamics and host evolution. However, the study of phage-host interactions is hindered by a paucity of model systems from natural environments. Here, we investigate phage-host interactions in the "pink berry" consortia, which are naturally occurring, low-diversity, macroscopic bacterial aggregates that are found in the Sippewissett Salt Marsh (Falmouth, MA, USA). We leverage metagenomic sequence data and a comparative genomics approach to identify eight compete phage genomes, infer their bacterial hosts from host-encoded clustered regularly interspaced short palindromic repeats (CRISPRs), and observe the potential evolutionary consequences of these interactions. Seven of the eight phages identified infect known pink berry symbionts, namely, sp. PB-SRB1, sp. PB-PSB1, and sp. A2, and they are largely divergent from known viruses. In contrast to the conserved bacterial community structure of pink berries, the distribution of these phages across aggregates is highly variable. Two phages persisted over a period of seven years with high sequence conservation, allowing us to identify gene gain and loss. Increased nucleotide variation in a conserved phage capsid gene that is commonly targeted by host CRISPR systems suggests that CRISPRs may drive phage evolution in pink berries. Finally, we identified a predicted phage lysin gene that was horizontally transferred to its bacterial host, potentially via a transposon intermediary. Taken together, our results demonstrate that pink berry consortia contain diverse and variable phages as well as provide evidence for phage-host coevolution via multiple mechanisms in a natural microbial system. Phages, which are viruses that infect bacteria, are important components of all microbial systems, in which they drive the turnover of organic matter by lysing host cells, facilitate horizontal gene transfer (HGT), and coevolve with their bacterial hosts. Bacteria resist phage infection, which is often costly or lethal, through a diversity of mechanisms. One of these mechanisms is CRISPR systems, which encode arrays of phage-derived sequences from past infections to block subsequent infection with related phages. Here, we investigate the bacteria and phage populations from a simple marine microbial community, known as "pink berries", found in salt marshes of Falmouth, Massachusetts, as a model of phage-host coevolution. We identify eight novel phages and characterize a case of putative CRISPR-driven phage evolution as well as an instance of HGT between a phage and its host, together suggesting that phages have large evolutionary impacts in a naturally occurring microbial community.
噬菌体(phages)是感染细菌的病毒,是微生物群落中最丰富的组成部分,在群落动态和宿主进化中发挥作用。然而,由于缺乏来自自然环境的模型系统,噬菌体-宿主相互作用的研究受到了阻碍。在这里,我们研究了自然发生的、低多样性的宏观细菌聚集体——“粉色浆果”(pinkberry)中的噬菌体-宿主相互作用。这些聚集体存在于美国马萨诸塞州法尔茅斯的锡皮怀塞特盐沼(Sippewissett Salt Marsh)中。我们利用宏基因组序列数据和比较基因组学方法,鉴定了 8 个完整的噬菌体基因组,从宿主编码的簇状规则间隔短回文重复序列(CRISPRs)中推断出它们的细菌宿主,并观察了这些相互作用的潜在进化后果。鉴定出的 8 个噬菌体中有 7 个感染了已知的粉色浆果共生体,即 sp. PB-SRB1、sp. PB-PSB1 和 sp. A2,它们与已知的病毒有很大的差异。与粉色浆果细菌群落结构的保守性形成对比的是,这些噬菌体在聚集体中的分布具有高度的可变性。两种噬菌体在长达七年的时间里保持着高度的序列保守性,这使得我们能够识别基因的获得和丢失。一个保守的噬菌体衣壳基因的核苷酸变异增加,而这个基因通常是宿主 CRISPR 系统的靶标,这表明 CRISPR 系统可能在粉色浆果中推动了噬菌体的进化。最后,我们鉴定出一个预测的噬菌体溶菌酶基因,该基因通过转座子中间体发生了水平转移,进入其细菌宿主。总的来说,我们的研究结果表明,粉色浆果聚集体中含有多样化和可变的噬菌体,并为在自然微生物系统中通过多种机制进行的噬菌体-宿主共同进化提供了证据。噬菌体是感染细菌的病毒,是所有微生物系统的重要组成部分,它们通过裂解宿主细胞来推动有机质的转化,促进水平基因转移(HGT),并与细菌宿主共同进化。细菌通过多种机制来抵抗噬菌体的感染,这种感染通常是代价高昂或致命的。其中一种机制是 CRISPR 系统,它编码了过去感染的噬菌体衍生序列的数组,以阻止后续与相关噬菌体的感染。在这里,我们以马萨诸塞州法尔茅斯的盐沼中的一种简单海洋微生物群落——“粉色浆果”(pinkberry)为模型,研究了细菌和噬菌体种群。我们鉴定了 8 个新的噬菌体,并描述了一个可能由 CRISPR 驱动的噬菌体进化案例,以及一个噬菌体与其宿主之间的 HGT 实例,这表明噬菌体在自然发生的微生物群落中具有很大的进化影响。