Labonté Jessica M, Pachiadaki Maria, Fergusson Elizabeth, McNichol Jesse, Grosche Ashley, Gulmann Lara K, Vetriani Costantino, Sievert Stefan M, Stepanauskas Ramunas
Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States.
Department of Marine Biology, Texas A&M University at Galveston, Galveston, TX, United States.
Front Microbiol. 2019 Jun 12;10:1262. doi: 10.3389/fmicb.2019.01262. eCollection 2019.
Phage-host interactions likely play a major role in the composition and functioning of many microbiomes, yet remain poorly understood. Here, we employed single cell genomics to investigate phage-host interactions in a diffuse-flow, low-temperature hydrothermal vent that may be reflective of a broadly distributed biosphere in the subseafloor. We identified putative prophages in 13 of 126 sequenced single amplified genomes (SAGs), with no evidence for lytic infections, which is in stark contrast to findings in the surface ocean. Most were distantly related to known prophages, while their hosts included bacterial phyla Campylobacterota, Bacteroidetes, Chlorobi, Proteobacteria, Lentisphaerae, Spirochaetes, and Thermotogae. Our results suggest the predominance of lysogeny over lytic interaction in diffuse-flow, deep-sea hydrothermal vents, despite the high activity of the dominant Campylobacteria that would favor lytic infections. We show that some of the identified lysogens have co-evolved with their host over geological time scales and that their genes are transcribed in the environment. Functional annotations of lysogeny-related genes suggest involvement in horizontal gene transfer enabling host's protection against toxic metals and antibacterial compounds.
噬菌体与宿主的相互作用可能在许多微生物群落的组成和功能中发挥重要作用，但目前仍知之甚少。在这里，我们利用单细胞基因组学研究了一种扩散流低温热液喷口处的噬菌体与宿主的相互作用，这种热液喷口可能反映了广泛分布于海底以下的生物圈。我们在126个测序的单扩增基因组（SAG）中的13个中鉴定出推定的原噬菌体，没有发现裂解感染的证据，这与在表层海洋中的发现形成了鲜明对比。大多数原噬菌体与已知原噬菌体的亲缘关系较远，而它们的宿主包括弯曲杆菌门、拟杆菌门、绿菌门、变形菌门、慢生根瘤菌门、螺旋体门和栖热袍菌门。我们的结果表明，在扩散流深海热液喷口中，溶原性比裂解相互作用更为普遍，尽管占主导地位的弯曲杆菌活性很高，有利于裂解感染。我们表明，一些已鉴定的溶原菌在地质时间尺度上与其宿主共同进化，并且它们的基因在环境中被转录。与溶原性相关基因的功能注释表明，这些基因参与水平基因转移，使宿主能够抵御有毒金属和抗菌化合物。
