Microbes and their associated viruses are key drivers of biogeochemical processes in marine and soil biomes. While viruses of phototrophic cyanobacteria are well-represented in model systems, challenges of isolating marine microbial heterotrophs and their viruses have hampered experimental approaches to quantify the importance of viruses in nutrient recycling. A resurgence in cultivation efforts has improved the availability of fastidious bacteria for hypothesis testing, but this has not been matched by similar efforts to cultivate their associated bacteriophages. Here, we describe a high-throughput method for isolating important virus–host systems for fastidious heterotrophic bacteria that couples advances in culturing of hosts with sequential enrichment and isolation of associated phages. Applied to six monthly samples from the Western English Channel, we first isolated one new member of the globally dominant bacterial SAR11 clade and three new members of the methylotrophic bacterial clade OM43. We used these as bait to isolate 117 new phages, including the first known siphophage-infecting SAR11, and the first isolated phage for OM43. Genomic analyses of 13 novel viruses revealed representatives of three new viral genera, and infection assays showed that the viruses infecting SAR11 have ecotype-specific host ranges. Similar to the abundant human-associated phage ɸCrAss001, infection dynamics within the majority of isolates suggested either prevalent lysogeny or chronic infection, despite a lack of associated genes, or host phenotypic bistability with lysis putatively maintained within a susceptible subpopulation. Broader representation of important virus–host systems in culture collections and genomic databases will improve both our understanding of virus–host interactions, and accuracy of computational approaches to evaluate ecological patterns from metagenomic data.

微生物及其相关病毒是海洋和土壤生物群落生物地球化学过程的关键驱动因素。虽然光养蓝细菌的病毒在模型系统中得到了很好的体现，但分离海洋微生物异养生物及其病毒的挑战阻碍了量化病毒在营养物循环中的重要性的实验方法。培养工作的复兴提高了用于假设检验的挑剔细菌的可用性，但这并没有与培养相关噬菌体的类似努力相匹配。在这里，我们描述了一种用于分离挑剔异养细菌的重要病毒-宿主系统的高通量方法，该方法将宿主培养的进展与相关噬菌体的连续富集和分离相结合。应用来自西英吉利海峡的六个月样本，我们首先分离出全球占主导地位的细菌 SAR11 分支的一个新成员和甲基营养细菌分支 OM43 的三个新成员。我们使用这些作为诱饵分离出 117 个新噬菌体，包括第一个已知的噬菌体感染 SAR11 和第一个分离的 OM43 噬菌体。对 13 种新型病毒的基因组分析揭示了三种新病毒属的代表，感染分析表明感染 SAR11 的病毒具有生态型特异性宿主范围。与丰富的人类相关噬菌体 ɸCrAss001 类似，大多数分离株内的感染动态表明，尽管缺乏相关基因，但普遍存在溶原性或慢性感染，或者在易感亚群中假定维持裂解的宿主表型双稳定性。在培养物保藏中心和基因组数据库中更广泛地表征重要的病毒-宿主系统将提高我们对病毒-宿主相互作用的理解，以及根据宏基因组数据评估生态模式的计算方法的准确性。