Bacteriophages play significant roles in the composition, diversity, and evolution of bacterial communities. Despite their importance, it remains unclear how phage diversity and phage-host interactions are spatially structured. Local adaptation may play a key role. Nitrogen-fixing symbiotic bacteria, known as rhizobia, have been shown to locally adapt to domesticated common bean at its Mesoamerican and Andean sites of origin. This may affect phage-rhizobium interactions. However, knowledge about the diversity and coevolution of phages with their respective Rhizobium populations is lacking. Here, through the study of four phage-Rhizobium communities in Mexico and Argentina, we show that both phage and host diversity is spatially structured. Cross-infection experiments demonstrated that phage infection rates were higher overall in sympatric rhizobia than in allopatric rhizobia except for one Argentinean community, indicating phage local adaptation and host maladaptation. Phage-host interactions were shaped by the genetic identity and geographic origin of both the phage and the host. The phages ranged from specialists to generalists, revealing a nested network of interactions. Our results suggest a key role of local adaptation to resident host bacterial communities in shaping the phage genetic and phenotypic composition, following a similar spatial pattern of diversity and coevolution to that in the host.

噬菌体在细菌群落的组成、多样性和进化中发挥着重要作用。尽管噬菌体多样性和噬菌体-宿主相互作用很重要，但其空间结构仍不清楚。当地的适应可能发挥关键作用。固氮共生细菌（称为根瘤菌）已被证明能够适应中美洲和安第斯起源地的驯化普通豆。这可能会影响噬菌体-根瘤菌的相互作用。然而，关于噬菌体及其各自根瘤菌种群的多样性和共同进化的知识仍然缺乏。在这里，通过对墨西哥和阿根廷的四个噬菌体-根瘤菌群落的研究，我们表明噬菌体和宿主多样性都是空间结构的。交叉感染实验表明，除阿根廷的一个群落外，同域根瘤菌中的噬菌体感染率总体高于异域根瘤菌中的噬菌体感染率，这表明噬菌体局部适应和宿主适应不良。噬菌体与宿主的相互作用是由噬菌体和宿主的遗传特性和地理起源决定的。噬菌体的范围从专家到通才，揭示了一个嵌套的相互作用网络。我们的结果表明，对常驻宿主细菌群落的局部适应在塑造噬菌体遗传和表型组成方面发挥着关键作用，遵循与宿主相似的多样性和共同进化的空间模式。