Data from: The impact of bacteriophages on phyllosphere bacterial abundance and composition

Interactions between bacteria and bacteriophage viruses (phages) are known to influence pathogen growth and virulence, microbial diversity, and even biogeochemical cycling. Lytic phages in particular infect and lyse their host cells, and can therefore have significant effects on cell densities as well as competitive dynamics within microbial communities. Despite the known impacts of lytic phages on the ecology and evolution of bacteria in free-living communities, little is known about the role of lytic phages in host-associated microbiomes. We set out to characterize the impact of phages in the tomato phyllosphere, i.e., the bacteria associated with above-ground plant tissues, by transferring microbial communities from field-grown tomato plants to juvenile plants grown under mostly sterile conditions in either the presence or absence of their associated phage community. In three separate experiments, we found that the presence of phages affects overall bacterial abundance during colonization of new host plants. Furthermore, bacterial community analysis using 16S rRNA amplicon sequencing shows that phages significantly alter the relative abundance of dominant community members and can influence both within- and among-host diversity. These results underscore the importance of lytic phages in host-associated microbiomes and are relevant to microbiome transplantation approaches, as they suggest transferring non-bacterial components of the microbiome among hosts is likely to have a strong impact on growth of both the resident and donor microbiota.细菌与噬菌体（bacteriophage viruses，简称phages）之间的相互作用已被证实会影响病原菌的生长与毒力、微生物多样性，乃至生物地球化学循环。裂解性噬菌体（lytic phages）可通过侵染并裂解宿主细胞，对微生物群落内的细胞密度及竞争动态产生显著影响。尽管裂解性噬菌体对自由生活群落中细菌的生态学与进化过程具有明确影响，但学界对其在宿主相关微生物组（microbiome）中的作用仍知之甚少。本研究以番茄叶际（tomato phyllosphere，即附着于植物地上组织的细菌群落）为研究对象，将田间种植番茄的微生物群落移植到近乎无菌环境下培育的幼株中，并设置是否保留其伴随噬菌体群落的两组处理，以此表征噬菌体对番茄叶际的影响。在三组独立实验中，研究团队发现噬菌体的存在会影响新宿主植物定殖过程中的总细菌丰度。此外，通过16S rRNA扩增子测序（16S rRNA amplicon sequencing）开展的细菌群落分析显示，噬菌体会显著改变群落优势类群的相对丰度，并可对宿主内部及宿主间的微生物多样性产生影响。本研究结果凸显了裂解性噬菌体在宿主相关微生物组中的重要性，同时对微生物组移植策略具有参考价值：研究表明，在宿主间转移微生物组的非细菌组分，可能会对定植菌群与供体菌群的生长均产生显著影响。