摘要

尽管从水生环境中分离的病毒的研究变得越来越频繁，但其中大多数仅限于病毒分类学的表征。细菌在viromes中的读数很丰富，但这种遗传物质在水生微生物学生态学中的作用程度仍不清楚。为了达到这个目的，我们开发了一种有用的方法来表征水生环境中的病毒和微生物群落，特别关注鉴定病毒中含有的微生物基因。从横跨兰布罗河收集的水样，从春季到高度都市化的米兰地区分离出病毒样颗粒。通过鸟枪法宏基因组测序分析衍生的病毒，寻找细菌基因的存在，相对丰富，特别关注那些涉及抗微生物剂抗性机制的基因。所有维氏菌样品中已经鉴定出抗生素和重金属抗性基因，并具有高丰度的分配给细胞过程和信号传导的读数。 Virome数据与从同一样本中分离出的微生物组中鉴定出的数据相比，显示出功能类别及其相对丰度方面的差异。为了验证水生病毒群体在细菌基因转移中的作用，用低剂量的四环素使水基细胞受到扰动或不受扰动。通过qPCR分析获得的结果揭示了virome和微生物组中tet基因丰度的变化，突出了病毒种群在微生物基因动员中的相关作用。

Despite studies of viromes isolated from aquatic environments are becoming increasingly frequent, most of them are limited to the characterization of viral taxonomy. Bacterial reads in viromes are abundant but the extent to which this genetic material is playing a role in the ecology of aquatic microbiology remains unclear. To this aim, we developed of a useful approach for the characterization of viral and microbial communities of aquatic environments with a particular focus on the identification of microbial genes harbored in the viromes. Virus-like particles were isolated from water samples collected across the Lambro River, from the spring to the high urbanized Milan area. The derived viromes were analyzed by shotgun metagenomic sequencing looking for the presence, relative abundance of bacterial genes with particular focus on those genes involved in antimicrobial resistance mechanisms. Antibiotic and heavy metal resistance genes have been identified in all virome samples together with a high abundance of reads assigned to cellular processes and signaling. Virome data compared to those identified in the microbiome isolated from the same sample revealed differences in terms of functional categories and their relative abundance. To verify the role of aquatic viral population in bacterial gene transfer, water-based mesocosms were perturbed or not perturbed with a low dose of tetracycline. The results obtained by qPCR assays revealed variation in abundance of tetgenes in the virome and microbiome highlighting a relevant role of viral populations in microbial gene mobilization.

https://www.frontiersin.org/articles/10.3389/fmicb.2017.01095/full