Viromes As Genetic Reservoir for the Microbial Communities in Aquatic Environments: A Focus on Antimicrobial-Resistance Genes.
Viromes As Genetic Reservoir for the Microbial Communities in Aquatic Environments: A Focus on Antimicrobial-Resistance Genes.
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DOI：
10.3389/fmicb.2017.01095
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发表时间：
2017
影响因子：
5.2
通讯作者：
Mora D
中科院分区：
文献类型：
--
作者：
Colombo S;Arioli S;Neri E;Della Scala G;Gargari G;Mora D
尽管对从水生环境中分离出的病毒组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。病毒体中的细菌读数非常丰富，但这种遗传物质在水生微生物生态学中发挥作用的程度仍不清楚。为此，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，特别关注病毒体中蕴藏的微生物基因的识别。从兰布罗河（从泉水到米兰高度城市化地区）收集的水样中分离出病毒样颗粒。通过鸟枪法宏基因组测序对衍生的病毒组进行分析，寻找细菌基因的存在和相对丰度，特别关注那些涉及抗菌素耐药机制的基因。所有病毒组样本中均已鉴定出抗生素和重金属抗性基因，以及分配给细胞过程和信号传导的大量读数。病毒组数据与从同一样本中分离出的微生物组中鉴定的数据相比，揭示了功能类别及其相对丰度方面的差异。为了验证水生病毒种群在细菌基因转移中的作用，用低剂量的四环素扰动或不扰动水基中生态系统。 qPCR 检测获得的结果揭示了病毒组和微生物组中 tet 基因丰度的变化，凸显了病毒群体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 tet genes in the virome and microbiome highlighting a relevant role of viral populations in microbial gene mobilization.