Abstract
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.
Highlights
Studies of the environments through metagenomics analysis are becoming increasingly frequent and the development of instruments, techniques and databases makes the study and the characterization of viral communities with a shotgun metagenomics approach more and more informative
We developed a method for the comprehensive characterization of viral and microbial communities by shotgun metagenomics focusing the attention on the presence and relative abundance of microbial gene sequences in viromes isolated from the Lambro River flow, from the spring to the high urbanized/industrialized Milan area
The sample A was characterized by the largest abundance of bacterial reads (93%), and only 7% were identified as viral reads
Summary
Studies of the environments through metagenomics analysis are becoming increasingly frequent and the development of instruments, techniques and databases makes the study and the characterization of viral communities with a shotgun metagenomics approach more and more informative. Water is an ideal medium for bacterial life, characterized by accessible dissolved nutrients, as well as protection from desiccation and UV light. In this context, the high frequency of encounters between bacteria and bacteriophages strongly favors, through transduction, the Viromes As Genetic Reservoir for the Microbial Communities mobilization of genetic material. The extent to which these viromeassociated microbial genes are accessible to members of the environmental microbiota remains unclear. In this context, those factors triggering the mobilization and spreading of microbial genes by the viral communities in water environments are still processes not completely understood. A part from the water environments, the role of viruses in mobilization of ARGs in the human and mice microbiota after exposure to antibiotics has been recently experimentally documented, showing that the treatment with antibiotics leads to an increase in the ARGs abundance in the virome (Fancello et al, 2013; Modi et al, 2013; Abeles et al, 2015)
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