Sanguino Laura, Franqueville Laure, Vogel Timothy M, Larose Catherine
Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Ecole Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France.
Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Ecole Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France
FEMS Microbiol Ecol. 2015 May;91(5). doi: 10.1093/femsec/fiv046. Epub 2015 Apr 22.
The ecological pressure that viruses place on microbial communities is not only based on predation, but also on gene transfer. In order to determine the potential impact of viruses and transduction, we need a better understanding of the dynamics of interactions between viruses and their hosts in the environment. Data on environmental viruses are scarce, and methods for tracking their interactions with prokaryotes are needed. Clustered regularly interspaced short palindromic repeats (CRISPRs), which contain viral sequences in bacterial genomes, might help document the history of virus-host interactions in the environment. In this study, a bioinformatics network linking viruses and their hosts using CRISPR sequences obtained from metagenomic data was developed and applied to metagenomes from Arctic glacial ice and soil. The application of our network approach showed that putative interactions were more commonly detected in the ice samples than the soil which would be consistent with the ice viral-bacterial interactions being more dynamic than those in soil. Further analysis of the viral sequences in the CRISPRs indicated that Ralstonia phages might be agents of transduction in the Arctic glacial ice.
病毒对微生物群落施加的生态压力不仅基于捕食，还基于基因转移。为了确定病毒和转导的潜在影响，我们需要更好地了解环境中病毒与其宿主之间相互作用的动态。关于环境病毒的数据稀缺，因此需要追踪它们与原核生物相互作用的方法。成簇规律间隔短回文重复序列（CRISPRs）在细菌基因组中包含病毒序列，可能有助于记录环境中病毒-宿主相互作用的历史。在本研究中，开发了一种利用从宏基因组数据获得的CRISPR序列将病毒与其宿主联系起来的生物信息学网络，并将其应用于北极冰川冰和土壤的宏基因组。我们网络方法的应用表明，与土壤相比，在冰样本中更常检测到假定的相互作用，这与冰中病毒-细菌相互作用比土壤中更具动态性一致。对CRISPRs中病毒序列的进一步分析表明，罗尔斯通氏菌噬菌体可能是北极冰川冰中转导的媒介。
