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首页> 外文期刊>Applied Microbiology >New Approaches Indicate Constant Viral Diversity despite Shifts in Assemblage Structure in an Australian Hypersaline Lake
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New Approaches Indicate Constant Viral Diversity despite Shifts in Assemblage Structure in an Australian Hypersaline Lake

机译：尽管澳大利亚高盐湖的集结结构发生了变化，但新方法仍显示出恒定的病毒多样性

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It is widely stated that viruses represent the most significant source of biodiversity on Earth, yet characterizing the diversity of viral assemblages in natural systems remains difficult. Viral diversity studies are challenging because viruses lack universally present, phylogenetically informative genes. Here, we developed an approach to estimate viral diversity using a series of functional and novel conserved genes. This approach provides direct estimates of viral assemblage diversity while retaining resolution at the level of individual viral populations in a natural system. We characterized viral assemblages in eight samples from hypersaline Lake Tyrrell (LT), Victoria, Australia, using 39,636 viral contigs. We defined viral operational taxonomic units (OTUs) in two ways. First, we used genes with three different functional predictions that were abundantly represented in the data set. Second, we clustered proteins of unknown function based on sequence similarity, and we chose genes represented by three clusters with numerous members to define OTUs. In combination, diversity metrics indicated between 412 and 735 sampled populations, and the number of populations remained relatively constant across samples. We determined the relative representation of each viral OTU in each sample and found that viral assemblage structures correlate with salinity and solution chemistry. LT viral assemblages were near-replicates from the same site sampled a few days apart but differed significantly on other spatial and temporal scales. The OTU definition approach proposed here paves the way for metagenomics-based analyses of viral assemblages using ecological models previously applied to bacteria and archaea.
机译：人们普遍认为，病毒是地球上生物多样性的最重要来源，但要表征自然系统中病毒组合的多样性仍然很困难。病毒多样性研究具有挑战性，因为病毒缺乏普遍存在的系统发育信息基因。在这里，我们开发了一种使用一系列功能和新颖的保守基因估算病毒多样性的方法。这种方法可以直接估算病毒的多样性，同时在自然系统中保持单个病毒种群水平的分辨率。我们使用39,636个病毒重叠群，对来自澳大利亚维多利亚州超盐湖泰瑞尔（LT）的八个样本中的病毒组合进行了表征。我们通过两种方式定义了病毒操作分类单位（OTU）。首先，我们使用具有三种不同功能预测的基因，这些预测在数据集中得到了充分的体现。其次，我们基于序列相似性将功能未知的蛋白质聚类，并选择由具有多个成员的三个聚类代表的基因来定义OTU。总体而言，多样性指标表明在412个到735个样本人口之间，并且样本之间的人口数量保持相对恒定。我们确定了每个样品中每个病毒OTU的相对表示，发现病毒组装结构与盐度和溶液化学相关。 LT病毒集合体是从几天间隔采样的同一位置复制的，但在其他时空尺度上差异很大。本文提出的OTU定义方法为使用以前应用于细菌和古细菌的生态模型为基于宏基因组学的病毒组合分析铺平了道路。

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