The study of natural archaeal assemblages requires community context, namely, a concurrent assessment of the dynamics of archaeal, bacterial, and viral populations. Here, we use filter size-resolved metagenomic analyses to report the dynamics of 101 archaeal and bacterial OTUs and 140 viral populations across 17 samples collected over different timescales from 2007–2010 from Australian hypersaline Lake Tyrrell (LT). All samples were dominated by Archaea (75–95%). Archaeal, bacterial, and viral populations were found to be dynamic on timescales of months to years, and different viral assemblages were present in planktonic, relative to host-associated (active and provirus) size fractions. Analyses of clustered regularly interspaced short palindromic repeat (CRISPR) regions indicate that both rare and abundant viruses were targeted, primarily by lower abundance hosts. Although very few spacers had hits to the NCBI nr database or to the 140 LT viral populations, 21% had hits to unassembled LT viral concentrate reads. This suggests local adaptation to LT-specific viruses and/or undersampling of haloviral assemblages in public databases, along with successful CRISPR-mediated maintenance of viral populations at abundances low enough to preclude genomic assembly. This is the first metagenomic report evaluating widespread archaeal dynamics at the population level on short timescales in a hypersaline system. 1. Introduction As the most abundant and ubiquitous biological entities, viruses influence host mortality and community structure, food web dynamics, and geochemical cycles [1, 2]. In order to better characterize the potential influence that viruses have on archaeal evolution and ecology, it is important to understand the coupled dynamics of viruses and their archaeal hosts in natural systems. Although previous studies have demonstrated dynamics in virus-host populations, most of these studies have focused on bacterial hosts, often restricted to targeted groups of virus-host pairs, and little is known about archaeal virus-host dynamics in natural systems. Community-scale virus-host analyses have often been based on low-resolution measurements of the whole community, relying on techniques such as denaturing gradient gel electrophoresis (DGGE), pulsed-field gel electrophoresis (PFGE), and microscopic counts (e.g., [3–5]). One exception is a study that examined viral and microbial dynamics through single read-based metagenomic analyses in four aquatic environments, including an archaea-dominated hypersaline crystallizer pond [6]. In that work, it was proposed
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