Abstract
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.
Highlights
As the most abundant and ubiquitous biological entities, viruses influence host mortality and community structure, food web dynamics, and geochemical cycles [1, 2]
Though we acknowledge that a comparison of 16S rRNA gene microbial OTUs to >10 kb viral contig OTUs is an imperfect proxy for comparing the diversity of these groups, we find approximately 10 viral populations in the viral concentrate size fraction per host OTU in most samples, suggesting that planktonic virus diversity and host diversity scale approximately with abundance, which has previously been established to be approximately 10 : 1 in most environments (e.g., [31])
The San Diego (SD) study suggested stability of viral populations in that system, and we previously demonstrated through a reanalysis of the SD data that the most abundant viral populations from that study were dynamic [8], so it is possible that different sequencing and analytical methods would have revealed dynamics in archaeal and bacterial populations at the SD site as well
Summary
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. In a reanalysis of some of those data by our group using metagenomic assembly, we concluded that viruses were dynamic at the population (taxon) level in that system [7]. This result suggests that further analyses are necessary to determine whether archaeal populations tend to be dynamic or stable in hypersaline systems on short timescales
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
