ArticleApplied and environmental microbiology2013
New approaches indicate constant viral diversity despite shifts in assemblage structure in an Australian hypersaline lake.
Article in Applied and environmental microbiology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Viral diversity of brine and precipitated halite of Tuz Lake, an inland hypersaline lake in Turkey.Archives of virology · 2025Article
- Arctic Ocean virus communities and their seasonality, bipolarity, and prokaryotic associations.Nature communications · 2025Article
- Article
- Viral but not bacterial community successional patterns reflect extreme turnover shortly after rewetting dry soils.Nature ecology & evolution · 2023Article
- A Tale of Two Seasons: Distinct Seasonal Viral Communities in a Thermokarst Lake.Microorganisms · 2023Article
- Microbiome and metagenomic analysis of Lake Hillier Australia reveals pigment-rich polyextremophiles and wide-ranging metabolic adaptations.Environmental microbiome · 2022Article
- Isolation of a virus causing a chronic infection in the archaeal model organismProceedings of the National Academy of Sciences of the United States of America · 2022Article
- Role of Phylogenetic Structure in the Dynamics of Coastal Viral Assemblages.Applied and environmental microbiology · 2021Article
- Article
- JMT-1: a novel, spherical lytic halotolerant phage isolated from Yuncheng saline lake.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2018Article
- Characterization of ecologically diverse viruses infecting co-occurring strains of cosmopolitan hyperhalophilic Bacteroidetes.The ISME journal · 2018Article
- Temporal dynamics of uncultured viruses: a new dimension in viral diversity.The ISME journal · 2018Article
- Assessing Species Diversity Using Metavirome Data: Methods and Challenges.Computational and structural biotechnology journal · 2017Review
- Article
- Acidianus Tailed Spindle Virus: a New Archaeal Large Tailed Spindle Virus Discovered by Culture-Independent Methods.Journal of virology · 2016Article
- Metaviromics of Namib Desert Salt Pans: A Novel Lineage of Haloarchaeal Salterproviruses and a Rich Source of ssDNA Viruses.Viruses · 2016Article
- Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers.PloS one · 2016Article
- A novel Halomonas ventosae-specific virulent halovirus isolated from the Qiaohou salt mine in Yunnan, Southwest China.Extremophiles : life under extreme conditions · 2016Article
- Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem.The ISME journal · 2015Article
- Diversity of the cell-wall associated genomic island of the archaeon Haloquadratum walsbyi.BMC genomics · 2015Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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