ArticleViruses2019
Evaluation of Sequencing Library Preparation Protocols for Viral Metagenomic Analysis from Pristine Aquifer Groundwaters.
Article in Viruses, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Article
- High niche specificity and host genetic diversity of groundwater viruses.The ISME journal · 2024Article
- Evaluation of multiple displacement amplification for metagenomic analysis of low biomass samples.ISME communications · 2024Article
- The smallest in the deepest: the enigmatic role of viruses in the deep biosphere.National science review · 2023Review
- Combining Flow Cytometry and Metagenomics Improves Recovery of Metagenome-Assembled Genomes in a Cell Culture from Activated Sludge.Microorganisms · 2023Article
- Novel Virus Identification through Metagenomics: A Systematic Review.Life (Basel, Switzerland) · 2022Review
- Comprehensive Evaluation of RNA and DNA Viromic Methods Based on Species Richness and Abundance Analyses Using Marmot Rectal Samples.mSystems · 2022Article
- Assessment of Rapid MinION Nanopore DNA Virus Meta-Genomics Using Calves Experimentally Infected with Bovine Herpes Virus-1.Viruses · 2022Article
- Women in the European Virus Bioinformatics Center.Viruses · 2022Article
- Deep Impact of Random Amplification and Library Construction Methods on Viral Metagenomics Results.Viruses · 2021Article
- Viruses and Their Interactions With Bacteria and Archaea of Hypersaline Great Salt Lake.Frontiers in microbiology · 2021Article
- Article
- Temporal Variability of Virioplankton during aMicroorganisms · 2020Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Viral ecology of terrestrial habitats is yet-to be extensively explored, in particular the terrestrial subsurface. One problem in obtaining viral sequences from groundwater aquifer samples is the relatively low amount of virus particles. As a result, the amount of extracted DNA may not be sufficient for direct sequencing of such samples. Here we compared three DNA amplification methods to enrich viral DNA from three pristine limestone aquifer assemblages of the Hainich Critical Zone Exploratory to evaluate potential bias created by the different amplification methods as determined by viral metagenomics. Linker amplification shotgun libraries resulted in lowest redundancy among the sequencing reads and showed the highest diversity, while multiple displacement amplification produced the highest number of contigs with the longest average contig size, suggesting a combination of these two methods is suitable for the successful enrichment of viral DNA from pristine groundwater samples. In total, we identified 27,173, 5,886 and 32,613 viral contigs from the three samples from which 11.92 to 18.65% could be assigned to taxonomy using blast. Among these, members of the
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