Viral metagenomes of Lake Soyang, the largest freshwater lake in South Korea

Abstract

A high number of viral metagenomes have revealed countless genomes of putative bacteriophages that have not yet been identified due to limitations in bacteriophage cultures. However, most virome studies have been focused on marine or gut environments, thereby leaving the viral community structure of freshwater lakes unclear. Because the lakes located around the globe have independent ecosystems with unique characteristics, viral community structures are also distinctive but comparable. Here, we present data on viral metagenomes that were seasonally collected at a depth of 1 m from Lake Soyang, the largest freshwater reservoir in South Korea. Through shotgun metagenome sequencing using the Illumina MiSeq platform, 3.08 to 5.54-Gbps of reads per virome were obtained. To predict the viral genome sequences within Lake Soyang, contigs were constructed and 648 to 1,004 putative viral contigs were obtained per sample. We expect that both viral metagenome reads and viral contigs would contribute in comparing and understanding of viral communities among different freshwater lakes depending on seasonal changes.

Comparison of ultrafiltration and iron chloride flocculation in the preparation of aquatic viromes from contrasting sample types

“…We compared two approaches for concentrating and purifying viruses, iron chloride flocculation and ultrafiltration, and applied them to four water matrices for the preparation of high-quality viral DNA extracts for metagenomics. Both concentration methods are widely used for virome studies ( Brum et al, 2015 ; Beaulaurier et al, 2020 ; Gregory et al, 2019 ; Moon et al, 2020a ; Moon et al, 2020b ; Aguirre de Carcer et al, 2015 ; Roux et al, 2016a ; Breitbart et al, 2002 ; Breitbart et al, 2003 ; Petrovich et al, 2019 ; Mohiuddin & Schellhorn, 2015 ; Skvortsov et al, 2016 ; Roux et al, 2012 ), but there has not been a systematic study evaluating stepwise performance and viral recovery through the concentration and purification processes across multiple matrices. As our end goal was the preparation of amplification-free sequencing libraries suitable for both short and long read sequencing, the ideal preparation method would generate sufficient mass of high molecular weight DNA for these purposes.…”

“…Non-viral DNA contamination was evaluated by the 16S rRNA gene concentration factor and the virus to 16S rRNA enrichment. 18S rRNA gene concentrations were not assessed in this study, as previous studies have demonstrated greater contamination of prokaryotic DNA in viromes as compared to eukaryotic DNA ( Hurwitz et al, 2013 ; Kleiner, Hooper & Duerkop, 2015 ; Moon et al, 2020b ). Both methods performed similarly at removing 16S rRNA gene copies, but the greater ability to concentrate viruses with the ultrafiltration steps resulted in a greater enrichment of viral genomes relative to 16S rRNA gene copies.…”

“…In this study, we evaluated the impact of sample matrix on the performance of two commonly applied concentration methods, ultrafiltration and iron chloride flocculation. Ultrafiltration and iron chloride flocculation were selected because they have been widely used for marine and freshwater virome studies ( Brum et al, 2015 ; Hurwitz et al, 2013 ; Beaulaurier et al, 2020 ; Gregory et al, 2019 ; Moon et al, 2020a ; Moon et al, 2020b ; Aguirre de Carcer et al, 2015 ). Using virus spike-and-recovery experiments, a step-wise assessment of each method was performed for four contrasting sample types that varied in their solids content and salinity: wastewater influent (i.e., raw sewage), wastewater secondary effluent (i.e., post carbon removal, pre-disinfection), river water, and seawater.…”

A Snapshot of the Global Drinking Water Virome: Diversity and Metabolic Potential Vary with Residual Disinfectant Use

“…It is therefore unsurprising that only 2% of the viral populations in the drinking water distribution systems samples analyzed in our study had a taxonomic assignment. In addition to the lack of drinking water virome studies to date, groundwater and surface water, which are typically used as source waters for drinking water production, also have been less frequently studied than marine aquatic environments (Kallies et al, 2019;Kothari et al, 2021;Malki et al, 2020;Moon et al, 2020;Paez-Espino et al, 2016;Roux et al, 2012;Skvortsov et al, 2016).…”

Comparison of ultrafiltration and iron chloride flocculation in the preparation of aquatic viromes from contrasting sample types

“…Ultrafiltration and iron chloride flocculation were selected because they have been widely used for marine and freshwater virome studies (7,24,(36)(37)(38)(39)(40). Using virus spike-and-recovery experiments, a step-wise assessment of each method was performed for four contrasting sample types that varied in their solids content and salinity: wastewater influent (i.e., raw sewage), wastewater secondary effluent (i.e., post carbon removal, pre-disinfection), river water, and seawater.…”