Spatial and temporal dynamics of virus occurrence in two freshwater lakes captured through metagenomic analysis

Abstract

Viruses are the most abundant microorganisms in the aquatic environment, yet the identification of viruses and assessing their diversity still remains a challenge. Here, we present a robust, routinely usable approach to identify viruses from two freshwater lakes of the lower Great Lakes region, Lake Ontario, and Lake Erie. We collected water samples from six different beaches of these two lakes during the summer period of 2012 and 2013, and separated into three distinct fractions, namely a bacterial fraction, a virus like particle (VLP) fraction, and a fraction of eDNA (environmental DNA). DNA extracted from all three fractions was sequenced and bioinformatic analyses of sequences revealed the presence of viruses from major viral families. The analyzed viral sequences were dominated by bacteriophage sequences, but also contained many plant and animal viruses. Within the context of this study, geographic location does not appear to have a major impact on viral abundance and diversity, since virome composition of both lakes were similar. Comparative analyses between eDNA and viral fractions showed that eDNA can be used in combination with VLP fractions to identify viruses from the environment.

Geospatial distribution of viromes in tropical freshwater ecosystems

“…In this geospatial metagenomics study, we identified virome abundance and diversity in different reservoirs and tributaries. Due to insufficient viral genome sequencing information in the NCBI, 41.4% of the virome genome had no significant hits and bacteriophages were the most abundant organisms in the matrix, which is in agreement with previous studies of surface water viromes (Mohiuddin and Schellhorn, 2015;Skvortsov et al, 2016;Tseng et al, 2013). Phages, considered to be the most abundant and diverse biological entities on Earth, play an important role in shaping biological and geochemical processes at the global scale (Díaz-Muñoz and Koskella, 2014).…”

Comparative study of viromes from freshwater samples of the Ile-Balkhash region of Kazakhstan captured through metagenomic analysis

“…Nucleic acids were isolated from the collected samples in the amount of 2.5-4 lg per 1 L water sample, which corresponds to the average number of isolated nucleic acids from the same volume [29]. Considering that rather small input amounts of ng are sufficient for sequencing of nucleic acid with Illumina HiSeq [30], in further studies it will be possible to reduce the volume of water samples in order to decrease the time and cost of isolation of nucleic acids.…”

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

“…Instead, virus-focused metagenomics studies either concentrate virus-genomes via their virions or enrich for double-stranded RNA that is a broadly shared feature of virus replication. The virus-enriched nucleic acids are then sequenced by shotgun metagenomics methods (Bibby 2013) for the detection of viruses in environmental material, including marine water (Schmidt et al 2014), fresh water (Mohiuddin & Schellhorn 2015), soil (Ballaud et al 2016), crop plants (Aw et al 2016), native plants and weed plant species (Blouin et al 2016). We remain unable to recommend a single molecular approach to comprehensively target all of the diversity of viral material for metabarcoding studies in an unbiased manner, i.e.…”