Metagenomic analysis of virus diversity and relative abundance in a eutrophic freshwater harbour

Abstract

Aquatic viruses have been extensively studied over the past decade, yet fundamental aspects of freshwater virus communities remain poorly described. Our goal was to characterize particle-associated virus communities seasonally and spatially in a freshwater harbour. Community DNA was extracted from water samples and sequenced on an Illumina HiSeq platform. Assembled contigs were annotated as belonging to the virus families Caudovirales, Mimiviridae, Phycodnaviridae, and virophages (Lavidaviridae), or to other groups of undefined viruses. Diverse Mimiviridae contigs were detected in the samples, but the two sites contained distinct Mimiviridae communities. Virophages were often the most abundant group, and discrete virophage taxa were remarkably stable across sites and dates despite fluctuations in Mimiviridae community composition. Caudovirales were present at low abundances in most samples, contrasting other studies of freshwater environments. Similarly, Phycodnaviridae abundances were surprisingly low in all samples despite the harbour’s capacity to support high algal biomass during the summer and autumn months, suggesting that Mimiviridae are the dominant algae-infecting viruses in this system. Overall, our findings provided insights into freshwater virus community assemblages by expanding the documented diversity of freshwater virus communities, highlighting the potential ecological importance of virophages, and revealing distinct communities over small spatial scales.

Comparing the diversity and relative abundance of free and particle-associated aquatic viruses

“…This leads to a higher likelihood of annotating Caudovirales sequences as originating from discrete taxa compared to virophage sequences. Our observations of disproportionally high virophage abundances compared to reference databases aligns with previous observations of their high relative abundances in larger, cell-associated size fractions (15,17), and reinforces the notion that sequence annotations are only as good as the databases from which they are derived.…”

“…Compared to prokaryote and eukaryote sequences, virus sequences are underrepresented in reference databases influencing the reported diversity of viruses in metagenomes (discussed in detail in C. N. Palermo et al (15)). This inevitably leads to a large portion of sequences in environmental metagenomes remaining unclassified and being discarded at the annotation step in the data processing pipeline.…”

“…In particular, metagenomic data has rapidly expanded virus sequence databases and the documented diversity of viruses (7)(8)(9)(10)(11)(12)(13)(14)(15). Early metagenomic studies revealed the incredible diversity of viruses on a local scale, but limited global diversity, with the majority of viruses present at low abundances in the environment but acting as seedbanks for future infection (16).…”

“…We previously studied virus communities in Hamilton Harbour (15), an urban eutrophic freshwater embayment of Lake Ontario, Canada that is well-studied due to its economic importance and long-term remediation efforts. We mined viral sequences from metagenome libraries derived from > 0.22 µm size fractions originally collected to study cellular communities.…”

Seasonal Regime Shift in the Viral Communities of a Permafrost Thaw Lake

“…Viruses are major players in aquatic ecosystem function [ 22 , 23 , 24 ], including in freshwater environments [ 25 , 26 , 27 , 28 ]. They catalyze the exchange of genes between their hosts [ 29 ], which can affect a community’s adaptive responses.…”