Metagenomic characterization of the viral community of the South Scotia Ridge

Abstract

Viruses are the most abundant biological entities in aquatic ecosystems and harbor an enormous genetic diversity. While their great influence on the marine ecosystems is widely acknowledged, current information about their diversity remains scarce. A viral metagenomic analysis of two surfaces and one bottom water sample was conducted from sites on the South Scotia Ridge (SSR) near the Antarctic Peninsula, during the austral summer 2016. The taxonomic composition and diversity of the viral communities were investigated and a functional assessment of the sequences was determined. Phylotypic analysis showed that most viruses belonging to the order Caudovirales, in particular, the family Podoviridae (41.92-48.7%), which is similar to the viral communities from the Pacific Ocean. Functional analysis revealed a relatively high frequency of phage-associated and metabolism genes. Phylogenetic analyses of phage TerL and Capsid_NCLDV (nucleocytoplasmic large DNA viruses) marker genes indicated that many of the sequences associated with Caudovirales and NCLDV were novel and distinct from known complete phage genomes. High Phaeocystis globosa virus virophage (Pgvv) signatures were found in SSR area and complete and partial Pgvv-like were obtained which may have an influence on host-virus interactions in the area during summer. Our study expands the existing knowledge of viral communities and their diversities from the Antarctic region and provides basic data for further exploring polar microbiomes.Importance In this study, we used high-throughput sequencing and bioinformatics analysis to analyze the viral community structure and biodiversity of SSR in the open sea near the Antarctic Peninsula. The results showed that the SSR viromes are novel, oceanic-related viromes and a high proportion of sequence reads was classified as unknown. Among known virus counterparts, members of the order Caudovirales were most abundant which is consistent with viromes from the Pacific Ocean. In addition, phylogenetic analyses based on the viral marker genes (TerL and MCP) illustrate the high diversity among Caudovirales and NCLDV. Combining deep sequencing and a random subsampling assembly approach, a new Pgvv-like group was also found in this region, which may a signification factor regulating virus-host interactions.

Saline lakes on the Qinghai-Tibet Plateau harbor unique viral assemblages mediating microbial environmental adaption

“…Only a few viral sequences of the six viromes could be assigned to a taxonomic rank, which is similar to previous viral metagenomic studies (Liang et al, 2019;Roux et al, 2016;Yang et al, 2019a). Caudovirales were abundant in QhL and XQL, which had low to moderate salinities (Ackermann, 1998).…”

“…Caudovirales were abundant in QhL and XQL, which had low to moderate salinities (Ackermann, 1998). This distribution is similar to other environments, including seawater, freshwater lakes, soil, and marine sediments (Fancello et al, 2013;Jasna et al, 2018;Kim et al, 2017;Parmar et al, 2018;Segobola et al, 2018;Skvortsov et al, 2016;Yang et al, 2019a;Zhang et al, 2021a;Zheng et al, 2021). However, viruses of DQL, a hypersaline lake, were unique and dominated by haloviruses (Figure 1).…”

“…Some NCLDVs were detected in XQL and QhL10, which had moderate salinities (Figure 1); most of these were similar to phycodnaviruses that infect microalgae (Figure S4B) (Schulz et al, 2020). This occurrence pattern is similar to marine viral communities (Yang et al, 2019a). The NCLDV supergroup is commonly abundant and diverse in oceans but can also be found in freshwater and associated with most major eukaryotic lineages; it might be the most important contributor to the control of primary production in hypersaline environments despite the low biomass (Schulz et al, 2020;Uritskiy et al, 2019).…”

“…The clean reads were picked from the raw reads by Novogene. Then, the high-quality paired-end reads were filtered using cutadapt and Perl scripts using the following conditions: (1) without N; (2) no more than 20% bases with a quality score less than 20; (3) no more than 30% bases with a quality score less than 30 Yang et al, 2019a).…”

Virioplankton assemblages from challenger deep, the deepest place in the oceans

“…The scores of the top High Scoring Pairs (HSPs) of virome A against virome B were then summed (S AB ). Ultimately, the similarity scores for each pair of viromes were normalized as the distance matrix (dis = 1-log(S AB )/log(S AA )) for performing PCoA and NMDS analysis using the Vegan R package (Dixon, 2003;Yang et al, 2019). Additionally, 10 viromes from epipelagic and bathypelagic South China Sea and 32 bathypelagic Pacific and Atlantic viromes were also downloaded for comparing (De Corte et al, 2019;Liang et al, 2019).…”