Viral Diversity and Its Relationship With Environmental Factors at the Surface and Deep Sea of Prydz Bay, Antarctica

Abstract

A viral metagenomic analysis of five surface and two bottom water (878 meters below surface, mbs, and 3,357 mbs) samples from Prydz Bay, was conducted during February–March 2015. The results demonstrated that most of the DNA viruses were dsDNA viruses (79.73–94.06%, except at PBI1, 37.51%). Of these, Caudovirales (Siphoviridae, Myoviridae, and Podoviridae) phages were most abundant in surface seawater (67.67–71.99%), while nucleocytoplasmic large DNA viruses (NCLDVs) (Phycodnaviridae, Mimiviridae, and Pandoraviridae accounted for >30% of dsDNA viruses) were most abundant in the bottom water (3,357 mbs). Of the ssDNA viruses, Microviridae was the dominant family in PBI2, PBI3, PBOs, and PBI4b (57.09–87.55%), while Inoviridae (58.16%) was the dominant family in PBI1. Cellulophaga phages (phi38:1 and phi10:1) and Flavobacterium phage 11b, infecting the possible host strains affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes, were abundant in surface water dsDNA viromes. The long contig (PBI2_1_C) from the viral metagenomes were most similar to the genome architectures of Cellulophaga phage phi10:1 and Flavobacterium phage 11b from the Arctic Ocean. Comparative analysis showed that the surface viral community of Prydz Bay could be clearly separated from other marine and freshwater environments. The deep sea viral community was similar to the deep sea viral metagenome at A Long-term Oligotrophic Habitat Assessment Station (ALOHA, at 22°45′N, 158°00′W). The multivariable analysis indicated that nutrients probably played an important role in shaping the local viral community structure. This study revealed the preliminary characteristics of the viral community in Prydz Bay, from both the surface and the deep sea. It provided evidence of the relationships between the virome and the environment in Prydz Bay and provided the first data from the deep sea viral community of the Southern Ocean.

Temporal Variability of Virioplankton during a Gymnodinium catenatum Algal Bloom

“…In addition, the most dominant dsDNA viruses were from the order Caudovirales. Previous viral metagenome studies on marine environments have also found a high abundance of Caudovirales [53,54]. Our analysis indicated that the relative abundance of Caudovirales increased from the pre-bloom stage (YT1 and YT3) to the growth and peak stages (YT4 to YT6); it reached its highest values at YT5 (50.6%) and subsequently decreased during the post-bloom stage (YT8, YT10, and YT11) ( Figure 1).…”

“…Similarly, the abundance of the other members (such as Phycodnaviridae and Microviridae) showed a dramatic increase during the G. catenatum bloom and were enriched (with abundances of more than 10%) at the end of bloom. Siphoviridae, Podoviridae, and Myoviridae were the major members, which is not surprising because these species have been found to be the most abundant groups of viruses in the aquatic environment [54,56,57]. Previous metagenome investigations of environmental samples have shown ubiquitous dsDNA eukaryotic viruses (such as Iridoviridae, Phycodnaviridae, Mimiviridae, Poxviridae, and Polydnaviridae) in the DNA viromes.…”

“…In our study, only Phycodnaviridae and Mimiviridae were detected, and they accounted for a relatively low proportion of the whole. The main reason for this was likely our choice of sampling sites: Gong et al [54] used samples from deep sea areas, whereas our samples were collected near shore in a phycosphere environment. The relatively higher abundance of Phycodnaviridae and Mimiviridae in this work indicates that they were the main species associated with G. catenatum and perhaps participated in the decline of algal bloom [58][59][60][61].…”

“…In a previous study, Hwang et al [56] found that Pelagibacter phage HTVC010P, Ostreococcus lucimarinus OIV5/OIV1, and Roseobacter phage SIO1 were the most common species in Goseong Bay. Gong et al [54] suggested that Cellulophaga phages, Pseudomonas phages, and Vibrio phages were responsible for the high percentage of surface water viromes in Prydz Bay. In Chile Bay, an integrative omics study demonstrated that the phage community associated with bacterioplankton was dominated by a new Pseudoalteromonas virus (PpCBA) during a diatom-dominated phytoplankton bloom [64].…”

Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

“…The case is well illustrated by the families Microviridae and Leviviridae, which have received relatively little attention from the ICTV (i.e., two subfamilies, six genera and 21 species versus two genera and four species, respectively). Environmental studies have indicated that the family Microviridae contains at least five unclassified subfamilies [40][41][42][43][44][45][46][47]. Recently, Callanan et al [48] predicted 331 species and 247 genera among the single-stranded RNA phages, potentially leading to a significant expansion of the family Leviviridae.…”