Metagenomic Exploration of Viruses throughout the Indian Ocean

Abstract

The characterization of global marine microbial taxonomic and functional diversity is a primary goal of the Global Ocean Sampling Expedition. As part of this study, 19 water samples were collected aboard the Sorcerer II sailing vessel from the southern Indian Ocean in an effort to more thoroughly understand the lifestyle strategies of the microbial inhabitants of this ultra-oligotrophic region. No investigations of whole virioplankton assemblages have been conducted on waters collected from the Indian Ocean or across multiple size fractions thus far. Therefore, the goals of this study were to examine the effect of size fractionation on viral consortia structure and function and understand the diversity and functional potential of the Indian Ocean virome. Five samples were selected for comprehensive metagenomic exploration; and sequencing was performed on the microbes captured on 3.0-, 0.8- and 0.1 µm membrane filters as well as the viral fraction (<0.1 µm). Phylogenetic approaches were also used to identify predicted proteins of viral origin in the larger fractions of data from all Indian Ocean samples, which were included in subsequent metagenomic analyses. Taxonomic profiling of viral sequences suggested that size fractionation of marine microbial communities enriches for specific groups of viruses within the different size classes and functional characterization further substantiated this observation. Functional analyses also revealed a relative enrichment for metabolic proteins of viral origin that potentially reflect the physiological condition of host cells in the Indian Ocean including those involved in nitrogen metabolism and oxidative phosphorylation. A novel classification method, MGTAXA, was used to assess virus-host relationships in the Indian Ocean by predicting the taxonomy of putative host genera, with Prochlorococcus, Acanthochlois and members of the SAR86 cluster comprising the most abundant predictions. This is the first study to holistically explore virioplankton dynamics across multiple size classes and provides unprecedented insight into virus diversity, metabolic potential and virus-host interactions.

Genome of a SAR116 bacteriophage shows the prevalence of this phage type in the oceans

“…These seven viromes, all from the ocean surface, included four from the Indian Ocean (13) and three from the Pacific Ocean (Table 1 and Table S3; see SI Materials and Methods for the selection process, brief description, and sequence processing). Each read from the selected viromes was used as a query in BLASTN analyses against a genome database that included HMO-2011 and 4,541 other viruses and was assigned to a single best-matching reference genome.…”

“…Recent metagenomic studies of the oceans have revealed the numerous novel genetic repertoires of marine viromes (8)(9)(10)(11)(12)(13)(14). However, most genome fragments in these viromes cannot be categorized into any known viral group (8,9,13,14).…”

“…However, most genome fragments in these viromes cannot be categorized into any known viral group (8,9,13,14). Because most marine viruses are believed to be phages (15), a more thorough understanding of the ecological and evolutionary roles of marine viruses and a better interpretation of the rapidly increasing virome sequences require the isolation and genomic analysis of individual viruses, especially phages infecting diverse marine bacterioplankton.…”

Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone

“…However, a direct comparison of protein-coding gene content between fractions was not presented, and high-resolution taxonomic surveys from these analyses are not available. Although such comparisons identified functional differences in size-fractionated picoeukaryote ) and viral (Williamson et al, 2012) communities, to the best of our knowledge only two other studies Smith et al 2013), focusing on temperate sites in the North Pacific, have directly compared microbial (Bacteria and Archaea) functional gene content between filter size fractions. Here, we use metagenome and 16S rRNA gene amplicon sequencing to compare microbial communities from two size classes in the ETSP OMZ.…”

Using Signature Genes as Tools To Assess Environmental Viral Ecology and Diversity

“…As an example, we have generated a g23 tree that combines several viral metagenomics data sets from freshwater environments (Lake Pavin, France [102] and El Berbera Saharan pond [107]) and ma-rine environments (M6O1K, Indian Ocean [108] and LJ12S and LJ26S, Pacific Ocean [109]) with isolated T4-like phages (Fig. 1).…”