Comparative Metagenomics of Viral Assemblages Inhabiting Four Phyla of Marine Invertebrates

Brent M Gudenkauf,Ian Hewson

doi:10.3389/fmars.2016.00023

Abstract

Viruses are the most abundant biological entities on Earth, killing 10-20% of oceanic biomass each day. However, despite their ecological importance, viruses inhabiting many echinoderms, cnidarians, urochordates, and marine arthropods have not been investigated with significant breadth. We conducted a broad survey of the viral assemblages inhabiting these hosts through viral metagenomics and phylogenetic analysis. Results indicate that different invertebrate groups harbor distinct viral assemblages. Interestingly, however, no significant difference is observed between the viral assemblages of echinoderms and arthropods. These similarities and differences may be due to cellular, immunological, geographical, and ecological differences amongst host phyla, although mechanistic determination is beyond the purview of this work. Additionally, we present evidence of the detection of several viral families that have not yet been observed in these hosts. Finally, we confirm the result of previous investigation that method of library construction significantly biases metagenomic results by altering the representation of of ssDNA and dsDNA viral genomes.

Highlights

Viruses are the most abundant biological entities on Earth, with an estimated 1030 viruses in the oceans (Suttle, 2007)
Recent viral metagenomic studies have exposed novel families of invertebrate viruses (e.g., Ng, 2010; Rosario et al, 2011, 2012; Dunlap et al, 2013). This technique may be used as Comparative Metagenomics of Invertebrate Viruses viral surveillance (Ng, 2010), or as a starting point for further investigation into microbe–microbe interactions, microbe–host interactions, pathogenesis, and disease diagnosis
Between 0.06 and 88.03% matched viral genomes, with the remaining sequences corresponding to bacterial, archaeal, or eukaryotic genome fragments. This is similar to the results of previous studies that utilized similar viral genome isolation protocols, and likely results from DNA released from host, bacterial, and/or archaeal cells during the tissue homogenization process (Hewson et al, 2011a, 2013; Gudenkauf et al, 2014)

Summary

Introduction

Viruses are the most abundant biological entities on Earth, with an estimated 1030 viruses in the oceans (Suttle, 2007). Surface seawater typically harbors 107 viral particles mL−1, with fewer viruses at depth (105 mL−1), and greater abundance in algal blooms (Wommack and Colwell, 2000) These viruses cause mortality in 10–20% of oceanic biomass each day (Munn, 2006; Suttle, 2007). Viruses associated with metazoan host microbiomes include viruses that infect hosts (i.e., pathogens, neutral-effect viruses, and endogenous viruses), and viruses that infect non-metazoan components, including bacterial, archaeal, and eukaryotic microbial constituents Despite their significance as agents of mortality, investigation of viruses associated with marine invertebrates has historically been limited. Viruses of many ecologically important marine invertebrate faunae have not yet been investigated; Entire phyla lack described viruses (Suttle, 2005). Metaviromics provides a strong starting point for future study of viral–host relationships

Methods

Results

Conclusion