Abstract
In this study, we analyzed viral metagenomes (viromes) in the sedimentary habitats of three geographically and geologically distinct (hado)pelagic environments in the northwest Pacific; the Izu-Ogasawara Trench (water depth = 9,760 m) (OG), the Challenger Deep in the Mariana Trench (10,325 m) (MA), and the forearc basin off the Shimokita Peninsula (1,181 m) (SH). Virus abundance ranged from 106 to 1011 viruses/cm3 of sediments (down to 30 cm below the seafloor [cmbsf]). We recovered viral DNA assemblages (viromes) from the (hado)pelagic sediment samples and obtained a total of 37,458, 39,882, and 70,882 sequence reads by 454 GS FLX Titanium pyrosequencing from the virome libraries of the OG, MA, and SH (hado)pelagic sediments, respectively. Only 24−30% of the sequence reads from each virome library exhibited significant similarities to the sequences deposited in the public nr protein database (E-value <10−3 in BLAST). Among the sequences identified as potential viral genes based on the BLAST search, 95−99% of the sequence reads in each library were related to genes from single-stranded DNA (ssDNA) viral families, including Microviridae, Circoviridae, and Geminiviridae. A relatively high abundance of sequences related to the genetic markers (major capsid protein [VP1] and replication protein [Rep]) of two ssDNA viral groups were also detected in these libraries, thereby revealing a high genotypic diversity of their viruses (833 genotypes for VP1 and 2,551 genotypes for Rep). A majority of the viral genes predicted from each library were classified into three ssDNA viral protein categories: Rep, VP1, and minor capsid protein. The deep-sea sedimentary viromes were distinct from the viromes obtained from the oceanic and fresh waters and marine eukaryotes, and thus, deep-sea sediments harbor novel viromes, including previously unidentified ssDNA viruses.
Highlights
Viruses represent the most abundant number of biological components by far in aquatic ecosystems [1], and viral ecology in environments such as oceanic surface waters, coastal, and fresh waters have been intensively investigated [2]
Most of the potentially virus-originating sequences from the deep-sea shallow subseafloor sediments were similar to sequences from single-stranded DNA (ssDNA) viruses, such as the families of Microviridae, Circoviridae, Nanoviridae, and Geminiviridae (Fig. 3B)
These ssDNA viruses have been isolated only from terrestrial environments; recently, both isolation and metagenomic studies have revealed the existence of ssDNA viruses in marine environments
Summary
Viruses represent the most abundant number of biological components by far in aquatic ecosystems [1], and viral ecology in environments such as oceanic surface waters, coastal, and fresh waters have been intensively investigated [2]. Viral activity in aquatic environments is known to regulate the dynamics and mortality of the host microbial community [3,4,5,6,7,8,9]. Viruses have been noted as natural genetic vectors for horizontal gene transfer events [13,14]. Despite their ecological and evolutionary importance, our current knowledge of marine viruses is restricted to the euphotic zone of the habitat, which represents only a limited portion of the oceanic biosphere [15]. Viral ecology in sedimentary environments has been poorly studied, the seafloor sediments cover almost two-thirds of the Earth’s surface and serve as highly vital and dynamic interface habitats in global ocean biogeochemical cycles [16]
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