Transporting Ocean Viromes: Invasion of the Aquatic Biosphere

RESEARCH ARTICLE Transporting Ocean Viromes: Invasion of the Aquatic Biosphere Yiseul Kim1*, Tiong Gim Aw2, Joan B. Rose1,2 1 Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America, 2 Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, United States of America * Abstract a11111 OPEN ACCESS Citation: Kim Y, Aw TG, Rose JB (2016) Transporting Ocean Viromes: Invasion of the Aquatic Biosphere. PLoS ONE 11(4): e0152671. doi:10.1371/ journal.pone.0152671 Editor: Senjie Lin, University of Connecticut, UNITED STATES Received: October 28, 2015 Accepted: March 17, 2016 Studies of marine viromes (viral metagenomes) have revealed that DNA viruses are highly diverse and exhibit biogeographic patterns. However, little is known about the diversity of RNA viruses, which are mostly composed of eukaryotic viruses, and their biogeographic patterns in the oceans. A growth in global commerce and maritime traffic may accelerate spread of diverse and non-cosmopolitan DNA viruses and potentially RNA viruses from one part of the world to another. Here, we demonstrated through metagenomic analyses that failure to comply with mid-ocean ballast water exchange regulation could result in movement of viromes including both DNA viruses and RNA viruses (including potential viral pathogens) unique to geographic and environmental niches. Furthermore, our results showed that virus richness (known and unknown viruses) in ballast water is associated with distance between ballast water exchange location and its nearest shoreline as well as length of water storage time in ballast tanks (voyage duration). However, richness of only known viruses is governed by local environmental conditions and different viral groups have different responses to environmental variation. Overall, these results identified ballast water as a factor contributing to ocean virome transport and potentially increased exposure of the aquatic bioshpere to viral invasion. Published: April 7, 2016 Copyright: © 2016 Kim et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: Data sets for all samples are available in the NCBI Short Read Archive under accession number SRP061842. Funding: This study was supported by the National Science Foundation, Partnerships for International Research and Education (OISE-0530174). Competing Interests: The authors have declared that no competing interests exist. Introduction Viruses are the most undiscovered and mysterious part of the biosphere. Their role as pathogenic entities is well recognized and the array of viral infections throughout the tree of life, including archaea, bacteria, and eukaryotes, is immense. However, we have only scratched the surface to reveal the global genetic diversity of viruses. This has limited our understanding of the ecological role of phages and other viral groups in biogeochemical cycling, as well as gene exchange [1]. Our knowledge of the viral predator-prey interactions is poor and viral life histories have not been well described. Viral-host specificity that was once considered a well-known biological principal is now being challenged, as even the concept of plant viral infections of humans and other animals is being proposed [2]. PLOS ONE | DOI:10.1371/journal.pone.0152671 April 7, 2016 1 / 18 Transporting Ocean Viromes During the past decade, metagenomics with dramatic evolution of sequencing technologies have revolutionized environmental virological studies and enabled the in-depth characterization of viral communities that would not have been possible with traditional methods. Since the first viral metagenome (virome) study by Breitbart et al. [3], research has demonstrated the feasibility of metagenomic approaches to examine viral communities in various complex environmental systems, mostly focused on natural aquatic environments, marine [4–10] and freshwater [11–17]. Among these, two global surveys of the ocean virome, which focused mainly on DNA viruses infecting bacteria, have suggested that marine viruses, particularly phages are highly diverse and can exhibit distinctive biogeographic patterns [4,10]. While these studies have revealed a diverse array of DNA phages (e.g., Microviridae, Myoviridae, Podoviridae, and Siphoviridae) in marine environments and that local environmental conditions play an important role in structuring their diversity, little is known about the diversity of RNA viruses and eukaryotic viruses in the oceans and their global transport and disease potential. Oceanic and coastal anthropogenic pollution is growing in part as a function of global commerce and increasing maritime traffic. It is estimated that ocean-going cargo vessels transport as high as 12 billion tons of ballast water each year, transferring the aquatic life from one part of the world to another [18]. Global movement of nonindigenous species within ballast tanks across natural barriers has threatened coastal ecosystem and biodiversity. The metazoan ballast invaders have been well studied and described since about the 1980s [19,20]. However, the mechanisms of microbial invasions are still unclear despite the potential of microorganisms to influence the ecological functioning of biological communities and ecosystems at a global scale [21]. Ruiz et al. [22] provided a hypothesis that the likelihood of invasions goes up with increasing inoculation concentration and that genetic diversity of the microbial component in ballast water including viruses must be examined to further understand the global transport of pathogens. More than a decade later, this call to improve our scientific knowledge has remained unanswered despite the advancement of metagenomics using high-throughput sequencing. Here, we integrated environmental virology, metagenomics, and bioinformatics to examine variation in virome composition of ballast water between geographic locations and demonstrated that ballast water moves around ocean viromes (including potential viral pathogens) from one part of the world to another. Materials and Methods Ethics Statement Access to the Port of Los Angeles/Long Beach (LA/LB) was gained by California State Lands Commission, and the ballast water sampling was approved by the captains of vessels. Access to the Port of Singapore was gained by Port of Singapore Authority, and the ballast water sampling was approved by an anonymous shipping company and by the captains of vessels. At both locations, the sampling was conducted under the supervision of the captains and chief officers of vessels. Samples collected from the Port of Singapore were transported to Michigan State University (MSU) with the import permit approved by United States Centers for D (...truncated)