Global shipping activities transport 12 billion tons of water across regions each year. This so called ballast water contains a variety of biological materials and has been considered to transfer non−native species between biomes, resulting in potential ecological, economic, and public health problems in major ports worldwide. Despite the large amount of ballast water transported around the globe and its negative impact on native ecosystems, relatively little attention has been paid to viral invasions via ballast water due to technical challenges in detecting the wide range of viruses. The limitations of virus discovery using traditional approaches can now be overcome with the emergence of metagenomics, which enables unprecedented views of viral diversity and functions. This dissertation brought together environmental virology, metagenomics, and bioinformatics for the first time in order to examine taxonomic composition and diversity of viruses in ballast and harbor waters collected from a freshwater system, and to investigate global transport of viruses through ballast water and effect of engineered, management, and environmental parameters associated with ballast water on ocean viruses. Viral communities in ballast water in the Great Lakes were examined due to the long history of non−native species invasions in this region of the world. Five ballast and three harbor waters were collected from the Port of Duluth−Superior on May 2013. Bioinformatics analyses of over 550 million Illumina reads showed that the viral sequences had mostly no homologs in the public database, indicating that our knowledge about viral diversity is still very limited. Among the sequences homologous to known viruses (22.3 ± 6.2%), ballast and harbor waters contained a diversity of viruses, which were largely dominated by double–stranded (ds) DNA phages, including Myoviridae, Podoviridae, and Siphoviridae. Along with these phage families, viruses that could infect a broad range of hosts, including archaea, fungi, invertebrate, plant, protist, and vertebrate, some of which are highly pathogenic to fish and shrimp, were present at different levels in the viral metagenomes (viromes). Comparative virome analyses showed that viromes were distinct among the Great Lakes and formed a specific group of temperate freshwater viromes, separate from viromes associated with marine environments and engineered freshwater systems.The scope of this research was expanded to examine viral communities in marine environments. Sixteen ballast and eight harbor waters were collected from the Port of Los Angeles/Long Beach and the Port of Singapore from March through May 2014. Bioinformatics analyses of 3.8 billion Illumina reads revealed that taxonomic profile of the sequences homologous to known viruses (30.6 ± 0.03%) was similar to that observed in the Great Lakes viromes, which were largely dominated by dsDNA phages. Moreover, this research was able to detect sequences most similar to viruses infecting human, fish, and shrimp, which are related to significant public health problems or direct economic impact. Variations in virome composition of ballast and harbor waters were found between geographic locations, suggesting that the movement of ballast water across the global shipping network transports the ocean viromes. Importantly, this research showed that virus richness (type of viruses) in ballast water was not governed by engineered or management variables but by conditions of local environment where viruses arise from showing associations with latittude. Outcomes of the present research represent the most detailed characterization to date of viruses in ballast water, defining the role of ballast water in the transport of freshwater and ocean viromes and an increased risk of exposure of aquatic fauna and flora to viruses. The present findings emphasize the need for implementing ballast water discharge limits for viruses and treatment. More research is needed on host population structure to better understand the impact of the transport of viruses between biomes.
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