Metagenomic Survey of Viral Diversity Obtained from Feces of Subantarctic and South American Fur Seals

RESEARCH ARTICLE Metagenomic Survey of Viral Diversity Obtained from Feces of Subantarctic and South American Fur Seals Mariana Kluge1, Fabrício Souza Campos1, Maurício Tavares2, Derek Blaese de Amorim2, Fernanda Pedone Valdez3, Adriana Giongo4, Paulo Michel Roehe1, Ana Claudia Franco1* 1 Virology Laboratory, Department of Microbiology, Immunology and Parasitology, Institute of Basic Health Sciences, UFRGS (Federal University of Rio Grande do Sul), Porto Alegre, Rio Grande do Sul, Brazil, 2 CECLIMAR (Center for Coastal, Limnology and Marine Studies), UFRGS (Federal University of Rio Grande do Sul), Imbé, Rio Grande do Sul, Brazil, 3 Genomic and Molecular Biology Laboratory, PUCRS (Pontifical Catholic University of Rio Grande do Sul), Porto Alegre, Rio Grande do Sul, Brazil, 4 IPR (Institute of Petroleum and Natural Resources), PUCRS (Pontifical Catholic University of Rio Grande do Sul), Porto Alegre, Rio Grande do Sul, Brazil * OPEN ACCESS Citation: Kluge M, Campos FS, Tavares M, de Amorim DB, Valdez FP, Giongo A, et al. (2016) Metagenomic Survey of Viral Diversity Obtained from Feces of Subantarctic and South American Fur Seals. PLoS ONE 11(3): e0151921. doi:10.1371/ journal.pone.0151921 Editor: Ulrike Gertrud Munderloh, University of Minnesota, UNITED STATES Received: November 26, 2015 Accepted: March 7, 2016 Published: March 17, 2016 Copyright: © 2016 Kluge 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: All sequence data is available from the NIH Sequence Read Archive (SRA —http://www.ncbi.nlm.nih.gov/sra/) database (accession number SRP070196). Funding: The research leading to these results has received funding from the National Council for the Improvement of Higher Education (CAPES—http:// www.capes.gov.br/), the National Council for Scientific and Technological Development (CNPq— http://www.cnpq.br/), and the Study and Project Funding Agency (FINEP—http://www.finep.gov.br/). The funders had no role in study design, data Abstract The Brazilian South coast seasonally hosts numerous marine species, observed particularly during winter months. Some animals, including fur seals, are found dead or debilitated along the shore and may harbor potential pathogens within their microbiota. In the present study, a metagenomic approach was performed to evaluate the viral diversity in feces of fur seals found deceased along the coast of the state of Rio Grande do Sul. The fecal virome of two fur seal species was characterized: the South American fur seal (Arctocephalus australis) and the Subantarctic fur seal (Arctocephalus tropicalis). Fecal samples from 10 specimens (A. australis, n = 5; A. tropicalis, n = 5) were collected and viral particles were purified, extracted and amplified with a random PCR. The products were sequenced through Ion Torrent and Illumina platforms and assembled reads were submitted to BLASTx searches. Both viromes were dominated by bacteriophages and included a number of potentially novel virus genomes. Sequences of picobirnaviruses, picornaviruses and a hepevirus-like were identified in A. australis. A rotavirus related to group C, a novel member of the Sakobuvirus and a sapovirus very similar to California sea lion sapovirus 1 were found in A. tropicalis. Additionally, sequences of members of the Anelloviridae and Parvoviridae families were detected in both fur seal species. This is the first metagenomic study to screen the fecal virome of fur seals, contributing to a better understanding of the complexity of the viral community present in the intestinal microbiota of these animals. Introduction Every year, hundreds of marine species arrive at the coast of Rio Grande do Sul, the southernmost state in Brazil. Among these species, which include birds, turtles and mammals, fur seals PLOS ONE | DOI:10.1371/journal.pone.0151921 March 17, 2016 1 / 24 Viral Diversity in Fur Seals collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. are regular visitors that can be observed near or on-shore. These animals are driven to this region by the Malvinas current, particularly during winter months [1–3]. Although some fur seals may reach the coast to rest, several are found dead or debilitated along the shore and the cause of their weakness or death cannot always be determined [4,5]. Few studies have attempted to identify the pathogens that infect these populations and their roles as etiological agents of diseases and as potential zoonotic agents, especially those concerned with viruses [6– 10]. While the virome of marine mammals has already been investigated [11], these studies have been restricted to species native to the northern hemisphere. Little is known about the viruses that infect marine mammals limited to the southern hemisphere and the effects of this geographical difference on their virome profiles. Here, we evaluated the viral diversity of two species of pinnipeds from the Otariidae family from the southern hemisphere: the South American fur seal (Arctocephalus australis) and the Subantarctic fur seal (Arctocephalus tropicalis). While the South American fur seal is found along the Pacific and Atlantic coast of South America, the Subantarctic fur seal has a broader range that extends from the South Atlantic to Indian ocean islands. The South American fur seal is more frequently sighted in Rio Grande do Sul coast, mostly juveniles, due to the proximity of its closest breeding colony, located in the neighboring country of Uruguay. By contrast, the closest Subantarctic fur seals colonies are located at more than 4,000 km away at the south Atlantic islands of Gough and Tristan da Cunha [3,12]. Juveniles and adults specimens of Subantarctic fur seals reach the Atlantic coast with the help of ocean currents, and it is known that juveniles do not stay in the colonies during breeding seasons, while adults can travel long distances after mating [1,13]. The aim of this study was to examine the fecal virome of two species of fur seals whose cadavers were found along the shore of Rio Grande do Sul state. Anelloviruses, parvoviruses and picornaviruses were identified, as well as potential new members of Sakobuvirus, Picobirnavirus and Rotavirus. A sapovirus very similar to California sea lion sapovirus 1 was found in the Subantarctic fur seal, and a hepevirus-like sequence was identified. The data provides a preliminary characterization of the viruses that occur within fur seals populations of the southern hemisphere. Materials and Methods Sample Collection Fecal samples from 10 specimens (A. australis, n = 5; A. tropicalis, n = 5) were collected directly from the intestines of deceased fur seals found along shores between August (...truncated)