Metagenomic analysis of lacustrine viral diversity along a latitudinal transect of the Antarctic Peninsula

FEMS Microbiology Ecology, 92, 2016, fiw074 doi: 10.1093/femsec/fiw074 Advance Access Publication Date: 7 April 2016 Research Article RESEARCH ARTICLE Daniel Aguirre de Cárcer1,† , Alberto López-Bueno1,† , Juan M. Alonso-Lobo1 , Antonio Quesada2 and Antonio Alcamı́1,∗ 1 Centro de Biologı́a Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientı́ficas (CSIC)–Universidad Autónoma de Madrid, 28049 Madrid, Spain and 2 Departamento de Biologı́a, Universidad Autónoma de Madrid, 28049 Madrid, Spain ∗ Corresponding author: Centro de Biologı́a Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco, 28049 Madrid, Spain. Tel: +34-91-1964560; E-mail: † DAG and ALB contributed equally to this work. One sentence summary: Lacustrine viral diversity along the Antarctic Peninsula. Editor: Max Häggblom ABSTRACT Environmental viruses constitute the most abundant biological entities on earth, and harbor an enormous genetic diversity. While their strong influence on the ecosystem is widely acknowledged, current knowledge about their diversity and distribution remains limited. Here we present the metagenomic study of viral communities from freshwater bodies located along a transect of the Antarctic Peninsula. These ecosystems were chosen on the basis of environmental and biogeographical variation. The results obtained indicate that the virus assemblages were diverse, and that the larger fraction represented viruses with no close relatives in the databases. Comparisons to existing metaviromes showed that the communities studied were dissimilar to other freshwater viromes including those from the Arctic. Finally, we observed no indication of there being a reduction in either viral richness or diversity estimates with increasing latitude along the studied transect, further adding to the controversy regarding the possible existence of latitudinal gradients of diversity in the microbial world. Keywords: Antarctic Peninsula; lacustrine environments; viruses; metagenomics; latitudinal gradient; ssDNA viruses INTRODUCTION Viruses are numerically dominant in the environment, and comprise a large fraction of the genetic diversity on Earth (Suttle 2005; Ignacio-Espinoza, Solonenko and Sullivan 2013). They influence microbial community structure (Fuhrman 1999), genetic diversity and evolution (Mann et al. 2003; Williamson et al. 2008). Overall, viruses exert a profound effect on the food web and affect global geochemical cycles (Evans, Pearce and Brussaard 2009; Weitz et al. 2015), yet most of what we know about viral ecology comes from marine environments (for a review, see Bre- itbart 2012). Hence, there is a need to better understand their ecology in freshwater systems, significantly since previous studies have shown the existence of distinct viral clades in freshwater and marine environments (Short and Suttle 2005; Chenard and Suttle 2008; Roux et al. 2012). Antarctic freshwater environments constitute a unique model to understand viral ecology and biodiversity, since these simple ecosystems commonly present limited nutrient input and short food webs dominated by microorganisms. Moreover, there is an increasing recognition that microbial diversity in polar freshwater bodies can serve as sentinels of global Received: 10 December 2015; Accepted: 4 April 2016  C FEMS 2016. All rights reserved. For permissions, please e-mail: 1 Metagenomic analysis of lacustrine viral diversity along a latitudinal transect of the Antarctic Peninsula 2 FEMS Microbiology Ecology, 2016, Vol. 92, No. 6 environmental change (Camacho et al. 2012). Specially so in the case of the Antarctic Peninsula, which has been experiencing some of the most rapid temperature increases on Earth (2◦ C since 1960s) (Quayle et al. 2002; Turner et al. 2005; Steig et al. 2009). However, limited knowledge about viruses in Antarctic freshwater ecosystems and the environmental factors that influence their diversity and distribution hampers our understanding of the microbial ecology of these pristine habitats. Another source of interest in the study of Antarctic viral diversity is the increasingly recognized hypothesis that polar regions could represent hotspots of microbial diversity and evolution (Anesio and Bellas 2011). This hypothesis is grounded on accumulating evidence that periodic glaciation events (particularly the Neoproterozoic glaciation known as ‘snowball Earth’) could have been periods of intense diversification rather than periods of major extinctions in microbial communities (Corsetti, Olcott and Bakermans 2006; Moczydlowska 2008). Moreover, the high relative diversity of ancestral lineages of microbial eukaryotes found in cold habitats (Stoeck et al. 2007) is consistent with the idea that old and diverse lineages of microbes may have persisted in cold refuges throughout the Earth’s history, serving as life’s reservoir during catastrophic glaciations (Boetius et al. 2015). The initial study of an Antarctic lake virome (Lopez-Bueno et al. 2009) uncovered a diverse community of small eukaryotic viruses, unexpected for such an extreme and high latitude ecosystem. Here we present the metagenomic analysis of lacustrine viral communities sampled across a transect of the Antarctic Peninsula. The in-depth analysis of the re- sulting metagenomic dataset allows us to sustain the notion that Antarctic freshwater viral communities are diverse, with the larger fraction representing viruses with no close relatives in the databases, and dissimilar to freshwater viromes previously described, including the recently described Arctic viromes (Aguirre de Carcer et al. 2015). Moreover, confronting the metagenomic dataset with matching environmental data revealed, among other things, that the studied communities did not follow the latitudinal diversity gradient and distance decay phenomena observed for cellular organisms (Nekola and White 1999; Hawkins 2001). MATERIALS AND METHODS Sampling sites Samples were taken from several freshwater bodies following a transect along a latitudinal gradient (ca. 670 km) of the Antarctic Peninsula (Fig. 1, Fig. S1, Supporting Information; Table 1). The freshwater bodies investigated were included within the Antarctic Conservation Biogeographic Region 3, covering the northwest Antarctic Peninsula and offshore islands environmental domains sensu (Terauds et al. 2012). The sampling sites were chosen covering the maximum expanse of this biogeographic region based also on their accessibility by ship and represented lacustrine ecosystems subjected apparently to different ecological conditions (e.g. age, proximity to glaciers and proximity to marine animal colonies). A portable probe (YSI 556 MPS Water Figure 1. Diagram depicting the location of the freshwater bodies studied along the Antarctic Peninsula. A close up of the Livingston Island is shown to better localize the three lakes sampled in this island. Domo (Byers Peninsula, Livingston Island. ASPA126. Position −62.64 −60.97). (...truncated)