Ciliate Diversity, Community Structure, and Novel Taxa in Lakes of the Mcmurdo Dry Valleys, Antarctica
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Reference: Biol. Bull. 227: 175–190. (October 2014) © 2014 Marine Biological Laboratory Ciliate Diversity, Community Structure, and Novel Taxa in Lakes of the McMurdo Dry Valleys, Antarctica YUAN XU1,*†, TRISTA VICK-MAJORS2, RACHAEL MORGAN-KISS3, JOHN C. PRISCU2, AND LINDA AMARAL-ZETTLER4,5,* 1Laboratory of Protozoology, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; 2Montana State University, Department of Land Resources and Environmental Sciences, 334 Leon Johnson Hall, Bozeman, Montana 59717; 3Department of Microbiology, Miami University, Oxford, Ohio 45056; 4The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts 02543; and 5Department of Earth, Environmental and Planetary Sciences, Brown University, Providence, Rhode Island 02912 Abstract. We report an in-depth survey of next-genera- trends in dissolved oxygen concentration and salinity may tion DNA sequencing of ciliate diversity and community play a critical role in structuring ciliate communities. A structure in two permanently ice-covered McMurdo Dry PCR-based strategy capitalizing on divergent eukaryotic V9 Valley lakes during the austral summer and autumn (No- hypervariable region ribosomal RNA gene targets unveiled vember 2007 and March 2008). We tested hypotheses on the two new genera in these lakes. A novel taxon belonging to relationship between species richness and environmental an unknown class most closely related to Cryptocaryon conditions including environmental extremes, nutrient sta- irritans was also inferred from separate gene phylogenies. tus, and day length. On the basis of the unique environment that exists in these high-latitude lakes, we expected that Introduction novel taxa would be present. Alpha diversity analyses showed that extreme conditions—that is, high salinity, low The McMurdo Dry Valleys (MCM), Antarctica, harbor oxygen, and extreme changes in day length—did not impact numerous perennially ice-covered lakes in our planet’s ciliate richness; however, ciliate richness was 30% higher in coldest and driest desert (Priscu et al., 1998). The physico- samples with higher dissolved organic matter. Beta diver- chemical conditions in these lakes can be extreme, with sity analyses revealed that ciliate communities clustered by salinities ranging from fresh to as much as 5 times seawater, dissolved oxygen, depth, and salinity, but not by season temperatures below Ϫ4 °C, and oxygen ranging from (i.e., day length). The permutational analysis of variance Ͼ200% supersaturation in the upper photic zones to suboxic test indicated that depth, dissolved oxygen, and salinity had below permanent chemoclines (Spigel and Priscu, 1998; significant influences on the ciliate community for the abun- Vick and Priscu, 2012). In addition to environmental ex- dance matrices of resampled data, while lake and season tremes, solar radiation fluctuates from 24-h sunlight in the were not significant. This result suggests that the vertical austral summer to complete darkness in the austral winter, imposing additional stresses on the microbiota that domi- * Authors contributed equally. nate these polar habitats. There are 4 mon of full incident To whom correspondence should be addressed. E-mail: amaral@mbl. sunlight (November to February) and 4 mon of total dark- edu ness (May to August) with twilight in between. The remote † Current address: State Key Laboratory of Estuarine and Coastal Re- geographical nature of the lakes, the Ͻ3-m-thick perennial search, East China Normal University, Shanghai 200062, China. Abbreviations: ELB, East Lobe Bonney; GAST, Global Alignment for ice covers on the lakes, and the circumpolar oceans sur- Sequence Taxonomy; MCM, McMurdo Dry Valleys; OTU, operational rounding Antarctica create a barrier to colonization (Spauld- taxonomic unit; WLB, West Lobe Bonney. ing et al., 2010) that makes these ecosystems ideal locations 175 176 Y. XU ET AL. to search for endemic novel taxa in a biogeographically isolated environment. The lakes contain no fish; microorganisms dominate the food web. Among the microbiota that inhabit the MCM lakes are microbial eukaryotes, mainly protists representing a broad range of evolutionary lineages inclusive of photo- trophs, mixotrophs, and heterotrophs (Kong et al., 2012; Thurman et al., 2012). Protist communities are important in carbon and nutrient cycling, occupying both the bottom (primary production) and top (predation) of the truncated MCM food web (Bielewicz et al., 2011). Among the hetero- trophs, ciliates, often regarded as “flagship” taxa because of their conspicuous size and morphology (Foissner, 2005), have been the object of past morphology-based biodiversity investigations in the MCM lakes. These studies suggested that ciliate populations in the lakes were more diverse than anticipated (Kepner et al., 1999). While the diversity of bacteria and archaea in MCM lakes has been studied using Figure 1. Locations of Lake Fryxell and Lake West Lobe Bonney molecular methods (Brambilla et al., 2001; Karr et al., 2006), (WLB) sampled in this study. The white areas represent glaciers; darker the biodiversity of protists, especially ciliates, in these lakes shades represent exposed soils. Both lakes are located within the Taylor Valley of the McMurdo Dry Valleys (see inset). has been largely limited to analysis with morphology-based approaches (Laybourn-Parry et al., 1996; Roberts et al., 2000; Song and Wilbert, 2002), except for a single clone and to determine potentially endemic taxa, we used next- library based sequencing study (Bielewicz et al., 2011). generation amplicon sequencing to examine ciliate diversity In aquatic ecosystems, ciliates are a main component of and community structure in two MCM lakes, Lake Fryxell the microbial loop (Azam et al., 1983) and play an impor- and Lake West Lobe Bonney (Fig. 1). tant role in the microbial food web by controlling bacterial We exploited the unique nature of the MCM lakes, as prey populations, redistributing organic sources of nutrients well as their remote location, to test the following hypoth- and carbon, and linking the microbial loop with higher eses regarding ciliate biogeography and species richness: trophic levels (Finlay and Esteban, 1998). With short life (1) the extreme environmental conditions encountered in the cycles and delicate external membranes, ciliates may re- MCM Lakes (i.e., high salinity (Ͼ80 PSU), cold, and low spond more quickly than metazoa to environmental changes oxygen at depth) result in overall low richness of ciliate (Coppellotti and Matarazzo, 2000) and thus represent sen- populations; (2) ciliate richness increases with nutrient con- sitive indicator species (Xu et al., 2011a, b). Many ciliates centrations via interactions with bacterial communities (i.e., can tolerate extremes in environmental conditions and have nitrate, dissolved organic carbon, etc.), as most ciliates feed been reported in a range of extreme environments (Coppel- on bacteria and organics; (3) according to the day-length lotti and Matarazzo, 2000; Jiang et al., 2007). The food web hypothesis of Gilbert et al. (2010), which postulates that day in the MCM lakes is dominated by the microbial loop in length might be a primary determinant of the seasonality of which ciliates likely represent the top predators and there- marine bacterial communities, richness of ciliate popula- fore are important in carbon and nutrient cycling in these tions is higher in autumn than in summer, a situation that aquatic systems. Indeed, in Lake Fryxell (Fig. 1), ciliates characterizes Antarctic marine bacterioplankton (Ghiglione occur in high abundance (Laybourn-Parry et al., 1996), and Murray, 2012); and (4) given the isolated and extreme providing a good proxy for the study of biodiversity physical and chemical nature of the MCM lakes environ- changes in this environment as a whole. ment, our deep sequencing efforts would identify endemic An estimated 83%–89% of the 4500 known free-living and/or novel ciliate species. ciliate morphospecies remain to be formally described (Foissner et al., 2009; Xu et al., 2011a). Morphological- Materials and Methods based identification has shown that more than 20% of the Sample collection and next-generation sequencing taxa found in the MCM lakes are novel (Petz et al., 2007). Despite a wealth of morphological features, the identifica- This study was part of the Microbial Inventory Research tion of ciliates at the species level is laborious, often sub- Across Diverse Aquatic Long Term Ecological Research jective, and requires skilled taxonomic expertise that can Sites (MIRADA-LTERS) Project with the broad goal of miss rare species (Xu et al., 2011a, b). To gain more documenting, describing, and discovering novel diversity at information on ciliate diversity and community structure aquatic LTER locations. The MCM-LTER site (MIRADA CILIATE BIODIVERSITY IN MCM LAKES 177 Table 1 Contextual data from our study Sample ID Contextual Data MCM1 MCM2 MCM3 MCM4 MCM5 MCM6 MCM7 MCM8 Collection Date (UTC) 11/22/07 11/22/07 11/30/07 11/30/07 3/17/08 3/17/08 3/25/08 3/25/08 Depth (Meters) 6 9 13 18 13 18 6 9 Lake (Name) Lake Fryxell Lake Fryxell Lake WLB Lake WLB Lake WLB Lake WLB Lake Fryxell Lake Fryxell Latitude (Decimal Degree) Ϫ77.61031 Ϫ77.61031 Ϫ77.72006 Ϫ77.72006 Ϫ77.72006 Ϫ77.720072006 Ϫ77.61031 Ϫ77.61031 Longitude (Decimal Degree) 85.53597 85.53597 84.57732 84.57732 84.57732 84.57732 85.53597 85.53597 Ammonium (mol lϪ1) 0.3 0.17 0.96