Molecular Phylogeny of Euglyphid Testate Amoebae
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Molecular Phylogenetics and Evolution 55 (2010) 113–122 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev Molecular phylogeny of euglyphid testate amoebae (Cercozoa: Euglyphida) suggests transitions between marine supralittoral and freshwater/terrestrial environments are infrequent Thierry J. Heger a,b,c,d,e,*, Edward A.D. Mitchell a,b,c, Milcho Todorov f, Vassil Golemansky f, Enrique Lara c, Brian S. Leander e, Jan Pawlowski d a Ecosystem Boundaries Research Unit, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), CH-1015 Lausanne, Switzerland b Environmental Engineering Institute, École Polytechnique Fédérale de Lausanne (EPFL), Station 2, CH-1015 Lausanne, Switzerland c Institute of Biology, University of Neuchâtel, CH-2009 Neuchâtel, Switzerland d Department of Zoology and Animal Biology, University of Geneva, Sciences III, CH-1211 Geneva 4, Switzerland e Departments of Zoology and Botany, University of British Columbia, Vancouver, BC, Canada V6T 1Z4 f Institute of Zoology, Bulgarian Academy of Sciences, 1000 Sofia, Bulgaria article info abstract Article history: Marine and freshwater ecosystems are fundamentally different regarding many biotic and abiotic factors. Received 24 June 2009 The physiological adaptations required for an organism to pass the salinity barrier are considerable. Many Revised 22 November 2009 eukaryotic lineages are restricted to either freshwater or marine environments. Molecular phylogenetic Accepted 25 November 2009 analyses generally demonstrate that freshwater species and marine species segregate into different Available online 22 December 2009 sub-clades, indicating that transitions between these two environments occur only rarely in the course of evolution. It is, however, unclear if the transitions between freshwater and environments characterized Keywords: by highly variable salinities, such as the marine supralittoral zone, are also infrequent. Here, we use tes- Cryptic species tate amoebae within the Euglyphida to assess the phylogenetic interrelationships between marine supr- Cyphoderia Cyphoderiidae alittoral and freshwater taxa. Euglyphid testate amoebae are mainly present in freshwater habitats but Euglyphida also occur in marine supralittoral environments. Accordingly, we generated and analyzed partial SSU Freshwater rRNA gene sequences from 49 new marine/supralittoral and freshwater Cyphoderiidae sequences, 20 Marine supralittoral sequences of the Paulinellidae, Trinematidae, Assulinidae, and Euglyphidae families as well as 21 Gen- Phylogeny Bank sequences of unidentified taxa derived from environmental PCR surveys. Both the molecular and Protista morphological data suggest that the diversity of Cyphoderiidae is strongly underestimated. The results Rhizaria of our phylogenetic analyses demonstrated that marine supralittoral and freshwater euglyphid testate SEM amoeba species are segregated into distinct sub-clades, suggesting that transitions between these two SSU rRNA gene Testate amoebae habitats occurred only infrequently. Ó 2009 Elsevier Inc. All rights reserved. 1. Introduction foraminiferans, most haptophytes, and pelagophytes are marine, whereas no representative of the Mycetozoa has ever been found The biotic and abiotic factors in marine and freshwater eco- in saltwater. In contrast, other eukaryote lineages occur in both systems differ considerably and impose physiological constraints marine and freshwater/terrestrial habitats. For instance, crypto- on organisms that pass through this salinity barrier. As a conse- phytes, diatoms and dinoflagellates are abundant in both envi- quence, the taxonomic compositions of the communities encoun- ronments. But even within these groups, phylogenetic studies tered in both environments are quite divergent. Some major have indicated a limited number of marine/freshwater transi- eukaryotic lineages are restricted to either marine or freshwater tions, suggesting that such events are rare in the evolutionary environments. For example, radiolarians, echinoderms, most history of different lineages (von der Heyden and Cavalier-Smith, 2005; Alverson et al., 2007; Cavalier-Smith and von der Heyden, * Corresponding author. Address: Wetlands Research Group, Ecosystem Bound- 2007; Logares et al., 2007; Shalchian-Tabrizi et al., 2008; Cava- aries Research Unit, WSL, Swiss Federal Institute for Forest, Snow and Landscape lier-Smith, 2009). Likewise, even though at the morphospecies Research, Station 2, CH-1015 Lausanne, Switzerland. Fax: +41 21 693 39 13. level several microeukaryotic lineages appear to have wide salin- E-mail addresses: thierry.heger@epfl.ch (T.J. Heger), [email protected] ity ranges, molecular phylogenies show that they are uncommon (E.A.D. Mitchell), [email protected] (M. Todorov), [email protected] bas.bg (V. Golemansky), [email protected] (E. Lara), bleander@interchan- (Koch and Ekelund, 2005; Finlay et al., 2006; Scheckenbach et al., ge.ubc.ca (B.S. Leander), [email protected] (J. Pawlowski). 2006; Bass et al., 2007). 1055-7903/$ - see front matter Ó 2009 Elsevier Inc. All rights reserved. doi:10.1016/j.ympev.2009.11.023 114 T.J. Heger et al. / Molecular Phylogenetics and Evolution 55 (2010) 113–122 The order Euglyphida Copeland, 1956, is a group of testate amoe- orythion species belong to the Cyphoderiidae family although they bae with filamentous pseudopodia that build self-secreted silica were initially described as members of the Psammonobiotidae tests. Euglyphids are currently divided into five families: the Assu- family (Golemansky, 1970; Valkanov, 1970; Chardez, 1991). In this linidae, Euglyphidae, Trinematidae, Paulinellidae and Cyphoderii- paper we use the terms ‘‘Euglyphid testate amoebae”, or ‘‘euglyph- dae (Meisterfeld, 2002; Adl et al., 2005; Lara et al., 2007). These ids” to refer to the Euglyphida sensu stricto. organisms were considered as exclusive inhabitants of soil and freshwater habitats up to the second part of the 20th century. Early 2.2. Testate amoebae isolation for DNA extractions and scanning reports of Euglyphida from subsurface waters of the Pacific Ocean electronic imaging (Wailes, 1927) were interpreted as imports from continental fresh- waters. Since then, Euglyphida were more intensively investigated The testate amoebae were isolated by sieving and back sieving. in marine supralittoral environments and today, more than 50 spe- With the exception of Cyphoderia cf. compressa, all samples from cies were described from the marine supralittoral of the Black Sea the marine sand beaches were incubated between 4 and 8 weeks and other marine habitats of the World (Golemansky, 1974, 2007; in the laboratory, at about 20 °C prior to the isolation. For each Ogden and Couteaux, 1989; Chardez, 1991; Golemansky and Todo- DNA preparation, between 5 and 100 individuals were isolated rov, 1999). While the Assulinidae, Euglyphidae and Trinematidae individually under light microscope using fine diameter glass pip- have been found almost exclusively in terrestrial or freshwater hab- ettes. Cells were washed by transferring them three times into dis- itats (for simplicity hereafter referred to as freshwater), the Cypho- tilled water. A guanidine thiocyanate protocol was used to extract deriidae and the Paulinellidae are found also in the marine DNA (Chomczynski and Sacchi, 1987). The shell ultrastructure of supralittoral zone (Meisterfeld, 2002). selected individuals from each populations, excepting Cyphoderia The marine supralittoral environment is characterized by vari- ampulla from Dragichevo, C. ampulla from Sofia and C. cf. compressa able salinity values, which can fluctuate relatively rapidly between from Tsawassen, were investigated by scanning electron micros- typical seawater to less than 10‰ (Todorov and Golemansky, 2007; copy (SEM) by Todorov et al. (2009) or in the present study (Figs. 1 Todorov et al., 2009). Thus, organisms inhabiting such an environ- and 2). For SEM, testate amoeba shells were mounted on stubs and ment must face huge selective pressure to adapt to these harsh kept for 2 weeks in a desiccator. The shells were coated with gold conditions. The Cyphoderiidae are one of the few microeukaryotic in a vacuum coating unit and observed either with a JEOL JSM- groups that have successfully colonised both environments. There- 5510 microscope at a tension of 10 kV or with a PHILIPS XL30 fore, they represent an excellent model group to study the impact FEG microscope at a tension of 5 kV. of salinity in eukaryotic cell evolution. The current Euglyphida taxonomy is largely based on shell char- 2.3. SSU rDNA amplification and sequencing acters. Shells are composed of secreted plates which often differ in shape, size and arrangement among species (Meisterfeld, 2002). The 30 terminal fragment (708–765 bp) of the SSU rRNA gene and However, morphological data alone are often unreliable for testing a selected number of near full-length (1697–1795 bp) portions of hypotheses of colonization processes because such characters can this gene were amplified by nested polymerase chain reaction be subject to convergent evolution during the marine to freshwater (PCR) with the universal eukaryotic primers in the first PCR (Table 2) transition (or vice versa) (Lee and Bell, 1999). and then using a specific Cyphoderiidae primer and a universal In order to overcome these current limitations, a detailed phy- eukaryotic primer in the second PCR (Table 2). The PCR cycling pro- logenetic study of freshwater