Morphological and Phylogenetic Characterization of New Gephyrocapsa Isolates Suggests Introgressive Hybridization in the Emiliania/Gephyrocapsa Complex (Haptophyta)

The coccolithophore genus Gephyrocapsa contains a cosmopolitan assemblage of pelagic species, including the bloom-forming Gephyrocapsa oceanica, and is closely related to the emblematic coccolithophore Emiliania huxleyi within the Noëlaerhabdaceae. These two species have been extensively studied and are well represented in culture collections, whereas cultures of other species of this family are lacking. We report on three new strains of Gephyrocapsa isolated into culture from samples from the Chilean coastal upwelling zone using a novel flow cytometric single-cell sorting technique. The strains were characterized by morphological analysis using scanning electron microscopy and phylogenetic analysis of 6 genes (nuclear 18S and 28S rDNA, plastidial 16S and tufA, and mitochondrial cox1 and cox3 genes). Morphometric features of the coccoliths indicate that these isolates are distinct from G. oceanica and best correspond to G. muellerae. Surprisingly, both plastidial and mitochondrial gene phylogenies placed these strains within the E. huxleyi clade and well separated from G. oceanica isolates, making Emiliania appear polyphyletic. The only nuclear sequence difference, 1 bp in the 28S rDNA region, also grouped E. huxleyi with the new Gephyrocapsa isolates and apart from G. oceanica. Specifically, the G. muellerae morphotype strains clustered with the mitochondrial β clade of E. huxleyi, which, like G. muellerae, has been associated with cold (temperate and sub-polar) waters. Among putative evolutionary scenarios that could explain these results we discuss the possibility that E. huxleyi is not a valid taxonomic unit, or, alternatively the possibility of past hybridization and introgression between each E. huxleyi clade and older Gephyrocapsa clades. In either case, the results support the transfer of Emiliania to Gephyrocapsa. These results have important implications for relating morphological species concepts to ecological and evolutionary units of diversity.

Morphological and Phylogenetic Characterization of New Gephyrocapsa Isolates Suggests Introgressive Hybridization in the Emiliania/Gephyrocapsa Complex (Haptophyta)

The coccolithophore genus Gephyrocapsa contains a cosmopolitan assemblage of pelagic species, including the bloom-forming Gephyrocapsa oceanica, and is closely related to the emblematic coccolithophore Emiliania huxleyi within the Noëlaerhabdaceae. These two species have been extensively studied and are well represented in culture collections, whereas cultures of other species of this family are lacking. We report on three new strains of Gephyrocapsa isolated into culture from samples from the Chilean coastal upwelling zone using a novel flow cytometric single-cell sorting technique. The strains were characterized by morphological analysis using scanning electron microscopy and phylogenetic analysis of 6 genes (nuclear 18S and 28S rDNA, plastidial 16S and tufA, and mitochondrial cox1 and cox3 genes). Morphometric features of the coccoliths indicate that these isolates are distinct from G. oceanica and best correspond to G. muellerae. Surprisingly, both plastidial and mitochondrial gene phylogenies placed these strains within the E. huxleyi clade and well separated from G. oceanica isolates, making Emiliania appear polyphyletic. The only nuclear sequence difference, 1 bp in the 28S rDNA region, also grouped E. huxleyi with the new Gephyrocapsa isolates and apart from G. oceanica. Specifically, the G. muellerae morphotype strains clustered with the mitochondrial β clade of E. huxleyi, which, like G. muellerae, has been associated with cold (temperate and sub-polar) waters. Among putative evolutionary scenarios that could explain these results we discuss the possibility that E. huxleyi is not a valid taxonomic unit, or, alternatively the possibility of past hybridization and introgression between each E. huxleyi clade and older Gephyrocapsa clades. In either case, the results support the transfer of Emiliania to Gephyrocapsa. These results have important implications for relating morphological species concepts to ecological and evolutionary units of diversity.

Application of microarrays (phylochips) for analysis of community diversity by species identification

Abstract Molecular probe-based methods (Fluorescent in-situ hybridisation or FISH, Next Generation Sequencing or NGS) have proved successful in improving both the efficiency and accuracy of the identification of microorganisms, especially those that lack distinct morphological features, such as picoplankton. However, FISH methods have the major drawback that they can only identify one or just a few species at a time because of the reduced number of available fluorochromes that can be added to the probe. Although the length of sequence that can be obtained is continually improving, NGS still requires a great deal of handling time, its analysis time is still months and with a PCR step it will always be sensitive to natural enzyme inhibitors. With the use of DNA microarrays, it is possible to identify large numbers of taxa on a single-glass slide, the so-called phylochip, which can be semi-quantitative. This review details the major steps in probe design, design and production of a phylochip and validation of the array. Finally, major microarray studies in the phytoplankton community are reviewed to demonstrate the scope of the method.

Application of microarrays (phylochips) for analysis of community diversity by species identification

Abstract Molecular probe-based methods (Fluorescent in-situ hybridisation or FISH, Next Generation Sequencing or NGS) have proved successful in improving both the efficiency and accuracy of the identification of microorganisms, especially those that lack distinct morphological features, such as picoplankton. However, FISH methods have the major drawback that they can only identify one or just a few species at a time because of the reduced number of available fluorochromes that can be added to the probe. Although the length of sequence that can be obtained is continually improving, NGS still requires a great deal of handling time, its analysis time is still months and with a PCR step it will always be sensitive to natural enzyme inhibitors. With the use of DNA microarrays, it is possible to identify large numbers of taxa on a single-glass slide, the so-called phylochip, which can be semi-quantitative. This review details the major steps in probe design, design and production of a phylochip and validation of the array. Finally, major microarray studies in the phytoplankton community are reviewed to demonstrate the scope of the method.