Methodology for Single-Cell Genetic Analysis of Planktonic Foraminifera for Studies of Protist Diversity and Evolution

Type Article
Date 2016
Language English
Author(s) Weiner Agnes K. M.1, 2, Morard Raphael1, Weinkauf Manuel F. G.1, 3, Darling Kate F.4, 5, André Aurore6, Quillévéré Frédéric7, Ujiie Yurika8, Douady Christophe J.9, 10, de Vargas Colomban11, 12, Kucera Michal1
Affiliation(s) 1 : MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
2 : Department of Marine Biodiversity Research, Japan Agency for Marine Earth Science and Technology (JAMSTEC), Yokosuka, Japan
3 : Department of Earth Sciences, University of Geneva, Geneva, Switzerland
4 : School of GeoSciences, University of Edinburgh, Edinburgh, UK
5 : School of Geography and GeoSciences, University of St. Andrews, St. Andrews, UK
6 : UFR Sciences Exactes et Naturelles, Université de Reims-Champagne-Ardenne, Reims, France
7 : Centre Nationnal de la Recherche Scientifique (CNRS), École Normale Supérieure (ENS) de Lyon, University of Lyon, Villeurbanne, France
8 : Center for Advanced Marine Core Research, Kochi University, Kochi, Japan
9 : Laboratoire d'Ecologie des Hydrosystémes Naturels et Anthropisés, Univ Lyon, Université Lyon 1, CNRS UMR 5023, ENTPE, Villeurbanne, France
10 : Institut Universitaire de France, Paris, France
11 : Centre Nationnal de la Recherche Scientifique (CNRS), UMR 7144, Station Biologique de Roscoff, Roscoff, France
12 : Station Biologique de Roscoff, Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Roscoff, France
Source Frontiers In Marine Science (2296-7745) (Frontiers Media SA), 2016 , Vol. 3 , N. 255 , P. 1-15
DOI 10.3389/fmars.2016.00255
WOS© Times Cited 28
Keyword(s) foraminifera, protists, single-cell genetics, cryptic diversity, comparability, methods, laboratory protocols, standardization
Abstract

Single-cell genetic analysis is an essential method to investigate the biodiversity and evolutionary ecology of marine protists. In protist groups that do not reproduce under laboratory conditions, this approach provides the only means to directly associate molecular sequences with cell morphology. The resulting unambiguous taxonomic identification of the DNA sequences is a prerequisite for barcoding and analyses of environmental metagenomic data. Extensive single-cell genetic studies have been carried out on planktonic foraminifera over the past 20 years to elucidate their phylogeny, cryptic diversity, biogeography, and the relationship between genetic and morphological variability. In the course of these investigations, it has become evident that genetic analysis at the individual specimen level is confronted by innumerable challenges ranging from the negligible amount of DNA present in the single cell to the substantial amount of DNA contamination introduced by endosymbionts or food particles. Consequently, a range of methods has been developed and applied throughout the years for the genetic analysis of planktonic foraminifera in order to enhance DNA amplification success rates. Yet, the description of these methods in the literature rarely occurred with equivalent levels of detail and the different approaches have never been compared in terms of their efficiency and reproducibility. Here, aiming at a standardization of methods, we provide a comprehensive review of all methods that have been employed for the single-cell genetic analysis of planktonic foraminifera. We compile data on success rates of DNA amplification and use these to evaluate the effects of key parameters associated with the methods of sample collection, storage and extraction of single-cell DNA. We show that the chosen methods influence the success rates of single-cell genetic studies, but the differences between them are not sufficient to hinder comparisons between studies carried out by different methods. The review thus not only provides a comprehensive reference with guidelines for future genetic studies on foraminifera, but it also establishes an important benchmark for investigations using existing single-cell datasets. The methods are widely applicable and the review may help to establish similar standard principles for their utilization in other protist groups.

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Publisher's official version 15 2 MB Open access
Table 1 20 KB Open access
Table 2 17 KB Open access
Table 3 112 KB Open access
Data sheet 1 17 477 KB Open access
Data sheet 2 3 601 KB Open access
Data sheet 3 2 136 KB Open access
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How to cite 

Weiner Agnes K. M., Morard Raphael, Weinkauf Manuel F. G., Darling Kate F., André Aurore, Quillévéré Frédéric, Ujiie Yurika, Douady Christophe J., de Vargas Colomban, Kucera Michal (2016). Methodology for Single-Cell Genetic Analysis of Planktonic Foraminifera for Studies of Protist Diversity and Evolution. Frontiers In Marine Science, 3(255), 1-15. Publisher's official version : https://doi.org/10.3389/fmars.2016.00255 , Open Access version : https://archimer.ifremer.fr/doc/00383/49460/