Molecular Assessment of Benthic Foraminiferal Diversity

Lecroq, Béatrice

doi:10.1007/978-4-431-54388-6_6

Cited by 5 publications

(3 citation statements)

References 19 publications

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“…Specimens can be stored either individually, directly in DNA extraction buffer or dried and frozen on cardboard faunal slides (Figure 2, details in Supplementary Data Sheet 1). Preservation in ethanol, a hypothetical third option commonly used for metazoans, is not recommended for foraminifera as it inhibits the amplification of DNA by PCR (Holzmann and Pawlowski, 1996;Lecroq, 2014). Drying and freezing has been used preferably in the last years, since it allows faster handling of foraminiferal specimens (André et al, 2013;Weiner et al, 2014Weiner et al, , 2015.…”

Section: Preservation Of Specimensmentioning

confidence: 99%

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

et al. 2016

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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 Weiner et al.Single-Cell Genetic Analysis of Foraminifera 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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Section: Preservation Of Specimensmentioning

confidence: 99%

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

et al. 2016

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“…williamsoni were present; which comprised up to 80% of the living benthic foraminiferal assemblage. This species is easily identified through the yellow/brown-coloured protoplasm extensively distributed across the entire foraminiferal tests, except in the last chambers [25,44]. Previously, the naturally intense protoplasm colour has been widely used as an indicator of viable foraminiferal individuals [45], and additional observation of pseudopodia activity confirmed that these individuals were alive.…”

Section: Methodsmentioning

confidence: 99%

“…Calcein-labelled specimens were randomly selected and transferred into foraminiferal culture chambers containing a tissue cell culture insert with a silica layer [29,43,44]. As specimens of E .…”

Section: Methodsmentioning

confidence: 99%

Impacts of ocean acidification on intertidal benthic foraminiferal growth and calcification

et al. 2019

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Foraminifera are expected to be particularly susceptible to future changes in ocean carbonate chemistry as a function of increased atmospheric CO 2 . Studies in an experimental recirculating seawater system were performed with a dominant benthic foraminiferal species collected from intertidal mudflats. We investigated the experimental impacts of ocean acidification on survival, growth/calcification, morphology and the biometric features of a calcareous species Elphidium williamsoni . Foraminifera were exposed for 6 weeks to four different pH treatments that replicated future scenarios of a high CO 2 atmosphere resulting in lower seawater pH. Results revealed that declining seawater pH caused a decline in foraminiferal survival rate and growth/calcification (mainly through test weight reduction). Scanning electron microscopy image analysis of live specimens at the end of the experimental period show changes in foraminiferal morphology with clear signs of corrosion and cracking on the test surface, septal bridges, sutures and feeding structures of specimens exposed to the lowest pH conditions. These findings suggest that the morphological changes observed in shell feeding structures may serve to alter: (1) foraminiferal feeding efficiency and their long-term ecological competitiveness, (2) the energy transferred within the benthic food web with a subsequent shift in benthic community structures and (3) carbon cycling and total CaCO 3 production, both highly significant processes in coastal waters. These experimental results open-up the possibility of modelling future impacts of ocean acidification on both calcification and dissolution in benthic foraminifera within mid-latitude intertidal environments, with potential implications for understanding the changing marine carbon cycle.

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NGS-metabarcoding revealing novel foraminiferal diversity in the Western Pacific Magellan Seamount sediments

Shi

Lei

et al. 2021

J. Ocean. Limnol.

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Molecular Assessment of Benthic Foraminiferal Diversity

Cited by 5 publications

References 19 publications

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

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

Impacts of ocean acidification on intertidal benthic foraminiferal growth and calcification

NGS-metabarcoding revealing novel foraminiferal diversity in the Western Pacific Magellan Seamount sediments

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