Molecular Assessment of Benthic Foraminiferal Diversity

Abstract

Recent advances in molecular biology have extended our possibilities to investigate biodiversity and evolution of small organisms. This is especially true for the hyper-diverse benthic foraminifera, which can now be identified by their DNA sequences rather than only by their morphology trough time-consuming observations under the microscope. In this chapter, we will introduce two general methods for the molecular assessment of benthic foraminiferal diversity. The first one is "the single-cell approach" and consists in isolating a single living specimen before extracting, amplifying, cloning and sequencing its DNA. The second method is "the environmental DNA approach", which aims to extract the DNA from the overall fauna present in the sediment before specifically amplifying foraminiferal fragments and massively sequence them. For both approaches, we will present some core experimental protocols with specificities and possible optimizations.