Large benthic foraminifera under the pipette: Method development and ecological assessment in the Spermonde Archipelago

Coral reefs are described as the rainforest of the seas, because they form a marine hotspot of biodiversity. Some coral reefs live and thrive in murky waters; they are important to study because they might provide refugia for corals and other reef organisms in face of climatic instability, especially the rise of sea water temperature. To assess this concept and to monitor the dynamics of coral reefs over time and space, multiple methods were developed, including the use of bioindicator species. Large benthic foraminifera (LBF), millimetre-sized unicellular marine protists, has proven to be very useful in assessing environmental conditions in coral reefs. Compiling 25 years of research from turbid coral reefs located in the Spermonde Archipelago, South Sulawesi, Indonesia, I answer three main questions: 1) Can LBF communities be used as a warning signal for reef benthic community shift? 2) Can molecular methods be used to assess LBF community compositions reliably? 3) Which environmental factors trigger the spatial distribution of LBF species? This work contributes to the greater understanding of the ecology of LBF by the means of morphological and molecular data analysis. Building upon thirty years of pioneer molecular research in foraminifera, I demonstrated the strength of LBF in monitoring reefs using molecular methods in a quantitative manner. Finally, I underscored how the combination of multiple LBF taxa provide complementary information on the reef environmental conditions in terms of water quality and substrate characteristics. This information is essential to picture ancient reefs and to anticipate future changes of present coral reefs.