DNA metabarcoding and microscopic analyses of sea turtles biofilms: Complementary to understand turtle behavior

Abstract

Sea turtles are distributed in tropical and subtropical seas worldwide. They play several ecological roles and are considered important indicators of the health of marine ecosystems. Studying epibiotic diatoms living on turtle shells suggestively has great potential in the study of turtle behavior because diatoms are always there. However, diatom identification at the species level is time consuming, requires well-trained specialists, and there is a high probability of finding new taxa growing on turtle shells, which makes identification tricky. An alternative approach based on DNA barcoding and high throughput sequencing (HTS), metabarcoding, has been developed in recent years to identify species at the community level by using a DNA reference library. The suitabilities of morphological and molecular approaches were compared. Diatom assemblages were sampled from seven juvenile green turtles (Chelonia mydas) from Mayotte Island, France. The structures of the epibiotic diatom assemblages differed between both approaches. This resulted in different clustering of the turtles based on their diatom communities. Metabarcoding allowed better discrimination between turtles based on their epibiotic diatom assemblages and put into evidence the presence of a cryptic diatom diversity. Microscopy, for its part, provided more ecological information of sea turtles based on historical bibliographical data and the abundances of ecological guilds of the diatom species present in the samples. This study shows the complementary nature of these two methods for studying turtle behavior.

A fundamental difference between macrobiota and microbial eukaryotes: protistan plankton has a species maximum in the freshwater‐marine transition zone of the Baltic Sea

“…The technical biases of microscopy and molecular protistan diversity studies are well known and have been discussed in detail by several authors (see e.g. Bachy et al ., ; Stoeck et al ., ; Visco et al ., ; Rivera et al ., ). For discussions of biases among molecular‐based diversity studies including PCR biases, metabarcode regions, taxonomic classifications, OTU cluster algorithms, (relative) abundance patterns, and also the potential influence of ancient DNA we refer to, for example, Stoeck et al ., ; Stoeck et al ., ; Pinto and Raskin, ; Bachy et al ., ; Stoeck et al ., ; Hu et al ., ; Forster et al ., ; Singer et al ., .…”

“…The technical biases of microscopy and molecular protistan diversity studies are well known and have been discussed in detail by several authors (see e.g. Bachy et al, 2013;Stoeck et al, 2014;Visco et al, 2015;Rivera et al, 2018). For discussions of biases among molecularbased diversity studies including PCR biases, metabarcode regions, taxonomic classifications, OTU cluster algorithms, (relative) abundance patterns, and also the potential influence of ancient DNA we refer to, for example, Stoeck et al, 2007;Stoeck et al, 2010;Pinto and Raskin, 2012;Bachy et al, 2013;Stoeck et al, 2014;Hu et al, 2015;Forster et al, 2016;Singer et al, 2016. Regarding biological differences, dinoflagellates, diatoms and dictyochophytes belong to the most important phytoplankton classes in the Baltic Sea, sensitively reacting to seasonal changes by forming extensive spring blooms, predominantly in the western Baltic Sea (Wasmund et al, 2013;Wasmund et al, 2016).…”

The impact of OTU sequence similarity threshold on diatom‐based bioassessment: A case study of the rivers of Mayotte (France, Indian Ocean)

“…Even though the number of species included in the DNA reference libraries is constantly increasing (Rivera, Vasselon, Jacquet, et al, 2018b), the proportion of OTUs that can be assigned to the species level remains far from satisfying. Published reports have described a wide range of classification coverage, including 35.7% , -Perret-Gentil et al, 2017), 23% (Rivera, Vasselon, Jacquet, et al, 2018b), and as low as 10% for marine samples (Rivera, Vasselon, Ballorain, et al, 2018a). Our approach is similar to those of Stevenson, Pan, & Van Dam, 2010) and in reference sites where nutrient limitation has selected for a limited number of taxa Stevenson, Hill, Herlihy, Yuan, & Norton, 2008).…”

Six new epibioticProschkinia(Bacillariophyta) species and new insights into the genus phylogeny

“…Following the first reports focused on sea turtleassociated diatoms (Frankovich et al, 2015;Majewska et al, 2015a,b), the number of studies investigating microbial epibionts of sea turtles and new epizoic diatom species has grown steadily (Frankovich et al, 2016;Robinson et al, 2016;Majewska et al, 2017aRiaux-Gobin et al, 2017a,b;Kaleli et al, 2018;Rivera et al, 2018). Several diatom species belonging to known or new genera have been described in the last four years (Frankovich et al, 2015(Frankovich et al, , 2016Majewska et al, 2015aMajewska et al, , 2017aRiaux-Gobin et al, 2017a,b;Kaleli et al, 2018).…”