Supplementary figure <i>C. janiceae</i>

A: C. janiceae ovipositor; B: C. uniseries ovipositor; C: C. janiceae male anal appendages; D: C. uniseries anal appendages.</p

A dragon in a trap! A record of using an aquatic trap to collect the Southeast Asian Water Monitor, Varanus salvator macromaculatus (Deraniyagala, 1944), in Indonesia (Squamata: Varanidae)

International audienceA record of using an aquatic trap to collect the Southeast Asian Water Monitor (Varanus salvator macromaculatus) in Indonesi

The phylum Chloroflexi and their SAR202 clade dominate the microbiome of two marine sponges living in extreme environmental conditions

The capacity of marine sponges to cope with environmental changes is often attributed to the specific composition of their bacterial communities. In this study, we assessed the bacterial microbiome of two dominant sponges, Rhabdastrella globostellata (Rg) and Hyrtios erectus (He), living in the Bouraké lagoon (New Caledonia), where abiotic conditions daily fluctuate according to the tide. Sponge specimens, sediment and seawater samples were collected at 2–3 m depth. The bacterial communities were assessed using 16S rRNA metabarcoding, and variations between the two sponges were compared using PCA biplots. Chloroflexi was the dominant phyla in both He and Rg with an average relative abundance of 41.2% and 53.2%, respectively, while it was absent in sediment and seawater. Among the phylum Chloroflexi, SAR202 clade was dominant in both sponges, reaching an average relative abundance of 53.2% (He) and 78.7% (Rg). Principal component analysis (PCA) was used to identify the main variables driving the bacterial community structure in both sponges. The results indicated that the bacterial community structure in both sponges was strongly associated with Chloroflexi (70.9% of the phyla variance) and SAR202 clade (86.6% of the clade variance). The high relative abundance of the phylum Chloroflexi and the SAR202 clade observed in this study is the highest reported so far in the literature in marine sponges. Such a high relative abundance of these bacteria could suggest their involvement in the well-being of sponges in the extreme environmental conditions of Bouraké

Limited interspecific variation in grazing susceptibility of the brown alga Lobophora to herbivory

The genus Lobophora is a notable benthic algal component of tropical coral reefs, capable of dominating large reef areas following coral mortality and herbivory declines. The alga, however, has been the object of contradictory observations in terms of susceptibility to herbivory. Unaware of the species-richness of this genus, most studies referred to Lobophora variegata, a species assumed to present various morphotypes and chemotypes, occupying diverse ecological niches. Variation in susceptibility to herbivory has been consequently interpreted as intraspecific variation in terms of morphology and chemical composition as well as differences in herbivore guild compositions and diet across different locations (e.g., habitat, reef, region). Recent taxonomic studies of Lobophora disclosed a high species diversity, which could explain previous conflicting observations. The present study tested the grazing susceptibility of seven species of Lobophora (L. dimorpha, L. hederacea, L. monticola, L. obscura, L. rosacea, L. sonderi and L. undulata), which differ in growth form as well as in their chemical composition and fine-scale ecological niche on coral reefs in the southern lagoon in New Caledonia, to two important herbivores in New Caledonia, the rabbitfish Siganus lineatus and the sea urchin Diadema setosum using tank, cage, and in situ experiments. All seven Lobophora species were markedly consumed in situ and by the two herbivores. Differences in consumption among the Lobophora species were small but statistically significant. Lobophora rosacea, characterized by a distinct secondary metabolome, was significantly more consumed by the two herbivores. Conversely, L. sonderi was always among the least consumed species. These results point to the possible role of chemical defense, and suggest that L. rosacea may produce less or different chemical deterrents than the other Lobophora species, and that L. sonderi may produce deterrents active over a wider range of herbivores. However, the limited interspecific differences in consumption point to the greater importance of associational and spatial refuges as defense strategies against herbivores over chemical or morphological defenses in the genus Lobophora

Colour plasticity in the shells and pearls of animal graft model Pinctada margaritifera assessed by HSV colour quantification

The bivalve Pinctada margaritifera has the capacity to produce the most varied and colourful pearls in the world. Colour expression in the inner shell is under combined genetic and environmental control and is correlated with the colour of pearls produced when the same individual is used as a graft donor. One major limitation when studying colour phenotypes is grader subjectivity, which leads to inconsistent colour qualification and quantification. Through the use of HSV (Hue Saturation Value) colour space, we created an R package named ‘ImaginR’ to characterise inner shell colour variations in P. margaritifera. Using a machine-learning protocol with a training dataset, ImaginR was able to reassign individual oysters and pearls to predefined human-based phenotype categories. We then tested the package on samples obtained in an experiment testing the effects of donor conditioning depth on the colour of the donor inner shell and colour of the pearls harvested from recipients following grafting and 20 months of culture in situ. These analyses successfully detected donor shell colour modifications due to depth-related plasticity and the maintenance of these modifications through to the harvested pearls. Besides its potential interest for standardization in the pearl industry, this new method is relevant to other research projects using biological models

Identifying genes associated with genetic control of color polymorphism in the pearl oyster Pinctada margaritifera var. cumingii (Linnaeus 1758) using a comparative whole genome pool‐sequencing approach

International audienceFor hundreds of years, the color diversity of Mollusca shells has been a topic of interest for humanity. However, the genetic control underlying color expression is still poorly understood in mollusks. The pearl oyster Pinctada margaritifera is increasingly becoming a biological model to study this process due to its ability to produce a large range of colors. Previous breeding experiments demonstrated that color phenotypes were partly under genetic control, and while a few genes were found in comparative transcriptomics and epigenetic experiments, genetic variants associated to the phenotypes have not yet been investigated. Here, we used a pooled-sequencing approach on 172 individuals to investigate color-associated variants on three color phenotypes of economic interest for pearl farming, in three wild and one hatchery populations. While our results uncovered SNPs targeting pigment-related genes already identified in previous studies, such as PBGD, tyrosinases, GST, or FECH, we also identified new colorrelated genes occurring in the same pathways, like CYP4F8, CYP3A4 and CYP2R1. Moreover, we identified new genes involved in novel pathways unknown to be involved in shell coloration for P. margaritifera, like the carotenoid pathway, BCO1. These findings are essential to possibly implement future breeding programs focused on individual selection for specific color production in pearl oysters and improve the footprint of perliculture on Polynesian lagoon by producing less, but with a better quality

Potential of high-throughput eDNA sequencing of soil fungi and bacteria for monitoring ecological restoration in ultramafic substrates: The case study of the New Caledonian biodiversity hotspot

International audienceDue to their central role in ecosystems functioning and their ability to rapidly respond to environmental changes, soil microorganisms could potentially be used for monitoring ecosystems recovery in the context of degraded land restoration. However, these belowground organisms have been, to date, largely neglected. Here, we investigated fungal and bacterial community diversity, composition, and structure from ultramafic soils in New Caledonia, an archipelago in the southwest Pacific recognized as a priority for conservation and restoration. The emerging approach of high-throughput amplicon sequencing of environmental DNA (eDNA)-metabarcoding of eDNAwas used to compare soil microbial communities from four different native vegetation types, representing different stages of a chronosequence and defined as reference ecosystems, to five distinct post-mining sites revegetated several years ago. Our results clearly revealed changes in soil microbial phyla and functional groups along the reference chronosequence and variable responses at the different revegetated sites, with two of the five sites showing a good trajectory of recovery. We thus propose three ratios as metrics for monitoring the restoration trajectory of soil microorganisms: the Ascomycota:Basidiomycota and Saprotrophic:Ectomycorrhizal ratios for fungi, and the Cyanobacteria:Chloroflexi ratios for bacteria. Our study, combined with recent works undertaken in other geographical areas, underpins the great promise that could represent soil microbial eDNA metabarcoding for monitoring restoration progress and success. With the emergence of these new cost-effective and scalable sequencing technologies, soil microbes could, in the near future, be included in guidelines for restoration operations in complement to more conventional approaches

Environmentally Driven Color Variation in the Pearl Oyster Pinctada margaritifera var. cumingii (Linnaeus, 1758) Is Associated With Differential Methylation of CpGs in Pigment- and Biomineralization-Related Genes

Today, it is common knowledge that environmental factors can change the color of many animals. Studies have shown that the molecular mechanisms underlying such modifications could involve epigenetic factors. Since 2013, the pearl oyster Pinctada margaritifera var. cumingii has become a biological model for questions on color expression and variation in Mollusca. A previous study reported color plasticity in response to water depth variation, specifically a general darkening of the nacre color at greater depth. However, the molecular mechanisms behind this plasticity are still unknown. In this paper, we investigate the possible implication of epigenetic factors controlling shell color variation through a depth variation experiment associated with a DNA methylation study performed at the whole genome level with a constant genetic background. Our results revealed six genes presenting differentially methylated CpGs in response to the environmental change, among which four are linked to pigmentation processes or regulations (GART, ABCC1, MAPKAP1, and GRL101), especially those leading to darker phenotypes. Interestingly, the genes perlucin and MGAT1, both involved in the biomineralization process (deposition of aragonite and calcite crystals), also showed differential methylation, suggesting that a possible difference in the physical/spatial organization of the crystals could cause darkening (iridescence or transparency modification of the biomineral). These findings are of great interest for the pearl production industry, since wholly black pearls and their opposite, the palest pearls, command a higher value on several markets. They also open the route of epigenetic improvement as a new means for pearl production improvement

First data on three bivalve species exposed to an intra-harbour polymetallic contamination (La Rochelle, France)

International audienceEvaluating diffuse sediment contamination in the environment is a major concern with the aim of reaching a good chemical and ecological state of the littoral zone. In this study the risks of chronic chemical contamination and consequences in the bivalves Crassostrea gigas, Mytilus sp. and Mimachlamys varia were evaluated in coastal environments. The objective here was to understand the anthropological phenomena that affect the functioning of the marina of La Rochelle (semi-closed environment). Harbours seeking ecomanagement accreditations (such as the international reference ISO 14001) constitute zones of interest to implement biomonitoring studies. The biological effects of chemical pollution in the Marina of La Rochelle were studied to develop a multi-biomarker biomonitoring approach on specific marine species of this site. Moreover, a genetic (DNA barcoding) approach was applied to validate the species identity of collected bivalves. Of the three species tested the scallop, M. varia, was the most sensitive to metal exposure

Molecular Pathways and Pigments Underlying the Colors of the Pearl Oyster Pinctada margaritifera var. cumingii (Linnaeus 1758)

The shell color of the Mollusca has attracted naturalists and collectors for hundreds of years, while the molecular pathways regulating pigment production and the pigments themselves remain poorly described. In this study, our aim was to identify the main pigments and their molecular pathways in the pearl oyster Pinctada margaritifera—the species displaying the broadest range of colors. Three inner shell colors were investigated—red, yellow, and green. To maximize phenotypic homogeneity, a controlled population approach combined with common garden conditioning was used. Comparative analysis of transcriptomes (RNA-seq) of P. margaritifera with different shell colors revealed the central role of the heme pathway, which is involved in the production of red (uroporphyrin and derivates), yellow (bilirubin), and green (biliverdin and cobalamin forms) pigments. In addition, the Raper–Mason, and purine metabolism pathways were shown to produce yellow pigments (pheomelanin and xanthine) and the black pigment eumelanin. The presence of these pigments in pigmented shell was validated by Raman spectroscopy. This method also highlighted that all the identified pathways and pigments are expressed ubiquitously and that the dominant color of the shell is due to the preferential expression of one pathway compared with another. These pathways could likely be extrapolated to many other organisms presenting broad chromatic variatio