Biology subjects

Planes, S.

Publications and source records attributed to Planes, S..

12 recordsLinked to original sources

bioRxiv2026

Diversity, host-specificity, and environmental drivers of the coral reef eukaryome

Coral reefs are among the most diverse ecosystems on Earth, yet the diversity and structure of their associated microeukaryotic communities remain poorly resolved. We characterized reef-associated eukaryomes across 113 reefs spanning the Pacific Ocean using more than 6,300 samples from corals, seawater, and sediments during the Tara Pacific expedition. We identified [~]121,000 eukaryotic ASVs, revealing one of Earths largest undocumented reservoirs of eukaryotic diversity; over 80% of the recovered diversity was previously undetected in global ocean surveys and fewer than 2% of sequences matched reference databases. Reef habitats supported highly distinct communities, with sediments and seawater harboring 20-40-fold higher richness than corals. Unexpectedly, coral-associated communities across 29 host lineages were consistently dominated by small metazoans, particularly demosponges and maxillopods, identifying these taxa as pervasive and previously unrecognized components of coral eukaryomes alongside Apicomplexa. Across the Pacific, eukaryome composition was strongly structured by environmental gradients, with thermal stress emerging as the primary driver of community turnover. Together, these results identify coral reefs as a globally important reservoir of hidden eukaryotic diversity and reveal the reef eukaryome as a sensitive indicator of ecosystem reorganization under climate change.

systems biology↗

bioRxiv2026

HIDDEN APICOMPLEXAN PARASITE DIVERSITY LINKS CORAL AND PLANKTON MICROBIOMES ACROSS REEF SEASCAPES

Parasitism is one of the most widespread trophic strategies in nature, though its diversity and ecological distribution in marine ecosystems remain poorly characterized. Apicomplexa are a major clade of obligate parasites best known for medically important taxa, yet their diversity and distribution in the ocean is still largely unresolved. Here, we used metabarcoding data from the Tara expeditions to investigate the diversity, distribution, and environmental drivers of Apicomplexa across coral reef ecosystems and adjacent oceanic habitats. By integrating samples spanning planktonic communities, coral tissues, and marine sediments across multiple oceanic regions, we substantially expand the known phylogenetic breadth of marine apicomplexans. Although apicomplexans were generally low in relative abundance, they were widely distributed across marine environments. Community composition differed markedly among habitats. Corallicolid lineages were consistently associated with coral hosts, whereas planktonic samples harbored a greater diversity of apicomplexans, dominated by crustacean-associated gregarines. Sediments contained particularly high apicomplexan richness, including several poorly characterized groups. Capitalizing on the pan-Pacific transect of the expedition, we resolved biogeographic patterns in apicomplexan diversity across ocean basins: tropical regions showed the highest overall diversity, while polar environments contained distinct apicomplexan assemblages not detected in other ocean biomes. Together, these results highlight the extensive and previously underappreciated diversity of marine Apicomplexa and demonstrate that integrating multiple marine biomes is essential for resolving the phylogenetic and ecological breadth of parasitism in the ocean.

genomics↗

bioRxiv2026

Ocean-scale transcriptomic analysis of corallicolids (Apicomplexa) reveals their ubiquity and molecular interactions with Pocillopora corals.

Corals are complex holobionts, encompassing numerous prokaryotes, viruses, and protists. This associated microbial community strongly influences coral health and its resilience to global ocean warming. Corallicolid apicomplexans are widespread coral-infecting parasites, yet their impact on the coral host remains poorly understood. This knowledge gap largely stems from the low abundance of these parasites in coral tissues, which makes them difficult to isolate and access to their genetic material. Here we analyzed nearly 1,000 Pocillopora coral colonies collected from 32 islands during the Tara Pacific expedition to identify the drivers of corallicolid prevalence and abundance. Corallicolids were detected in almost all Pocillopora colonies with variable relative abundances between islands. The high abundance of specific corallicolid populations correlates with seawater temperature and levels of host protein carbonylation. We used a large collection of 297 metatranscriptomes to assemble a corallicolid transcriptome and we identified apicomplexan parasite signature genes, including the GRA9 and PV2 confirming the close phylogenetic relationship with the family of Eimeriidae. Gene expression patterns indicate that the high abundance of corallicolids correlates with a high transcription of genes encoding apical complex proteins and genes involved in the control of host immune defenses. Overall, this study provides new insights into corallicolid biology and its interaction with the coral host by combining a newly generated transcriptome with a large-scale sampling of Pocillopora corals across the Pacific Ocean.

genomics↗

bioRxiv2024

Genome-resolved diversity and biosynthetic potential of the coral reef microbiome

Coral reefs are marine biodiversity hotspots that provide a wide range of ecosystem services. They are also reservoirs of bioactive compounds, many of which are produced by microbial symbionts associated with reef invertebrate hosts. However, for the keystone species of coral reefs--the reef-building corals themselves--we still lack a systematic assessment of their microbially encoded biosynthetic potential, and thus the molecular resources that may be at stake due to the alarming decline in reef biodiversity and cover. Here, we analysed microbial genomes reconstructed from 820 reef-building coral samples of three representative coral genera collected at 99 reefs across 32 islands during a two-year expedition throughout the Pacific Ocean (Tara Pacific). By contextualising our analyses with the microbiomes of other reef species, we found that genomic information was previously available for only 10% of the 4,224 microbial species overall and for less than 1% of the 645 species exclusively identified in Tara Pacific samples. We found reef-building coral microbiomes to be host-specific and their biosynthetic potential to rival or even surpass that found in traditional targets for natural product discovery, such as sponges and soft corals. Fire corals were not only particularly diverse in microbially encoded biosynthetic gene clusters (BGCs), but also in BGC-rich bacteria, including Acidobacteriota spp., which have been recently highlighted for their promising natural product repertoire. Together, this study unveils new candidate sources for bioactive compound discovery, prioritises targets for microbial isolation, and underscores the importance of conservation efforts by linking macro-organismal biodiversity loss to host-specific microbiomes and their biotechnological potential.

microbiology↗

bioRxiv2022

From genome wide SNPs to genomic islands of differentiation: the quest for species diagnostic markers in two scleractinian corals, Pocillopora and Porites

Coral reefs are of paramount importance in marine ecosystems, where they provide support for a large part of the biodiversity. Being quite sensitive to global changes, they are therefore the prime targets for biodiversity conservation policies. However, such conservation goals require accurate species identification, which are notoriously difficult to get in these highly morphologically variable organisms, rich in cryptic species. There is an acute need for easy-to-use and resolutive species diagnostic molecular markers. The present study builds on the huge sequencing effort developed during the TARA Pacific expedition to develop a genotyping strategy to assign coral samples to the correct species within two coral genera (Porites and Pocillopora). For this purpose, we developed a technique that we called "Divergent Fragment" based on the sequencing of a less than 2kb long diagnostic genomic fragment determined from the metagenomic data of a subset of the corals collected. This method has proven to be rapid, resolvable and cost-effective. Sequencing of PCR fragments nested along the species diagnostic fragment allowed us to assign 232 individuals of the genus Pocillopora and 247 individuals of the genus Porites to previously identified independent genetic lineages (i.e. species). This genotyping method will allow to fully analyze the coral samples collected across the Pacific during the Tara Pacific expedition and opens technological perspectives in the field of population genomics-guided conservation.

evolutionary biology↗

bioRxiv2022

Disparate patterns of genetic divergence in three widespread corals across a pan-Pacific environmental gradient highlights species-specific adaptation trajectories.

Tropical coral reefs are among the worst affected ecosystems by climate change with predictions ranging between a 70-90% loss of reefs in the coming decades. Effective conservation strategies that maximize ecosystem resilience, and potential for recovery, must be informed by the accurate characterization of extant genetic diversity and population structure together with an understanding of the adaptive potential of keystone species. Here, we analyzed samples from the Tara Pacific Expedition (2016 to 2018) that completed an 18,000 km longitudinal transect of the Pacific Ocean sampling three widespread corals - Pocillopora meandrina, Porites lobata, and Millepora cf. platyphylla - across 33 sites from 11 islands. Using deep metagenomic sequencing of 269 colonies in conjunction with morphological analyses and climate variability data we can show that the sampled transect encompasses multiple morphologically cryptic species that exhibit disparate biogeographic patterns, and most importantly, distinct evolutionary patterns, despite exposure to identical environmental regimes. Our findings demonstrate on a basin-scale that evolutionary trajectories are species-specific and complex, and can only in part be predicted from the environment. This highlights that conservation strategies must integrate multi-species investigations to consider the distinct genomic footprints shaped by selection as well as the genetic potential for adaptive change.

genetics↗

bioRxiv2022

Pervasive gene duplications as a major evolutionary driver of coral biology

Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central to these ecosystems, providing habitat and food to a great diversity of species. In the frame of the Tara Pacific expedition, we generated two coral genomes, Porites lobata and Pocillopora meandrina with vastly improved contiguity that allowed us to study the functional organisation of these genomes. We annotated their gene catalog and report a relatively higher gene number (43,000 and 32,000 genes respectively) than that found in other public coral genome sequences. This finding is explained by a high number of tandemly duplicated genes (almost a third of the predicted genes). We show that these duplicated genes originate from multiple and distinct duplication events throughout the coral lineage. They contribute to the amplification of gene families, mostly related to immune system and disease-resistance, which we suggest to be functionally linked to coral host resilience. At large, we show the importance of duplicated genes to inform the biology of reef-building corals and provide novel avenues to understand and screen for differences in stress resilience.

genomics↗

bioRxiv2020

Dual RNAseq highlights the kinetics of skin microbiome and fish host responsiveness to bacterial infection

a) BackgroundTenacibaculum maritimum is a worldwide-distributed fish pathogen known for causing dramatic damages on a broad range of wild and farmed marine fish populations. Recently sequenced genome of T. maritimum strain NCIMB 2154T provided unprecedented information on the possible molecular mechanisms involved in virulence for this species. However, little is known on the dynamic on the infection in vivo, and information are lacking on both the intrinsic host response (gene expression) and its associated microbiome community. Here, we applied complementary omic approaches, including dual RNAseq and 16S rRNA gene metabarcoding sequencing using Nanopore and short-reads Illumina technologies to unravel the host-pathogens interplay in experimental infection system using the tropical fish Platax orbicularis as model. b) ResultsWe show that T. maritimum transcriptomic landscape during infection is characterized by an enhancement of antibiotic catalytic and glucan catalytic functions while decreasing specific sulphate assimilation process, compared to in vitro cultures. Simultaneously, fish host display a large palette of immune effectors, notably involving innate response and triggering acute inflammatory response. In addition, results suggest that fish activate adaptive immune response visible through stimulation of T-helper cells, Th17, with congruent reduction of Th2 and T-regulatory cells. Fish were however largely sensitive to infection, and less than 25% of them survived after 96hpi. These surviving fish showed no evidence of stress (cortisol levels) as well as no significant difference in microbiome diversity compared to control at the same sampling time. The presence of Tenacibaculum in resistant fish skin and the total absence of any skin lesion suggest that these fish did not escape contact with the pathogen but rather prevent the pathogen entry. In these individuals we detected the up-regulation of specific immune-related genes differentiating resistant from control at 96hpi, which suggests a possible genomic basis of resistance while no genetic variations in coding regions was reported. c) ConclusionHere we refine the interplay between common fish pathogens and host immune response during experimental infection. We further highlight key actors of defense response, pathogenicity and possible genomic bases of resistance to T. maritimum.

genomics↗

bioRxiv2020

A framework for in situ molecular characterization of coral holobionts using nanopore sequencing

Molecular characterization of the coral host and the microbial assemblages associated with it (referred to as the coral holobiont) is currently undertaken via marker gene sequencing. This requires bulky instruments and controlled laboratory conditions which are impractical for environmental experiments in remote areas. Recent advances in sequencing technologies now permit rapid sequencing in the field; however, development of specific protocols and pipelines for the effective processing of complex microbial systems are currently lacking. Here, we used a combination of 3 marker genes targeting the coral animal host, its symbiotic alga, and the associated bacterial microbiome to characterize 60 coral colonies collected and processed in situ, during the Tara Pacific expedition. We used Oxford Nanopore Technologies to sequence marker gene amplicons and developed bioinformatics pipelines to analyze nanopore reads on a laptop, obtaining results in less than 24 hours. Reef scale network analysis of coral-associated bacteria reveals broadly distributed taxa, as well as host-specific associations. Protocols and tools used in this work may be applicable for rapid coral holobiont surveys, immediate adaptation of sampling strategy in the field, and to make informed and timely decisions in the context of the current challenges affecting coral reefs worldwide.

genomics↗

bioRxiv2019

Kinship does not predict the structure of a shark social network

Genetic relatedness in animal societies is often a factor that drives the structure of social groups. In the marine world, most studies which have investigated this question have focused on marine mammals such as whales and dolphins. For sharks, recent studies have demonstrated preferential associations among individuals from which social communities emerge. Assortment patterns have been found according to phenotypic or behavioural traits but the role of genetic relatedness in shaping the social structure of adult shark populations has, to the best our knowledge, never been investigated. Here, we used a social network analysis crossed with DNA microsatellite genotyping to investigate the role of the genetic relatedness in the social structure of a blacktip reef shark (Carcharhinus melanopterus) population. Based on data from 156 groups of sharks, we used generalized affiliation indices to isolate social preferences from non-social associations, controlling for the contribution of sex, size, gregariousness, spatial and temporal overlap on social associations, to test for the influence of genetic relatedness on social structure. A double permutation procedure was employed to confirm our results and account for issues arising from potentially elevated type I and type II error rates. Kinship was not a predictor of associations and affiliations among sharks at the dyad or community levels as individuals tended to associate independently of the genetic relatedness among them. The lack of parental care in this species may contribute to the breakdown of family links in the population early in life, thereby preventing the formation of kin-based social networks.

animal behavior and cognition↗

bioRxiv2019

A DNA barcode reference library of the French Polynesian shore fishes

The emergence of DNA barcoding and metabarcoding opened new ways to study biological diversity, however, the completion of DNA barcode libraries is fundamental for such approaches to succeed. This dataset is a DNA barcode reference library (fragment of Cytochrome Oxydase I gene) for 2,190 specimens representing at least 540 species of shore fishes collected over 10 years at 154 sites across the four volcanic archipelagos of French Polynesia; the Austral, Gambier, Marquesas and Society Islands, a 5,000,000 km2 area. At present, 65% of the known shore fish species of these archipelagoes possess a DNA barcode associated with preserved, photographed, tissue sampled and cataloged specimens, and extensive collection locality data. This dataset represents one of the most comprehensive DNA barcoding efforts for a vertebrate fauna to date. Considering the challenges associated with the conservation of coral reef fishes and the difficulties of accurately identifying species using morphological characters, this publicly available library is expected to be helpful for both authorities and academics in various fields.

zoology↗

bioRxiv2018

Dispersal limitations of early life stages and sibling aggregations in a broadcasting Millepora hydrocoral, as revealed by parentage analysis

Dispersal is a critical process for the persistence and productivity of marine populations. For many reef species, there is increasing evidence that local demography and self-recruitment have major consequences on their genetic diversity and adaptation to environmental change. Yet empirical data of dispersal patterns in reef-building species remain scarce. Here, we document the first genetic estimates of local dispersal and self-recruitment in a broadcasting reef-builder, the hydrocoral Millepora platyphylla. Using microsatellite markers, we gathered genotypic information from 3160 georeferenced colonies collected over 9000 m2 of reef in three adjacent habitats in Moorea, French Polynesia; the mid slope, upper slope and back reef. Our parentage analysis revealed a predominance of self-recruitment with 58% of sexual propagules produced locally. Sexual propagules often settled at less than 10 meters from their parents and dispersal events decrease with increasing geographic distance. Limited dispersal among adjacent habitats via cross-reef transport was also detected. Sibship analysis showed that both full and half siblings recruit together on the reef, resulting in sibling aggregations. The identification of local families revealed discrepancies between dispersal patterns of sexual and asexual propagules. Self-recruits are dispersed with along-reef currents and settled in alignment with the location of their parents, while the dispersal of asexual fragments is heavily influenced by wave-driven cross-reef currents. Our findings highlight the importance of self-recruitment together with clonality in stabilising population dynamics, as it can enhance local sustainability and resilience to disturbance, but also raise uncertainties on the widely accepted high dispersal ability of broadcasting reef species.

ecology↗