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Coral reefs are considered one of the most emblematic ecosystems in our oceans, but their existence is increasingly threatened by climate change. In this study, natural populations of two reef-building coral genera, Pocillopora spp. and Porites spp., and one hydrocoral Millepora cf. platyphylla from two different marine provinces in the Pacific Ocean were investigated using a multi-omics approach as part of the Tara Pacific expedition. Here, we propose a standardised method consisting of a biphasic extraction method followed by metabolomics analysis using mass spectrometry for the lipidome and ¹H nuclear magnetic resonance for hydrophilic metabolites. Our study assessed a broad range of the metabolome and is the first to identify and add 24 compounds by NMR and over 200 lipids by MS analyses for corals. Metabolic profiles were distinct among genera but not within genotypes of the cnidarian corals. Although endosymbiotic dinoflagellates of the family Symbiodiniaceae are known to play a central role in the metabolomic signature of the coral holobiont, they did not account for all differences. This suggests that a combined effect by different members of the coral holobiont and an interaction with the environment might be at play. Our study provides foundational knowledge on the coral holobiont metabolome. Communications Earth & Environment, 4 (1) ISSN:2662-4435

With climate projections questioning the future survival of stony corals and their dominance as tropical reef builders, it is critical to understand the adaptive capacity of corals to ongoing climate change. Biological mediation of the carbonate chemistry of the coral calcifying fluid is a fundamental component for assessing the response of corals to global threats. The Tara Pacific expedition (2016–2018) provided an opportunity to investigate calcification patterns in extant corals throughout the Pacific Ocean. Cores from colonies of the massive Porites and Diploastrea genera were collected from different environments to assess calcification parameters of long-lived reef-building corals. At the basin scale of the Pacific Ocean, we show that both genera systematically up-regulate their calcifying fluid pH and dissolved inorganic carbon to achieve efficient skeletal precipitation. However, while Porites corals increase the aragonite saturation state of the calcifying fluid (Ωcf) at higher temperatures to enhance their calcification capacity, Diploastrea show a steady homeostatic Ωcf across the Pacific temperature gradient. Thus, the extent to which Diploastrea responds to ocean warming and/or acidification is unclear, and it deserves further attention whether this is beneficial or detrimental to future survival of this coral genus. International audience

The family of Malacoherpesviridae is currently represented by only two viruses infecting molluscs, Ostreid herpesvirus 1 (OsHV-1) and Haliotid herpesvirus 1 (HaHV-1), both causing detrimental infections in aquaculture species. Malacoherpesvirus-like sequences were also detected through genome sequencing projects in amphioxus (Branchiostoma species) and annelid worm (Capitella teleta), suggesting the existence of a hidden diversity of malacoherpesviruses in aquatic animals. Here, to extend the knowledge on malacoherpesvirus diversity, we searched for the presence of malacoherpesvirus relatives in genomic, transcriptomic and metagenomic datasets, including from the Tara Oceans expedition, and report 4 novel malacoherpesvirus-like genomes (MalacoHV1-4). Genomic analysis suggested gastropods and bivalves as the most probable hosts for these new malacoherpesviruses. Phylogenetic analysis based on the family B DNA polymerase placed the novel MalacoHV1 and MalacoHV3 as sister lineages of OsHV-1 and HaHV-1, respectively, whereas MalacoHV2 and MalacoHV4 showed higher divergence. The viral genome found associated with amphioxus together with MalacoHV4 formed a sister clade to the mollusc and annelid malacoherpesviruses, suggesting an early divergence of the two virus assemblages. In conclusion, although relatively rare in the available sequence databases, the previously undescribed malacoherpesviruses, MalacoHV1-4, circulate in aquatic ecosystems and should be considered as possible emerging viruses under changing environmental conditions. International audience

Tropical coral reefs are among the most affected ecosystems by climate change and face increasing loss in the coming decades. Effective conservation strategies that maximize ecosystem resilience 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 (2016–2018) 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 despite a targeted sampling the transect encompasses multiple cryptic species. These species exhibit disparate biogeographic patterns and, most importantly, distinct evolutionary patterns in identical environmental regimes. Our findings demonstrate on a basin scale that evolutionary trajectories are species-specific and can only in part be predicted from the environment. This highlights that conservation strategies must integrate multi-species investigations to discern the distinct genomic footprints shaped by selection as well as the genetic potential for adaptive change. published

AbstractPublic sequencing databases contain vast amounts of biological information, yet they are largely underutilized as one cannot efficiently search them for any sequence(s) of interest. We presentkmindex, an innovative approach that can index thousands of highly complex metagenomes and perform sequence searches in a fraction of a second. The index construction is an order of magnitude faster than previous methods, while search times are two orders of magnitude faster. With negligible false positive rates below 0.01%,kmindexoutperforms the precision of existing approaches by four orders of magnitude. We demonstrate the scalability ofkmindexby successfully indexing 1,393 complex marine seawater metagenome samples from theTaraOceans project. Additionally, we introduce the publicly accessible web server “Ocean Read Atlas” (ORA) athttps://ocean-read-atlas.mio.osupytheas.fr/, which enables real-time queries on theTaraOceans dataset. The open-sourcekmindexsoftware is available athttps://github.com/tlemane/kmindex.

Abstract Coral reefs are among the most diverse ecosystems on Earth. They support high biodiversity of multicellular organisms that strongly rely on associated microorganisms for health and nutrition. However, the extent of the coral reef microbiome diversity and its distribution at the oceanic basin-scale remains to be explored. Here, we systematically sampled 3 coral morphotypes, 2 fish species, and planktonic communities in 99 reefs from 32 islands across the Pacific Ocean, to assess reef microbiome composition and biogeography. We show a very large richness of reef microorganisms compared to other environments, which extrapolated to all fishes and corals of the Pacific, approximates the current estimated total prokaryotic diversity for the entire Earth. Microbial communities vary among and within the 3 animal biomes (coral, fish, plankton), and geographically. For corals, the cross-ocean patterns of diversity are different from those known for other multicellular organisms. Within each coral morphotype, community composition is always determined by geographic distance first, both at the island and across ocean scale, and then by environment. Our unprecedented sampling effort of coral reef microbiomes, as part of the Tara Pacific expedition, provides new insight into the global microbial diversity, the factors driving their distribution, and the biocomplexity of reef ecosystems. International audience

Background: 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 coral reef ecosystems, providing habitat to a great diversity of species. Results: In the frame of the Tara Pacific expedition, we assemble two coral genomes, Porites lobata and Pocillopora cf. effusa, with vastly improved contiguity that allows us to study the functional organization of these genomes. We annotate their gene catalog and report a relatively higher gene number than that found in other public coral genome sequences, 43,000 and 32,000 genes, respectively. This finding is explained by a high number of tandemly duplicated genes, accounting for 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 the immune system and disease resistance, which we suggest to be functionally linked to coral host resilience. Conclusions: 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. Genome Biology, 24 (1) ISSN:1474-760X