Metabolomic profiling reveals deep chemical divergence between two morphotypes of the zoanthid Parazoanthus axinellae

Divergence in metabolomic profile in clownfish and damselfish skin mucus

Introduction

The clownfish - sea anemone mutualism was suggested to have triggered the adaptive radiation of clownfishes, but the origin of clownfish resistance to stinging tentacles of host anemones remains unclear. The presence of specific compounds in the mucus of clownfishes conferring them the unique ability to prevent nematocyst discharge from their hosts has been the most supported hypothesis. Yet the mystery regarding the types of compounds found in clownfish skin mucus remains unsolved.

Methods

We analyzed the chemical composition of clownfish and damselfish mucus using an untargeted metabolomics (HILIC-HRMS) and lipidomics (RPLC-HRMS) approach.

Results and Discussion

The polar and lipid metabolome signatures were highly specific and allowed to discriminate between the clownfish and damselfish clades. The most discriminative part of the signature was the sphingolipid profile, displaying a broader diversity of ceramides present in significantly higher levels in clownfish mucus. Importantly, the inter-specific variability of metabolic signature was significantly higher in clownfishes, although their diversification is evolutionarily more recent, thus implying the impact of symbiosis on metabolic variability and adaptation. Furthermore, specialists and generalists clownfish species displayed distinctive metabolite signature. Two strict clownfish specialists, which are phylogenetically distant but share the same host species, clustered together based on their molecular signature, suggesting a link with their mutualistic nature. Overall, comparative analyses of metabolic signatures highlight differences in chemical composition of clownfish mucus and provide insight into biochemical pathways potentially implicated in clownfish adaptation to inhabit sea anemones and consequently diversify.

Metabolomics on the study of marine organisms

BACKGROUND

Marine ecosystems are hosts to a vast array of organisms, being among the most richly biodiverse locations on the planet. The study of these ecosystems is very important, as they are not only a significant source of food for the world but also have, in recent years, become a prolific source of compounds with therapeutic potential. Studies of aspects of marine life have involved diverse fields of marine science, and the use of metabolomics as an experimental approach has increased in recent years. As part of the "omics" technologies, metabolomics has been used to deepen the understanding of interactions between marine organisms and their environment at a metabolic level and to discover new metabolites produced by these organisms.

AIM OF REVIEW

This review provides an overview of the use of metabolomics in the study of marine organisms. It also explores the use of metabolomics tools common to other fields such as plants and human metabolomics that could potentially contribute to marine organism studies. It deals with the entire process of a metabolomic study, from sample collection considerations, metabolite extraction, analytical techniques, and data analysis. It also includes an overview of recent applications of metabolomics in fields such as marine ecology and drug discovery and future perspectives of its use in the study of marine organisms.

KEY SCIENTIFIC CONCEPTS OF REVIEW

The review covers all the steps involved in metabolomic studies of marine organisms including, collection, extraction methods, analytical tools, statistical analysis, and dereplication. It aims to provide insight into all aspects that a newcomer to the field should consider when undertaking marine metabolomics.

Marine Biodiscovery in a Changing World

The term "marine biodiscovery" has been recently been adopted to describe the area of marine natural products dedicated to the search of new drugs. Several maritime countries such as Australia, New Zealand, South Korea, and Japan as well as some European countries have invested significantly in this area of research over the last 50 years. In the late 2000s, research in this field has received significant interest and support in Ireland for exploring new marine bioresources from the nutrient-rich waters of the Northeastern Atlantic Ocean. Despite undeniable success exemplified by the marketing of new drugs, especially in oncology, the integration of new technical but also environmental aspects should be considered. Indeed, global change, particularly in our oceans, such as climate change, biodiversity loss, and the emergence of microbial pathogens, not only affects the environment but ultimately contributes to social inequalities. In this contribution, new avenues and best practices are proposed, such as the development of biorepositories and shared data for the future of marine biodiscovery research. The extension of this type of scientific work will allow humanity to finally make the optimum use of marine bioresources.

Comparison of sequence-capture and ddRAD approaches in resolving species and populations in hexacorallian anthozoans

Genome-level sequencing is the next step in understanding species-level relationships within Anthozoa (soft corals, anemones, stony corals, and their kin) as morphological and PCR-directed (single-locus) sequencing methods often fall short of differentiating species. The sea anemone genus Metridium is a common northern temperate sea anemone whose species are difficult to differentiate using morphology alone. Here we use Metridium as a case study to confirm the low level of information available in six loci for species differentiation commonly sequenced for Actiniaria and explore and compare the efficacy of ddRAD and sequence-capture methods in species-level systematics and biogeographic studies. We produce phylogenetic trees from concatenated datasets and perform DAPC and STRUCTURE analyses using SNP data. The six conventional loci are not able to consistently differentiate species within Metridium. The sequence-capture dataset resulted in high support and resolution for both current species and relationships between geographic areas. The ddRAD datasets displayed ambiguity among species, and support between major geographic groupings was not as high as the sequence-capture datasets. The level of resolution and support resulting from the sequence-capture data, combined with the ability to add additional individuals and expand beyond the genus Metridium over time, emphasizes the utility of sequence-capture methods for both systematics and future biogeographic studies within anthozoans. We discuss the strengths and weaknesses of the genomic approaches in light of our findings and suggest potential implications for the biogeography of Metridium based on our sampling.

Evidence of genetic isolation between two Mediterranean morphotypes of Parazoanthus axinellae

Coralligenous assemblages are among the most species-rich and vulnerable habitats of the Mediterranean Sea. Nevertheless, data on connectivity patterns on species inhabiting these habitats, crucial to define management and protection priorities, are largely lacking. Moreover, unreliable species-level taxonomy can confound ecological studies and mislead management strategies. In the northwestern Mediterranean two Parazoanthus axinellae morphotypes differing in size, color and preferred substrate are found in sympatry. In this study, we used COI and ITS sequence polymorphism to assess (1) the genetic divergence between the two morphotypes, (2) their connectivity patterns and (3) their phylogenetic position within the Parazoanthidae. Specimens of P. axinellae were sampled in 11 locations along the northwestern Mediterranean; in 6 locations, samples of the two morphotypes were collected in sympatry. Small genetic diversity and structure were found within morphotypes, while marked and consistent differentiation was detected between them. Moreover, the less widespread morphotype appeared to be closer to Pacific species as P. juanfernandezii and P. elongatus. Our findings confirmed the limited knowledge on Parazoanthus species complex, and how this gap can have important implication for the conservation strategies of this widespread and valuable genus in the Mediterranean Sea.

Marine natural products from zoantharians: bioactivity, biosynthesis, systematics, and ecological roles

The dazzling marine zoantharians represent a reservoir of chemical diversity that remains to be unveiled. These fragile animals have so far been found to harbour the highly bioactive palytoxins or zoanthamines but also the harmless ecdysteroids or zoanthozanthins.

Metabolomic variability of four macroalgal species of the genus Lobophora using diverse approaches

Among comparative metabolomic studies used in marine sciences, only few of them are dedicated to macroalgae despite their ecological importance in marine ecosystems. Therefore, experimental data are needed to assess the scopes and limitations of different metabolomic techniques applied to macroalgal models. Species of the genus Lobophora belong to marine brown algae (Family: Dictyotaceae) and are widely distributed, especially in tropical coral reefs. The species richness of this genus has only been unveiled recently and it includes species of diverse morphologies and habitats, with some species interacting with corals. This study aims to assess the potential of different metabolomic fingerprinting approaches in the discrimination of four well known Lobophora species (L. rosacea, L. sonderii, L. obscura and L. monticola). These species present distinct morphologies and are found in various habitats in the New Caledonian lagoon (South-Western Pacific). We compared and combined different untargeted metabolomic techniques: liquid chromatography-mass spectrometry (LC-MS), nuclear magnetic resonance (1H-NMR) and gas chromatography (GC-MS). Metabolomic separations were observed between each Lobophora species, with significant differences according to the techniques used. LC-MS was the best approach for metabotype distinction but a combination of approaches was also useful and allowed identification of chemomarkers for some species. These comparisons provide important data on the use of metabolomic approaches in the Lobophora genus and will pave the way for further studies on the sources of metabolomic variations for this ecologically important macroalgae.

Halogenated Tyrosine Derivatives from the Tropical Eastern Pacific Zoantharians Antipathozoanthus hickmani and Parazoanthus darwini

In the search for bioactive marine natural products from zoantharians of the Tropical Eastern Pacific, four new tyrosine dipeptides, named valdiviamides A-D (1-4), were isolated from Antipathozoanthus hickmani, and two new tyramine derivatives, 5 and 6, from Parazoanthus darwini. The phenols of all six tyrosine derivatives are substituted by bromine and/or iodine atoms at the ortho positions of the hydroxyl. The planar structures of these aromatic alkaloids were elucidated from 1D and 2D NMR experiments in combination with HRESIMS data, and the absolute configurations of 1-4 were deduced from comparison between experimental and calculated electronic circular dichroism spectra. As halogenated tyrosine derivatives could represent chemotaxonomic markers of these genera, we decided to undertake the first chemical investigation of another species, Terrazoanthus cf. patagonichus. As expected, no halogenated metabolite was evidenced in the species, but we report herein the identification of two new zoanthoxanthin derivatives, named zoamides E (7) and F (8), from this species. Antimicrobial and cytotoxicity bioassays revealed that valdiviamide B (2) displayed moderate cytotoxicity against the HepG2 cell line with an IC₅₀ value of 7.8 μM.

Response diversity in Mediterranean coralligenous assemblages facing climate change: Insights from a multispecific thermotolerance experiment

Climate change threatens coastal benthic communities on a global scale. However, the potential effects of ongoing warming on mesophotic temperate reefs at the community level remain poorly understood. Investigating how different members of these communities will respond to the future expected environmental conditions is, therefore, key to anticipating their future trajectories and developing specific management and conservation strategies. Here, we examined the responses of some of the main components of the highly diverse Mediterranean coralligenous assemblages to thermal stress. We performed thermotolerance experiments with different temperature treatments (from 26 to 29°C) with 10 species from different phyla (three anthozoans, six sponges and one ascidian) and different structural roles. Overall, we observed species-specific contrasting responses to warming regardless of phyla or growth form. Moreover, the responses ranged from highly resistant species to sensitive species and were mostly in agreement with previous field observations from mass mortality events (MMEs) linked to Mediterranean marine heat waves. Our results unravel the diversity of responses to warming in coralligenous outcrops and suggest the presence of potential winners and losers in the face of climate change. Finally, this study highlights the importance of accounting for species-specific vulnerabilities and response diversity when forecasting the future trajectories of temperate benthic communities in a warming ocean.

NR3E receptors in cnidarians: A new family of steroid receptor relatives extends the possible mechanisms for ligand binding

Steroid hormone receptors are important regulators of development and physiology in bilaterian animals, but the role of steroid signaling in cnidarians has been contentious. Cnidarians produce steroids, including A-ring aromatic steroids with a side-chain, but these are probably made through pathways different than the one used by vertebrates to make their A-ring aromatic steroids. Here we present comparative genomic analyses indicating the presence of a previously undescribed nuclear receptor family within medusozoan cnidarians, that we propose to call NR3E. This family predates the diversification of ERR/ER/SR in bilaterians, indicating that the first NR3 evolved in the common ancestor of the placozoan and cnidarian-bilaterian with lineage-specific loss in the anthozoans, even though multiple species in this lineage have been shown to produce aromatic steroids, whose function remain unclear. We discovered serendipitously that a cytoplasmic factor within epidermal cells of transgenic Hydra vulgaris can trigger the nuclear translocation of heterologously expressed human ERα. This led us to hypothesize that aromatic steroids may also be present in the medusozoan cnidarian lineage, which includes Hydra, and may explain the translocation of human ERα. Docking experiments with paraestrol A, a cnidarian A-ring aromatic steroid, into the ligand-binding pocket of Hydra NR3E indicates that, if an aromatic steroid is indeed the true ligand, which remains to be demonstrated, it would bind to the pocket through a partially distinct mechanism from the manner in which estradiol binds to vertebrate ER.

Assessing the Zoantharian Diversity of the Tropical Eastern Pacific through an Integrative Approach

Zoantharians represent a group of marine invertebrates widely distributed from shallow waters to the deep sea. Despite a high diversity and abundance in the rocky reefs of the Pacific Ocean, very few studies have been reported on the diversity of this group in the Tropical Eastern Pacific coasts. While molecular techniques recently clarified some taxonomic relationships within the order, the taxonomy of zoantharians is still highly challenging due to a lack of clear morphological characters and confusing use of different data in previous studies. Our first insight into the zoantharian diversity at El Pelado Marine Protected Area - Ecuador led to the identification of six species: Terrazoanthus patagonichus; Terrazoanthus sp.; Antipathozoanthus hickmani; Parazoanthus darwini; Zoanthus cf. pulchellus; and Zoanthus cf. sociatus. A metabolomic approach using UHPLC-HRMS was proven to be very efficient as a complementary tool in the systematics of these species and specialized metabolites of the ecdysteroid and alkaloid families were identified as key biomarkers for interspecific discrimination. These results show good promise for an application of this integrative approach to other zoantharians.

Metabolomic Profiles of Dinophysis acuminata and Dinophysis acuta Using Non-Targeted High-Resolution Mass Spectrometry: Effect of Nutritional Status and Prey

Photosynthetic species of the genus Dinophysis are obligate mixotrophs with temporary plastids (kleptoplastids) that are acquired from the ciliate Mesodinium rubrum, which feeds on cryptophytes of the Teleaulax-Plagioselmis-Geminigera clade. A metabolomic study of the three-species food chain Dinophysis-Mesodinium-Teleaulax was carried out using mass spectrometric analysis of extracts of batch-cultured cells of each level of that food chain. The main goal was to compare the metabolomic expression of Galician strains of Dinophysis acuminata and D. acuta that were subjected to different feeding regimes (well-fed and prey-limited) and feeding on two Mesodinium (Spanish and Danish) strains. Both Dinophysis species were able to grow while feeding on both Mesodinium strains, although differences in growth rates were observed. Toxin and metabolomic profiles of the two Dinophysis species were significantly different, and also varied between different feeding regimes and different prey organisms. Furthermore, significantly different metabolomes were expressed by a strain of D. acuminata that was feeding on different strains of the ciliate Mesodinium rubrum. Both species-specific metabolites and those common to D. acuminata and D. acuta were tentatively identified by screening of METLIN and Marine Natural Products Dictionary databases. This first metabolomic study applied to Dinophysis acuminata and D.acuta in culture establishes a basis for the chemical inventory of these species.

Ecdysonelactones, Ecdysteroids from the Tropical Eastern Pacific Zoantharian Antipathozoanthus hickmani

Despite a large occurrence, especially over the Pacific Ocean, the chemical diversity of marine invertebrates belonging to the order Zoantharia is largely underexplored. For the two species of the genus Antipathozoanthus no chemical study has been reported so far. The first chemical investigation of Antipathozoanthus hickmani collected at the Marine Protected Area “El Pelado”, Santa Elena, Ecuador, led to the isolation of four new ecdysteroid derivatives named ecdysonelactones. The structures of ecdysonelactones A–D (1–4) were determined based on their spectroscopy data, including 1D and 2D NMR and HRMS. The four compounds of this family of ecdysteroids feature an unprecedented γ-lactone fused at the C-2/C-3 position of ring A. These derivatives exhibited neither antimicrobial nor cytotoxic activities.

Inter- and Intraspecific Variability of Nitrogenated Compounds in Gorgonian Corals via Application of a Fast One-Step Analytical Protocol

Gorgonian corals play a structural role in temperate and tropical biogenic reefs, forming animal forests and creating biodiversity hot spots. In the Mediterranean Sea, slow-growing and long-lived gorgonian species are threatened by human disturbances and global environmental changes and concern about their conservation is rising. Alkaloid metabolites have proven to be essential in protecting these species from environmental stressors. Traditional profiling methodologies to detect these metabolites require a large quantity of living tissue. Here, the chemodiversity of gorgonian alkaloids was investigated by applying a fast and effective protocol combining extraction and derivatization using small-scale tissue samples and GC/MS analysis. The method was effective in identifying and quantifying alkaloids and guanine-based compounds. Eight N-heterocyclic compounds were found in six Mediterranean gorgonians differing for types and quantity. The metabolomic profile was conservative in species of the Eunicella genus, with three species sharing the same pattern. Conversely, Paramuricea clavata displayed a noticeable spatial pattern of variation among colonies collected in different locations. The analytical approach presented here proved to be effective, allowing rare, endangered, and small-sized species to be screened rapidly for detection of new compounds in order to explore their biological and ecological functions.

Chemical profiling of two congeneric sea mat corals along the Brazilian coast: adaptive and functional patterns

Multisource metabolomics of two congeneric sea mat corals along the Brazilian coast suggested the major influence of environment on chemical divergence.

Bio-invasive ascidians in Ireland: A threat for the shellfish industry but also a source of high added value products

In October 2016, a rapid assessment survey of ascidian species was conducted in shellfish farms at Killary Fjord, in the west of Ireland. Two non-indigenous solitary ascidians Ascidiella aspersa and Corella eumoyta were recorded for the first time in shellfish farms at this location. Both invasive ascidians have the potential to greatly reduce mussel production in Killary Fjord by competing with shellfish for food and habitat. Their high abundance also causes an increase in maintenance costs leading to economic losses for aquaculture farmers. Prompted by our finding of two invasive ascidians in Killary Fjord, we provide a brief review of the ecological role of ascidians and the potential of harnessing biomass from such invasive species for the production of high added value marine natural products.

Passive Sampling and High Resolution Mass Spectrometry for Chemical Profiling of French Coastal Areas with a Focus on Marine Biotoxins

Passive samplers (solid phase adsorption toxin tracking: SPATT) are able to accumulate biotoxins produced by microalgae directly from seawater, thus providing useful information for monitoring of the marine environment. SPATTs containing 0.3, 3, and 10 g of resin were deployed at four different coastal areas in France and analyzed using liquid chromatography coupled to high resolution mass spectrometry. Quantitative targeted screening provided insights into toxin profiles and showed that toxin concentrations and profiles in SPATTs were dependent on the amount of resin used. Between the three amounts of resin tested, SPATTs containing 3 g of resin appeared to be the best compromise, which is consistent with the use of 3 g of resin in SPATTs by previous studies. MassHunter and Mass Profiler Professional softwares were used for data reprocessing and statistical analyses. A differential profiling approach was developed to investigate and compare the overall chemical diversity of dissolved substances in different coastal water bodies. Principal component analysis (PCA) allowed for spatial differentiation between areas. Similarly, SPATTs retrieved from the same location at early, medium, and late deployment periods were also differentiated by PCA, reflecting seasonal variations in chemical profiles and in the microalgal community. This study used an untargeted metabolomic approach for spatial and temporal differentiation of marine environmental chemical profiles using SPATTs, and we propose this approach as a step forward in the discovery of chemical markers of short- or long-term changes in the microbial community structure.

Secondary Metabolome Variability and Inducible Chemical Defenses in the Mediterranean Sponge Aplysina cavernicola

Secondary metabolites play a crucial role in marine invertebrate chemical ecology. Thus, it is of great importance to understand factors regulating their production and sources of variability. This work aimed to study the variability of the bromotyrosine derivatives in the Mediterranean sponge Aplysina cavernicola, and also to better understand how biotic (reproductive state) and abiotic factors (seawater temperature) could partly explain this variability. Results showed that the A. cavernicola reproductive cycle has little effect on the variability of the sponges' secondary metabolism, whereas water temperature has a significant influence on the production level of secondary metabolites. Temporal variability analysis of the sponge methanolic extracts showed that bioactivity variability was related to the presence of the minor secondary metabolite dienone, which accounted for 50 % of the bioactivity observed. Further bioassays coupled to HPLC extract fractionation confirmed that dienone was the only compound from Aplysina alkaloids to display a strong bioactivity. Both dienone production and bioactivity showed a notable increase in October 2008, after a late-summer warming episode, indicating that A. cavernicola might be able to induce chemical changes to cope with environmental stressors.