Immune parameter data

This archive file contains the data files for the expression levels of the range of immune parameters presented in the manuscript: 1) Chromoprotein expression levels, 2) Fluorescent protein expression levels, 3) Immune gene expression levels and 4) PO and tpPO activity levels. Each file contains a description of the samples and sample names used

Fluorescent Protein Analysis Methodology

This archive file contains the files required for the fluorescent protein spectral analysis. The input file Wounding_Aaspera_fl.csv containing the raw fluorescence values and sample protein concentration is provided along with the reference fluorescent protein data file modelspecs_interp_25sh.csv (based on the spectrum of purified Acropora millepora fluorescent proteins) and the spectral decomposition script specs_regression_WF.R. The reference fluorescent protein data and the script were provided by Mikhail Matz

Host-microbe interactions in octocoral holobionts - recent advances and perspectives

Abstract Octocorals are one of the most ubiquitous benthic organisms in marine ecosystems from the shallow tropics to the Antarctic deep sea, providing habitat for numerous organisms as well as ecosystem services for humans. In contrast to the holobionts of reef-building scleractinian corals, the holobionts of octocorals have received relatively little attention, despite the devastating effects of disease outbreaks on many populations. Recent advances have shown that octocorals possess remarkably stable bacterial communities on geographical and temporal scales as well as under environmental stress. This may be the result of their high capacity to regulate their microbiome through the production of antimicrobial and quorum-sensing interfering compounds. Despite decades of research relating to octocoral-microbe interactions, a synthesis of this expanding field has not been conducted to date. We therefore provide an urgently needed review on our current knowledge about octocoral holobionts. Specifically, we briefly introduce the ecological role of octocorals and the concept of holobiont before providing detailed overviews of (I) the symbiosis between octocorals and the algal symbiont Symbiodinium; (II) the main fungal, viral, and bacterial taxa associated with octocorals; (III) the dominance of the microbial assemblages by a few microbial species, the stability of these associations, and their evolutionary history with the host organism; (IV) octocoral diseases; (V) how octocorals use their immune system to fight pathogens; (VI) microbiome regulation by the octocoral and its associated microbes; and (VII) the discovery of natural products with microbiome regulatory activities. Finally, we present our perspectives on how the field of octocoral research should move forward, and the recognition that these organisms may be suitable model organisms to study coral-microbe symbioses

16S rRNA amplicon sequencing - QIIME analysis

This archive file contains all input and output files required for and produced by the QIIME pipeline in the 'dataset' folder. The quality file Wound.qual and the sequence file Wound.fna along with the mapping files Map.txt and Map_corrected2.txt are the primary input files. Output files include the complete selection of OTU tables (otu_table.biom, Normalised_otu_table.biom as well the weighted and unweighted Unifrac tables). Additional special files required for analysis can be found in the 'input' folder. The script 'QIIME Analysis script.txt' was used for data analysis and the file 'Sample names.txt' should be used to determine the biological sample / treatment corresponding to each sample. Sequences have been deposited in the NCBI Sequence Read Archive (SRA) database under study accession number SRP052969

Holobiont responses of mesophotic precious red coral Corallium rubrum to thermal anomalies

Abstract Marine heat waves (MHWs) have increased in frequency and intensity worldwide, causing mass mortality of benthic organisms and loss of biodiversity in shallow waters. The Mediterranean Sea is no exception, with shallow populations of habitat-forming octocorals facing the threat of local extinction. The mesophotic zone, which is less affected by MHWs, may be of ecological importance in conservation strategies for these species. However, our understanding of the response of mesophotic octocoral holobionts to changes in seawater temperature remains limited. To address this knowledge gap, we conducted a study on an iconic Mediterranean octocoral, the red coral Corallium rubrum sampled at 60 m depth and 15 °C. We exposed the colonies to temperatures they occasionally experience (18 °C) and temperatures that could occur at the end of the century if global warming continues (21 °C). We also tested their response to extremely cold and warm temperatures (12 °C and 24 °C). Our results show a high tolerance of C. rubrum to a two-month long exposure to temperatures ranging from 12 to 21 °C as no colony showed signs of tissue loss, reduced feeding ability, stress-induced gene expression, or disruption of host-bacterial symbioses. At 24 °C, however, we measured a sharp decrease in the relative abundance of Spirochaetaceae, which are the predominant bacterial symbionts under healthy conditions, along with a relative increase in Vibrionaceae. Tissue loss and overexpression of the tumor necrosis factor receptor 1 gene were also observed after two weeks of exposure. In light of ongoing global warming, our study helps predict the consequences of MHWs on mesophotic coralligenous reefs and the biodiversity that depends on them

Absence of skeleton deposition in juveniles of the scleractinian coral Acropora millepora

[Extract] Deposition of aragonite skeletons by scleractinian corals typically starts immediately after larval settlement and metamorphosis. However, following the November 2011 coral mass spawning event, we observed that many of our experimental Acropora millepora recruits still lacked a skeleton at 30 days following spawning

Ultra-violet radiation has a limited impact on seasonal differences in the acropora muricata holobiont

International audienceEnvironmental conditions are known to influence corals and their associated communities of microorganisms. However, our insights into the impacts of seasonal changes in ultraviolet radiation (UVR) on both coral physiology and microbiome remain very limited. To address this challenge, we maintained the coral Acropora muricata shaded from UVR or under ambient UVR levels during two contrasting seasons, i.e. summer and winter, and assessed the impact of UVR on the coral holobiont at each season. To this end, we analyzed the physiology (e.g., calcification, protein content, photosynthesis-related parameters) and coral microbiota composition, as well as the abundance and composition of the microbial communities and organic matter contents of the surrounding seawater. Our results show major seasonal effects on coral phenotype: (1) a lower host biomass and photosynthesizing, but fast calcifying phenotype in summer, and (2) a higher host biomass and photosynthesizing, but slow calcifying phenotype in winter. UVR had only a significant impact on Symbiodinium functioning. Specifically, high UVR levels reduced photosynthesis efficiency in summer, but an increase in chlorophyll a content may have compensated for this effect. The coral microbiota, which was variable but generally dominated by Endozoicomonas, was not affected by UVR, but its composition differed between seasons. In contrast, UVR had a major, but differential impact on the seawater microbial communities at both seasons. Particularly in summer, bacteria from the Alteromonadaceae were significantly more abundant (15-fold; up to 75%) in seawater under ambient UVR levels. Overall, our study suggests that UVR has only a limited impact on coral holobiont composition and functioning, despite major fluctuations in the surrounding seawater microbiome; seasonal changes in the holobiont are thus mostly driven by other environmental factors

Temporal patterns in innate immunity parameters in reef-building corals and linkages with local climatic conditions

Extremes in seasonal environmental conditions can significantly impact the health and physiological functioning of reef corals, underscoring the need for knowledge of seasonally specific baselines from which to monitor and forecast impending stress. Increases above summertime means in seawater temperature, sunlight intensity, turbidity, or sedimentation may reduce coral immunocompetency and increase disease and bleaching susceptibility. We analyzed temporal patterns in innate immunity parameters over nine time points throughout one year to establish baseline levels from which anomalies might be detected for representative species from three major reef-building coral families (Acroporidae, Faviidae, and Poritidae). Temporal patterns in both phenoloxidase activity and expression of green fluorescent protein-like proteins varied among the three families, as did overall constitutive levels. For example, Porites cylindrica had 2.8-fold higher yearly average levels of phenoloxidase activity than Acropora millepora, which had the lowest levels. In contrast, mean fluorescence was lowest in Acropora millepora and highest in Echinopora mammiformis. Relationships between the potential physical drivers (seasonal variation in seawater temperature, rainfall, salinity) and temporal patterns in these parameters also differed among the three species. For example, phenoloxidase activity was positively correlated with seawater temperature in A. millepora, but negatively correlated in both E. mammiformis and P. cylindrica. Distinctions in constitutive levels and temporal patterns in these parameters among species suggest that corals from these three families have evolved different strategies for investing resources into innate immune parameters. Such differences highlight the need for species-specific baselines and long-Term assessments to accurately predict coral reef trajectories in rapidly changing environments

Comparative immune responses of corals to stressors associated with offshore reef-based tourist platforms

Unravelling the contributions of local anthropogenic and seasonal environmental factors in suppressing the coral immune system is important for prioritizing management actions at reefs exposed to high levels of human activities. Here, we monitor health of the model coral Acropora millepora adjacent to a high-use and an unused reef-based tourist platform, plus a nearby control site without a platform, over 7 months spanning a typical austral summer. Comparisons of temporal patterns in a range of biochemical and genetic immune parameters (Toll-like receptor signalling pathway, lectin-complement system, prophenoloxidase-activating system and green fluorescent protein-like proteins) among healthy, injured and diseased corals revealed that corals exhibit a diverse array of immune responses to environmental and anthropogenic stressors. In healthy corals at the control site, expression of genes involved in the Toll-like receptor signalling pathway (MAPK p38, MEKK1, cFos and ATF4/5) and complement system (C3 and Bf) was modulated by seasonal environmental factors in summer months. Corals at reef platform sites experienced additional stressors over the summer, as evidenced by increased expression of various immune genes, including MAPK p38 and MEKK1. Despite increased expression of immune genes, signs of white syndromes were detected in 31% of study corals near tourist platforms in the warmest summer month. Evidence that colonies developing disease showed reduced expression of genes involved in the complement pathway prior to disease onset suggests that their immune systems may have been compromised. Responses to disease and physical damage primarily involved the melanization cascade and GFP-like proteins, and appeared to be sufficient for recovery when summer heat stress subsided. Overall, seasonal and anthropogenic factors may have interacted synergistically to overwhelm the immune systems of corals near reef platforms, leading to increased disease prevalence in summer at these sites

Diazotrophic community and associated dinitrogen fixation within the temperate coral Oculina patagonica

Dinitrogen (N-2) fixing bacteria (diazotrophs) are an important source of new nitrogen in oligotrophic environments and represent stable members of the microbiome in tropical corals, while information on corals from temperate oligotrophic regions is lacking. Therefore, this study provides new insights into the diversity and activity of diazotrophs associated with the temperate coral Oculina patagonica from the Mediterranean Sea by combining metabarcoding sequencing of amplicons of both the 16S rRNA and nifH genes and N-15(2) stable isotope tracer analysis to assess diazotroph-derived nitrogen (DDN) assimilation by the coral. Results show that the diazotrophic community of O. patagonica is dominated by autotrophic bacteria (i.e. Cyanobacteria and Chlorobia). The majority of DDN was assimilated into the tissue and skeletal matrix, and DDN assimilation significantly increased in bleached corals. Thus, diazotrophs may constitute an additional nitrogen source for the coral host, when nutrient exchange with Symbiodinium is disrupted (e.g. bleaching) and external food supply is limited (e.g. oligotrophic summer season). Furthermore, we hypothesize that DDN can facilitate the fast proliferation of endolithic algae, which provide an alternative carbon source for bleached O. patagonica. Overall, O. patagonica could serve as a good model for investigating the importance of diazotrophs in coral recovery from bleaching