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Seasonal Stability in the Microbiomes of Temperate Gorgonians and the Red Coral Corallium Rubrum Across the Mediterranean Sea

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Seasonal Stability in the Microbiomes of Temperate Gorgonians and the Red Coral Corallium Rubrum Across the Mediterranean Sea Erschienen in: Microbial ecology ; 75 (2018), 1. - S. 274-288 https://dx.doi.org/10.1007/s00248-017-1006-y Seasonal Stability in the Microbiomes of Temperate Gorgonians and the Red Coral Corallium rubrum Across the Mediterranean Sea Jeroen A. J. M. van de Water1 & Christian R. Voolstra2 & Cecile Rottier1 & Silvia Cocito3 & Andrea Peirano3 & Denis Allemand1 & Christine Ferrier-Pagès1 Abstract Populations of key benthic habitat-forming relatively consistent over time at each location for each octocoral species have declined significantly in the octocoral species. However, differences in microbiome com- Mediterranean Sea due to mass mortality events caused by position and seasonal dynamics were observed between loca- microbial disease outbreaks linked to high summer seawater tions and could primarily be attributed to locally variant bac- temperatures. Recently, we showed that the microbial commu- teria. Overall, our data provide further evidence of the intricate nities of these octocorals are relatively structured; however, symbiotic relationships that exist between Mediterranean our knowledge on the seasonal dynamics of these octocorals and their associated microbes, which are ancient microbiomes is still limited. To investigate their seasonal sta- and highly conserved over both space and time, and suggest bility, we collected four soft gorgonian species (Eunicella regulation of the microbiome composition by the host, de- singularis, Eunicella cavolini, Eunicella verrucosa and pending on local conditions. Leptogorgia sarmentosa) and the precious red coral (Corallium rubrum) from two coastal locations with different Keywords Endozoicomonas . Spirochaetes . Red coral . terrestrial impact levels in the Mediterranean Sea, and used Gorgonian . 16S rRNA gene . Bacterial community . next-generation amplicon sequencing of the 16S rRNA gene. Holobiont . Evolution . Microbiome . Symbiosis The microbiomes of all soft gorgonian species were dominat- ed by the same ‘core microbiome’ bacteria belonging to the Endozoicomonas and the Cellvibrionales clade BD1-7, Introduction whereas the red coral microbiome was primarily composed of ‘core’ Spirochaetes, Oceanospirillales ME2 and The ‘holobiont’ is a collective term for the inter-kingdom Parcubacteria. The associations with these bacterial taxa were assemblages of host organisms and their microbial symbionts, including bacteria, archaea, viruses, fungi and algae. Bacterial symbioses have been recognized as essential for the health of eukaryotes and are integral to their adaptation and acclimation potential to environmental change [1, 2]. Increasing research efforts have endeavoured to identify the specific and obligate * Jeroen A. J. M. van de Water symbioses between prokaryotes and corals, among the thou- [email protected] sands of bacterial phylotypes associated with individual coral colonies [3]. Recent studies have shown that the coral ‘ ’ 1 Centre Scientifique de Monaco, 8 Quai Antoine 1er, holobiont contains a core microbiome [4, 5], consisting of 98000 Monaco, Monaco microbes that are consistently found within a species, as well 2 Red Sea Research Center, Division of Biological and Environmental as microbes whose presence depends on local conditions, and Science and Engineering (BESE), King Abdullah University of transient microbial associates [6, 7]. While the functional roles Science and Technology (KAUST), Thuwal 23955-6900, Saudi of the cnidarian-associated microbiota are still largely un- Arabia known, they have been implicated in many services beneficial 3 Marine Environment Research Centre, ENEA, La Spezia, Italy to the host, such as nitrogen fixation [8, 9], sulphur-cycling Konstanzer Online-Publikations-System (KOPS) URL: http://nbn-resolving.de/urn:nbn:de:bsz:352-2-tptc3cnfpcgl1 275 [10] and microbiome regulation through the secretion of anti- Mediterranean Sea at a clear and turbid location. We show biotics [11–14] and exclusion of pathogens by occupying (1) that the microbiomes associated with octocorals are dis- available microbial niches [15, 16]. As such, it is essential tinct from the microbial communities in the surrounding sea- for holobiont fitness to maintain a stable multi-functional mi- water and (2) that the highly structured bacterial assemblages crobial community. In contrast to the highly diverse are stable over time, but that local conditions may influence microbiomes of tropical corals, Mediterranean octocorals microbial community composition. Overall, our results pro- have been shown to harbour highly structured bacterial assem- vide new insights into the unique, specific associations be- blages dominated for >90% by only a few species [17, 18], tween gorgonians and their microbial symbionts. making them ideal model organisms to study cnidarian- microbe interactions. In the Mediterranean Sea, gorgonians are the most impor- Material and Methods tant habitat-forming species of benthic communities, contrib- uting significantly to the structural complexity, biomass and Study Species and Sampling Regime biodiversity of these ecosystems [19]. The success of gorgo- nians can at least in part be attributed to the specific symbioses Octocoral samples were collected at 30–40 m depth near with bacteria, which were recently found to be relatively sta- Cassis, France (43° 12′ N05°28′ E) and at 16–20 m depth ble across spatial scales [7, 18]. In species belonging to the on Dante Shoal near La Spezia, Italy (44° 01′ N09°50′ E) Gorgoniidae family, bacteria from the genus Endozoicomonas every 3 months (±1–2 weeks) between May 2014 and have been found to be the most prevalent [20–23], with some July 2015 (Fig. 1;Table1). The La Spezia sampling location lesser contributions from clade BD1-7 [7]. Endozoicomonas is characterized by high turbidity, which is highest in spring- have been found in numerous marine invertebrates and have summer and the lowest in fall-winter (total suspended solids been identified as crucial to the health of corals (expertly concentration ranging between 1.61 and 2.65 mg L−1 [37]) reviewed in [24]), with a loss of these bacteria having a severe and is the result of terrestrial runoff from the Magra River negative impact on holobiont functioning. In tropical and sewage from the city of La Spezia, both of which get octocorals and deep-sea gorgonians, especially the precious caught up in the westward Ligurian current [38]. In contrast, red coral Corallium rubrum, Spirochaetes may be one of the the sampling location near Cassis is not impacted by terrestrial (co-)dominant microbial associates [18, 25, 26], which may runoff, as no river is present within a 60 km radius, and sew- play roles in nitrogen and carbon fixation, as seen in the age input from the town of ~7000 inhabitants is limited, cor- Spirochaete-termite symbiosis [27, 28]. The spatial stability responding with low turbidity levels. While Eunicella of these bacteria-host associations, which may reside in the singularis, Eunicella verrucosa and Leptogorgia sarmentosa same habitat and location, suggests strong selection mecha- were sampled at both locations; samples of Corallium rubrum nisms employed by the holobiont of Mediterranean gorgo- and Eunicella cavolini were only obtained near Cassis as these nians. Indeed, gorgonian tissue extracts are known to interfere species were not present at the La Spezia location. Fragments with bacterial quorum-sensing and have potent antimicrobial of five visually healthy colonies that did not show any mac- activity [29–32]. Local disturbances and elevated seawater roscopic signs of epibiosis or partial mortality, were collected temperatures have, however, been linked to disruptions in at each location and time point, with the exception of the microbiome of gorgonians [7, 33]. Recent mass mortality July 2015 when only three replicate fragments were collected events caused by microbial disease outbreaks and thermal at Cassis. Samples were rinsed twice with 0.2-μm filtered anomalies have resulted in significant population declines seawater to remove exogenous, loosely associated microor- [34, 35]. This suggests that shifts in the gorgonian microbiome ganisms and stored in ice-cold RNAlater (ThermoFisher towards an ‘unhealthy’, dysbiotic state could occur on a sea- Scientific) at 4 °C. In addition, three samples of 2 l of seawater sonal scale, particularly during the summer months. each were collected next to the octocoral colonies and filtered Mediterranean octocorals experience large variations in sea- sequentially through 8, 3 and 0.2-μm Whatman Nuclepore water temperatures, from a minimum of 12 °C in winter to at Track-Etched filters (Sigma-Aldrich), and the retentate was least23°Cinsummer[36] and may experience significant kept in RNAlater at 4 °C. river discharges, which brings sediment, turbidity and pollu- tion, following rain in coastal areas, particularly in spring and DNA Extraction and 16S rRNA Gene Amplicon Library autumn. It is therefore important to understand the seasonal Preparation variability in the gorgonian-associated bacterial assemblages or determine whether it is as stable as across spatial scales. To extract DNA from tissues and seawater filter retentate, we Here, we describe the temporal patterns in the microbiome used the Genomic DNA buffer set and Genomic-tip 20/G of five closely (genera Eunicella and Leptogorgia) and dis- columns (QIAGEN, Hilden, Germany) following the manu- tantly (genus Corallium) related octocorals from the facturer’s sample preparation and lysis protocol for tissues— 276 libraries of the red
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