Cnidarian Interaction with Microbial Communities: From Aid to Animal's Health to Rejection Responses

Cassiopea xamachana microbiome across anatomy, development, and geography

The upside-down jellyfish holobiont, Cassiopea xamachana, is a useful model system for tri-partite interactions between the cnidarian host, the photosymbiont, and the bacterial microbiome. While the interaction between the host and photosymbiont has been well studied, less is understood of the associated bacterial community. To date, the bacterial microbiome of wild C. xamachana has remained largely uncharacterized. Thus, wild medusae (n=6) and larvae (n=3) were collected from two sites in the Florida Keys. Bacterial community composition was characterized via amplicon sequencing of the 16S rRNA gene V4 region. The medusa bacterial community was dominated by members of the Alphaproteobacteria and Gammaproteobacteria, while Planctomycetota, Actinomycetota, Bacteroidota, and Bacillota were also present, among others. Community composition was consistent between locations and across medusa structures (oral arm, bell, and gonad). The larval bacterial community clustered apart from the medusa community in beta diversity analysis and was characterized by the presence of several Pseudomonadota taxa that were not present in the medusa, including the Alteromonas, Pseudoalteromonas, and Thalassobius genera. A bacterial isolate library encompassing much of the amplicon sequencing diversity was also developed and tested via metabolic assays in a separate culture-dependent analysis of isolates from medusa bells, oral arms, and laplets. Most characteristics were not correlated with host sex or medusa structure, but gelatinase production was more common in laplet isolates, while lactose fermentation was more common in female oral arm isolates. The Endozoicomonas genus was dominant in both amplicon sequencing and in our isolate library, and was equally prevalent across all medusa structures and in both sexes. Understanding the bacterial component of the C. xamachana holobiont will allow us to further develop this important model cnidarian holobiont.

Chlamydiae in corals: shared functional potential despite broad taxonomic diversity

Cnidarians, such as corals and sea anemones, associate with a wide range of bacteria that have essential functions, including nutrient cycling and the production of antimicrobial compounds. Within cnidarians, bacteria can colonize all microhabitats including the tissues. Among them are obligate intracellular bacteria of the phylum Chlamydiota (chlamydiae) whose impact on cnidarian hosts and holobionts, especially corals, remain unknown. Here, we conducted a meta-analysis of previously published 16S rRNA gene metabarcoding data from cnidarians (e.g. coral, jellyfish, and anemones), eight metagenome-assembled genomes (MAGs) of coral-associated chlamydiae, and one MAG of jellyfish-associated chlamydiae to decipher their diversity and functional potential. While the metabarcoding dataset showed an enormous diversity of cnidarian-associated chlamydiae, six out of nine MAGs were affiliated with the Simkaniaceae family. The other three MAGs were assigned to the Parasimkaniaceae, Rhabdochlamydiaceae, and Anoxychlamydiaceae, respectively. All MAGs lacked the genes necessary for an independent existence, lacking any nucleotide or vitamin and most amino acid biosynthesis pathways. Hallmark chlamydial genes, such as a type III secretion system, nucleotide transporters, and genes for host interaction, were encoded in all MAGs. Together these observations suggest an obligate intracellular lifestyle of coral-associated chlamydiae. No unique genes were found in coral-associated chlamydiae, suggesting a lack of host specificity. Additional studies are needed to understand how chlamydiae interact with their coral host, and other microbes in coral holobionts. This first study of the diversity and functional potential of coral-associated chlamydiae improves our understanding of both the coral microbiome and the chlamydial lifestyle and host range.

The Effect of Pollen on Coral Health

Corals are facing a range of threats, including rises in sea surface temperature and ocean acidification. Some now argue that keeping corals ex situ (in aquaria), may be not only important but necessary to prevent local extinction, for example in the Florida Reef Tract. Such collections or are already becoming common place, especially in the Caribbean, and may act as an ark, preserving and growing rare or endangered species in years to come. However, corals housed in aquaria face their own unique set of threats. For example, hobbyists (who have housed corals for decades) have noticed seasonal mortality is commonplace, incidentally following months of peak pollen production. So, could corals suffer from hay fever? If so, what does the future hold? In short, the answer to the first question is simple, and it is no, corals cannot suffer from hay fever, primarily because corals lack an adaptive immune system, which is necessary for the diagnosis of such an allergy. However, the threat from pollen could still be real. In this review, we explore how such seasonal mortality could play out. We explore increases in reactive oxygen species, the role of additional nutrients and how the microbiome of the pollen may introduce disease or cause dysbiosis in the holobiont.

Systematic review of cnidarian microbiomes reveals insights into the structure, specificity, and fidelity of marine associations

Microorganisms play essential roles in the health and resilience of cnidarians. Understanding the factors influencing cnidarian microbiomes requires cross study comparisons, yet the plethora of protocols used hampers dataset integration. We unify 16S rRNA gene sequences from cnidarian microbiome studies under a single analysis pipeline. We reprocess 12,010 cnidarian microbiome samples from 186 studies, alongside 3,388 poriferan, 370 seawater samples, and 245 cultured Symbiodiniaceae, unifying ~6.5 billion sequence reads. Samples are partitioned by hypervariable region and sequencing platform to reduce sequencing variability. This systematic review uncovers an incredible diversity of 86 archaeal and bacterial phyla associated with Cnidaria, and highlights key bacteria hosted across host sub-phylum, depth, and microhabitat. Shallow (< 30 m) water Alcyonacea and Actinaria are characterized by highly shared and relatively abundant microbial communities, unlike Scleractinia and most deeper cnidarians. Utilizing the V4 region, we find that cnidarian microbial composition, richness, diversity, and structure are primarily influenced by host phylogeny, sampling depth, and ocean body, followed by microhabitat and sampling date. We identify host and geographical generalist and specific Endozoicomonas clades within Cnidaria and Porifera. This systematic review forms a framework for understanding factors governing cnidarian microbiomes and creates a baseline for assessing stress associated dysbiosis.

Selecting 16S rRNA Primers for Microbiome Analysis in a Host-Microbe System: The Case of the Jellyfish Rhopilema nomadica

Amplicon sequencing of the 16S rRNA gene is extensively used to characterize bacterial communities, including those living in association with eukaryotic hosts. Deciding which region of the 16S rRNA gene to analyze and selecting the appropriate PCR primers remains a major decision when initiating any new microbiome study. Based on a detailed literature survey of studies focusing on cnidarian microbiomes, we compared three commonly used primers targeting different hypervariable regions of the 16S rRNA gene, V1V2, V3V4, and V4V5, using the jellyfish Rhopilema nomadica as a model. Although all primers exhibit a similar pattern in bacterial community composition, the performance of the V3V4 primer set was superior to V1V2 and V4V5. The V1V2 primers misclassified bacteria from the Bacilli class and exhibited low classification resolution for Rickettsiales, which represent the second most abundant 16S rRNA gene sequence in all the primers. The V4V5 primer set detected almost the same community composition as the V3V4, but the ability of these primers to also amplify the eukaryotic 18S rRNA gene may hinder bacterial community observations. However, after overcoming the challenges possessed by each one of those primers, we found that all three of them show very similar bacterial community dynamics and compositions. Nevertheless, based on our results, we propose that the V3V4 primer set is potentially the most suitable for studying jellyfish-associated bacterial communities. Our results suggest that, at least for jellyfish samples, it may be feasible to directly compare microbial community estimates from different studies, each using different primers but otherwise similar experimental protocols. More generally, we recommend specifically testing different primers for each new organism or system as a prelude to large-scale 16S rRNA gene amplicon analyses, especially of previously unstudied host-microbe associations.

The complex role of microbial metabolic activity in fossilization

Bacteria play an important role in the fossilization of soft tissues; their metabolic activities drive the destruction of the tissues and also strongly influence mineralization. Some environmental conditions, such as anoxia, cold temperatures, and high salinity, are considered widely to promote fossilization by modulating bacterial activity. However, bacteria are extremely diverse, and have developed metabolic adaptations to a wide range of stressful conditions. Therefore, the influence of the environment on bacterial activity, and of their metabolic activity on fossilization, is complex. A number of examples illustrate that simple, general assumptions about the role of bacteria in soft tissue fossilization cannot explain all preservational pathways: (i) experimental results show that soft tissues of cnidaria decay less in oxic than anoxic conditions, and in the fossil record are found more commonly in fossil sites deposited under oxic conditions rather than anoxic environments; (ii) siderite concretions, which often entomb soft tissue fossils, precipitate due to a complex mixture of sulfate- and iron reduction by some bacterial species, running counter to original theories that iron reduction is the primary driver of siderite concretion growth; (iii) arthropod brains, now widely accepted to be preserved in many Cambrian fossil sites, are one of the first structures to decay in taphonomic experiments, indicating that their fossilization processes are complex and influenced by bacterial activity. In order to expand our understanding of the complex process of bacterially driven soft tissue fossilization, more research needs to be done, on fossils themselves and in taphonomic experiments, to determine how the complex variation in microbial metabolic activity influences decay and mineralization.

Mesoglea Extracellular Matrix Reorganization during Regenerative Process in Anemonia viridis (Forskål, 1775)

Given the anatomical simplicity and the extraordinary ability to regenerate missing parts of the body, Cnidaria represent an excellent model for the study of the mechanisms regulating regenerative processes. They possess the mesoglea, an amorphous and practically acellular extracellular matrix (ECM) located between the epidermis and the gastrodermis of the body and tentacles and consists of the same molecules present in the ECM of vertebrates, such as collagen, laminin, fibronectin and proteoglycans. This feature makes cnidarians anthozoans valid models for understanding the ECM role during regenerative processes. Indeed, it is now clear that its role in animal tissues is not just tissue support, but instead plays a key role during wound healing and tissue regeneration. This study aims to explore regenerative events after tentacle amputation in the Mediterranean anemone Anemonia viridis, focusing in detail on the reorganization of the ECM mesoglea. In this context, both enzymatic, biometric and histological experiments reveal how this gelatinous connective layer plays a fundamental role in the correct restoration of the original structures by modifying its consistency and stiffness. Indeed, through the deposition of collagen I, it might act as a scaffold and as a guide for the reconstruction of missing tissues and parts, such as amputated tentacles.

Differences in the microbiota of native and non-indigenous gelatinous zooplankton organisms in a low saline environment

The translocation of non-indigenous species (NIS) around the world, especially in marine systems, is increasingly being recognized as a matter of concern. Species translocations have been shown to lead to wide ranging changes in food web structure and functioning. In addition to the direct effects of NIS, they could facilitate the accumulation or translocation of bacteria as part of their microbiomes. The Baltic Sea harbours many non-indigenous species, with most recent detection of the jellyfish Blackfordia virginica and the comb jelly Mnemiopsis leidyi in the low saline southwestern Baltic Sea. In this study, we used a multidisciplinary approach and investigated three gelatinous zooplankton species that co-occur in the same environment and feed on similar zooplankton food sources but show different histories of origin. The aim was to conduct a comparative microbiome analysis of indigenous and non-indigenous gelatinous zooplankton species in the low-saline southwestern Baltic Sea. Next-generation 16S rRNA marker gene sequencing of the V1/V2 region was employed to study the bacterial microbiome compositions. All tested species showed significant differences in their microbiome compositions (one way ANOSIM, R = 1, P < 0.008) with dissimilarities ranging from 85 to 92%. The indigenous jellyfish Aurelia aurita showed the highest bacterial operational taxonomic unit (OTU) richness. The overall differentiation between microbiomes was driven by eight indicator OTUs, which included Mycoplasma and Vibrio species. These bacteria can be problematic, as they include known pathogenic strains that are relevant to human health and aquaculture activities. Our results suggest that the impact assessment of NIS should consider potential pathogenic bacteria, enriched in the environment due to invasion, as potential risks to aquaculture activities.

The Microbial Community Associated with Rhizostoma pulmo: Ecological Significance and Potential Consequences for Marine Organisms and Human Health

Jellyfish blooms are frequent and widespread in coastal areas worldwide, often associated with significant ecological and socio-economic consequences. Recent studies have also suggested cnidarian jellyfish may act as vectors of bacterial pathogens. The scyphomedusa Rhizostoma pulmo is an outbreak-forming jellyfish widely occurring across the Mediterranean basin. Using combination of culture-based approaches and a high-throughput amplicon sequencing (HTS), and based on available knowledge on a warm-affinity jellyfish-associated microbiome, we compared the microbial community associated with R. pulmo adult jellyfish in the Gulf of Taranto (Ionian Sea) between summer (July 2016) and winter (February 2017) sampling periods. The jellyfish-associated microbiota was investigated in three distinct compartments, namely umbrella, oral arms, and the mucus secretion. Actinobacteria, Bacteroidetes, Chlamydiae, Cyanobacteria, Deinococcus-Thermus, Firmicutes, Fusobacteria, Planctomycetes, Proteobacteria, Rhodothermaeota, Spirochaetes, Tenericutes, and Thaumarchaeota were the phyla isolated from all the three R. pulmo compartments in the sampling times. In particular, the main genera Mycoplasma and Spiroplasma, belonging to the class Mollicutes (phylum Tenericutes), have been identified in all the three jellyfish compartments. The taxonomic microbial data were coupled with metabolic profiles resulting from the utilization of 31 different carbon sources by the BIOLOG Eco-Plate system. Microorganisms associated with mucus are characterized by great diversity. The counts of culturable heterotrophic bacteria and potential metabolic activities are also remarkable. Results are discussed in terms of R. pulmo ecology, the potential health hazard for marine and human life as well as the potential biotechnological applications related to the associated microbiome.

Jellyfish summer outbreaks as bacterial vectors and potential hazards for marine animals and humans health? The case of Rhizostoma pulmo (Scyphozoa, Cnidaria)

Jellyfish represent an important component of marine food webs characterized by large fluctuations of population density, with the ability to abruptly form outbreaks, followed by rarity periods. In spite of considerable efforts to investigate how jellyfish populations are responding globally to anthropogenic change, available evidence still remains unclear. In the last 50 years, jellyfish are seemingly on the rise in a number of coastal areas, including the Mediterranean Sea, where jellyfish blooms periodically become an issue to marine and maritime human activities. Their impacts on marine organism welfare have been poorly quantified. The jellyfish, Rhizostoma pulmo, is an outbreak-forming scyphomedusa whose large populations spread across the Mediterranean, with increasing periodicity and variable abundance. Studies on cnidarian jellyfish suggested being important vectors of bacterial pathogens. In the present study, by combination of conventional culture-based methods and a high-throughput amplicon sequencing (HTS) approach, we characterized the diversity of the bacterial community associated with this jellyfish during their summer outbreak. Three distinct jellyfish compartments, namely umbrella, oral arms, and the mucus secretion obtained from whole specimens were screened for specifically associated microbiota. A total of 17 phyla, 30 classes, 73 orders, 146 families and 329 genera of microbial organisms were represented in R. pulmo samples with three major clades (i.e. Spiroplasma, Mycoplasma and Wolinella) representing over 90% of the retrieved total sequences. The taxonomic microbial inventory was then combined with metabolic profiling data obtained from the Biolog Eco-Plate system. Significant differences among the jellyfish compartments were detected in terms of bacterial abundance, diversity and metabolic utilization of 31 different carbon sources with the highest value of abundance and metabolic potential in the mucus secretion compared to the umbrella and oral arms. Results are discussed in the framework of the species ecology as well as the potential health hazard for marine organisms and humans.

The role of chromatin dynamics under global warming response in the symbiotic coral model Aiptasia

Extreme weather events frequency and scale are altered due to climate change. Symbiosis between corals and their endosymbiotic-dinoflagellates (Symbiodinium) is susceptible to these events and can lead to what is known as bleaching. However, there is evidence for coral adaptive plasticity in the role of epigenetic that have acclimated to high-temperature environments. We have implemented ATAC-seq and RNA-seq to study the cnidarian-dinoflagellate model Exaptasia pallida (Aiptasia) and expose the role of chromatin-dynamics in response to thermal-stress. We have identified 1309 genomic sites that change their accessibility in response to thermal changes. Moreover, apo-symbiotic Aiptasia accessible sites were enriched with NFAT, ATF4, GATA3, SOX14, and PAX3 motifs and expressed genes related to immunological pathways. Symbiotic Aiptasia accessible sites were enriched with NKx3-1, HNF4A, IRF4 motifs and expressed genes related to oxidative-stress pathways. Our work opens a new path towards understanding thermal-stress gene regulation in association with gene activity and chromatin-dynamics.

Jellyfish-Associated Microbiome in the Marine Environment: Exploring Its Biotechnological Potential

Despite accumulating evidence of the importance of the jellyfish-associated microbiome to jellyfish, its potential relevance to blue biotechnology has only recently been recognized. In this review, we emphasize the biotechnological potential of host⁻microorganism systems and focus on gelatinous zooplankton as a host for the microbiome with biotechnological potential. The basic characteristics of jellyfish-associated microbial communities, the mechanisms underlying the jellyfish-microbe relationship, and the role/function of the jellyfish-associated microbiome and its biotechnological potential are reviewed. It appears that the jellyfish-associated microbiome is discrete from the microbial community in the ambient seawater, exhibiting a certain degree of specialization with some preferences for specific jellyfish taxa and for specific jellyfish populations, life stages, and body parts. In addition, different sampling approaches and methodologies to study the phylogenetic diversity of the jellyfish-associated microbiome are described and discussed. Finally, some general conclusions are drawn from the existing literature and future research directions are highlighted on the jellyfish-associated microbiome.