Jellyfish-associated bacterial communities and bacterioplankton in Indonesian Marine lakes

Diversity, composition and potential roles of sedimentary microbial communities in different coastal substrates around subtropical Okinawa Island, Japan

BACKGROUND

Marine benthic prokaryotic communities play crucial roles in material recycling within coastal environments, including coral reefs. Coastal sedimentary microbiomes are particularly important as potential reservoirs of symbiotic, beneficial, and pathogenic bacteria in coral reef environments, and therefore presumably play a core role in local ecosystem functioning. However, there is a lack of studies comparing different environments with multiple sites on the island scale, particularly studies focusing on prokaryotic communities, as previous investigations have focused mainly on a single site or on specific environmental conditions. In our study, we collected coastal sediments from seven sites around Okinawa Island, Japan, including three different benthic types; sandy bottoms, seagrass meadows, and hard substratum with living scleractinian corals. We then used metabarcoding to identify prokaryotic compositions and estimate enzymes encoded by genes to infer their functions.

RESULTS

The results showed that the three substrata had significantly different prokaryotic compositions. Seagrass meadow sites exhibited significantly higher prokaryotic alpha-diversity compared to sandy bottom sites. ANCOM analysis revealed that multiple bacterial orders were differentially abundant within each substratum. At coral reef sites, putative disease- and thermal stress-related opportunistic bacteria such as Rhodobacterales, Verrucomicrobiales, and Cytophagales were comparatively abundant, while seagrass meadow sites abundantly harbored Desulfobacterales, Steroidobacterales and Chromatiales, which are common bacterial orders in seagrass meadows. According to our gene-coded enzyme analyses the numbers of differentially abundant enzymes were highest in coral reef sites. Notably, superoxide dismutase, an important enzyme for anti-oxidative stress in coral tissue, was abundant at coral sites. Our results provide a list of prokaryotes to look into in each substrate, and further emphasize the importance of considering the microbiome, especially when focusing on environmental conservation.

CONCLUSION

Our findings prove that prokaryotic metabarcoding is capable of capturing compositional differences and the diversity of microbial communities in three different environments. Furthermore, several taxa were suggested to be differentially more abundant in specific environments, and gene-coded enzymic compositions also showed possible differences in ecological functions. Further study, in combination with field observations and temporal sampling, is key to achieving a better understanding of the interactions between the local microbiome and the surrounding benthic community.

Bioactivity Profiling and Untargeted Metabolomics of Microbiota Associated with Mesopelagic Jellyfish Periphylla periphylla

The marine mesopelagic zone extends from water depths of 200 m to 1000 m and is home to a vast number and diversity of species. It is one of the least understood regions of the marine environment with untapped resources of pharmaceutical relevance. The mesopelagic jellyfish Periphylla periphylla is a well-known and widely distributed species in the mesopelagic zone; however, the diversity or the pharmaceutical potential of its cultivable microbiota has not been explored. In this study, we isolated microorganisms associated with the inner and outer umbrella of P. periphylla collected in Irminger Sea by a culture-dependent approach, and profiled their chemical composition and biological activities. Sixteen mostly gram-negative bacterial isolates were selected and subjected to an OSMAC cultivation regime approach using liquid and solid marine broth (MB) and glucose-yeast-malt (GYM) media. Their ethyl acetate (EtOAc) extracts were assessed for cytotoxicity and antimicrobial activity against fish and human pathogens. All, except one extract, displayed diverse levels of antimicrobial activities. Based on low IC₅₀ values, four most bioactive gram-negative strains; Polaribacter sp. SU124, Shewanella sp. SU126, Psychrobacter sp. SU143 and Psychrobacter sp. SU137, were prioritized for an in-depth comparative and untargeted metabolomics analysis using feature-based molecular networking. Various chemical classes such as diketopiperazines, polyhydroxybutyrates (PHBs), bile acids and other lipids were putatively annotated, highlighting the biotechnological potential in P. periphylla-associated microbiota as well as gram-negative bacteria. This is the first study providing an insight into the cultivable bacterial community associated with the mesopelagic jellyfish P. periphylla and, indeed, the first to mine the metabolome and antimicrobial activities of these microorganisms.

First record of hydrozoan genera Eucheilota McCrady, 1859 and Mitrocomella Haeckel, 1879 and species Porpitaporpita (Linnaeus, 1758) and Physaliaphysalis (Linnaeus, 1758) in Bali, Indonesia

This report documents the first record of the genera Eucheilota and Mitrocomella and species Porpitaporpita and Physaliaphysalis in Bali, Indonesia, based on observed occurrences in different times and sites. The coincidence of the annual stranding of Physaliaphysalis in the east Bali and south Java coasts during the monsoon periods in Indonesia suggests a link with the upwelling events in the areas. However, more work is needed to analyse this phenomenon and study the occurrences of other Hydromedusae due to the limited data on hydrozoans in Indonesian waters. Overall, this report provides primary data to contribute to the general understanding of the biodiversity of marine organisms in Indonesia.

An Alum-Free Jellyfish Treatment for Food Applications

Jellyfish, marketed and consumed as food in The Far East, are traditionally processed using salt and alum mixtures. In recent years, the interest of Western consumers in jellyfish (JF) as a food source is increasing. In Europe [European Union (EU)], JF-derived food products are regulated by a novel food law, but methods for JF treatment and processing have not been developed yet. In this study, a protocol for the stabilization and processing of JF into semi-finished food products without the use of alum is proposed for the first time. Safety and quality parameters, together with a series of technological and nutritional traits, were used to monitor the proposed process and for the characterization of the JF-derived products. Calcium lactate (E327), calcium citrate (E333), and calcium acetate (E263), which are food thickening/stabilizing agents allowed by EU regulations, were used in order to control the presence of possible microbial pathogens and spoilage species. The use of calcium lactate and citrate led to an increase in texture values (~1.7-1.8-fold higher than in starting raw materials) and in several nutritional traits such as antioxidant activity, and protein and fatty acid content. In particular, the combination of JF treatments with calcium salts and phenolic compounds resulted in an antioxidant activity increase of up to 8-fold, protein concentration increase of up to 2.6-fold, fatty acid composition maintenance, and a ω6/ω3 ratio lower than 1. For the first time, the application of phenolic compounds to improve JF technological and nutritional features was verified. This study proposes a new procedure for JF treatment and stabilization useful for future potential food applications in Western countries.

Bacterial Communities Associated With Four Blooming Scyphozoan Jellyfish: Potential Species-Specific Consequences for Marine Organisms and Humans Health

Cnidarians have large surface areas available for colonization by microbial organisms, which serve a multitude of functions in the environment. However, relatively few studies have been conducted on scyphozoan-associated microbial communities. Blooms of scyphozoan species are common worldwide and can have numerous deleterious consequences on the marine ecosystem. Four scyphozoan species, Aurelia coerulea, Cyanea nozakii, Nemopilema nomurai, and Rhopilema esculentum, form large blooms in Chinese seas. In this study, we analyzed the bacterial communities associated with these four jellyfish based on 16S rRNA gene sequencing. We found that the bacterial communities associated with each scyphozoan species were significantly different from each other and from those of the surrounding seawater. There were no significant differences between the bacterial communities associated with different body parts of the four scyphozoan jellyfish. Core bacteria in various compartments of the four scyphozoan taxa comprised 57 OTUs (Operational Taxonomic Units), dominated by genera Mycoplasma, Vibrio, Ralstonia, Tenacibaculum, Shingomonas and Phyllobacterium. FAPROTAX function prediction revealed that jellyfish could influence microbially mediated biogeochemical cycles, compound degradation and transmit pathogens in regions where they proliferate. Finally, Six genera of potentially pathogenic bacteria associated with the scyphozoans were detected: Vibrio, Mycoplasma, Ralstonia, Tenacibaculum, Nautella, and Acinetobacter. Our study suggests that blooms of these four common scyphozoans may cause jellyfish species-specific impacts on element cycling in marine ecosystems, and serve as vectors of pathogenic bacteria to threaten other marine organisms and human health.

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.

Prokaryote Communities Inhabiting Endemic and Newly Discovered Sponges and Octocorals from the Red Sea

In the present study, we assessed prokaryotic communities of demosponges, a calcareous sponge, octocorals, sediment and seawater in coral reef habitat of the central Red Sea, including endemic species and species new to science. Goals of the study were to compare the prokaryotic communities of demosponges with the calcareous sponge and octocorals and to assign preliminary high microbial abundance (HMA) or low microbial abundance (LMA) status to the sponge species based on compositional trait data. Based on the compositional data, we were able to assign preliminary LMA or HMA status to all sponge species. Certain species, however, had traits of both LMA and HMA species. For example, the sponge Ectyoplasia coccinea, which appeared to be a LMA species, had traits, including a relatively high abundance of Chloroflexi members, that were more typical of HMA species. This included dominant OTUs assigned to two different classes within the Chloroflexi. The calcareous sponge clustered together with seawater, the known LMA sponge Stylissa carteri and other presumable LMA species. The two dominant OTUs of this species were assigned to the Deltaproteobacteria and had no close relatives in the GenBank database. The octocoral species in the present study had prokaryotic communities that were distinct from sediment, seawater and all sponge species. These were characterised by OTUs assigned to the orders Rhodospirillales, Cellvibrionales, Spirochaetales and the genus Endozoicomonas, which were rare or absent in samples from other biotopes.

Geographical location and habitat predict variation in prokaryotic community composition of Suberites diversicolor

Purpose

Marine lakes are unique habitats that house diverse assemblages of benthic and planktonic organisms including endemic species. In this study, we aimed to assess to what extent geographical location (Berau versus Papua) and the degree of marine lake connectivity (relatively open versus closed) to the surrounding marine environment structures the prokaryotic community composition of the sponge species Suberites diversicolor.

Methods

Sponge specimens were sampled in five marine lakes in Borneo and Papua and one open sea habitat in Taiwan.

Result

Prokaryotic communities of S. diversicolor were dominated by members assigned to the Proteobacteria (particularly Alphaproteobacteria and Gammaproteobacteria) and Cyanobacteria, which together made up from 78 to 87% of sequences in all samples. The dominant operational taxonomic units (OTUs) in most samples, OTUs 1 and 3, were both assigned to the alphaproteobacterial order Rhodospirillales with OTU-1 dominant in the marine lakes of Berau and Papua and OTU-3 in Taiwan. OTU-3 was also largely absent from Papuan samples but present in all Berau samples. Compositionally, S. diversicolor samples clustered according to geographical location with the main axis of variation separating marine lake samples collected in Berau from those collected in Papua and the second axis of variation separating open sea samples collected in Taiwan from all marine lake samples. In addition, our results suggest that the degree of lake connectivity to the open sea also influences prokaryotic composition.

Conclusion

Although previous studies have shown that sponge-associated microbial communities tend to be stable across different geographical and environmental gradients, in the present study, both geography and local environmental conditions were significant predictors of variation in prokaryotic community composition of S. diversicolor.

The Diversity of the Endobiotic Bacterial Communities in the Four Jellyfish Species

The associated microbiota plays an essential role in the life process of jellyfish. The endobiotic bacterial communities from four common jellyfish Phyllorhiza punctata, Cyanea capillata, Chrysaora melanaster, and Aurelia coerulea were comparatively analyzed by 16S rDNA sequencing in this study. Several 1049 OTUs were harvested from a total of 130 183 reads. Tenericutes (68.4%) and Firmicutes (82.1%) are the most abundant phyla in P. punctata and C. melanaster, whereas C. capillata and A. coerulea share the same top phylum Proteobacteria (76.9% vs. 78.3%). The classified OTUs and bacterial abundance greatly decrease from the phylum to genus level. The top 20 matched genera only account for 9.03% of the total community in P. punctata, 48.9% in C. capillata, 83.05% in C. melanaster, and 58.1% in A. coerulea, respectively. The heatmap of the top 50 genera shows that the relative abundances in A. coerulea and C. capillata are far richer than that in P. punctata and C. melanaster. Moreover, a total of 41 predictive functional categories at KEGG level 2 were identified. Our study indicates the independent diversity of the bacterial communities in the four common Scyphomedusae, which might involve in the metabolism and environmental information processing of the hosts.

The associated microbiota plays an essential role in the life process of jellyfish. The endobiotic bacterial communities from four common jellyfish Phyllorhiza punctata, Cyanea capillata, Chrysaora melanaster, and Aurelia coerulea were comparatively analyzed by 16S rDNA sequencing in this study. Several 1049 OTUs were harvested from a total of 130 183 reads. Tenericutes (68.4%) and Firmicutes (82.1%) are the most abundant phyla in P. punctata and C. melanaster, whereas C. capillata and A. coerulea share the same top phylum Proteobacteria (76.9% vs. 78.3%). The classified OTUs and bacterial abundance greatly decrease from the phylum to genus level. The top 20 matched genera only account for 9.03% of the total community in P. punctata, 48.9% in C. capillata, 83.05% in C. melanaster, and 58.1% in A. coerulea, respectively. The heatmap of the top 50 genera shows that the relative abundances in A. coerulea and C. capillata are far richer than that in P. punctata and C. melanaster. Moreover, a total of 41 predictive functional categories at KEGG level 2 were identified. Our study indicates the independent diversity of the bacterial communities in the four common Scyphomedusae, which might involve in the metabolism and environmental information processing of the hosts.

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.

Photosynthetic capacity of the endosymbiotic dinoflagellate Cladocopium sp. is preserved during digestion of its jellyfish host Mastigias papua by the anemone Entacmaea medusivora

The sea anemone Entacmaea medusivora (Actiniaria, Anthozoa) commonly feeds on the golden jellyfish Mastigias papua (Rhizostomeae, Scyphozoa) which harbours an endosymbiotic dinoflagellate of the genus Cladocopium (Symbiodiniaceae). In this study, we monitored the photosynthetic activity of the endosymbiotic microalgae while their host jellyfish were ingested and digested by starved medusivorous anemones. By analyzing the photosynthetic yield of photosystem II, we observed that Cladocopium cells remain photosynthetically competent during the whole digestion process, thus confirming the exceptional resistance of Symbiodiniaceae to digestive enzymes. In the gastric cavity of E. medusivora, Cladocopium cells release oxygen, which could broadly stimulate the gastric microbiotic flora of the sea anemone. Ultimately, E. medusivora is not able to retain Cladocopium cells more than few days and physiologically-unaltered cells are therefore expelled in faecal pellets. The potential contribution of E. medusivora to maintain a reservoir of Cladocopium symbionts and its role in the life cycle of M. papua is discussed.

The sponge microbiome within the greater coral reef microbial metacommunity

Much recent marine microbial research has focused on sponges, but very little is known about how the sponge microbiome fits in the greater coral reef microbial metacommunity. Here, we present an extensive survey of the prokaryote communities of a wide range of biotopes from Indo-Pacific coral reef environments. We find a large variation in operational taxonomic unit (OTU) richness, with algae, chitons, stony corals and sea cucumbers housing the most diverse prokaryote communities. These biotopes share a higher percentage and number of OTUs with sediment and are particularly enriched in members of the phylum Planctomycetes. Despite having lower OTU richness, sponges share the greatest percentage (>90%) of OTUs with >100 sequences with the environment (sediment and/or seawater) although there is considerable variation among sponge species. Our results, furthermore, highlight that prokaryote microorganisms are shared among multiple coral reef biotopes, and that, although compositionally distinct, the sponge prokaryote community does not appear to be as sponge-specific as previously thought.

Fate of 14C-acetyl sulfamethoxazole during the activated sludge process

Compared to antibiotic parent molecule, human metabolites are generally more polar and sometimes not less toxic in wastewater. However, most researches focus on the fate of parent molecule. Therefore, behaviors of human metabolites are little known. Moreover, though much has been done on the fate of antibiotics during activated sludge process, there are still some limitations and gaps. In the present study, [Ring-¹⁴C] acetyl sulfamethoxazole (¹⁴C-Ac-SMX) was used to investigate the fate of human metabolite of SMX during activated sludge process at environmentally relevant concentration. At the end of 216 h, 3.1% of the spiked activity in the initial aqueous phase was mineralized, 50% was adsorbed onto the solid phase, and 36.5% still remained in the aqueous phase, indicating that adsorption, not biodegradation, was the main dissipation pathway. In the existence of microbial activities, accumulation into the solid phase was much higher, which was less bioavailable by chemical sequential extraction. The multimedia kinetic model simultaneously depicted the fate of Ac-SMX in the gas, aqueous, and solid phases, and demonstrated that microbially accelerated accumulation onto the solid phase was attributed to lower desorption rate from the solid phase to the aqueous phase, where adsorption rate was not the key factor. Therefore, Ac-SMX cannot be efficiently mineralized and remain in the aqueous or the solid phases. The accumulation in the solid phase is less bioavailable and is hard to be desorbed in the existence of microbial activities, and should not be easily degraded, and may lead to the development of antibiotic-resistant bacteria and genes after discharge into the environment.

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.

Bacteria associated with moon jellyfish during bloom and post-bloom periods in the Gulf of Trieste (northern Adriatic)

Jellyfish are a prominent component of the plankton community. They frequently form conspicuous blooms which may interfere with different human enterprises. Among the aspects that remain understudied are jellyfish associations with microorganisms having potentially important implications for organic matter cycling. To the best of our knowledge, this study is the first to investigate the bacterial community associated with live moon jellyfish (Aurelia solida, Scyohozoa) in the Adriatic Sea. Using 16S rRNA clone libraries and culture-based methods, we have analyzed the bacterial community composition of different body parts: the exumbrella surface, oral arms, and gastric cavity, and investigated possible differences in medusa-associated bacterial community structure at the time of the jellyfish population peak, and during the senescent phase at the end of bloom. Microbiota associated with moon jellyfish was different from ambient seawater bacterial assemblage and varied between different body parts. Betaproteobacteria (Burkholderia, Cupriavidus and Achromobacter) dominated community in the gastral cavity of medusa, while Alphaproteobacteria (Phaeobacter, Ruegeria) and Gammaproteobacteria (Stenotrophomonas, Alteromonas, Pseudoalteromonas and Vibrio) prevailed on ‘outer’ body parts. Bacterial community structure changed during senescent phase, at the end of the jellyfish bloom, showing an increased abundance of Gammaproteobacteria, exclusively Vibrio. The results of cultured bacterial isolates showed the dominance of Gammaproeteobacteria, especially Vibrio and Pseudoalteromonas in all body parts. Our results suggest that jellyfish associated bacterial community might have an important role for the host, and that anthropogenic pollution in the Gulf of Trieste might affect their community structure.

Microbiome dynamics of two differentially resilient corals

Coral bleaching and disease are 2 common occurrences that are contributing to global coral cover decline. Understanding the interactions between the coral animal and its microbial associates, and how they may change in the presence of stressors such as warming and acidification, is a crucial component to understanding both susceptibility and resistance to disease and bleaching. The coral Diploria labyrinthiformis has been shown to be more disease resistant than its relative Pseudodiploria strigosa, providing an ideal study system for disease resistance. In this study, we examined the bacterial communities of these 2 coral species on the Florida Reef tract every 6 mo for 18 mo (in situ sampling), and under experimental (laboratory) thermal and pH manipulation. The in situ sampling encompassed wide fluctuations in temperature, including an anomalously warm summer period. The laboratory experiments involved exposure to both increased temperature (31°C) and lowered pH (7.7). The in situ bacterial communities of both coral species were highly similar in the winter, but diverged during summer, with the D. labyrinthiformis bacterial community being more stable than that of P. strigosa. Differences in the bacterial community between the 2 coral species included 29 operational taxonomic units (OTUs) that were specific to D. labyrinthiformis in all seasons, while only 2 OTUs were specific to P. strigosa. The comparative stability of the D. labyrinthiformis microbiome, in addition to harboring a more specific microbiome, may be a key component of the relative disease resistance of this coral.

Bacterial Communities Inhabiting the Sponge Biemna fortis, Sediment and Water in Marine Lakes and the Open Sea

Marine lakes are small bodies of landlocked seawater that are isolated from the open sea and have been shown to house numerous rare and unique taxa. The environmental conditions of the lakes are also characterised by lower pH and salinity and higher temperatures than generally found in the open sea. In the present study, we used a 16S rRNA gene barcoded pyrosequencing approach and a predictive metagenomic approach (PICRUSt) to examine bacterial composition and function in three distinct biotopes (sediment, water and the sponge species Biemna fortis) in three habitats (two marine lakes and the open sea) of the Berau reef system, Indonesia. Both biotope and habitat were significant predictors of higher taxon abundance and compositional variation. Most of the variation in operational taxonomic unit (OTU) composition was related to the biotope (42% for biotope alone versus 9% for habitat alone and 15% combined). Most OTUs were also restricted to a single biotope (1047 for B. fortis, 6120 for sediment and 471 for water). Only 98 OTUs were shared across all three biotopes. Bacterial communities from B. fortis, sediment and water samples were, however, also distinct in marine lake and open sea habitats. This was evident in the abundance of higher bacterial taxa. For example, the phylum Cyanobacteria was significantly more abundant in samples from marine lakes than from the open sea. This difference was most pronounced in the sponge B. fortis. In line with the compositional differences, there were pronounced differences in predicted relative gene count abundance among biotopes and habitats. Of particular interest was the predicted enrichment in B. fortis from the marine lakes for pathways including DNA replication and repair and the glutathione metabolism. This may facilitate adaptation of host and microbes to life in 'stressful' low pH, low salinity and/or high temperature environments such as those encountered in marine lakes.

Jellyfish Life Stages Shape Associated Microbial Communities, While a Core Microbiome Is Maintained Across All

The key to 650 million years of evolutionary success in jellyfish is adaptability: with alternating benthic and pelagic generations, sexual and asexual reproductive modes, multitudes of body forms and a cosmopolitan distribution, jellyfish are likely to have established a plenitude of microbial associations. Here we explored bacterial assemblages in the scyphozoan jellyfish Chrysaora plocamia (Lesson 1832). Life stages involved in propagation through cyst formation, i.e., the mother polyp, its dormant cysts (podocysts), and polyps recently excysted (excysts) from podocysts – were investigated. Associated bacterial assemblages were assessed using MiSeq Illumina paired-end tag sequencing of the V1V2 region of the 16S rRNA gene. A microbial core-community was identified as present through all investigated life stages, including bacteria with closest relatives known to be key drivers of carbon, nitrogen, phosphorus, and sulfur cycling. Moreover, the fact that half of C. plocamia’s core bacteria were also present in life stages of the jellyfish Aurelia aurita, suggests that this bacterial community might represent an intrinsic characteristic of scyphozoan jellyfish, contributing to their evolutionary success.

Endozoicomonas genomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts

Endozoicomonas bacteria are globally distributed and often abundantly associated with diverse marine hosts including reef-building corals, yet their function remains unknown. In this study we generated novel Endozoicomonas genomes from single cells and metagenomes obtained directly from the corals Stylophora pistillata, Pocillopora verrucosa, and Acropora humilis. We then compared these culture-independent genomes to existing genomes of bacterial isolates acquired from a sponge, sea slug, and coral to examine the functional landscape of this enigmatic genus. Sequencing and analysis of single cells and metagenomes resulted in four novel genomes with 60–76% and 81–90% genome completeness, respectively. These data also confirmed that Endozoicomonas genomes are large and are not streamlined for an obligate endosymbiotic lifestyle, implying that they have free-living stages. All genomes show an enrichment of genes associated with carbon sugar transport and utilization and protein secretion, potentially indicating that Endozoicomonas contribute to the cycling of carbohydrates and the provision of proteins to their respective hosts. Importantly, besides these commonalities, the genomes showed evidence for differential functional specificity and diversification, including genes for the production of amino acids. Given this metabolic diversity of Endozoicomonas we propose that different genotypes play disparate roles and have diversified in concert with their hosts.

Diversity and function of prevalent symbiotic marine bacteria in the genus Endozoicomonas

Endozoicomonas bacteria are emerging as extremely diverse and flexible symbionts of numerous marine hosts inhabiting oceans worldwide. Their hosts range from simple invertebrate species, such as sponges and corals, to complex vertebrates, such as fish. Although widely distributed, the functional role of Endozoicomonas within their host microenvironment is not well understood. In this review, we provide a summary of the currently recognized hosts of Endozoicomonas and their global distribution. Next, the potential functional roles of Endozoicomonas, particularly in light of recent microscopic, genomic, and genetic analyses, are discussed. These analyses suggest that Endozoicomonas typically reside in aggregates within host tissues, have a free-living stage due to their large genome sizes, show signs of host and local adaptation, participate in host-associated protein and carbohydrate transport and cycling, and harbour a high degree of genomic plasticity due to the large proportion of transposable elements residing in their genomes. This review will finish with a discussion on the methodological tools currently employed to study Endozoicomonas and host interactions and review future avenues for studying complex host-microbial symbioses.