Bacterial communities and species-specific associations with the mucus of Brazilian coral species

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.

Marine macroalgae and their associated bacterial communities affect larval settlement and survivorship of the coral Pocillopora damicornis

Macroalgae play crucial roles as major habitat-forming organisms in marine ecosystems, having significant impacts on coral recruitment and reef recovery. However, the interactions between marine macroalgae and coral larvae remain poorly understood. Furthermore, little is known whether differences in bacterial assemblages associated with macroalgae may play roles in this process. Here, we comprehensively investigated the impacts of different macroalgae and their associated microbiomes on larval settlement and survival of coral Pocillopora damicornis. The results revealed significant variations in larval settlement and survival rates when exposed to different macroalgal species. The highest settlement rate, reaching 90%, was observed in the presence of the red alga Hypnea pannosa, followed by green algae Caulerpa serrulata, C. racemosa, and brown algae Turbinaria gracilis, Sargassum polycystum. Correspondingly, similarities in bacterial compositions were observed between H. pannosa and C. racemosa, as well as between T. gracilis and S. polycystum, implying associated bacterial may be related with the algal functions. Furthermore, macroalgae that facilitate larval settlement exhibited higher abundances of amplicon sequence variants (ASVs) associated with the metabolism of dimethylsulfoniopropionate or the antagonism of known coral pathogens. However, the brown alga Padina boryana failed to induce larval settlement with survival rate of zero after 120 h. The algal species harbored more abundances of ASVs related to Rhizobiaceae. These findings highlight the significant impact of macroalgae and their associated microbiomes on coral recruitment, as they influence both larval settlement and survival rates.

Metabarcoding the Bacterial Assemblages Associated with Toxopneustes roseus in the Mexican Central Pacific

The Mexican Central Pacific (MCP) region has discontinuous coral ecosystems with different protection and anthropogenic disturbance. Characterizing the bacterial assemblage associated with the sea urchin Toxopneustes roseus and its relationship with environmental variables will contribute to understanding the species' physiology and ecology. We collected sea urchins from coral ecosystems at six sites in the MCP during the summer and winter for two consecutive years. The spatial scale represented the most important variation in the T. roseus bacteriome, particularly because of Isla Isabel National Park (PNII). Likewise, spatial differences correlated with habitat structure variables, mainly the sponge and live coral cover. The PNII exhibited highly diverse bacterial assemblages compared to other sites, characterized by families associated with diseases and environmental stress (Saprospiraceae, Flammeovirgaceae, and Xanthobacteraceae). The remaining five sites presented a constant spatiotemporal pattern, where the predominance of the Campylobacteraceae and Helicobacteraceae families was key to T. roseus' holobiont. However, the dominance of certain bacterial families, such as Enterobacteriaceae, in the second analyzed year suggests that Punto B and Islas e islotes de Bahía Chamela Sanctuary were exposed to sewage contamination. Overall, our results improve the understanding of host-associated bacterial assemblages in specific time and space and their relationship with the environmental condition.

Probiotics reshape the coral microbiome in situ without detectable off-target effects in the surrounding environment

Beneficial microorganisms for corals (BMCs), or probiotics, can enhance coral resilience against stressors in laboratory trials. However, the ability of probiotics to restructure the coral microbiome in situ is yet to be determined. As a first step to elucidate this, we inoculated putative probiotic bacteria (pBMCs) on healthy colonies of Pocillopora verrucosa in situ in the Red Sea, three times per week, during 3 months. pBMCs significantly influenced the coral microbiome, while bacteria of the surrounding seawater and sediment remained unchanged. The inoculated genera Halomonas, Pseudoalteromonas, and Bacillus were significantly enriched in probiotic-treated corals. Furthermore, the probiotic treatment also correlated with an increase in other beneficial groups (e.g., Ruegeria and Limosilactobacillus), and a decrease in potential coral pathogens, such as Vibrio. As all corals (treated and non-treated) remained healthy throughout the experiment, we could not track health improvements or protection against stress. Our data indicate that healthy, and therefore stable, coral microbiomes can be restructured in situ, although repeated and continuous inoculations may be required in these cases. Further, our study provides supporting evidence that, at the studied scale, pBMCs have no detectable off-target effects on the surrounding microbiomes of seawater and sediment near inoculated corals.

Reciprocal transplant experiment reveals multiple factors influencing changes in coral microbial communities across climate zones

Previous studies have demonstrated the influence of external factors (environmental factors and the coral host factors) on the community structure of coral-associated bacteria. However, the internal factors, e.g. the interaction within the bacterial community or bacteria itself, have often been overlooked in studies of the coral microbiome. Hence, we performed a reciprocal transplant of corals between two different climate zones to examine the resultant alterations in coral-associated bacterial communities. The findings highlight the significance of environmental factors, host selection, and highly resilient bacteria in shaping the coral microbial composition. The results support that coral species consistently harbor specific predominant bacterial groups influenced by host selection, while locations display unique bacterial taxa due to environmental variations. The transplantation of corals into new environments leads to a gradual shift in the bacterial community, from initially resembling that of the native location to eventually resembling that of the transplanted location, emphasizing the crucial role of bacterial community composition for coral survival under changing ambient conditions. Furthermore, highly resilient bacteria that persisted throughout the reciprocal transplant experiment demonstrated their adaptability to environmental and host changes, suggesting the presence of robust adaptation or resistance mechanisms in bacterial communities. Genetic adaptations within the prevalent bacterial group, Endozoicomonas, were also observed, suggesting variations in resilience and adaptation capabilities among different phylotypes. This study highlights the need to conduct further investigations into the coral-associated bacteria themselves, as they may hold some key insights into understanding the dynamics of coral-associated microbial communities. These data also highlight some key species of coral-associated bacteria which could benefit coral in response to alterations in ambient environment.

The bacterial signature offers vision into the machinery of coral fitness across high-latitude coral reef in the South China Sea

Coral-bacterial interaction is a major driver in coral acclimatization to the stressful environment. 16S rRNA High-throughput sequencing was used to classify the role of different coral reef compartments; sediment, water, and tissue; in the South China Sea (SCS), as well as different locations in shaping the microbial community. The majority of OTUs significantly shifted at impacted sites and indicated distinction in the relative abundance of bacteria compartment/site-wise. Richness and diversity were higher, and more taxa were enriched in the sediment communities. Proteobacteria dominated sediment samples, while Cyanobacteria dominated water samples. Coral tissue showed a shift among different sites with Proteobacteria remaining the dominant Phylum. Moreover, we report a dominance of Chlorobium genus in the healthy coral tissue sample collected from the severely damaged Site B, suggesting a contribution to tolerance and adaptation to the disturbing environment. Thus, revealing the complex functionally diverse microbial patterns associated with biotic and abiotic disturbed coral reefs will deliver understanding of the symbiotic connections and competitive benefit inside the hosts niche and can reveal a measurable footprint of the environmental impacts on coral ecosystems. We hence, urge scientists to draw more attention towards using coral microbiome as a self-sustaining tool in coral restoration.

Community Structure and Predicted Functions of Actively Growing Bacteria Responsive to Released Coral Mucus in Surrounding Seawater

A direct relationship exists between diverse corals and fish farming in Keten Bay, Amami-Oshima, Japan. The release of coral mucus has a significant impact on the microbial activity of surrounding seawater. To obtain a more detailed understanding of biogeochemical cycles in this environment, the effects of coral mucus on the community structure and function of bacteria in surrounding seawater need to be elucidated. We herein used a bromodeoxyuridine approach to investigate the structures and functions of bacterial communities growing close to mucus derived from two different Acropora corals, AC1 and AC2. The alpha diversities of actively growing bacteria (AGB) were lower in mucus-containing seawater than in control seawater and their community structures significantly differed, suggesting that the growth of specific bacteria was modulated by coral mucus. Rhodobacteraceae and Cryomorphaceae species were the most dominant AGB in response to the mucus of Acropora AC1 and AC2, respectively. In contrast, the growth of Actinomarinaceae, Alteromonadaceae, Flavobacteriaceae, and SAR86 clade bacteria was inhibited by coral mucus. The results of a Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) ana-lysis suggested that the predicted functions of AGB in mucus-containing seawater differed from those in seawater. These functions were related to the biosynthesis and degradation of the constituents of coral mucus, such as polysaccharides, sugar acids, and aromatic compounds. The present study demonstrated that complex bacterial community structures and functions may be shaped by coral mucus, suggesting that corals foster diverse bacterial communities that enhance the ecological resilience of this fish farming area.

Population Differences and Host Species Predict Variation in the Diversity of Host-Associated Microbes in Hydra

Most animals co-exist with diverse host-associated microbial organisms that often form complex communities varying between individuals, habitats, species and higher taxonomic levels. Factors driving variation in the diversity of host-associated microbes are complex and still poorly understood. Here, we describe the bacterial composition of field-collected Hydra, a freshwater cnidarian that forms stable associations with microbial species in the laboratory and displays complex interactions with components of the microbiota. We sampled Hydra polyps from 21 Central European water bodies and identified bacterial taxa through 16S rRNA sequencing. We asked whether diversity and taxonomic composition of host-associated bacteria depends on sampling location, habitat type, host species or host reproductive mode (sexual vs. asexual). Bacterial diversity was most strongly explained by sampling location, suggesting that the source environment plays an important role in the assembly of bacterial communities associated with Hydra polyps. We also found significant differences between host species in their bacterial composition that partly mirrored variations observed in lab strains. Furthermore, we detected a minor effect of host reproductive mode on bacterial diversity. Overall, our results suggest that extrinsic (habitat identity) factors predict the diversity of host-associated bacterial communities more strongly than intrinsic (species identity) factors, however, only a combination of both factors determines microbiota composition in Hydra.

CPR and DPANN Have an Overlooked Role in Corals' Microbial Community Structure

Understanding how microbial communities are structured in coral holobionts is important to estimate local and global impacts and provide efficient environment management strategies. Several studies investigated the relationship between corals and their microbial communities, including the environmental drivers of shifts in this relationship, associated with diseases and coral cover loss. However, these studies are often geographically or taxonomically restricted and usually focused on the most abundant microbial groups, neglecting the rare biosphere, including archaea in the group DPANN and the recently discovered bacterial members of the candidate phyla radiation (CPR). Although it is known that rare microbes can play essential roles in several environments, we still lack understanding about which taxa comprise the rare biosphere of corals' microbiome. Here, we investigated the host-related and technical factors influencing coral microbial community structure and the importance of CPR and DPANN in this context by analyzing more than a hundred coral metagenomes from independent studies worldwide. We show that coral genera are the main biotic factor shaping coral microbial communities. We also detected several CPR and DPANN phyla comprising corals' rare biosphere for the first time and showed that they significantly contribute to shaping coral microbial communities.

Best practices for generating and analyzing 16S rRNA amplicon data to track coral microbiome dynamics

Over the past two decades, researchers have searched for methods to better understand the relationship between coral hosts and their microbiomes. Data on how coral-associated bacteria are involved in their host's responses to stressors that cause bleaching, disease, and other deleterious effects can elucidate how they may mediate, ameliorate, and exacerbate interactions between the coral and the surrounding environment. At the same time tracking coral bacteria dynamics can reveal previously undiscovered mechanisms of coral resilience, acclimatization, and evolutionary adaptation. Although modern techniques have reduced the cost of conducting high-throughput sequencing of coral microbes, to explore the composition, function, and dynamics of coral-associated bacteria, it is necessary that the entire procedure, from collection to sequencing, and subsequent analysis be carried out in an objective and effective way. Corals represent a difficult host with which to work, and unique steps in the process of microbiome assessment are necessary to avoid inaccuracies or unusable data in microbiome libraries, such as off-target amplification of host sequences. Here, we review, compare and contrast, and recommend methods for sample collection, preservation, and processing (e.g., DNA extraction) pipelines to best generate 16S amplicon libraries with the aim of tracking coral microbiome dynamics. We also discuss some basic quality assurance and general bioinformatic methods to analyze the diversity, composition, and taxonomic profiles of the microbiomes. This review aims to be a generalizable guide for researchers interested in starting and modifying the molecular biology aspects of coral microbiome research, highlighting best practices and tricks of the trade.

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.

Detection of hydrocarbon-degrading bacteria on deepwater corals of the northeast Atlantic using CARD-FISH

Recently, studies have begun to identify oil-degrading bacteria and host-taxon specific bacterial assemblages associated with the coral holobiont, including deep-sea cold-water corals, which are thought to provide metabolic functions and additional carbon sources to their coral hosts. Here, we describe the identification of Marinobacter on the soft tissue of Lophelia pertusa coral polyps by Catalyzed Reporter Deposition Fluorescence in situ Hybridization (CARD-FISH). L. pertusa samples from three reef sites in the northeast Atlantic (Logachev, Mingulay and Pisces) were collected at depth by vacuum seal to eliminate contamination issues. After decalcification, histological processing and sagittal sectioning of the soft coral polyp tissues, the 16S rRNA-targeted oligonucleotide HRP-labelled probe Mrb-0625-a, and Cyanine 3 (Cy3)-labelled tyramides, were used to identify members of the hydrocarbon-degrading genus Marinobacter. Mrb-0625-a-hybridized bacterial cell signals were detected in different anatomical sites of all polyps collected from each of the three reef sites, suggesting a close, possibly intimate, association between them, but the purpose of which remains unknown. We posit that Marinobacter, and possibly other hydrocarbon-degrading bacteria associated with Lophelia, may confer the coral with the ability to cope with toxic levels of hydrocarbons in regions of natural oil seepage and where there is an active oil and gas industry presence.

The diversity and metabolic potential of the microbial functional gene associated with Porites pukoensis

Coral reef ecosystems usually distribute in oligotrophic tropical and subtropical marine environments, but they possess great biodiversity and high productivity. It may attribute to its efficient internal nutrient cycle system. However, the knowledge of functional microbial community structure is still limited. In this study, both functional gene array (Geochip 5.0) and nifH Illumina sequencing were used to profile the overall functional genes and diazotrophic communities associated with coral Porites pukoensis. More than 7500 microbial functional genes were detected from archaea, bacteria, and fungi. Most of these genes are related to the transformation of carbon, nitrogen, sulfur, and phosphorus, providing evidence that microbes in the coral holobiont play important roles in the biogeochemical cycle of coral reef ecosystems. Our results indicated a high diversity of diazotrophs associated with corals. The dominant diazotrophic groups were related to phyla Alphaproteobacteria, Deltaproteobacteria, Cyanobacteria, and Gammaproteobacteria. And the dominant diazotrophic communities were divided into four clusters. They were affiliated with nifH sequences from genera Zymomonas, Halorhodospira, Leptolyngbya, Trichormus, and Desulfovibrio, indicating these groups may play a more important role in the nitrogen-fixing process in the coral holobiont. This study revealed functional gene diversity and suggested the roles they played in the biogeochemical cycling of the coral holobiont.

The microbial profile of a tissue necrosis affecting the Atlantic invasive coral Tubastraea tagusensis

The Southwestern Atlantic rocky reef ecosystems are undergoing significant changes due to sun-corals (Tubastraea tagusensis and T. coccinea) invasion. At Búzios Island, on the northern coast of São Paulo State, where the abundance of T. tagusensis is particularly high, some colonies are displaying tissue necrosis, a phenomenon never reported for this invasive nor any other azooxanthellate coral species. Using next-generation sequencing, we sought to understand the relationship between T. tagusensis tissue necrosis and its microbiota. Thus, through amplicon sequencing, we studied both healthy and diseased coral colonies. Results indicate a wide variety of bacteria associated with healthy colonies and an even higher diversity associated with those corals presenting tissue necrosis, which displayed nearly 25% more microorganisms. Also, as the microbial community associated with the seven healthy colonies did not alter composition significantly, it was possible to verify the microbial succession during different stages of tissue necrosis (i.e., initial, intermediate, and advanced). Comparing the microbiome from healthy corals to those in early tissue necrosis suggests 21 potential pathogens, which might act as the promoters of such disease.

Differential Patterns of Microbiota Recovery in Symbiotic and Aposymbiotic Corals following Antibiotic Disturbance

Microbial relationships are critical to coral health, and changes in microbiomes are often exhibited following environmental disturbance. However, the dynamics of coral-microbial composition and external factors that govern coral microbiome assembly and response to disturbance remain largely uncharacterized. Here, we investigated how antibiotic-induced disturbance affects the coral mucus microbiota in the facultatively symbiotic temperate coral Astrangia poculata, which occurs naturally with high (symbiotic) or low (aposymbiotic) densities of the endosymbiotic dinoflagellate Breviolum psygmophilum. We also explored how differences in the mucus microbiome of natural and disturbed A. poculata colonies affected levels of extracellular superoxide, a reactive oxygen species thought to have both beneficial and detrimental effects on coral health. Using a bacterial and archaeal small-subunit (SSU) rRNA gene sequencing approach, we found that antibiotic exposure significantly altered the composition of the mucus microbiota but that it did not influence superoxide levels, suggesting that superoxide production in A. poculata is not influenced by the mucus microbiota. In antibiotic-treated A. poculata exposed to ambient seawater, mucus microbiota recovered to its initial state within 2 weeks following exposure, and six bacterial taxa played a prominent role in this reassembly. Microbial composition among symbiotic colonies was more similar throughout the 2-week recovery period than that among aposymbiotic colonies, whose microbiota exhibited significantly more interindividual variability after antibiotic treatment and during recovery. This work suggests that the A. poculata mucus microbiome can rapidly reestablish itself and that the presence of B. psygmophilum, perhaps by supplying nutrients, photosynthate, or other signaling molecules, exerts influence on this process.

IMPORTANCE Corals are animals whose health is often maintained by symbiotic microalgae and other microorganisms, yet they are highly susceptible to environmental-related disturbances. Here, we used a known disruptor, antibiotics, to understand how the coral mucus microbial community reassembles itself following disturbance. We show that the Astrangia poculata microbiome can recover from this disturbance and that individuals with algal symbionts reestablish their microbiomes in a more consistent manner compared to corals lacking symbionts. This work is important because it suggests that this coral may be able to recover its mucus microbiome following disturbance, it identifies specific microbes that may be important to reassembly, and it demonstrates that algal symbionts may play a previously undocumented role in microbial recovery and resilience to environmental change.

Diversity of Bacterioplankton and Bacteriobenthos from the Veracruz Reef System, Southwestern Gulf of Mexico

Bacterial diversity was explored among field samples and cultured isolates from coral reefs within the Veracruz Reef System. Bacterioplankton and bacteriobenthos were characterized by pyrosequencing 16S rRNA genes. Identified sequences belonged to the kingdom Bacteria and classified into 33 phyla. Proteobacteria (likely SAR11 clade) dominated in collective field samples, whereas Firmicutes were the most abundant taxa among cultured isolates. Bioinformatic sorting of sequences to family level revealed 223 bacterial families. Pseudomonadaceae, Exiguobacteraceae and Bacillaceae were dominant among cultured isolates. Vibrionaceae, Alteromonadaceae, and Flavobacteriaceae dominated in reef-associated sediments, whereas Rickettsiaceae and Synechoccaceae were more highly represented in the water column. Bacterial communities from sediments were more diverse than from the water column. This study reveals cryptic bacterial diversity among microenvironmental components of marine microbial reef communities subject to differential influence of anthropogenic stressors. Such investigations are critical for constructing scenarios of environmentally induced shifts in bacterial biodiversity and species composition.

Microbiome of the Southwestern Atlantic invasive scleractinian coral, Tubastraea tagusensis

Background

Commonly known as sun-coral, Tubastraea tagusensis is an azooxanthellate scleractinian coral that successfully invaded the Southwestern Atlantic causing significant seascape changes. Today it is reported to over 3500 km along the Brazilian coast, with several rocky shores displaying high substrate coverage. Apart from its singular invasiveness capacity, the documentation and, therefore, understanding of the role of symbiotic microorganisms in the sun-coral invasion is still scarce. However, in general, the broad and constant relationship between corals and microorganisms led to the development of co-evolution hypotheses. As such, it has been shown that the microbial community responds to environmental factors, adjustment of the holobiont, adapting its microbiome, and improving the hosts’ fitness in a short space of time. Here we describe the microbial community (i.e. Bacteria) associated with sun-coral larvae and adult colonies from a locality displaying a high invasion development.

Results

The usage of high throughput sequencing indicates a great diversity of Bacteria associated with T. tagusensis, with Cyanobacteria, Proteobacteria, Bacteroidetes, Actinobacteria, Planctomycetes, and Firmicutes corresponding to the majority of the microbiome in all samples. However, T. tagusensis’ microbial core consists of only eight genera for colonies, and, within them, three are also present in the sequenced larvae. Overall, the microbiome from colonies sampled at different depths did not show significant differences. The microbiome of the larvae suggests a partial vertical transfer of the microbial core in this species.

Conclusion

Although diverse, the microbiome core of adult Tubastraea tagusensis is composed of only eight genera, of which three are transferred from the mother colony to their larvae. The remaining bacteria genera are acquired from the seawater, indicating that they might play a role in the host fitness and, therefore, facilitate the sun-coral invasion in the Southwestern Atlantic.

Patterns in microbiome composition differ with ocean acidification in anatomic compartments of the Mediterranean coral Astroides calycularis living at CO2 vents

Coral microbiomes, the complex microbial communities associated with the different anatomic compartments of the coral, provide important functions for the host's survival, such as nutrient cycling at the host's surface, prevention of pathogens colonization, and promotion of nutrient uptake. Microbiomes are generally referred to as plastic entities, able to adapt their composition and functionality in response to environmental change, with a possible impact on coral acclimatization to phenomena related to climate change, such as ocean acidification. Ocean sites characterized by natural gradients of pCO₂ provide models for investigating the ability of marine organisms to acclimatize to decreasing seawater pH. Here we compared the microbiome of the temperate, shallow water, non-symbiotic solitary coral Astroides calycularis that naturally lives at a volcanic CO₂ vent in Ischia Island (Naples, Italy), with that of corals living in non-acidified sites at the same island. Bacterial DNA associated with the different anatomic compartments (mucus, tissue and skeleton) of A. calycularis was differentially extracted and a total of 68 samples were analyzed by 16S rRNA gene sequencing. In terms of phylogenetic composition, the microbiomes associated with the different coral anatomic compartments were different from each other and from the microbial communities of the surrounding seawater. Of all the anatomic compartments, the mucus-associated microbiome differed the most between the control and acidified sites. The differences detected in the microbial communities associated to the three anatomic compartments included a general increase in subdominant bacterial groups, some of which are known to be involved in different stages of the nitrogen cycle, such as potential nitrogen fixing bacteria and bacteria able to degrade organic nitrogen. Our data therefore suggests a potential increase of nitrogen fixation and recycling in A. calycularis living close to the CO₂ vent system.

Exceptional but vulnerable microbial diversity in coral reef animal surface microbiomes

Coral reefs host hundreds of thousands of animal species that are increasingly threatened by anthropogenic disturbances. These animals host microbial communities at their surface, playing crucial roles for their fitness. However, the diversity of such microbiomes is mostly described in a few coral species and still poorly defined in other invertebrates and vertebrates. Given the diversity of animal microbiomes, and the diversity of host species inhabiting coral reefs, the contribution of such microbiomes to the total microbial diversity of coral reefs could be important, yet potentially vulnerable to the loss of animal species. Analysis of the surface microbiome from 74 taxa, including teleost fishes, hard and soft corals, crustaceans, echinoderms, bivalves and sponges, revealed that more than 90% of their prokaryotic phylogenetic richness was specific and not recovered in surrounding plankton. Estimate of the total richness associated with coral reef animal surface microbiomes reached up to 2.5% of current estimates of Earth prokaryotic diversity. Therefore, coral reef animal surfaces should be recognized as a hotspot of marine microbial diversity. Loss of the most vulnerable reef animals expected under present-day scenarios of reef degradation would induce an erosion of 28% of the prokaryotic richness, with unknown consequences on coral reef ecosystem functioning.

Unraveling Heterogeneity of Coral Microbiome Assemblages in Tropical and Subtropical Corals in the South China Sea

Understanding the coral microbiome is critical for predicting the fidelity of coral symbiosis with growing surface seawater temperature (SST). However, how the coral microbiome will respond to increasing SST is still understudied. Here, we compared the coral microbiome assemblages among 73 samples across six typical South China Sea coral species in two thermal regimes. The results revealed that the composition of microbiome varied across both coral species and thermal regimes, except for Porites lutea. The tropical coral microbiome displayed stronger heterogeneity and had a more un-compacted ecological network than subtropical coral microbiome. The coral microbiome was more strongly determined by environmental factors than host specificity. γ- (32%) and α-proteobacteria (19%), Bacteroidetes (14%), Firmicutes (14%), Actinobacteria (6%) and Cyanobacteria (2%) dominated the coral microbiome. Additionally, bacteria inferred to play potential roles in host nutrients metabolism, several keystone bacteria detected in human and plant rhizospheric microbiome were retrieved in explored corals. This study not only disentangles how different host taxa and microbiome interact and how such an interaction is affected by thermal regimes, but also identifies previously unrecognized keystone bacteria in corals, and also infers the community structure of coral microbiome will be changed from a compacted to an un-compacted network under elevated SST.

Coral microbiome composition along the northern Red Sea suggests high plasticity of bacterial and specificity of endosymbiotic dinoflagellate communities

BACKGROUND

The capacity of reef-building corals to tolerate (or adapt to) heat stress is a key factor determining their resilience to future climate change. Changes in coral microbiome composition (particularly for microalgal endosymbionts and bacteria) is a potential mechanism that may assist corals to thrive in warm waters. The northern Red Sea experiences extreme temperatures anomalies, yet corals in this area rarely bleach suggesting possible refugia to climate change. However, the coral microbiome composition, and how it relates to the capacity to thrive in warm waters in this region, is entirely unknown.

RESULTS

We investigated microbiomes for six coral species (Porites nodifera, Favia favus, Pocillopora damicornis, Seriatopora hystrix, Xenia umbellata, and Sarcophyton trocheliophorum) from five sites in the northern Red Sea spanning 4° of latitude and summer mean temperature ranges from 26.6 °C to 29.3 °C. A total of 19 distinct dinoflagellate endosymbionts were identified as belonging to three genera in the family Symbiodiniaceae (Symbiodinium, Cladocopium, and Durusdinium). Of these, 86% belonged to the genus Cladocopium, with notably five novel types (19%). The endosymbiont community showed a high degree of host-specificity despite the latitudinal gradient. In contrast, the diversity and composition of bacterial communities of the surface mucus layer (SML)-a compartment particularly sensitive to environmental change-varied significantly between sites, however for any given coral was species-specific.

CONCLUSION

The conserved endosymbiotic community suggests high physiological plasticity to support holobiont productivity across the different latitudinal regimes. Further, the presence of five novel algal endosymbionts suggests selection of certain genotypes (or genetic adaptation) within the semi-isolated Red Sea. In contrast, the dynamic composition of bacteria associated with the SML across sites may contribute to holobiont function and broaden the ecological niche. In doing so, SML bacterial communities may aid holobiont local acclimatization (or adaptation) by readily responding to changes in the host environment. Our study provides novel insight about the selective and endemic nature of coral microbiomes along the northern Red Sea refugia.

Metagenomic analysis of microbial community associated with coral mucus from the Gulf of Aqaba

Coral-associated microbial communities contribute to a wide variety of useful roles regarding the their host, and therefore, the arrangement of the general microbiome network can emphatically impact coral wellbeing and survival. Various pollution sources can interfere and disrupt the microbial relationship with corals. Here, we adopted the bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP®) technique to investigate the shift of microbial communities associated with the mucus of the coral Stylophora pistillata collected from five sites (Marine Science Station, Industrial Complex, Oil Terminal, Public Beach, and Phosphate Port) along the Gulf of Aqaba (Red Sea). Our results revealed a high diversity in bacterial populations associated with coral mucus. Proteobacteria were observed to be the dominating phylum among all sampling sites. The identified bacterial taxa belong to the pathogenic bacteria from the genus Vibrio was presented in varying abundances at all sampling sites. Diversity and similarity analysis of microbial communists based on rarefaction curve and UniFrac cluster respectively demonstrated that there are variances in microbial groups associated with coral mucus along sites. The pollution sources among different locations along the Gulf of Aqaba seem to affect the coral-associated holobiont leading to changes in bacterial populations due to increasing human activities.

Establishment of Coral-Bacteria Symbioses Reveal Changes in the Core Bacterial Community With Host Ontogeny

Bacterial communities are fundamental symbionts of corals. However, the process by which bacterial communities are acquired across the life history of corals, particularly in larval and early juvenile stages, is still poorly characterized. Here, transfer of bacteria of the Scleractinian coral Acropora digitifera from adults to spawned egg-sperm bundles was analyzed, as well as acquisition across early developmental stages (larvae and newly settled spat), and 6-month-old juveniles. Larvae were reared under manipulated environmental conditions to determine the source (maternal, seawater, or sediment) of bacteria likely to establish symbiotic relationships with the host using amplicon sequencing of the 16S rRNA gene. Maternal colonies directly transferred bacteria from the families Rhodobacteraceae, Cryomorphaceae, and Endozoicimonaceae to egg-sperm bundles. Furthermore, significant differences in the microbial community structure were identified across generations, yet the structure of the coral bacterial community across early life history stages was not impacted by different environmental rearing conditions. These data indicate that the uptake and structure of bacterial communities is developmentally, rather than environmentally, regulated. Both maternal coral colonies and ubiquitous bacteria found across environmental substrates represent a potential source of symbionts important in establishing the coral microbiome. Uniquely, we report the presence of variation with ontogeny of both the core and resident bacterial communities, supporting the hypothesis that microbial communities are likely to play specific roles within the distinct life history stages of the coral host.

Microbial indicators of environmental perturbations in coral reef ecosystems

BACKGROUND

Coral reefs are facing unprecedented pressure on local and global scales. Sensitive and rapid markers for ecosystem stress are urgently needed to underpin effective management and restoration strategies. Although the fundamental contribution of microbes to the stability and functioning of coral reefs is widely recognised, it remains unclear how different reef microbiomes respond to environmental perturbations and whether microbiomes are sensitive enough to predict environmental anomalies that can lead to ecosystem stress. However, the lack of coral reef microbial baselines hinders our ability to study the link between shifts in microbiomes and ecosystem stress. In this study, we established a comprehensive microbial reference database for selected Great Barrier Reef sites to assess the diagnostic value of multiple free-living and host-associated reef microbiomes to infer the environmental state of coral reef ecosystems.

RESULTS

A comprehensive microbial reference database, originating from multiple coral reef microbiomes (i.e. seawater, sediment, corals, sponges and macroalgae), was generated by 16S rRNA gene sequencing for 381 samples collected over the course of 16 months. By coupling this database to environmental parameters, we showed that the seawater microbiome has the greatest diagnostic value to infer shifts in the surrounding reef environment. In fact, 56% of the observed compositional variation in the microbiome was explained by environmental parameters, and temporal successions in the seawater microbiome were characterised by uniform community assembly patterns. Host-associated microbiomes, in contrast, were five-times less responsive to the environment and their community assembly patterns were generally less uniform. By applying a suite of indicator value and machine learning approaches, we further showed that seawater microbial community data provide an accurate prediction of temperature and eutrophication state (i.e. chlorophyll concentration and turbidity).

CONCLUSION

Our results reveal that free-living microbial communities have a high potential to infer environmental parameters due to their environmental sensitivity and predictability. This highlights the diagnostic value of microorganisms and illustrates how long-term coral reef monitoring initiatives could be enhanced by incorporating assessments of microbial communities in seawater. We therefore recommend timely integration of microbial sampling into current coral reef monitoring initiatives.

Microbiomes of stony and soft deep-sea corals share rare core bacteria

BACKGROUND

Numerous studies have shown that bacteria form stable associations with host corals and have focused on identifying conserved "core microbiomes" of bacterial associates inferred to be serving key roles in the coral holobiont. Because studies tend to focus on only stony corals (order Scleractinia) or soft corals (order Alcyonacea), it is currently unknown if there are conserved bacteria that are shared by both. A meta-analysis was done of 16S rRNA amplicon data from multiple studies generated via identical methodology to allow direct comparisons of bacterial associates across seven deep-sea corals, including both stony and soft species: Anthothela grandiflora, Anthothela sp., Lateothela grandiflora, Lophelia pertusa, Paramuricea placomus, Primnoa pacifica, and Primnoa resedaeformis.

RESULTS

Twenty-three operational taxonomic units (OTUs) were consistently present in greater than 50% of the coral samples. Seven amplicon sequence variants (ASVs), five of which corresponded to a conserved OTU, were consistently present in greater than 30% of the coral samples including five or greater coral species. A majority of the conserved sequences had close matches with previously identified coral-associated bacteria. While known to dominate tropical and temperate coral microbiomes, Endozoicomonas were extremely rare or absent from these deep-sea corals. An Endozoicomonas OTU associated with Lo. pertusa in this study was most similar to those from shallow-water stony corals, while an OTU associated with Anthothela spp. was most similar to those from shallow-water gorgonians.

CONCLUSIONS

Bacterial sequences have been identified that are conserved at the level of class Anthozoa (i.e., found in both stony and soft corals, shallow and deep). These bacterial associates are therefore hypothesized to play important symbiotic roles and are highlighted for targeted future study. These conserved bacterial associates include taxa with the potential for nitrogen and sulfur cycling, detoxification, and hydrocarbon degradation. There is also some overlap with kit contaminants that need to be resolved. Rarely detected Endozoicomonas sequences are partitioned by whether the host is a stony coral or a soft coral, and the finer clustering pattern reflects the hosts' phylogeny.

Host genetic selection for cold tolerance shapes microbiome composition and modulates its response to temperature

The hologenome concept proposes that microbes and their host organism are an independent unit of selection. Motivated by this concept, we hypothesized that thermal acclimation in poikilothermic organisms, owing to their inability to maintain their body temperature, is connected to their microbiome composition. To test this hypothesis, we used a unique experimental setup with a transgenerational selective breeding scheme for cold tolerance in tropical tilapias. We tested the effects of the selection on the gut microbiome and on host transcriptomic response. Interestingly, we found that host genetic selection for thermal tolerance shapes the microbiome composition and its response to cold. The microbiomes of cold-resistant fish showed higher resilience to temperature changes, indicating that the microbiome is shaped by its host's selection. These findings are consistent with the hologenome concept and highlight the connection between the host and its microbiome's response to the environment.

Zoanthid mucus as new source of useful biologically active proteins

Palythoa caribaeorum is a very common colonial zoanthid in the coastal reefs of Brazil. It is known for its massive production of mucus, which is traditionally used in folk medicine by fishermen in northeastern Brazil. This study identified biologically active compounds in P. caribaerum mucus. Crude mucus was collected during low tides by the manual scraping of colonies; samples were maintained in an ice bath, homogenized, and centrifuged at 16,000 g for 1 h at 4 °C; the supernatant (mucus) was kept at -80 °C until use. The enzymatic (proteolytic and phospholipase A₂), inhibitory (metallo, cysteine and serine proteases), and hemagglutinating (human erythrocyte) activities were determined. The results showed high levels of cysteine and metallo proteases, intermediate levels of phosholipase A₂, low levels of trypsin, and no elastase and chymotrypsin like activities. The mucus showed potent inhibitory activity on snake venom metalloproteases and cysteine proteinase papain. In addition, it showed agglutinating activity towards O⁺, B⁺, and A⁺ erythrocyte types. The hemostatic results showed that the mucus prolongs the aPTT and PT, and strongly inhibited platelet aggregation induced by arachidonic acid, collagen, epinephrine, ADP, and thrombin. The antimicrobial activity was tested on 15 strains of bacteria and fungi through the radial diffusion assay in agar, and no activity was observed. Compounds in P. caribaeorum mucus were analyzed for the first time in this study, and our results show potential pharmacological activities in these compounds, which are relevant for use in physiopathological investigations. However, the demonstration of these activities indicates caution in the use of crude mucus in folk medicine. Furthermore, the present or absent activities identified in this mucus suggest that the studied P. caribaeorum colonies were in thermal stress conditions at the time of sample collection; these conditions may precede the bleaching process in zoanthids. Hence, the use of mucus as an indicator of this process should be evaluated in the future.

Inter-domain microbial diversity within the coral holobiont Siderastrea siderea from two depth habitats

Corals host diverse microbial communities that are involved in acclimatization, pathogen defense, and nutrient cycling. Surveys of coral-associated microbes have been particularly directed toward Symbiodinium and bacteria. However, a holistic understanding of the total microbiome has been hindered by a lack of analyses bridging taxonomically disparate groups. Using high-throughput amplicon sequencing, we simultaneously characterized the Symbiodinium, bacterial, and fungal communities associated with the Caribbean coral Siderastrea siderea collected from two depths (17 and 27 m) on Conch reef in the Florida Keys. S. siderea hosted an exceptionally diverse Symbiodinium community, structured differently between sampled depth habitats. While dominated at 27 m by a Symbiodinium belonging to clade C, at 17 m S. siderea primarily hosted a mixture of clade B types. Most fungal operational taxonomic units were distantly related to available reference sequences, indicating the presence of a high degree of fungal novelty within the S. siderea holobiont and a lack of knowledge on the diversity of fungi on coral reefs. Network analysis showed that co-occurrence patterns in the S. siderea holobiont were prevalent among bacteria, however, also detected between fungi and bacteria. Overall, our data show a drastic shift in the associated Symbiodinium community between depths on Conch Reef, which might indicate that alteration in this community is an important mechanism facilitating local physiological adaptation of the S. siderea holobiont. In contrast, bacterial and fungal communities were not structured differently between depth habitats.

Exploring coral microbiome assemblages in the South China Sea

Coral reefs are significant ecosystems. The ecological success of coral reefs relies on not only coral-algal symbiosis but also coral-microbial partnership. However, microbiome assemblages in the South China Sea corals remain largely unexplored. Here, we compared the microbiome assemblages of reef-building corals Galaxea (G. fascicularis) and Montipora (M. venosa, M. peltiformis, M. monasteriata) collected from five different locations in the South China Sea using massively-parallel sequencing of 16S rRNA gene and multivariate analysis. The results indicated that microbiome assemblages for each coral species were unique regardless of location and were different from the corresponding seawater. Host type appeared to drive the coral microbiome assemblages rather than location and seawater. Network analysis was employed to explore coral microbiome co-occurrence patterns, which revealed 61 and 80 co-occurring microbial species assembling the Galaxea and Montipora microbiomes, respectively. Most of these co-occurring microbial species were commonly found in corals and were inferred to play potential roles in host nutrient metabolism; carbon, nitrogen, sulfur cycles; host detoxification; and climate change. These findings suggest that the co-occurring microbial species explored might be essential to maintain the critical coral-microbial partnership. The present study provides new insights into coral microbiome assemblages in the South China Sea.

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.

Effects of suspended sediments and nutrient enrichment on juvenile corals

Three to six-month-old juveniles of Acropora tenuis, A. millepora and Pocillopora acuta were experimentally co-exposed to nutrient enrichment and suspended sediments (without light attenuation or sediment deposition) for 40days. Suspended sediments reduced survivorship of A. millepora strongly, proportional to the sediment concentration, but not in A. tenuis or P. acuta juveniles. However, juvenile growth of the latter two species was reduced to less than half or to zero, respectively. Additionally, suspended sediments increased effective quantum yields of symbionts associated with A. millepora and A. tenuis, but not those associated with P. acuta. Nutrient enrichment did not significantly affect juvenile survivorship, growth or photophysiology for any of the three species, either as a sole stressor or in combination with suspended sediments. Our results indicate that exposure to suspended sediments can be energetically costly for juveniles of some coral species, implying detrimental longer-term but species-specific repercussions for populations and coral cover.

Microbial processes driving coral reef organic carbon flow

Coral reefs are one of the most productive ecosystems on the planet, with primary production rates compared to that of rain forests. Benthic organisms release 10-50% of their gross organic production as mucus that stimulates heterotrophic microbial metabolism in the water column. As a result, coral reef microbes grow up to 50 times faster than open ocean communities. Anthropogenic disturbances cause once coral-dominated reefs to become dominated by fleshy organisms, with several outcomes for trophic relationships. Here we review microbial processes implicated in organic carbon flux in coral reefs displaying species phase shifts. The first section presents microbial players and interactions within the coral holobiont that contribute to reef carbon flow. In the second section, we identify four ecosystem-level microbial features that directly respond to benthic species phase shifts: community composition, biomass, metabolism and viral predation. The third section discusses the significance of microbial consumption of benthic organic matter to reef trophic relationships. In the fourth section, we propose that the 'microbial phase shifts' discussed here are conducive to lower resilience, facilitating the transition to new degradation states in coral reefs.

Diversity of culturable yeasts associated with zoanthids from Brazilian reef and its relation with anthropogenic disturbance

Some of the main threats to coral reefs come from human actions on marine environment, such as tourism, overfishing and pollution from urban development. While several studies have demonstrated an association between bacteria and corals, demonstrating how these communities react to different anthropogenic stressors, yeast communities associated with corals have received far less attention from researchers. The aim of this work was therefore to describe cultivable yeasts associated with three coral species and to evaluate the influence of sewage discharge on yeasts community. We obtained 130 isolates, mostly belonging to phylum Ascomycota and many of them had previously been isolated from human samples or are considered pathogens. The mycobiota was more similar among corals collected from the same reef, indicating that the composition of reef yeast community is more influenced by environmental conditions than host species. We suggest further studies to elucidate which factors are most influential on the composition of the coral-associated yeast community.

Bio-prospecting of coral (Porites lutea) mucus associated bacteria, Palk Bay reefs, Southeast coast of India

Coral mucus is one of the key localization in the coral holobiont, as this serves as an energy rich substrate for a wide range of abundant, diverse and multifunctional microbiota. However, very little is known about the functional role of bacterial communities in their associations with corals. In the present study, a total of 48 isolates were obtained from Porites lutea wherein the genus of Bacillus sp. and Vibrio sp. were predominant. Bio-prospecting the coral mucus revealed the existence of (10.42%) antagonistic bacteria against the tested bacterial pathogens. Molecular taxonomy (16S rRNA) proved the identity of these antagonistic bacteria belong to Enterobacter cloacae (CM1), Bacillus subtilis (CM2), Bacillus sp. (CM11) and Bacillus marisflavi (CM12). The secondary screening emphasized that the ethyl acetate extract of B. subtilis showed strong antagonistic effect, followed by the chloroform extract of E. cloacae and ethyl acetate extract of B. marisflavi. The antagonistic activity was statistically confirmed by Principal Component Analysis and Hierarchical Cluster Analysis. The privileged coral mucus associated bacterial (CMAB) solvent extracts inhibited the bacterial pathogens at 100 μg/ml (MIC) and ceased the growth at 200 μg/ml (MBC). The hemolytic and brine shrimp lethality assays disclosed the non-toxic nature of solvent extracts of CMAB. Altogether, the present investigation brought out the diversity of bacteria associated with the mucus of P. lutea. In addition, bio-prospecting corroborated the CMAB as the potential source of pharmacologically important bioactive compounds against a wide range of bacterial pathogens.

Functional diversity and redundancy across fish gut, sediment and water bacterial communities

This article explores the functional diversity and redundancy in a bacterial metacommunity constituted of three habitats (sediment, water column and fish gut) in a coastal lagoon under anthropogenic pressure. Comprehensive functional gene arrays covering a wide range of ecological processes and stress resistance genes to estimate the functional potential of bacterial communities were used. Then, diversity partitioning was used to characterize functional diversity and redundancy within (α), between (β) and across (γ) habitats. It was showed that all local communities exhibit a highly diversified potential for the realization of key ecological processes and resistance to various environmental conditions, supporting the growing evidence that macro-organisms microbiomes harbour a high functional potential and are integral components of functional gene dynamics in aquatic bacterial metacommunities. Several levels of functional redundancy at different scales of the bacterial metacommunity were observed (within local communities, within habitats and at the metacommunity level). The results suggested a high potential for the realization of spatial ecological insurance within this ecosystem, that is, the functional compensation among microorganisms for the realization and maintenance of key ecological processes, within and across habitats. Finally, the role of macro-organisms as dispersal vectors of microbes and their potential influence on marine metacommunity dynamics were discussed.

Long-Term Survey Is Necessary to Reveal Various Shifts of Microbial Composition in Corals

The coral holobiont is the assemblage of coral host and its microbial symbionts, which functions as a unit and is responsive to host species and environmental factors. Although monitoring surveys have been done to determine bacteria associated with coral, none have persisted for >1 year. Therefore, potential variations in minor or dominant community members that occur over extended intervals have not been characterized. In this study, 16S rRNA gene amplicon pyrosequencing was used to investigate the relationship between bacterial communities in healthy Stylophora pistillata in tropical and subtropical Taiwan over 2 years, apparently one of the longest surveys of coral-associated microbes. Dominant bacterial genera in S. pistillata had disparate changes in different geographical setups, whereas the constitution of minor bacteria fluctuated in abundance over time. We concluded that dominant bacteria (Acinetobacter, Propionibacterium, and Pseudomonas) were stable in composition, regardless of seasonal and geographical variations, whereas Endozoicomonas had a geographical preference. In addition, by combining current data with previous studies, we concluded that a minor bacteria symbiont, Ralstonia, was a keystone species in coral. Finally, we concluded that long-term surveys for coral microbial communities were necessary to detect compositional shifts, especially for minor bacterial members in corals.

Sustaining Rare Marine Microorganisms: Macroorganisms As Repositories and Dispersal Agents of Microbial Diversity

Recent analyses revealed that most of the biodiversity observed in marine microbial communities is represented by organisms with low abundance but, nonetheless essential for ecosystem dynamics and processes across both temporal and spatial scales. Surprisingly, few studies have considered the effect of macroorganism–microbe interactions on the ecology and distribution dynamics of rare microbial taxa. In this review, we synthesize several lines of evidence that these relationships cannot be neglected any longer. First, we provide empirical support that the microbiota of macroorganisms represents a significant part of marine bacterial biodiversity and that host-microbe interactions benefit to certain microbial populations which are part of the rare biosphere (i.e., opportunistic copiotrophic organisms). Second, we reveal the major role that macroorganisms may have on the dispersal and the geographic distribution of microbes. Third, we introduce an innovative and integrated view of the interactions between microbes and macroorganisms, namely sustaining the rares, which suggests that macroorganisms favor the maintenance of marine microbial diversity and are involved in the regulation of its richness and dynamics. Finally, we show how this hypothesis complements existing theories in microbial ecology and offers new perspectives about the importance of macroorganisms for the microbial biosphere, particularly the rare members.

Bacterial Community Associated with the Reef Coral Mussismilia braziliensis's Momentum Boundary Layer over a Diel Cycle

Corals display circadian physiological cycles, changing from autotrophy during the day to heterotrophy during the night. Such physiological transition offers distinct environments to the microbial community associated with corals: an oxygen-rich environment during daylight hours and an oxygen-depleted environment during the night. Most studies of coral reef microbes have been performed on samples taken during the day, representing a bias in the understanding of the composition and function of these communities. We hypothesized that coral circadian physiology alters the composition and function of microbial communities in reef boundary layers. Here, we analyzed microbial communities associated with the momentum boundary layer (MBL) of the Brazilian endemic reef coral Mussismilia braziliensis during a diurnal cycle, and compared them to the water column. We determined microbial abundance and nutrient concentration in samples taken within a few centimeters of the coral's surface every 6 h for 48 h, and sequenced microbial metagenomes from a subset of the samples. We found that dominant taxa and functions in the coral MBL community were stable over the time scale of our sampling, with no significant shifts between night and day samples. Interestingly, the two water column metagenomes sampled 1 m above the corals were also very similar to the MBL metagenomes. When all samples were analyzed together, nutrient concentration significantly explained 40% of the taxonomic dissimilarity among dominant genera in the community. Functional profiles were highly homogenous and not significantly predicted by any environmental variables measured. Our data indicated that water flow may overrule the effects of coral physiology in the MBL bacterial community, at the scale of centimeters, and suggested that sampling resolution at the scale of millimeters may be necessary to address diurnal variation in community composition.

Compositional shifts in bacterial communities associated with the coral Palythoa caribaeorum due to anthropogenic effects

Corals harbor abundant and diverse prokaryotic communities that may be strongly influenced by human activities, which in turn compromise the normal functioning of coral species and predispose them to opportunistic infections. In this study, we investigated the effect of sewage dumping on the bacterial communities associated with the soft coral Palythoa caribaeorum at two sites in the Brazilian coast. We observed a dominance of bacterial species classified as human pathogens at sites exposed to untreated sewage discharge. The microbial diversity of undisturbed sites was more homogeneous and diverse and showed greater abundance. In addition, bacterial communities differed substantially between the exposed and undisturbed areas. The microbial community associated with the samples collected from the exposed sites revealed the anthropogenic effect caused by organic matter from untreated sewage dumping, with an abundance of pathogenic bacterial species.

Microbiome variation in corals with distinct depth distribution ranges across a shallow-mesophotic gradient (15-85 m)

Mesophotic coral ecosystems (MCEs) are generally poorly studied, and our knowledge of lower MCEs (below 60 m depth) is largely limited to visual surveys. Here, we provide a first detailed assessment of the prokaryotic community associated with scleractinian corals over a depth gradient to the lower mesophotic realm (15-85 m). Specimens of three Caribbean coral species exhibiting differences in their depth distribution ranges (Agaricia grahamae, Madracis pharensis and Stephanocoenia intersepta) were collected with a manned submersible on the island of Curaçao, and their prokaryotic communities assessed using 16S rRNA gene sequencing analysis. Corals with narrower depth distribution ranges (depth-specialists) were associated with a stable prokaryotic community, whereas corals with a broader niche range (depth-generalists) revealed a higher variability in their prokaryotic community. The observed depth effects match previously described patterns in Symbiodinium depth zonation. This highlights the contribution of structured microbial communities over depth to the coral's ability to colonize a broader depth range.

Species-specific control of external superoxide levels by the coral holobiont during a natural bleaching event

The reactive oxygen species superoxide (O₂^·−) is both beneficial and detrimental to life. Within corals, superoxide may contribute to pathogen resistance but also bleaching, the loss of essential algal symbionts. Yet, the role of superoxide in coral health and physiology is not completely understood owing to a lack of direct in situ observations. By conducting field measurements of superoxide produced by corals during a bleaching event, we show substantial species-specific variation in external superoxide levels, which reflect the balance of production and degradation processes. Extracellular superoxide concentrations are independent of light, algal symbiont abundance and bleaching status, but depend on coral species and bacterial community composition. Furthermore, coral-derived superoxide concentrations ranged from levels below bulk seawater up to ∼120 nM, some of the highest superoxide concentrations observed in marine systems. Overall, these results unveil the ability of corals and/or their microbiomes to regulate superoxide in their immediate surroundings, which suggests species-specific roles of superoxide in coral health and physiology.

Corals may vary in their ability to regulate reactive oxygen species (ROS) that can influence coral health. Diaz and colleagues conduct in vivo measurements of the ROS superoxide at the surface of corals and find substantial species-level variation in superoxide regulation that is independent of bleaching status.

Comparative genomics of Paracoccus sp. SM22M-07 isolated from coral mucus: insights into bacteria-host interactions

One of the main goals of coral microbiology is to understand the ways in which coral-bacteria associations are established and maintained. This work describes the sequencing of the genome of Paracoccus sp. SM22M-07 isolated from the mucus of the endemic Brazilian coral species Mussismilia hispida. Comparative analysis was used to identify unique genomic features of SM22M-07 that might be involved in its adaptation to the marine ecosystem and the nutrient-rich environment provided by coral mucus, as well as in the establishment and strengthening of the interaction with the host. These features included genes related to the type IV protein secretion system, erythritol catabolism, and succinoglycan biosynthesis. We experimentally confirmed the production of succinoglycan by Paracoccus sp. SM22M-07 and we hypothesize that it may be involved in the association of the bacterium with coral surfaces.

Microbiome analysis shows enrichment for specific bacteria in separate anatomical regions of the deep-sea carnivorous sponge Chondrocladia grandis

The Cladorhizidae is a unique family of carnivorous marine sponges characterised by either the absence or reduction of the aquiferous system and by the presence of specialised structures to trap and digest mesoplanktonic prey. Previous studies have postulated a key role of host-associated bacteria in enabling carnivory in this family of sponges. In this study, we employed high-throughput Illumina-based sequencing to identify the bacterial community associated with four individuals of the deep-sea sponge Chondrocladia grandis sampled in the Gulf of Maine. By characterising the V6 through V8 region of the 16S rRNA gene, we compared the bacterial community composition and diversity in three distinct anatomical regions with predicted involvement in prey capture (sphere), support (axis) and benthic substrate attachment (root). A high abundance of Tenacibaculum, a known siderophore producing bacterial genus, was present in all anatomical regions and specimens. The abundance of Colwellia and Roseobacter was greater in sphere and axis samples, and bacteria from the hydrocarbon-degrading Robiginitomaculum genus were most abundant in the root. This first description of the bacterial community associated with C. grandis provides novel insights into the contribution of bacteria to the carnivorous lifestyle while laying foundations for future cladorhizid symbiosis studies.

Response of diatom-associated bacteria to host growth state, nutrient concentrations, and viral host infection in a model system

Diatoms are photosynthetic unicellular eukaryotes found ubiquitously in aquatic systems. Frequent physical associations with other microorganisms such as bacteria may influence diatom fitness. The predictability of bacterial-diatom interactions is hypothesized to depend on availability of nutrients as well as the physiological state of the host. Biotic and abiotic factors such as nutrient levels, host growth stage and host viral infection were manipulated to determine their effect on the ecological succession of bacterial communities associated with a single cell line of Chaetoceros sp. KBDT20; this was assessed using the relative abundance of bacterial phylotypes based on 16S rDNA sequences. A single bacterial family, Alteromonadaceae, dominated the attached-bacterial community (84.0%), with the most prevalent phylotypes belonging to the Alteromonas and Marinobacter genera. The taxa comprising the other 16% of the attached bacterial assemblage include Alphaproteobacteria, Betaproteobacteria, Bacilli, Deltaproteobacteria, other Gammaproteobacteria and Flavobacteria. Nutrient concentration and host growth stage had a statistically significant effect on the phylogenetic composition of the attached bacteria. It was inferred that interactions between attached bacteria, as well as the inherent stochasticity mediating contact may also contribute to diatom-bacterial associations.

The microbiome of coral surface mucus has a key role in mediating holobiont health and survival upon disturbance

Microbes are well-recognized members of the coral holobiont. However, little is known about the short-term dynamics of mucus-associated microbial communities under natural conditions and after disturbances, and how these dynamics relate to the host's health. Here we examined the natural variability of prokaryotic communities (based on 16S ribosomal RNA gene amplicon sequencing) associating with the surface mucus layer (SML) of Porites astreoides, a species exhibiting cyclical mucus aging and shedding. Shifts in the prokaryotic community composition during mucus aging led to the prevalence of opportunistic and potentially pathogenic bacteria (Verrucomicrobiaceae and Vibrionaceae) in aged mucus and to a twofold increase in prokaryotic abundance. After the release of aged mucus sheets, the community reverted to its original state, dominated by Endozoicimonaceae and Oxalobacteraceae. Furthermore, we followed the fate of the coral holobiont upon depletion of its natural mucus microbiome through antibiotics treatment. After re-introduction to the reef, healthy-looking microbe-depleted corals started exhibiting clear signs of bleaching and necrosis. Recovery versus mortality of the P. astreoides holobiont was related to the degree of change in abundance distribution of the mucus microbiome. We conclude that the natural prokaryotic community inhabiting the coral SML contributes to coral health and that cyclical mucus shedding has a key role in coral microbiome dynamics.

Endozoicomonas Are Specific, Facultative Symbionts of Sea Squirts

Ascidians are marine filter feeders and harbor diverse microbiota that can exhibit a high degree of host-specificity. Pharyngeal samples of Scandinavian and Mediterranean ascidians were screened for consistently associated bacteria by culture-dependent and -independent approaches. Representatives of the Endozoicomonas (Gammaproteobacteria, Hahellaceae) clade were detected in the ascidian species Ascidiella aspersa, Ascidiella scabra, Botryllus schlosseri, Ciona intestinalis, Styela clava, and multiple Ascidia/Ascidiella spp. In total, Endozoicomonas was detected in more than half of all specimens screened, and in 25-100% of the specimens for each species. The retrieved Endozoicomonas 16S rRNA gene sequences formed an ascidian-specific subclade, whose members were detected by fluorescence in situ hybridization (FISH) as extracellular microcolonies in the pharynx. Two strains of the ascidian-specific Endozoicomonas subclade were isolated in pure culture and characterized. Both strains are chemoorganoheterotrophs and grow on mucin (a mucus glycoprotein). The strains tested negative for cytotoxic or antibacterial activity. Based on these observations, we propose ascidian-associated Endozoicomonas to be commensals, living off the mucus continuously secreted into the pharynx. Members of the ascidian-specific Endozoicomonas subclade were also detected in seawater from the Scandinavian sampling site, which suggests acquisition of the symbionts by horizontal transmission. The combined results indicate a host-specific, yet facultative symbiosis between ascidians and Endozoicomonas.