Coral-associated bacteria and their role in the biogeochemical cycling of sulfur

The coral microbiome in sickness, in health and in a changing world

Stony corals, the engines and engineers of reef ecosystems, face unprecedented threats from anthropogenic environmental change. Corals are holobionts that comprise the cnidarian animal host and a diverse community of bacteria, archaea, viruses and eukaryotic microorganisms. Recent research shows that the bacterial microbiome has a pivotal role in coral biology. A healthy bacterial assemblage contributes to nutrient cycling and stress resilience, but pollution, overfishing and climate change can break down these symbiotic relationships, which results in disease, bleaching and, ultimately, coral death. Although progress has been made in characterizing the spatial-temporal diversity of bacteria, we are only beginning to appreciate their functional contribution. In this Review, we summarize the ecological and metabolic interactions between bacteria and other holobiont members, highlight the biotic and abiotic factors influencing the structure of bacterial communities and discuss the impact of climate change on these communities and their coral hosts. We emphasize how microbiome-based interventions can help to decipher key mechanisms underpinning coral health and promote reef resilience. Finally, we explore how recent technological developments may be harnessed to address some of the most pressing challenges in coral microbiology, providing a road map for future research in this field.

Microbiome heterogeneity in tissues of the coral, Fimbriaphyllia (Euphyllia) ancora

Coral microbiomes differ in the mucus, soft tissue and skeleton of a coral colony, but whether variations exist in different tissues of a single polyp is unknown. In the stony coral, Fimbriaphyllia ancora, we identified 8,994 amplicon sequencing variants (ASVs) in functionally differentiated polyp tissues, i.e., tentacles, body wall, mouth and pharynx, mesenterial filaments, and gonads (testes and ovaries), with a large proportion of ASVs specific to individual tissues. However, shared ASVs comprised the majority of microbiomes from all tissues in terms of relative abundance. No tissue-specific ASVs were found, except in testes, for which there were only two samples. At the generic level, Endozoicomonas was significantly less abundant in the body wall, where calicoblastic cells reside. On the other hand, several bacterial taxa presented significantly higher abundances in the mouth. Interestingly, although without statistical confirmation, gonadal tissues showed lower ASV richness and relatively high abundances of Endozoicomonas (in ovaries) and Pseudomonas (in testes). These findings provide evidence for microbiome heterogeneity between tissues within coral polyps, suggesting a promising field for future studies of functional interactions between corals and their bacterial symbionts.

A systematic review of antibiotics and antibiotic resistance genes (ARGs) in mariculture wastewater: Antibiotics removal by microalgal-bacterial symbiotic system (MBSS), ARGs characterization on the metagenomic

Antibiotic residues in mariculture wastewater seriously affect the aquatic environment. Antibiotic Resistance Genes (ARGs) produced under antibiotic stress flow through the environment and eventually enter the human body, seriously affecting human health. Microalgal-bacterial symbiotic system (MBSS) can remove antibiotics from mariculture and reduce the flow of ARGs into the environment. This review encapsulates the present scenario of mariculture wastewater, the removal mechanism of MBSS for antibiotics, and the biomolecular information under metagenomic assay. When confronted with antibiotics, there was a notable augmentation in the extracellular polymeric substances (EPS) content within MBSS, along with a concurrent elevation in the proportion of protein (PN) constituents within the EPS, which limits the entry of antibiotics into the cellular interior. Quorum sensing stimulates the microorganisms to produce biological responses (DNA synthesis - for adhesion) through signaling. Oxidative stress promotes gene expression (coupling, conjugation) to enhance horizontal gene transfer (HGT) in MBSS. The microbial community under metagenomic detection is dominated by aerobic bacteria in the bacterial-microalgal system. Compared to aerobic bacteria, anaerobic bacteria had the significant advantage of decreasing the distribution of ARGs. Overall, MBSS exhibits remarkable efficacy in mitigating the challenges posed by antibiotics and resistant genes from mariculture wastewater.

AI-2 quorum sensing signal disrupts coral symbiotic homeostasis and induces host bleaching

Symbiotic microorganisms play critical ecophysiological roles that facilitate the maintenance of coral health. Currently, information on the gene and protein pathways contributing to bleaching responses is lacking, including the role of autoinducers. Although the autoinducer AI-1 is well understood, information on AI-2 is insufficient. Here, we observed a 3.7-4.0 times higher abundance of the AI-2 synthesis gene luxS in bleached individuals relative to their healthy counterparts among reef-building coral samples from the natural environment. Laboratory tests further revealed that AI-2 contributed significantly to an increase in coral bleaching, altered the ratio of potential probiotic and pathogenic bacteria, and suppressed the antiviral activity of specific pathogenic bacteria while enhancing their functional potential, such as energy metabolism, chemotaxis, biofilm formation and virulence release. Structural equation modeling indicated that AI-2 influences the microbial composition, network structure, and pathogenic features, which collectively contribute to the coral bleaching status. Collectively, our results offer novel potential strategies for coral conservation based on a signal manipulation approach.

Bacteria associated with the in hospite Symbiodiniaceae's phycosphere

Symbiotic interactions between Symbiodiniaceae and bacteria are still poorly explored, especially those in hospite. Here, we adapted a technique that allows for the enrichment of intact and metabolically active in hospite Symbiodiniaceae cells (ihSC) and their associated bacteria from the tissue of the model coral Pocillopora damicornis, using a discontinuous gradient of solution of isotonic Percoll (SIP). The ihSC were concentrated in the 50% SIP fraction, as determined by microscopy. The presence of bacteria associated with ihSC was confirmed by fluorescence in situ hybridization, while microbiome analysis indicated that bacteria of the families Halieaceae, Flavobacteriaceae, and Alcanivoraceae are significantly associated with ihSC. Extracellular vesicles that could be exuding molecules were detected on the symbiosome membranes. Our technique and data contribute to elucidate ihSC-bacteria interactions.

A genome-centric view of the role of the Acropora kenti microbiome in coral health and resilience

Microbial diversity has been extensively explored in reef-building corals. However, the functional roles of coral-associated microorganisms remain poorly elucidated. Here, we recover 191 bacterial and 10 archaeal metagenome-assembled genomes (MAGs) from the coral Acropora kenti (formerly A. tenuis) and adjacent seawater, to identify microbial functions and metabolic interactions within the holobiont. We show that 82 MAGs were specific to the A. kenti holobiont, including members of the Pseudomonadota, Bacteroidota, and Desulfobacterota. A. kenti-specific MAGs displayed significant differences in their genomic features and functional potential relative to seawater-specific MAGs, with a higher prevalence of genes involved in host immune system evasion, nitrogen and carbon fixation, and synthesis of five essential B-vitamins. We find a diversity of A. kenti-specific MAGs encode the biosynthesis of essential amino acids, such as tryptophan, histidine, and lysine, which cannot be de novo synthesised by the host or Symbiodiniaceae. Across a water quality gradient spanning 2° of latitude, A. kenti microbial community composition is correlated to increased temperature and dissolved inorganic nitrogen, with corresponding enrichment in molecular chaperones, nitrate reductases, and a heat-shock protein. We reveal mechanisms of A. kenti-microbiome-symbiosis on the Great Barrier Reef, highlighting the interactions underpinning the health of this keystone holobiont.

A study into the diversity of coral-associated bacteria using culture-dependent and culture-independent approaches in coral Dipsastraea favus from the Gulf of Kutch

Corals harbour ~25 % of the marine diversity referring to biodiversity hotspots in marine ecosystems. Global efforts to find ways to restore the coral reef ecosystem from various threats can be complemented by studying coral-associated bacteria. Coral-associated bacteria are vital components of overall coral wellbeing. We explored the bacterial diversity associated with coral Dipsastraea favus (D. favus) collected from the Gulf of Kutch, India, using both culture-dependent and metagenomic approaches. In both approaches, phylum Proteobacteria, Firmicutes, and Actinobacteria predominated, comprising the genera Vibrio, Bacillus, Shewanella, Pseudoalteromonas, Exiguobacterium and Streptomyces. Moreover, the majority of culturable isolates showed multiple antibiotic resistance index ≥0.2. In this study, specific bacterial diversity associated with coral sp. D. favus and its possible role in managing coral health was established. Almost 43 strains from the samples were successfully cultured, creating a base for exploring these microbes for their potential use in coral conservation methods.

Microbiome composition and function within the Kellet's whelk perivitelline fluid

Microbiomes have gained significant attention in ecological research, owing to their diverse interactions and essential roles within different organismal ecosystems. Microorganisms, such as bacteria, archaea, and viruses, have profound impact on host health, influencing digestion, metabolism, immune function, tissue development, and behavior. This study investigates the microbiome diversity and function of Kellet's whelk (Kelletia kelletii) perivitelline fluid (PVF), which sustains thousands of developing K. kelletii embryos within a polysaccharide and protein matrix. Our core microbiome analysis reveals a diverse range of bacteria, with the Roseobacter genus being the most abundant. Additionally, genes related to host-microbe interactions, symbiosis, and quorum sensing were detected, indicating a potential symbiotic relationship between the microbiome and Kellet's whelk embryos. Furthermore, the microbiome exhibits gene expression related to antibiotic biosynthesis, suggesting a defensive role against pathogenic bacteria and potential discovery of novel antibiotics. Overall, this study sheds light on the microbiome's role in Kellet's whelk development, emphasizing the significance of host-microbe interactions in vulnerable life history stages. To our knowledge, ours is the first study to use 16S sequencing coupled with RNA sequencing (RNA-seq) to profile the microbiome of an invertebrate PVF.IMPORTANCEThis study provides novel insight to an encapsulated system with strong evidence of symbiosis between the microbial inhabitants and developing host embryos. The Kellet's whelk perivitelline fluid (PVF) contains microbial organisms of interest that may be providing symbiotic functions and potential antimicrobial properties during this vulnerable life history stage. This study, the first to utilize a comprehensive approach to investigating Kellet's whelk PVF microbiome, couples 16S rRNA gene long-read sequencing with RNA-seq. This research contributes to and expands our knowledge on the roles of beneficial host-associated microbes.

Evolutionary radiation and microbial community dynamics shape the thermal tolerance of Fungiidae in the southern South China Sea

Fungiidae have shown increased thermal adaptability in coral reef ecosystems under global warming. This study analyzes the evolutionary divergence and microbial communities of Fungiidae in the Sanjiao Reef of the southern South China Sea and explores the impact of coral evolution radiation and microbial dynamics on the heat tolerance of Fungiidae. The results found that Cycloseris was an ancient branch of Fungiidae, dating back approximately 147.8953 Mya, and Fungiidae differentiated into two ancestral clades (clades I and II) before 107.0312 Ma. Fungiidae exhibited specific symbioses with the Cladocopium C27 sub-clade. Notably, the Cladocopium C1 sub-clade has a high relative abundance in clade I, whereas the heat-tolerant Cladocopium C40 and C3u sub-clades subdominante in clade II. Regarding bacterial communities, Cycloseris costulata, the earliest divergent species, had higher bacterial β-diversity, while the latest divergent species, Lithophyllon scabra, displayed lower bacterial α-diversity and higher community stability. Beneficial bacteria dominante Fungiidae's bacterial community (54%). The co-occurrence network revealed that microbial networks in clade II exhibited lower complexity and greater resilience than those in clade I. Our study highlights that host evolutionary radiation and microbial communities shaped Fungiidae's thermal tolerance. The variability in subdominant Symbiodiniaceae populations may contribute to interspecific differences in thermal tolerance along the evolutionary branches of Fungiidae. The presence of abundant beneficial bacteria may further enhance the thermal ability of the Fungiidae. Furthermore, the later divergent species of Fungiidae have stronger heat tolerance, possibly driven by the increased regulation ability of the host on the bacterial community, greater microbial community stability, and interaction network resistance.IMPORTANCECoral reefs are facing significant threats due to global warming. The heat tolerance of coral holobionts depends on both the coral host and its microbiome. However, the association between coral evolutionary radiation and interspecific differences in microbial communities remains unclear. In this study, we investigated the role of evolutionary radiation and microbial community dynamics in shaping the thermal acclimation potential of Fungiidae in the Sanjiao Reef of the southern South China Sea. The study's results suggest that evolutionary radiation enhances the thermal tolerance of Fungiidae. Fungiidae species that have diverged more recently have exhibited a higher presence of heat-tolerant Symbiodiniaceae taxa, more stable bacterial communities, and a robust and resilient microbial interaction network, improving the thermal adaptability of Fungiidae. In summary, this study provides new insights into the thermal adaptation patterns of corals under global warming conditions.

Antimicrobial activity of coral-associated beneficial bacteria against coral disease-causing microbial pathogens

Microbial infection of immune-compromised corals influences disease severity, resulting in coral mortality. However, coral-associated beneficial bacteria are known to produce antimicrobial compounds that prevent the growth of potential pathogens and invading microbes. Hence, beneficial bacteria associated with coral Porites lutea were isolated and antimicrobial protein and bioactive secondary metabolites were extracted and tested for their antimicrobial activity against putative prokaryotic and eukaryotic coral pathogens. Bioactive secondary metabolites exhibited remarkable antagonism against various coral pathogens such as Serratia marcescens, Vibrio species, and Aspergillus sydowii. Besides, the metabolites of Cobetia marina, Cobetia amphilecti, Pseudoalteromonas neustonica, and Virgibacillus halodenitrificans manifested notable inhibition against the protozoan ciliates (Uronema marinum, Holosticha diademata, Cohnilembus verminus, and Euplotes vannus) and zooplankton that are known to be involved in the secondary pathogenesis in coral diseased lesion progression. Thus, the present study may benefit in understanding coral-associated beneficial bacteria for their antagonistic interactions with microbial pathogens, as well as their potential involvement in reducing coral disease severity.

DNA from non-viable bacteria biases diversity estimates in the corals Acropora loripes and Pocillopora acuta

BACKGROUND

Nucleic acid-based analytical methods have greatly expanded our understanding of global prokaryotic diversity, yet standard metabarcoding methods provide no information on the most fundamental physiological state of bacteria, viability. Scleractinian corals harbour a complex microbiome in which bacterial symbionts play critical roles in maintaining health and functioning of the holobiont. However, the coral holobiont contains both dead and living bacteria. The former can be the result of corals feeding on bacteria, rapid swings from hyper- to hypoxic conditions in the coral tissue, the presence of antimicrobial compounds in coral mucus, and an abundance of lytic bacteriophages.

RESULTS

By combining propidium monoazide (PMA) treatment with high-throughput sequencing on six coral species (Acropora loripes, A. millepora, A. kenti, Platygyra daedalea, Pocillopora acuta, and Porites lutea) we were able to obtain information on bacterial communities with little noise from non-viable microbial DNA. Metabarcoding of the 16S rRNA gene showed significantly higher community evenness (85%) and species diversity (31%) in untreated compared with PMA-treated tissue for A. loripes only. While PMA-treated coral did not differ significantly from untreated samples in terms of observed number of ASVs, > 30% of ASVs were identified in untreated samples only, suggesting that they originated from cell-free/non-viable DNA. Further, the bacterial community structure was significantly different between PMA-treated and untreated samples for A. loripes and P. acuta indicating that DNA from non-viable microbes can bias community composition data in coral species with low bacterial diversity.

CONCLUSIONS

Our study is highly relevant to microbiome studies on coral and other host organisms as it delivers a solution to excluding non-viable DNA in a complex community. These results provide novel insights into the dynamic nature of host-associated microbiomes and underline the importance of applying versatile tools in the analysis of metabarcoding or next-generation sequencing data sets.

Unveiling microbiome changes in Mediterranean octocorals during the 2022 marine heatwaves: quantifying key bacterial symbionts and potential pathogens

BACKGROUND

Climate change has accelerated the occurrence and severity of heatwaves in the Mediterranean Sea and poses a significant threat to the octocoral species that form the foundation of marine animal forests (MAFs). As coral health intricately relies on the symbiotic relationships established between corals and microbial communities, our goal was to gain a deeper understanding of the role of bacteria in the observed tissue loss of key octocoral species following the unprecedented heatwaves in 2022.

RESULTS

Using amplicon sequencing and taxon-specific qPCR analyses, we unexpectedly found that the absolute abundance of the major bacterial symbionts, Spirochaetaceae (C. rubrum) and Endozoicomonas (P. clavata), remained, in most cases, unchanged between colonies with 0% and 90% tissue loss. These results suggest that the impairment of coral health was not due to the loss of the main bacterial symbionts. However, we observed a significant increase in the total abundance of bacterial opportunists, including putative pathogens such as Vibrio, which was not evident when only their relative abundance was considered. In addition, there was no clear relation between bacterial symbiont loss and the intensity of thermal stress, suggesting that factors other than temperature may have influenced the differential response of octocoral microbiomes at different sampling sites.

CONCLUSIONS

Our results indicate that tissue loss in octocorals is not directly caused by the decline of the main bacterial symbionts but by the proliferation of opportunistic and pathogenic bacteria. Our findings thus underscore the significance of considering both relative and absolute quantification approaches when evaluating the impact of stressors on coral microbiome as the relative quantification does not accurately depict the actual changes in the microbiome. Consequently, this research enhances our comprehension of the intricate interplay between host organisms, their microbiomes, and environmental stressors, while offering valuable insights into the ecological implications of heatwaves on marine animal forests. Video Abstract.

Similar but different: Characterization of dddD gene-mediated DMSP metabolism among coral-associated Endozoicomonas

Endozoicomonas are often predominant bacteria and prominently important in coral health. Their role in dimethylsulfoniopropionate (DMSP) degradation has been a subject of discussion for over a decade. A previous study found that Endozoicomonas degraded DMSP through the dddD pathway. This process releases dimethyl sulfide, which is vital for corals coping with thermal stress. However, little is known about the related gene regulation and metabolic abilities of DMSP metabolism in Endozoicomonadaceae. In this study, we isolated a novel Endozoicomonas DMSP degrader and observed a distinct DMSP metabolic trend in two phylogenetically close dddD-harboring Endozoicomonas species, confirmed genetically by comparative transcriptomic profiling and visualization of the change of DMSP stable isotopes in bacterial cells using nanoscale secondary ion spectrometry. Furthermore, we found that DMSP cleavage enzymes are ubiquitous in coral Endozoicomonas with a preference for having DddD lyase. We speculate that harboring DMSP degrading genes enables Endozoicomonas to successfully colonize various coral species across the globe.

Rhodobacteraceae dominate the core microbiome of the sea star Odontaster validus (Koehler, 1906) in two opposite geographical sectors of the Antarctic Ocean

Microbiota plays essential roles in the health, physiology, and in adaptation of marine multi-cellular organisms to their environment. In Antarctica, marine organisms have a wide range of unique physiological functions and adaptive strategies, useful for coping with extremely cold conditions. However, the role of microbiota associated with Antarctic organisms in such adaptive strategies is underexplored. In the present study, we investigated the diversity and putative functions of the microbiome of the sea star Odontaster validus, one of the main keystone species of the Antarctic benthic ecosystems. We compared the whole-body bacterial microbiome of sea stars from different sites of the Antarctic Peninsula and Ross Sea, two areas located in two opposite geographical sectors of the Antarctic continent. The taxonomic composition of O. validus microbiomes changed both between and within the two Antarctic sectors, suggesting that environmental and biological factors acting both at large and local scales may influence microbiome diversity. Despite this, one bacterial family (Rhodobacteraceae) was shared among all sea star individuals from the two geographical sectors, representing up to 95% of the microbial core, and suggesting a key functional role of this taxon in holobiont metabolism and well-being. In addition, the genus Roseobacter belonging to this family was also present in the surrounding sediment, implying a potential horizontal acquisition of dominant bacterial core taxa via host-selection processes from the environment.

Microorganisms and dissolved metabolites distinguish Florida's Coral Reef habitats

As coral reef ecosystems experience unprecedented change, effective monitoring of reef features supports management, conservation, and intervention efforts. Omic techniques show promise in quantifying key components of reef ecosystems including dissolved metabolites and microorganisms that may serve as invisible sensors for reef ecosystem dynamics. Dissolved metabolites are released by reef organisms and transferred among microorganisms, acting as chemical currencies and contributing to nutrient cycling and signaling on reefs. Here, we applied four omic techniques (taxonomic microbiome via amplicon sequencing, functional microbiome via shotgun metagenomics, targeted metabolomics, and untargeted metabolomics) to waters overlying Florida's Coral Reef, as well as microbiome profiling on individual coral colonies from these reefs to understand how microbes and dissolved metabolites reflect biogeographical, benthic, and nutrient properties of this 500-km barrier reef. We show that the microbial and metabolite omic approaches each differentiated reef habitats based on geographic zone. Further, seawater microbiome profiling and targeted metabolomics were significantly related to more reef habitat characteristics, such as amount of hard and soft coral, compared to metagenomic sequencing and untargeted metabolomics. Across five coral species, microbiomes were also significantly related to reef zone, followed by species and disease status, suggesting that the geographic water circulation patterns in Florida also impact the microbiomes of reef builders. A combination of differential abundance and indicator species analyses revealed metabolite and microbial signatures of specific reef zones, which demonstrates the utility of these techniques to provide new insights into reef microbial and metabolite features that reflect broader ecosystem processes.

Genome analysis of a coral-associated bacterial consortium highlights complementary hydrocarbon degradation ability and other beneficial mechanisms for the host

Here we report the oil degradation genetic potential of six oil-degrading bacteria (ODB), previously used as a bioremediation consortium, isolated from the hydrocoral Millepora alcicornis and seawater. The strains were identified as Halomonas sp. (LC_1), Cobetia sp. (LC_6), Pseudoalteromonas shioyasakiensis (LC_2), Halopseudomonas aestusnigri (LC_3), Shewanella algae (LC_4), and Brucella intermedia (LC_5). The taxonomic identification differed from that of the original paper when we used whole genome gene markers instead of just 16S rRNA gene. Genes responsible for the degradation of aromatic hydrocarbons and n-alkanes were found in all genomes, although different (and complementary) steps of the metabolic pathways were unique to each strain. Genes for naphthalene and toluene degradation were found in various strains. We annotated quinate degradation genes in LC_6, while LC_3 and LC_5 presented genes for biosurfactant and rhamnolipid biosynthesis. We also annotated genes related to beneficial mechanisms for corals, such as genes involved in nitrogen and DMSP metabolism, cobalamin biosynthesis and antimicrobial compounds production. Our findings reinforce the importance of using bacterial consortia for bioremediation approaches instead of single strains, due to their complementary genomic arsenals. We also propose a genome-based framework to select complementary ODB that can provide additional benefits to coral health.

Symbiont Identity Impacts the Microbiome and Volatilome of a Model Cnidarian-Dinoflagellate Symbiosis

The symbiosis between cnidarians and dinoflagellates underpins the success of reef-building corals in otherwise nutrient-poor habitats. Alterations to symbiotic state can perturb metabolic homeostasis and thus alter the release of biogenic volatile organic compounds (BVOCs). While BVOCs can play important roles in metabolic regulation and signalling, how the symbiotic state affects BVOC output remains unexplored. We therefore characterised the suite of BVOCs that comprise the volatilome of the sea anemone Exaiptasia diaphana ('Aiptasia') when aposymbiotic and in symbiosis with either its native dinoflagellate symbiont Breviolum minutum or the non-native symbiont Durusdinium trenchii. In parallel, the bacterial community structure in these different symbiotic states was fully characterised to resolve the holobiont microbiome. Based on rRNA analyses, 147 unique amplicon sequence variants (ASVs) were observed across symbiotic states. Furthermore, the microbiomes were distinct across the different symbiotic states: bacteria in the family Vibrionaceae were the most abundant in aposymbiotic anemones; those in the family Crocinitomicaceae were the most abundant in anemones symbiotic with D. trenchii; and anemones symbiotic with B. minutum had the highest proportion of low-abundance ASVs. Across these different holobionts, 142 BVOCs were detected and classified into 17 groups based on their chemical structure, with BVOCs containing multiple functional groups being the most abundant. Isoprene was detected in higher abundance when anemones hosted their native symbiont, and dimethyl sulphide was detected in higher abundance in the volatilome of both Aiptasia-Symbiodiniaceae combinations relative to aposymbiotic anemones. The volatilomes of aposymbiotic anemones and anemones symbiotic with B. minutum were distinct, while the volatilome of anemones symbiotic with D. trenchii overlapped both of the others. Collectively, our results are consistent with previous reports that D. trenchii produces a metabolically sub-optimal symbiosis with Aiptasia, and add to our understanding of how symbiotic cnidarians, including corals, may respond to climate change should they acquire novel dinoflagellate partners.

Bacteria and microalgae associations in periphyton-mechanisms and biotechnological opportunities

Phototrophic and heterotrophic microorganisms coexist in complex and dynamic structures called periphyton. These structures shape the biogeochemistry and biodiversity of aquatic ecosystems. In particular, microalgae-bacteria interactions are a prominent focus of study by microbial ecologists and can provide biotechnological opportunities for numerous applications (i.e. microalgal bloom control, aquaculture, biorefinery, and wastewater bioremediation). In this review, we analyze the species dynamics (i.e. periphyton formation and factors determining the prevalence of one species over another), coexisting communities, exchange of resources, and communication mechanisms of periphytic microalgae and bacteria. We extend periphyton mathematical modelling as a tool to comprehend complex interactions. This review is expected to boost the applicability of microalgae-bacteria consortia, by drawing out knowledge from natural periphyton.

Concordance of microbial and visual health indicators of white-band disease in nursery reared Caribbean coral Acropora cervicornis

Background

Coral diseases are one of the leading causes of declines in coral populations. In the Caribbean, white band disease (WBD) has led to a substantial loss of Acropora corals. Although the etiologies of this disease have not been well described, characterizing the coral microbiome during the transition from a healthy to diseased state is critical for understanding disease progression. Coral nurseries provide unique opportunities to further understand the microbial changes associated with diseased and healthy corals, because corals are monitored over time. We characterized the microbiomes before and during an outbreak of WBD in Acropora cervicornis reared in an ocean nursery in Little Cayman, CI. We asked (1) do healthy corals show the same microbiome over time (before and during a disease outbreak) and (2) are there disease signatures on both lesioned and apparently healthy tissues on diseased coral colonies?

Methods

Microbial mucus-tissue slurries were collected from healthy coral colonies in 2017 (before the disease) and 2019 (during the disease onset). Diseased colonies were sampled at two separate locations on an individual coral colony: at the interface of Disease and ∼10 cm away on Apparently Healthy coral tissue. We sequenced the V4 region of the 16S rRNA gene to characterize bacterial and archaeal community composition in nursery-reared A. cervicornis. We assessed alpha diversity, beta diversity, and compositional differences to determine differences in microbial assemblages across health states (2019) and healthy corals between years (2017 and 2019).

Results

Microbial communities from healthy A. cervicornis from 2017 (before disease) and 2019 (after disease) did not differ significantly. Additionally, microbial communities from Apparently Healthy samples on an otherwise diseased coral colony were more similar to Healthy colonies than to the diseased portion on the same colony for both alpha diversity and community composition. Microbial communities from Diseased tissues had significantly higher alpha diversity than both Healthy and Apparently Healthy tissues but showed no significant difference in beta-diversity dispersion. Our results show that at the population scale, Healthy and Apparently Healthy coral tissues are distinct from microbial communities associated with Diseased tissues. Furthermore, our results suggest stability in Little Cayman nursery coral microbiomes over time. We show healthy Caymanian nursery corals had a stable microbiome over a two-year period, an important benchmark for evaluating coral health via their microbiome.

Recent advancements in coral health, microbiome interactions and climate change

Corals are the visible indicators of the disasters induced by global climate change and anthropogenic activities and have become a highly vulnerable ecosystem on the verge of extinction. Multiple stressors could act individually or synergistically which results in small to large scale tissue degradation, reduced coral covers, and makes the corals vulnerable to various diseases. The coralline diseases are like the Chicken pox in humans because they spread hastily throughout the coral ecosystem and can devastate the coral cover formed over centuries in an abbreviated time. The extinction of the entire reef ecosystem will alter the ocean and earth's amalgam of biogeochemical cycles causing a threat to the entire planet. The current manuscript provides an overview of the recent advancement in coral health, microbiome interactions and climate change. Culture dependent and independent approaches in studying the microbiome of corals, the diseases caused by microorganisms, and the reservoirs of coral pathogens are also discussed. Finally, we discuss the possibilities of protecting the coral reefs from diseases through microbiome transplantation and the capabilities of remote sensing in monitoring their health status.

Spatial, temporal and network analyses provide insights into the dynamics of the bacterial communities associated with two species of Caribbean octocorals and indicate possible key taxa

Despite the current decline of scleractinian coral populations, octocorals are thriving on reefs in the Caribbean Sea and western North Atlantic Ocean. These cnidarians are holobiont entities, interacting with a diverse array of microorganisms. Few studies have investigated the spatial and temporal stability of the bacterial communities associated with octocoral species and information regarding the co-occurrence and potential interactions between specific members of these bacterial communities remain sparse. To address this knowledge gap, this study investigated the stability of the bacterial assemblages associated with two common Caribbean octocoral species, Eunicea flexuosa and Antillogorgia americana, across time and geographical locations and performed network analyses to investigate potential bacterial interactions. Results demonstrated that general inferences regarding the spatial and temporal stability of octocoral-associated bacterial communities should not be made, as host-specific characteristics may influence these factors. In addition, network analyses revealed differences in the complexity of the interactions between bacteria among the octocoral species analyzed, while highlighting the presence of genera known to produce bioactive secondary metabolites in both octocorals that may play fundamental roles in structuring the octocoral-associated bacteriome.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13199-023-00923-x.

A bacterial symbiont in the gill of the marine scallop Argopecten irradians irradians metabolizes dimethylsulfoniopropionate

Microbial lysis of dimethylsulfoniopropionate (DMSP) is a key step in marine organic sulfur cycling and has been recently demonstrated to play an important role in mediating interactions between bacteria, algae, and zooplankton. To date, microbes that have been found to lyse DMSP are largely confined to free-living and surface-attached bacteria. In this study, we report for the first time that a symbiont (termed "Rhodobiaceae bacterium HWgs001") in the gill of the marine scallop Argopecten irradians irradians can lyse and metabolize DMSP. Analysis of 16S rRNA gene sequences suggested that HWgs001 accounted for up to 93% of the gill microbiota. Microscopic observations suggested that HWgs001 lived within the gill tissue. Unlike symbionts of other bivalves, HWgs001 belongs to Alphaproteobacteria rather than Gammaproteobacteria, and no genes for carbon fixation were identified in its small genome. Moreover, HWgs001 was found to possess a dddP gene, responsible for the lysis of DMSP to acrylate. The enzymatic activity of dddP was confirmed using the heterologous expression, and in situ transcription of the gene in scallop gill tissues was demonstrated using reverse-transcription PCR. Together, these results revealed a taxonomically and functionally unique symbiont, which represents the first-documented DMSP-metabolizing symbiont likely to play significant roles in coastal marine ecosystems.

Physiological changes during torpor favor association with Endozoicomonas endosymbionts in the urochordate Botrylloides leachii

Environmental perturbations evoke down-regulation of metabolism in some multicellular organisms, leading to dormancy, or torpor. Colonies of the urochordate Botrylloides leachii enter torpor in response to changes in seawater temperature and may survive for months as small vasculature remnants that lack feeding and reproductive organs but possess torpor-specific microbiota. Upon returning to milder conditions, the colonies rapidly restore their original morphology, cytology and functionality while harboring re-occurring microbiota, a phenomenon that has not been described in detail to date. Here we investigated the stability of B. leachii microbiome and its functionality in active and dormant colonies, using microscopy, qPCR, in situ hybridization, genomics and transcriptomics. A novel lineage of Endozoicomonas, proposed here as Candidatus Endozoicomonas endoleachii, was dominant in torpor animals (53-79% read abundance), and potentially occupied specific hemocytes found only in torpid animals. Functional analysis of the metagenome-assembled genome and genome-targeted transcriptomics revealed that Endozoicomonas can use various cellular substrates, like amino acids and sugars, potentially producing biotin and thiamine, but also expressing various features involved in autocatalytic symbiosis. Our study suggests that the microbiome can be linked to the metabolic and physiological states of the host, B. leachii, introducing a model organism for the study of symbioses during drastic physiological changes, such as torpor.

Different disease inoculations cause common responses of the host immune system and prokaryotic component of the microbiome in Acropora palmata

Reef-building corals contain a complex consortium of organisms, a holobiont, which responds dynamically to disease, making pathogen identification difficult. While coral transcriptomics and microbiome communities have previously been characterized, similarities and differences in their responses to different pathogenic sources has not yet been assessed. In this study, we inoculated four genets of the Caribbean branching coral Acropora palmata with a known coral pathogen (Serratia marcescens) and white band disease. We then characterized the coral's transcriptomic and prokaryotic microbiomes' (prokaryiome) responses to the disease inoculations, as well as how these responses were affected by a short-term heat stress prior to disease inoculation. We found strong commonality in both the transcriptomic and prokaryiomes responses, regardless of disease inoculation. Differences, however, were observed between inoculated corals that either remained healthy or developed active disease signs. Transcriptomic co-expression analysis identified that corals inoculated with disease increased gene expression of immune, wound healing, and fatty acid metabolic processes. Co-abundance analysis of the prokaryiome identified sets of both healthy-and-disease-state bacteria, while co-expression analysis of the prokaryiomes' inferred metagenomic function revealed infected corals' prokaryiomes shifted from free-living to biofilm states, as well as increasing metabolic processes. The short-term heat stress did not increase disease susceptibility for any of the four genets with any of the disease inoculations, and there was only a weak effect captured in the coral hosts' transcriptomic and prokaryiomes response. Genet identity, however, was a major driver of the transcriptomic variance, primarily due to differences in baseline immune gene expression. Despite genotypic differences in baseline gene expression, we have identified a common response for components of the coral holobiont to different disease inoculations. This work has identified genes and prokaryiome members that can be focused on for future coral disease work, specifically, putative disease diagnostic tools.

Identifying keystone species in microbial communities using deep learning

Previous studies suggested that microbial communities harbor keystone species whose removal can cause a dramatic shift in microbiome structure and functioning. Yet, an efficient method to systematically identify keystone species in microbial communities is still lacking. This is mainly due to our limited knowledge of microbial dynamics and the experimental and ethical difficulties of manipulating microbial communities. Here, we propose a Data-driven Keystone species Identification (DKI) framework based on deep learning to resolve this challenge. Our key idea is to implicitly learn the assembly rules of microbial communities from a particular habitat by training a deep learning model using microbiome samples collected from this habitat. The well-trained deep learning model enables us to quantify the community-specific keystoneness of each species in any microbiome sample from this habitat by conducting a thought experiment on species removal. We systematically validated this DKI framework using synthetic data generated from a classical population dynamics model in community ecology. We then applied DKI to analyze human gut, oral microbiome, soil, and coral microbiome data. We found that those taxa with high median keystoneness across different communities display strong community specificity, and many of them have been reported as keystone taxa in literature. The presented DKI framework demonstrates the power of machine learning in tackling a fundamental problem in community ecology, paving the way for the data-driven management of complex microbial communities.

Identification of quorum sensing-regulated Vibrio fortis as potential pathogenic bacteria for coral bleaching and the effects on the microbial shift

Coastal pollution, global warming, ocean acidification, and other reasons lead to the imbalance of the coral reef ecosystem, resulting in the increasingly serious problem of coral degradation. Coral bleaching is often accompanied by structural abnormalities of coral symbiotic microbiota, among which Vibrio is highly concerned. In this study, Vibrio fortis S10-1 (MCCC 1H00104), isolated from sea cucumber, was used for the bacterial infection on coral Seriatopora guttatus and Pocillopora damicornis. The infection of S10-1 led to coral bleaching and a significant reduction of photosynthetic function in coral holobiont, and the pathogenicity of V. fortis was regulated by quorum sensing. Meanwhile, Vibrio infection also caused a shift of coral symbiotic microbial community, with significantly increased abundant Proteobacteria and Actinobacteria and significantly reduced abundant Firmicutes; on genus level, the abundance of Bacillus decreased significantly and the abundance of Rhodococcus, Ralstonia, and Burkholderia-Caballeronia-Paraburkholderia increased significantly; S10-1 infection also significantly impacted the water quality in the micro-ecosystem. In contrast, S10-1 infection showed less effect on the microbial community of the live stone, which reflected that the microbes in the epiphytic environment of the live stone might have a stronger ability of self-regulation; the algal symbionts mainly consisted of Cladocopium sp. and showed no significant effect by the Vibrio infection. This study verified that V. fortis is the primary pathogenic bacterium causing coral bleaching, revealed changes in the microbial community caused by its infection, provided strong evidence for the "bacterial bleaching" hypothesis, and provided an experimental experience for the exploration of the interaction mechanism among microbial communities, especially coral-associated Vibrio in the coral ecosystem, and potential probiotic strategy or QS regulation on further coral disease control.

Microbiota of healthy and bleached corals of the species Siderastrea stellata in response to river influx and seasonality in Brazilian northeast

Although coral bleaching is increasing worldwide due to warming oceans exacerbated by climate change, there has been a growing recognition that local stressors may play an additional role. Important stressors include the physicochemical and microbiological influences that are related to river runoff. Here, we investigated the microbiota associated to mucus and tissue of endemic coral Siderastrea stellata, collected from Brazilian northeast coral reefs of Barra de Santo Antônio (subject to river runoff) and Maragogi (minimal river runoff) during both the rainy and dry seasons. We sequenced the V4 region of 16S rDNA and used multiple R packages to process raw data and performed statistical analysis to reveal the microbial community structure composition and functional predictions. Major dissimilarities between microbial communities were related to seasonality, while healthy and bleached specimens were mainly associated with the enrichment of several less abundant taxa involved in specific metabolic functions, mainly related to the nitrogen cycle. We were not able to observe the dominance of groups that has been previously associated with bleachings, such as Vibrionaceae or Burkholderiaceae. The influx of freshwater appears to increase the homogeneity between individuals in Barra de Santo Antonio, especially during the rainy season. By contrast, we observed an increased homogeneity between samples in Maragogi during the dry season. Understanding the dynamics of the coral microbiota and how bleaching appears in response to specific environmental variables, in addition to determining the conditions that lead to a more robust coral microbiota, is essential for choosing the most appropriate area and conservation methods, for example.

Microbial Interactions with Dissolved Organic Matter Are Central to Coral Reef Ecosystem Function and Resilience

To thrive in nutrient-poor waters, coral reefs must retain and recycle materials efficiently. This review centers microbial processes in facilitating the persistence and stability of coral reefs, specifically the role of these processes in transforming and recycling the dissolved organic matter (DOM) that acts as an invisible currency in reef production, nutrient exchange, and organismal interactions. The defining characteristics of coral reefs, including high productivity, balanced metabolism, high biodiversity, nutrient retention, and structural complexity, are inextricably linked to microbial processing of DOM. The composition of microbes and DOM in reefs is summarized, and the spatial and temporal dynamics of biogeochemical processes carried out by microorganisms in diverse reef habitats are explored in a variety of key reef processes, including decomposition, accretion, trophictransfer, and macronutrient recycling. Finally, we examine how widespread habitat degradation of reefs is altering these important microbe-DOM interactions, creating feedbacks that reduce reef resilience to global change.

Prevalence of differential microbiome in healthy, diseased and nipped colonies of corals, Porites lutea in the Gulf of Kachchh, north-west coast of India

Coral reefs are constantly subjected to multiple stresses like diseases and fish predation, which can profoundly influence the coral microbiome. This study investigated the differences in bacterial community structure of healthy, white syndrome affected and blenny nipped coral colonies of Porites lutea, collected from the coral reefs of Gulf of Kachchh, north-west coast of India. Present study observed that the stressed coral colonies harbored more OTUs and contained higher diversity values compared to healthy corals colonies. Similarly, beta diversity analysis indicated the dissimilarities among the three coral samples analyzed. Though the taxonomy analysis indicated bacterial phyla like Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria among the entire coral samples studied, there was a variation in their relative abundances. Huge variations were observed in the relative dominance at the bacterial genera level. About 13phyla and 11 genera was identified in healthy coral. The PBN sample was found to contain Proteobacteria, Cyanobacteria, Verrucomicrobia, and Lentisphaerae as dominant phyla and Endozoicomonas, Dyella, Woeseia, and Winogradskyella as dominant genera. The PWS sample contained Proteobacteria, Lentisphaerae, Spirochaetes, and Tenericutes as dominant phyla and Endozoicomonas, Arcobacter, Sunxiuqinia, and Carboxylicivirgia as dominant genera. Among the healthy samples, sequences belonging to Uncultured Rhodospirillaceae were dominant, while Woeseia and sequences belonging to Uncultured Rhodovibrionaceae were dominant among the blenny nipped white syndrome infected corals. Although any previously established pathogen was not identified, present study revealed the presence of a potentially pathogenic bacterium, Arcobacter, among the diseased corals. It also demonstrated a dynamic microbiome among the Porites lutea colonies on subjecting to various stresses.

Enriching the endophytic bacterial microbiota of Ginkgo roots

Bacterial endophytes of Ginkgo roots take part in the secondary metabolic processes of the fossil tree and contribute to plant growth, nutrient uptake, and systemic resistance. However, the diversity of bacterial endophytes in Ginkgo roots is highly underestimated due to the lack of successful isolates and enrichment collections. The resulting culture collection contains 455 unique bacterial isolates representing 8 classes, 20 orders, 42 families, and 67 genera from five phyla: Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Deinococcus-Thermus, using simply modified media (a mixed medium without any additional carbon sources [MM)] and two other mixed media with separately added starch [GM] and supplemented glucose [MSM]). A series of plant growth-promoting endophytes had multiple representatives within the culture collection. Moreover, we investigated the impact of refilling carbon sources on enrichment outcomes. Approximately 77% of the natural community of root-associated endophytes were predicted to have successfully cultivated the possibility based on a comparison of the 16S rRNA gene sequences between the enrichment collections and the Ginkgo root endophyte community. The rare or recalcitrant taxa in the root endosphere were mainly associated with Actinobacteria, Alphaproteobacteria, Blastocatellia, and Ktedonobacteria. By contrast, more operational taxonomic units (OTUs) (0.6% in the root endosphere) became significantly enriched in MM than in GM and MSM. We further found that the bacterial taxa of the root endosphere had strong metabolisms with the representative of aerobic chemoheterotrophy, while the functions of the enrichment collections were represented by the sulfur metabolism. In addition, the co-occurrence network analysis suggested that the substrate supplement could significantly impact bacterial interactions within the enrichment collections. Our results support the fact that it is better to use the enrichment to assess the cultivable potential and the interspecies interaction as well as to increase the detection/isolation of certain bacterial taxa. Taken together, this study will deepen our knowledge of the indoor endophytic culture and provide important insights into the substrate-driven enrichment.

Genomic view of the diversity and functional role of archaea and bacteria in the skeleton of the reef-building corals Porites lutea and Isopora palifera

At present, our knowledge on the compartmentalization of coral holobiont microbiomes is highly skewed toward the millimeter-thin coral tissue, leaving the diverse coral skeleton microbiome underexplored. Here, we present a genome-centric view of the skeleton of the reef-building corals Porites lutea and Isopora palifera, through a compendium of ∼400 high-quality bacterial and archaeal metagenome-assembled genomes (MAGs), spanning 34 phyla and 57 classes. Skeletal microbiomes harbored a diverse array of stress response genes, including dimethylsulfoniopropionate synthesis (dsyB) and metabolism (DMSP lyase). Furthermore, skeletal MAGs encoded an average of 22 ± 15 genes in P. lutea and 28 ± 23 in I. palifera with eukaryotic-like motifs thought to be involved in maintaining host association. We provide comprehensive insights into the putative functional role of the skeletal microbiome on key metabolic processes such as nitrogen fixation, dissimilatory and assimilatory nitrate, and sulfate reduction. Our study provides critical genomic resources for a better understanding of the coral skeletal microbiome and its role in holobiont functioning.

Benthic exometabolites and their ecological significance on threatened Caribbean coral reefs

Benthic organisms are the architectural framework supporting coral reef ecosystems, but their community composition has recently shifted on many reefs. Little is known about the metabolites released from these benthic organisms and how compositional shifts may influence other reef life, including prolific microorganisms. To investigate the metabolite composition of benthic exudates and their ecological significance for reef microbial communities, we harvested exudates from six species of Caribbean benthic organisms including stony corals, octocorals, and an invasive encrusting alga, and subjected these exudates to untargeted and targeted metabolomics approaches using liquid chromatography-mass spectrometry. Incubations with reef seawater microorganisms were conducted to monitor changes in microbial abundances and community composition using 16 S rRNA gene sequencing in relation to exudate source and three specific metabolites. Exudates were enriched in amino acids, nucleosides, vitamins, and indole-based metabolites, showing that benthic organisms contribute labile organic matter to reefs. Furthermore, exudate compositions were species-specific, and riboflavin and pantothenic acid emerged as significant coral-produced metabolites, while caffeine emerged as a significant invasive algal-produced metabolite. Microbial abundances and individual microbial taxa responded differently to exudates from stony corals and octocorals, demonstrating that exudate mixtures released from different coral species select for specific bacteria. In contrast, microbial communities did not respond to individual additions of riboflavin, pantothenic acid, or caffeine. This work indicates that recent shifts in benthic organisms alter exudate composition and likely impact microbial communities on coral reefs.

Climate Change Impacts on the Marine Cycling of Biogenic Sulfur: A Review

A key component of the marine sulfur cycle is the climate-active gas dimethylsulfide (DMS), which is synthesized by a range of organisms from phytoplankton to corals, and accounts for up to 80% of global biogenic sulfur emissions. The DMS cycle starts with the intracellular synthesis of the non-gaseous precursor dimethylsulfoniopropionate (DMSP), which is released to the water column by various food web processes such as zooplankton grazing. This dissolved DMSP pool is rapidly turned over by microbially mediated conversion using two known pathways: demethylation (releasing methanethiol) and cleavage (producing DMS). Some of the formed DMS is ventilated to the atmosphere, where it undergoes rapid oxidation and contributes to the formation of sulfate aerosols, with the potential to affect cloud microphysics, and thus the regional climate. The marine phase cycling of DMS is complex, however, as heterotrophs also contribute to the consumption of the newly formed dissolved DMS. Interestingly, due to microbial consumption and other water column sinks such as photolysis, the amount of DMS that enters the atmosphere is currently thought to be a relatively minor fraction of the total amount cycled through the marine food web—less than 10%. These microbial processes are mediated by water column temperature, but the response of marine microbial assemblages to ocean warming is poorly characterized, although bacterial degradation appears to increase with an increase in temperature. This review will focus on the potential impact of climate change on the key microbially mediated processes in the marine cycling of DMS. It is likely that the impact will vary across different biogeographical regions from polar to tropical. For example, in the rapidly warming polar oceans, microbial communities associated with the DMS cycle will likely change dramatically during the 21st century with the decline in sea ice. At lower latitudes, where corals form an important source of DMS (P), shifts in the microbiome composition have been observed during thermal stress with the potential to alter the DMS cycle.

Microbiome and Metabolome Contributions to Coral Health and Disease

AbstractCoral populations are declining worldwide as a result of increased environmental stressors, including disease. Coral health is greatly dependent on complex interactions between the host animal and its associated microbial symbionts. While relatively understudied, there is growing evidence that the coral microbiome contributes to the health and resilience of corals in a variety of ways, similar to more well-studied systems, such as the human microbiome. Many of these interactions are dependent upon the production and exchange of natural products, including antibacterial compounds, quorum-sensing molecules, internal signaling molecules, nutrients, and so on. While advances in sequencing, culturing, and metabolomic techniques have aided in moving forward the understanding of coral microbiome interactions, current sequence and metabolite databases are lacking, hindering detailed descriptions of the microbes and metabolites involved. This review focuses on the roles of coral microbiomes in health and disease processes of coral hosts, with special attention to the coral metabolome. We discuss what is currently known about the relationship between the coral microbiome and disease, of beneficial microbial products or services, and how the manipulation of the coral microbiome may chemically benefit the coral host against disease. Understanding coral microbiome-metabolome interactions is critical to assisting management, conservation, and restoration strategies.

Community structure of coral microbiomes is dependent on host morphology

BACKGROUND

The importance of symbiosis has long been recognized on coral reefs, where the photosynthetic dinoflagellates of corals (Symbiodiniaceae) are the primary symbiont. Numerous studies have now shown that a diverse assemblage of prokaryotes also make-up part of the microbiome of corals. A subset of these prokaryotes is capable of fixing nitrogen, known as diazotrophs, and is also present in the microbiome of scleractinian corals where they have been shown to supplement the holobiont nitrogen budget. Here, an analysis of the microbiomes of 16 coral species collected from Australia, Curaçao, and Hawai'i using three different marker genes (16S rRNA, nifH, and ITS2) is presented. These data were used to examine the effects of biogeography, coral traits, and ecological life history characteristics on the composition and diversity of the microbiome in corals and their diazotrophic communities.

RESULTS

The prokaryotic microbiome community composition (i.e., beta diversity) based on the 16S rRNA gene varied between sites and ecological life history characteristics, but coral morphology was the most significant factor affecting the microbiome of the corals studied. For 15 of the corals studied, only two species Pocillopora acuta and Seriotopora hystrix, both brooders, showed a weak relationship between the 16S rRNA gene community structure and the diazotrophic members of the microbiome using the nifH marker gene, suggesting that many corals support a microbiome with diazotrophic capabilities. The order Rhizobiales, a taxon that contains primarily diazotrophs, are common members of the coral microbiome and were eight times greater in relative abundances in Hawai'i compared to corals from either Curacao or Australia. However, for the diazotrophic component of the coral microbiome, only host species significantly influenced the composition and diversity of the community.

CONCLUSIONS

The roles and interactions between members of the coral holobiont are still not well understood, especially critical functions provided by the coral microbiome (e.g., nitrogen fixation), and the variation of these functions across species. The findings presented here show the significant effect of morphology, a coral "super trait," on the overall community structure of the microbiome in corals and that there is a strong association of the diazotrophic community within the microbiome of corals. However, the underlying coral traits linking the effects of host species on diazotrophic communities remain unknown. Video Abstract.

Effect of Various Local Anthropogenic Impacts on the Diversity of Coral Mucus-Associated Bacterial Communities

The global continued decline in coral reefs is intensifying the need to understand the response of corals to local environmental stressors. Coral-associated bacterial communities have been suggested to have a swift response to environmental pollutants. This study aims to determine the variation in the bacterial communities associated with the mucus of two coral species, Pocillopora damicornis (Linnaeus, 1758) and Stylophora pistillata (Esper, 1792), and the coral-surrounding seawater from three areas exposed to contamination at the Jordanian coast of the Gulf of Aqaba (Red Sea), and also explores the antibacterial activity of these bacteria. Corals were collected from three contaminated zones along the coast, and the bacteria were quantified and identified by conventional morphological and biochemical tests, as well as 16S rRNA gene sequencing. The average number of bacteria significantly varied among the coral mucus from the sampling zones and between the coral mucus and the surrounding seawater. The P. damicornis mucus-associated bacterial community was dominated by members of the classes Gammaproteobacteria, Cytophagia, and Actinomycetia, while the mucus of S. pistillata represented higher bacterial diversity, with the dominance of the bacterial classes Gammaproteobacteria, Actinomycetia, Alphaproteobacteria, and Bacilli. The effects of local anthropogenic impacts on coral mucus bacterial communities were represented in the increased abundance of bacterial species related to coral diseases. Furthermore, the results demonstrated the existence of bacterial isolates with antibacterial activity that possibly acted as a first line of defense to protect and maintain the coral host against pathogens. Indeed, the dynamics of coral-associated microbial communities highlight the importance of holistic studies that focus on microbial interactions across the coral reef ecosystem.

A roadmap to understanding diversity and function of coral reef-associated fungi

Tropical coral reefs are hotspots of marine productivity, owing to the association of reef-building corals with endosymbiotic algae and metabolically diverse bacterial communities. However, the functional importance of fungi, well-known for their contribution to shaping terrestrial ecosystems and global nutrient cycles, remains underexplored on coral reefs. We here conceptualize how fungal functional traits may have facilitated the spread, diversification, and ecological adaptation of marine fungi on coral reefs. We propose that functions of reef-associated fungi may be diverse and go beyond their hitherto described roles of pathogens and bioeroders, including but not limited to reef-scale biogeochemical cycles and the structuring of coral-associated and environmental microbiomes via chemical mediation. Recent technological and conceptual advances will allow the elucidation of the physiological, ecological, and chemical contributions of understudied marine fungi to coral holobiont and reef ecosystem functioning and health and may help provide an outlook for reef management actions.

Microbiome Restructuring: Dominant Coral Bacterium Endozoicomonas Species Respond Differentially to Environmental Changes

Bacteria in the coral microbiome play a crucial role in determining coral health and fitness, and the coral host often restructures its microbiome composition in response to external factors. An important but often neglected factor determining this microbiome restructuring is the ability of microbiome members to respond to changes in the environment. To address this issue, we examined how the microbiome structure of Acropora muricata corals changed over 9 months following a reciprocal transplant experiment. Using a combination of metabarcoding, genomics, and comparative genomics approaches, we found that coral colonies separated by a small distance harbored different dominant Endozoicomonas-related phylotypes belonging to two different species, including a novel species, “Candidatus Endozoicomonas penghunesis” 4G, whose chromosome-level (complete) genome was also sequenced in this study. Furthermore, the two dominant Endozoicomonas species had different potentials to scavenge reactive oxygen species, suggesting potential differences in responding to the environment. Differential capabilities of dominant members of the microbiome to respond to environmental change can (i) provide distinct advantages or disadvantages to coral hosts when subjected to changing environmental conditions and (ii) have positive or negative implications for future reefs.

IMPORTANCE The coral microbiome has been known to play a crucial role in host health. In recent years, we have known that the coral microbiome changes in response to external stressors and that coral hosts structure their microbiome in a host-specific manner. However, an important internal factor, the ability of microbiome members to respond to change, has been often neglected. In this study, we combine metabarcoding, culturing, and genomics to delineate the differential ability of two dominant Endozoicomonas species, including a novel “Ca. Endozoicomonas penghunesis” 4G, to respond to change in the environment following a reciprocal transplant experiment.

Enhanced wastewater treatment performance by understanding the interaction between algae and bacteria based on quorum sensing

In order to further obtain sustainable wastewater treatment technology, in-depth analysis based on algal-bacterial symbiosis, quorum sensing signal molecules and algal-bacterial relationship will lay the foundation for the synergistic algal-bacterial wastewater treatment process. The methods of enhancing algae and bacteria wastewater treatment technology were systematically explored, including promoting symbiosis, reducing algicidal behavior, eliminating the interference of quorum sensing inhibitor, and developing algae and bacteria granular sludge. These findings can provide guidance for sustainable economic and environmental development, and facilitate carbon emissions reduction by using algae and bacteria synergistic wastewater treatment technology in further attempts. The future work should be carried out in the following four aspects: (1) Screening of dominant microalgae and bacteria; (2) Coordination of stable (emerging) contaminants removal; (3) Utilization of algae to produce fertilizers and feed (additives), and (4) Constructing recombinant algae and bacteria for reducing carbon emissions and obtaining high value-added products.

Changes in coral forest microbiomes predict the impact of marine heatwaves on habitat-forming species down to mesophotic depths

Global warming is causing the increase in intensity and frequency of heatwaves, which are often associated with mass mortality events of marine organisms from shallow and mesophotic rocky habitats, including gorgonians and other sessile organisms. We investigated the microbiome responses of the gorgonians Paramuricea clavata, Eunicella cavolini, and the red coral Corallium rubrum to the episodic temperature anomalies detected in the North Western Mediterranean, during August 2011. Although the investigated corals showed no signs of visible necrosis, the abundance of associated Bacteria and Archaea increased with increasing seawater temperature, suggesting their temperature-dependent proliferation. Coral microbiomes were highly sensitive to thermal anomaly amplitude and exhibited increased bacterial diversity to greater thermal shifts. This effect was explained by the decline of dominant bacterial members and the increase of new, rare and opportunistic taxa, including pathogens, revealing a direct effect of heatwave-induced alteration of the microbiomes and not a secondary consequence of coral necrosis.

A Novel, NADH-Dependent Acrylate Reductase in Vibrio harveyi

Bacteria coping with oxygen deficiency use alternative terminal electron acceptors for NADH regeneration, particularly fumarate. Fumarate is reduced by the FAD_binding_2 domain of cytoplasmic fumarate reductase in many bacteria. The variability of the primary structure of this domain in homologous proteins suggests the existence of reducing activities with different specificities. Here, we produced and characterized one such protein encoded in the Vibrio harveyi genome (GenBank ID: AIV07243) and found it to be a specific NADH:acrylate oxidoreductase (ARD). This previously unknown enzyme is formed by the OYE-like, FMN_bind, and FAD_binding_2 domains and contains covalently bound flavin mononucleotide (FMN) and noncovalently bound flavin adenine dinucleotide (FAD) and FMN in a ratio of 1:1:1. The covalently bound FMN is absolutely required for activity and is attached by the specific flavin transferase, ApbE, to the FMN_bind domain. Quantitative reverse transcription PCR (RT-qPCR) and activity measurements indicated dramatic stimulation of ARD biosynthesis by acrylate in the V. harveyi cells grown aerobically. In contrast, the ard gene expression in the cells grown anaerobically without acrylate was higher than that in aerobic cultures and increased only 2-fold in the presence of acrylate. These findings suggest that the principal role of ARD in Vibrio is energy-saving detoxification of acrylate coming from the environment. IMPORTANCE The benefits of the massive genomic information accumulated in recent years for biological sciences have been limited by the lack of data on the function of most gene products. Approximately half of the known prokaryotic genes are annotated as "proteins with unknown functions," and many other genes are annotated incorrectly. Thus, the functional and structural characterization of the products of such genes, including identification of all existing enzymatic activities, is a pressing issue in modern biochemistry. In this work, we have shown that the product of the V. harveyi ard gene exhibits a yet-undescribed NADH:acrylate oxidoreductase activity. This activity may allow acrylate detoxification and its use as a terminal electron acceptor in anaerobic or substrate in aerobic respiration of marine and other bacteria.

Recent insights into oceanic dimethylsulfoniopropionate biosynthesis and catabolism

Dimethylsulfoniopropionate (DMSP), a globally important organosulfur compound is produced in prodigious amounts (2.0 Pg sulfur) annually in the marine environment by phytoplankton, macroalgae, heterotrophic bacteria, some corals and certain higher plants. It is an important marine osmolyte and a major precursor molecule for the production of climate-active volatile gas dimethyl sulfide (DMS). DMSP synthesis take place via three pathways: a transamination 'pathway-' in some marine bacteria and algae, a Met-methylation 'pathway-' in angiosperms and bacteria and a decarboxylation 'pathway-' in the dinoflagellate, Crypthecodinium. The enzymes DSYB and TpMMT are involved in the DMSP biosynthesis in eukaryotes while marine heterotrophic bacteria engage key enzymes such as DsyB and MmtN. Several marine bacterial communities import DMSP and degrade it via cleavage or demethylation pathways or oxidation pathway, thereby generating DMS, methanethiol, and dimethylsulfoxonium propionate, respectively. DMSP is cleaved through diverse DMSP lyase enzymes in bacteria and via Alma1 enzyme in phytoplankton. The demethylation pathway involves four different enzymes, namely DmdA, DmdB, DmdC and DmdD/AcuH. However, enzymes involved in the oxidation pathway have not been yet identified. We reviewed the recent advances on the synthesis and catabolism of DMSP and enzymes that are involved in these processes.

Thermal Stress Has Minimal Effects on Bacterial Communities of Thermotolerant Symbiodinium Cultures

Algae in the dinoflagellate family Symbiodiniaceae are endocellular photosymbionts of corals and other cnidarians. This close relationship is disrupted when seawater temperature increases, causing coral bleaching eventually affecting entire coral reefs. Although the relationship between animal host and photosymbiont has been well-studied, little is known about the bacterial community associated with Symbiodiniaceae in culture. We compared the microbial communities of three isolates from different species of the genus Symbiodinium (formerly known as Symbiodinium clade A) with different ecophysiology, levels of interaction with the animal host, and thermal adaptations. Two species, Symbiodinium microadriaticum and Symbiodinium necroappettens, exhibit intermediate thermotolerance, with a decrease of both growth rate and photochemical efficiency with increased temperature. The third species, Symbiodinium pilosum, has high thermotolerance with no difference in growth rate or photochemical efficiency at 32°C. Microbial communities were characterized after 27 days of growth under control (26°C) and high temperature (32°C). Data shows stronger grouping of bacterial assemblages based on Symbiodinium species than temperature. Microbial communities did not group phylogenetically. We found a shared set of fifteen ASVs belonging to four genera and three families that remained in all three Symbiodiniaceae species. These included Labrenzia, Phycisphaeraceae (SM1A02), Roseovarius, and Muricauda, which are all commonly associated with corals and Symbiodiniaceae cultures. Few ASVs differed significantly by temperature within species. S. pilosum displayed significantly lower levels of microbial diversity and greater individual variability in community composition at 32°C compared to 26°C. These results suggest that bacteria associated or co-cultured with thermotolerant Symbiodinium might play an important role in thermotolerance. Further research on the functional metabolic pathways of these bacteria might hold the key to understanding Symbiodinium’s ability to tolerate thermal stress.

Temporal Variation in the Microbiome of Tropical and Temperate Octocorals

Bacterial members of the coral holobiont play an important role in determining coral fitness. However, most knowledge of the coral microbiome has come from reef-building scleractinian corals, with far less known about the nature and importance of the microbiome of octocorals (subclass Octocorallia), which contribute significantly to reef biodiversity and functional complexity. We examined the diversity and structure of the bacterial component of octocoral microbiomes over summer and winter, with a focus on two temperate (Erythropodium hicksoni, Capnella gaboensis; Sydney Harbour) and two tropical (Sinularia sp., Sarcophyton sp.; Heron Island) species common to reefs in eastern Australia. Bacterial communities associated with these octocorals were also compared to common temperate (Plesiastrea versipora) and tropical (Acropora aspera) hard corals from the same reefs. Using 16S rRNA amplicon sequencing, bacterial diversity was found to be heterogeneous among octocorals, but we observed changes in composition between summer and winter for some species (C. gaboensis and Sinularia sp.), but not for others (E. hicksoni and Sarcophyton sp.). Bacterial community structure differed significantly between all octocoral species within both the temperate and tropical environments. However, on a seasonal basis, those differences were less pronounced. The microbiomes of C. gaboensis and Sinularia sp. were dominated by bacteria belonging to the genus Endozoicomonas, which were a key conserved feature of their core microbiomes. In contrast to previous studies, our analysis revealed that Endozoicomonas phylotypes are shared across different octocoral species, inhabiting different environments. Together, our data demonstrates that octocorals harbour a broad diversity of bacterial partners, some of which comprise 'core microbiomes' that potentially impart important functional roles to their hosts.

Long-Term Heat Selection of the Coral Endosymbiont Cladocopium C1acro (Symbiodiniaceae) Stabilizes Associated Bacterial Communities

Heat-tolerant strains of the coral endosymbiont, Cladocopium C1^acro (Symbiodiniaceae), have previously been developed via experimental evolution. Here, we examine physiological responses and bacterial community composition (using 16S rRNA gene metabarcoding) in cultures of 10 heat-evolved (SS) and 9 wild-type (WT) strains, which had been exposed for 6 years to 31 °C and 27 °C, respectively. We also examine whether the associated bacterial communities were affected by a three-week reciprocal transplantation to both temperatures. The SS strains had bacterial communities with lower diversities that showed more stability and lower variability when exposed to elevated temperatures compared with the WT strains. Amplicon sequence variants (ASVs) of the bacterial genera Labrenzia, Algiphilus, Hyphobacterium and Roseitalea were significantly more associated with the SS strains compared with the WT strains. WT strains showed higher abundance of ASVs assigned to the genera Fabibacter and Tropicimonas. We hypothesize that these compositional differences in associated bacterial communities between SS and WT strains also contribute to the thermal tolerance of the microalgae. Future research should explore functional potential between bacterial communities using metagenomics to unravel specific genomic adaptations.

Micronutrient content drives elementome variability amongst the Symbiodiniaceae

BACKGROUND

Elements are the basis of life on Earth, whereby organisms are essentially evolved chemical substances that dynamically interact with each other and their environment. Determining species elemental quotas (their elementome) is a key indicator for their success across environments with different resource availabilities. Elementomes remain undescribed for functionally diverse dinoflagellates within the family Symbiodiniaceae that includes coral endosymbionts. We used dry combustion and ICP-MS to assess whether Symbiodiniaceae (ten isolates spanning five genera Breviolum, Cladocopium, Durusdinium, Effrenium, Symbiodinium) maintained under long-term nutrient replete conditions have unique elementomes (six key macronutrients and nine micronutrients) that would reflect evolutionarily conserved preferential elemental acquisition. For three isolates we assessed how elevated temperature impacted their elementomes. Further, we tested whether Symbiodiniaceae conform to common stoichiometric hypotheses (e.g., the growth rate hypothesis) documented in other marine algae. This study considers whether Symbiodiniaceae isolates possess unique elementomes reflective of their natural ecologies, evolutionary histories, and resistance to environmental change.

RESULTS

Symbiodiniaceae isolates maintained under long-term luxury uptake conditions, all exhibited highly divergent elementomes from one another, driven primarily by differential content of micronutrients. All N:P and C:P ratios were below the Redfield ratio values, whereas C:N was close to the Redfield value. Elevated temperature resulted in a more homogenised elementome across isolates. The Family-level elementome was (C_19.8N_2.6 P_1.0S_18.8K_0.7Ca_0.1) · 1000 (Fe_55.7Mn_5.6Sr_2.3Zn_0.8Ni_0.5Se_0.3Cu_0.2Mo_0.1V_0.04) mmol Phosphorous^-1 versus (C_25.4N_3.1P_1.0S_23.1K_0.9Ca_0.4) · 1000 (Fe_66.7Mn_6.3Sr_7.2Zn_0.8Ni_0.4Se_0.2Cu_0.2Mo_0.2V_0.05) mmol Phosphorous ^-1 at 27.4 ± 0.4 °C and 30.7 ± 0.01 °C, respectively. Symbiodiniaceae isolates tested here conformed to some, but not all, stoichiometric principles.

CONCLUSIONS

Elementomes for Symbiodiniaceae diverge from those reported for other marine algae, primarily via lower C:N:P and different micronutrient expressions. Long-term maintenance of Symbiodiniaceae isolates in culture under common nutrient replete conditions suggests isolates have evolutionary conserved preferential uptake for certain elements that allows these unique elementomes to be identified. Micronutrient content (normalised to phosphorous) commonly increased in the Symbiodiniaceae isolates in response to elevated temperature, potentially indicating a common elemental signature to warming.

Biogeographical and seasonal dynamics of the marine Roseobacter community and ecological links to DMSP-producing phytoplankton

Ecological interactions between marine bacteria and phytoplankton play a pivotal role in governing the ocean's major biogeochemical cycles. Among these, members of the marine Roseobacter Group (MRG) can establish mutualistic relationships with phytoplankton that are, in part, maintained by exchanges of the organosulfur compound, dimethylsulfoniopropionate (DMSP). Yet most of what is known about these interactions has been derived from culture-based laboratory studies. To investigate temporal and spatial co-occurrence patterns between members of the MRG and DMSP-producing phytoplankton we analysed 16S and 18S rRNA gene amplicon sequence variants (ASVs) derived from 5 years of monthly samples from seven environmentally distinct Australian oceanographic time-series. The MRG and DMSP-producer communities often displayed contemporaneous seasonality, which was greater in subtropical and temperate environments compared to tropical environments. The relative abundance of both groups varied latitudinally, displaying a poleward increase, peaking (MRG at 33% of total bacteria, DMSP producers at 42% of eukaryotic phototrophs) during recurrent spring-summer phytoplankton blooms in the most temperate site (Maria Island, Tasmania). Network analysis identified 20,140 significant positive correlations between MRG ASVs and DMSP producers and revealed that MRGs exhibit significantly stronger correlations to high DMSP producers relative to other DMSP-degrading bacteria (Pelagibacter, SAR86 and Actinobacteria). By utilising the power of a continental network of oceanographic time-series, this study provides in situ confirmation of interactions found in laboratory studies and demonstrates that the ecological dynamics of an important group of marine bacteria are shaped by the production of an abundant and biogeochemically significant organosulfur compound.

Coral-microbe interactions: their importance to reef function and survival

Many different microorganisms associate with the coral host in a single entity known as the holobiont, and their interactions with the host contribute to coral health, thereby making them a fundamental part of reef function, survival, and conservation. As corals continue to be susceptible to bleaching due to environmental stress, coral-associated bacteria may have a potential role in alleviating bleaching. This review provides a synthesis of the various roles bacteria have in coral physiology and development, and explores the possibility that changes in the microbiome with environmental stress could have major implications in how corals acclimatize and survive. Recent studies on the interactions between the coral's algal and bacterial symbionts elucidate how bacteria may stabilize algal health and, therefore, mitigate bleaching. A summary of the innovative tools and experiments to examine host-microbe interactions in other cnidarians (a temperate coral, a jellyfish, two anemones, and a freshwater hydroid) is offered in this review to delineate our current knowledge of mechanisms underlying microbial establishment and maintenance in the animal host. A better understanding of these mechanisms may enhance the success of maintaining probiotics long-term in corals as a conservation strategy.

Antibiotics reduce bacterial load in Exaiptasia diaphana, but biofilms hinder its development as a gnotobiotic coral model

Coral reefs are declining due to anthropogenic disturbances, including climate change. Therefore, improving our understanding of coral ecosystems is vital, and the influence of bacteria on coral health has attracted particular interest. However, a gnotobiotic coral model that could enhance studies of coral–bacteria interactions is absent. To address this gap, we tested the ability of treatment with seven antibiotics for 3 weeks to deplete bacteria in Exaiptasia diaphana, a sea anemone widely used as a coral model. Digital droplet PCR (ddPCR) targeting anemone Ef1-α and bacterial 16S rRNA genes was used to quantify bacterial load, which was found to decrease six-fold. However, metabarcoding of bacterial 16S rRNA genes showed that alpha and beta diversity of the anemone-associated bacterial communities increased significantly. Therefore, gnotobiotic E. diaphana with simplified, uniform bacterial communities were not generated, with biofilm formation in the culture vessels most likely impeding efforts to eliminate bacteria. Despite this outcome, our work will inform future efforts to create a much needed gnotobiotic coral model.

Regulation of the Coral-Associated Bacteria and Symbiodiniaceae in Acropora valida Under Ocean Acidification

Ocean acidification is one of many stressors that coral reef ecosystems are currently contending with. Thus, understanding the response of key symbiotic microbes to ocean acidification is of great significance for understanding the adaptation mechanism and development trend of coral holobionts. Here, high-throughput sequencing technology was employed to investigate the coral-associated bacteria and Symbiodiniaceae of the ecologically important coral Acropora valida exposed to different pH gradients. After 30 days of acclimatization, we set four acidification gradients (pH 8.2, 7.8, 7.4, and 7.2, respectively), and each pH condition was applied for 10 days, with the whole experiment lasting for 70 days. Although the Symbiodiniaceae density decreased significantly, the coral did not appear to be bleached, and the real-time photosynthetic rate did not change significantly, indicating that A. valida has strong tolerance to acidification. Moreover, the Symbiodiniaceae community composition was hardly affected by ocean acidification, with the C1 subclade (Cladocopium goreaui) being dominant among the Symbiodiniaceae dominant types. The relative abundance of the Symbiodiniaceae background types was significantly higher at pH 7.2, indicating that ocean acidification might increase the stability of the community composition by regulating the Symbiodiniaceae rare biosphere. Furthermore, the stable symbiosis between the C1 subclade and coral host may contribute to the stability of the real-time photosynthetic efficiency. Finally, concerning the coral-associated bacteria, the stable symbiosis between Endozoicomonas and coral host is likely to help them adapt to ocean acidification. The significant increase in the relative abundance of Cyanobacteria at pH 7.2 may also compensate for the photosynthesis efficiency of a coral holobiont. In summary, this study suggests that the combined response of key symbiotic microbes helps the whole coral host resist the threats of ocean acidification.