Kistimonas asteriae gen. nov., sp. nov., a gammaproteobacterium isolated from Asterias amurensis

Parendozoicomonas callyspongiae sp. nov. Isolated from a Marine Sponge, Callyspongia elongate, and Reclassification of Sansalvadorimonas verongulae as Parendozoicomonas verongulae comb. nov

A strictly aerobic Gram-negative bacterium, designated 2012CJ34-2T, was isolated from marine sponge to Chuja-do in Jeju-island, Republic of Korea and taxonomically characterized. Cells were catalase- and oxidase-positive, and non-motile rods (without flagella). Growth was observed at 15-42 °C (optimum, 30 °C), pH 6-9 (optimum, pH 7), and in the presence of 0.5-10% (w/v) NaCl (optimum, 2-3%). The major cellular fatty acid and respiratory quinones were identified summed feature 3 (C16:1 ω7c/C16:1 ω6c), and Q-8 and Q-9, respectively. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminophospholipid, two unidentified phospholipids, and three unidentified lipids. The DNA G+C content was 48.0 mol%. Phylogenetic analyses based on 16S rRNA gene and whole genome sequences showed that strain 2012CJ34-2T formed a clade with Parendozoicomonas haliclonae S-B4-1UT and Sansalvadorimonas verongulae LMG 29871T within the family Endozoicomodaceae. Genome relatedness values, including dDDH, ANI and AF, and AAI and POCP, among strain 2012CJ34-2T, P. haliclonae S-B4-1UT, and S. verongulae LMG 29871T were within the range of the bacterial genus cut-off values. Based on the phylogenetic, chemotaxonomic, and genomic analyses, strain 2012CJ34-2T represents a novel bacterial species of the family Endozoicomodaceae, for which the name Parendozoicomonas callyspongiae sp. nov. is proposed. The type strain is 2012CJ34-2T (= KACC 22641T = LMG 32581T). Additionally, we proposed the reclassification of Sansalvadorimonas verongulae of the family Hahellaceae as Parendozoicomonas verongulae of the family Endozoicomonadaceae.

Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean

Health and resilience of the coral holobiont depend on diverse bacterial communities often dominated by key marine symbionts of the Endozoicomonadaceae family. The factors controlling their distribution and their functional diversity remain, however, poorly known. Here, we study the ecology of Endozoicomonadaceae at an ocean basin-scale by sampling specimens from three coral genera (Pocillopora, Porites, Millepora) on 99 reefs from 32 islands across the Pacific Ocean. The analysis of 2447 metabarcoding and 270 metagenomic samples reveals that each coral genus harbored a distinct new species of Endozoicomonadaceae. These species are composed of nine lineages that have distinct biogeographic patterns. The most common one, found in Pocillopora, appears to be a globally distributed symbiont with distinct metabolic capabilities, including the synthesis of amino acids and vitamins not produced by the host. The other lineages are structured partly by the host genetic lineage in Pocillopora and mainly by the geographic location in Porites. Millepora is more rarely associated to Endozoicomonadaceae. Our results show that different coral genera exhibit distinct strategies of host-Endozoicomonadaceae associations that are defined at the bacteria lineage level.

A Review of Asteroid Biology in the Context of Sea Star Wasting: Possible Causes and Consequences

AbstractSea star wasting-marked in a variety of sea star species as varying degrees of skin lesions followed by disintegration-recently caused one of the largest marine die-offs ever recorded on the west coast of North America, killing billions of sea stars. Despite the important ramifications this mortality had for coastal benthic ecosystems, such as increased abundance of prey, little is known about the causes of the disease or the mechanisms of its progression. Although there have been studies indicating a range of causal mechanisms, including viruses and environmental effects, the broad spatial and depth range of affected populations leaves many questions remaining about either infectious or non-infectious mechanisms. Wasting appears to start with degradation of mutable connective tissue in the body wall, leading to disintegration of the epidermis. Here, we briefly review basic sea star biology in the context of sea star wasting and present our current knowledge and hypotheses related to the symptoms, the microbiome, the viruses, and the associated environmental stressors. We also highlight throughout the article knowledge gaps and the data needed to better understand sea star wasting mechanistically, its causes, and potential management.

Microbiome differences between wild and aquarium whitespotted eagle rays (Aetobatus narinari)

Background

Animal-associated microbiomes can be influenced by both host and environmental factors. Comparing wild animals to those in zoos or aquariums can help disentangle the effects of host versus environmental factors, while also testing whether managed conditions foster a ‘natural’ host microbiome. Focusing on an endangered elasmobranch species—the whitespotted eagle ray Aetobatus narinari—we compared the skin, gill, and cloaca microbiomes of wild individuals to those at Georgia Aquarium. Whitespotted eagle ray microbiomes from Georgia Aquarium were also compared to those of cownose rays (Rhinoptera bonasus) in the same exhibit, allowing us to explore the effect of host identity on the ray microbiome.

Results

Long-term veterinary monitoring indicated that the rays in managed care did not have a history of disease and maintained health parameters consistent with those of wild individuals, with one exception. Aquarium whitespotted eagle rays were regularly treated to control parasite loads, but the effects on animal health were subclinical. Microbiome α- and β-diversity differed between wild versus aquarium whitespotted eagle rays at all body sites, with α-diversity significantly higher in wild individuals. β-diversity differences in wild versus aquarium whitespotted eagle rays were greater for skin and gill microbiomes compared to those of the cloaca. At each body site, we also detected microbial taxa shared between wild and aquarium eagle rays. Additionally, the cloaca, skin, and gill microbiomes of aquarium eagle rays differed from those of cownose rays in the same exhibit. Potentially pathogenic bacteria were at low abundance in all wild and aquarium rays.

Conclusion

For whitespotted eagle rays, managed care was associated with a microbiome differing significantly from that of wild individuals. These differences were not absolute, as the microbiome of aquarium rays shared members with that of wild counterparts and was distinct from that of a cohabitating ray species. Eagle rays under managed care appear healthy, suggesting that their microbiomes are not associated with compromised host health. However, the ray microbiome is dynamic, differing with both environmental factors and host identity. Monitoring of aquarium ray microbiomes over time may identify taxonomic patterns that co-vary with host health.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-022-00187-8.

Proposal of Zooshikellaceae fam. nov. to accommodate the genera Zooshikella and Spartinivicinus and reclassification of Zooshikella marina as a later heterotypic synonym of Zooshikella ganghwensis based on whole genome sequence analysis

The genus Spartinivicinus, affiliated to the class Gammaproteobacteria, is an important marine member that produces prodiginines. Currently, its taxonomic assignment to family level is not well presented. Phylogeny of 16S rRNA gene sequences indicated that Spartinivicinus forms a monophyletic clade with Zooshikella, which is neighboured by Aestuariirhabdus of the family Aestuariirhabdaceae and another monophyletic clade of the family Endozoicomonadaceae. The 16S rRNA gene of Spartinivicinus ruber S2-4-1H^T had sequence similarities to those of Aestuariirhabdus litorea GTF13^T, Zooshikella members and Endozoicomonas members of 93.4%, 93.2-93.4  and <92.5 %, respectively. Phylogenomic analysis based on 120 bacterial conserved single-copy genes highly supported placing Spartinivicinus as a sister member of Zooshikella, neighboured by Aestuariirhabdaceae and Endozoicomonadaceae members, indicating that Spartinivicinus and Zooshikella could be considered to belong to the same family. Thus, Zooshikellaceae fam. nov. is proposed to accommodate the two genera. Colonies of Spartinivicinus and Zooshikella are red-pigmented, which is different from Aestuariirhabdus (pale-yellow pigmented). The major respiratory quinone of S. ruber was ubiquinone (Q-9), similar to Zooshikella, but distinct from Aestuariirhabdus (Q-9 and Q-8). The predominant fatty acids and polar lipids of Spartinivicinus also showed a similar patterns to Zooshikella, but they were different from Aestuariirhabdus. Lastly, Spartinivicinus possessed a genome size of 6.68 Mbp and DNA G+C content of 40.1mol%, similar to Zooshikella, but much larger than Aestuariirhabdus. In addition, the 16S rRNA genes of Z. ganghwensis JC2044^T and Z. marina JC333^T possess sequence similarity of 99.79 %. Whole genome comparisons indicated that they shared 79.8 % digital DNA-DNA hybridization, 97.78 % average nucleotide identity and 97.31 % average amino acid identity values. Activities of catalase and oxidase for the two strains were positive. Hydrolysis of skimmed milk and Tweens (40, 60 and 80) was positive. Interestingly, the two strains produced different kinds of prodiginines. We propose that Z. marina is a later heterotypic synonym of Zooshikella ganghwensis.

Evidence That Microorganisms at the Animal-Water Interface Drive Sea Star Wasting Disease

Sea star wasting (SSW) disease describes a condition affecting asteroids that resulted in significant Northeastern Pacific population decline following a mass mortality event in 2013. The etiology of SSW is unresolved. We hypothesized that SSW is a sequela of microbial organic matter remineralization near respiratory surfaces, one consequence of which may be limited O₂ availability at the animal-water interface. Microbial assemblages inhabiting tissues and at the asteroid-water interface bore signatures of copiotroph proliferation before SSW onset, followed by the appearance of putatively facultative and strictly anaerobic taxa at the time of lesion genesis and as animals died. SSW lesions were induced in Pisaster ochraceus by enrichment with a variety of organic matter (OM) sources. These results together illustrate that depleted O₂ conditions at the animal-water interface may be established by heterotrophic microbial activity in response to organic matter loading. SSW was also induced by modestly (∼39%) depleted O₂ conditions in aquaria, suggesting that small perturbations in dissolved O₂ may exacerbate the condition. SSW susceptibility between species was significantly and positively correlated with surface rugosity, a key determinant of diffusive boundary layer thickness. Tissues of SSW-affected individuals collected in 2013–2014 bore δ¹⁵N signatures reflecting anaerobic processes, which suggests that this phenomenon may have affected asteroids during mass mortality at the time. The impacts of enhanced microbial activity and subsequent O₂ diffusion limitation may be more pronounced under higher temperatures due to lower O₂ solubility, in more rugose asteroid species due to restricted hydrodynamic flow, and in larger specimens due to their lower surface area to volume ratios which affects diffusive respiratory potential.

Aestuariirhabdus litorea gen. nov., sp. nov., isolated from a sea tidal flat and proposal of Aestuariirhabdaceae fam. nov

A Gram-negative, moderately halophilic and facultatively aerobic bacterium, designated strain GTF13^T, was isolated from a sea tidal flat. Cells were curved rods and motile by a single polar flagellum showing catalase and oxidase activities. Growth was observed at 20-37 °C, pH 5.0-8.5 and 1.0-6.0 % (w/v) NaCl. Strain GTF13^T contained C_16:0, summed feature 3 (comprising C_16 : 1  ω6c/C_16 : 1  ω7c), summed feature 8 (comprising C_18 : 1  ω6c/C_18 : 1  ω7c) and C_12 : 0 3-OH as major fatty acids and ubiquinone-9 and ubiquinone-8 as major quinones. Phosphatidylethanolamine and two unidentified phospholipids were detected as major polar lipids. The G+C content of the genomic DNA was 59.8 mol%. Strain GTF13^T was most closely related to Simiduia agarivorans SA1^T, Endozoicomonas montiporae CL-33^T and Pseudomonas segetis FR1439^T, belonging to different families or orders of the class Gammaproteobacteria, with less than 92.0 % 16S rRNA gene sequence similarities. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain GTF13^T formed a phylogenetic lineage with the family Litoricolaceae, but the genome-based phylogenomic tree showed that strain GTF13^T formed a distinct phylogenetic lineage within the order Oceanospirillales. The very low 16S rRNA gene sequence similarities and distinct phylogenetic relationships, together with distinct phenotypic and chemotaxonomic properties, served to differentiate strain GTF13^T from phylogenetically closely related families. Here, strain GTF13^T is proposed as a novel genus and species, for which the name Aestuariirhabdus litorea gen. nov., sp. nov. is proposed, within a new family Aestuariirhabdaceae fam. nov. of the order Oceanospirillales. The type strain is GTF13^T (=KACC 19788^T=JCM 32043^T).

Salinibius halmophilus gen. nov., sp. nov., isolated from a marine solar saltern

A novel Gram-stain-negative, facultatively anaerobic, flagellated and spiral-shaped bacterium, designated WDS2A16AT was isolated from a marine solar saltern in Weihai, PR China. Growth was observed at 20–40 °C (optimal 33–37 °C), 1–15 % (w/v) NaCl (optimal 3–4 %) and pH 6.0–9.0 (optimal pH 7.5). Major cellular fatty acids (>10 %) were C18 : 1ω7c and C16 : 0. Phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid were detected as the predominant polar lipids. The sole respiratory quinone was Q-8. The DNA G+C content of strain WDS2A16AT was 48.5 mol%. The 16S rRNA gene sequence similarities of WDS2A16AT with other species were less than 91 %. The average nucleotide identity, in silico DNA–DNA hybridization and amino acid identity of strain WDS2A16AT with the most related strain Gynuella sunshinyii YC6258 T were 66.1, 19.3 and 48.1 %, respectively. Comparative analysis of 16S rRNA gene sequences and phenotypic characterization indicated that strain WDS2A16AT represents a novel species in a new genus, for which the name Salinibius halmophilus gen. nov., sp. nov. is proposed. The type strain is WDS2A16AT (=KCTC 52225T=MCCC 1H00139T).

Exposure to TiO2 nanoparticles induces shifts in the microbiota composition of Mytilus galloprovincialis hemolymph

It is now recognized that host microbiome, the community of microorganisms that colonize the animal body (e.g. microbiota) and their genomes, play an important role in the health status of all organisms, from nutrient processing to protection from disease. In particular, the complex, bilateral interactions between the host innate immune system and the microbiota are crucial in maintaining whole body homeostasis. The development of nanotechnology is raising concern on the potential impact of nanoparticles-NPs on human and environmental health. Titanium dioxide-nTiO₂, one of the most widely NP in use, has been shown to affect the gut microbiota of mammals and fish, as well as to potentially alter microbial communities. In the marine bivalve Mytilus galloprovincialis, nTiO₂ has been previously shown to interact with hemolymph components, thus resulting in immunomodulation. However, no information is available on the possible impact of NPs on the microbiome of marine organisms. Bivalves host high microbial abundance and diversity, and alteration of their microbiota, in both tissues and hemolymph, in response to stressful conditions has been linked to a compromised health status and susceptibility to diseases. In this work, the effects of nTiO₂ exposure (100 μg/L, 4 days) on Mytilus hemolymph microbiota were investigated by 16S rRNA gene-based profiling. Immune parameters were also evaluated. Although hemolymph microbiota of control and nTiO₂-treated mussels revealed a similar core composition, nTiO₂ exposure affected the abundance of different genera, with decreases in some (e.g. Shewanella, Kistimonas, Vibrio) and increases in others (e.g. Stenotrophomonas). The immunomodulatory effects of nTiO₂ were confirmed by the increase in the bactericidal activity of whole hemolymph. These represent the first data on the effects of NPs on the microbiome of marine invertebrates, and suggest that the shift in hemolymph microbiome composition induced by nTiO₂ may result from the interplay between the microbiota and the immune system.

Taxonomic and functional heterogeneity of the gill microbiome in a symbiotic coastal mangrove lucinid species

Lucinidae clams harbor gammaproteobacterial thioautotrophic gill endosymbionts that are environmentally acquired. Thioautotrophic lucinid symbionts are related to metabolically similar symbionts associated with diverse marine host taxa and fall into three distinct phylogenetic clades. Most studies on the lucinid–bacteria chemosymbiosis have been done with seagrass-dwelling hosts, whose symbionts belong to the largest phylogenetic clade. In this study, we examined the taxonomy and functional repertoire of bacterial endosymbionts at an unprecedented resolution from Phacoides pectinatus retrieved from mangrove-lined coastal sediments, which are underrepresented in chemosymbiosis studies. The P. pectinatus thioautotrophic endosymbiont expressed metabolic gene variants for thioautotrophy, respiration, and nitrogen assimilation distinct from previously characterized lucinid thioautotrophic symbionts and other marine symbionts. At least two other bacterial species with different metabolisms were also consistently identified in the P. pectinatus gill microbiome, including a Kistimonas-like species and a Spirochaeta-like species. Bacterial transcripts involved in adhesion, growth, and virulence and mixotrophy were highly expressed, as were host-related hemoglobin and lysozyme transcripts indicative of sulfide/oxygen/CO₂ transport and bactericidal activity. This study suggests the potential roles of P. pectinatus and its gill microbiome species in mangrove sediment biogeochemistry and offers insights into host and microbe metabolisms in the habitat.

Crown-of-Thorns Sea Star Acanthaster cf. solaris Has Tissue-Characteristic Microbiomes with Potential Roles in Health and Reproduction

Outbreaks of coral-eating crown-of-thorns sea stars (CoTS; Acanthaster species complex) cause substantial coral loss; hence, there is considerable interest in developing prevention and control strategies. We characterized the microbiome of captive CoTS and assessed whether dysbiosis was evident in sea stars during a disease event. Most tissue types had a distinct microbiome. The exception was female gonads, in which the microbiomes were highly variable among individuals. Male gonads were dominated (>97% of reads) by a single Mollicutes-related operational taxonomic unit (OTU). Detailed phylogenetic and microscopy analysis demonstrated the presence of a novel Spiroplasma-related bacterium in the spermatogenic layer. Body wall samples had high relative abundance (43 to 64% of reads) of spirochetes, likely corresponding to subcuticular symbionts reported from many echinoderms. Tube feet were characterized by Hyphomonadaceae (24 to 55% of reads). Pyloric cecal microbiomes had high alpha diversity, comprising many taxa commonly found in gastrointestinal systems. The order Oceanospirillales (genera Endozoicomonas and Kistimonas) was detected in all tissues. A microbiome shift occurred in diseased individuals although differences between tissue types were retained. The relative abundance of spirochetes was significantly reduced in diseased individuals. Kistimonas was present in all diseased individuals and significantly associated with diseased tube feet, but its role in disease causation is unknown. While Arcobacter was significantly associated with diseased tissues and Vibrionaceae increased in diversity, no single OTU was detected in all diseased individuals, suggesting opportunistic proliferation of these taxa in this case. This study shows that CoTS have tissue-characteristic bacterial communities and identifies taxa that could play a role in reproduction and host health.

IMPORTANCE Coral-eating crown-of-thorns sea stars (CoTS; Acanthaster species complex) are native to the Indo-Pacific, but during periodic population outbreaks they can reach extreme densities (>1,000 starfish per hectare) and function as a pest species. On the Great Barrier Reef, Australia, CoTS have long been considered one of the major contributors to coral loss. There has been significant investment in a targeted control program using lethal injection, and there is interest in developing additional and complementary technologies that can increase culling efficiencies. The biology of CoTS has been studied extensively, but little is known about their associated microbiome. This cultivation-independent analysis of the CoTS microbiome provides a baseline for future analyses targeting the functional role of symbionts, the identification of pathogens, or the development of reproduction manipulators.

Description of Sansalvadorimonas verongulae gen. nov., sp. nov., a gammaproteobacterium isolated from the marine sponge Verongula gigantea

A Gram-stain-negative, strictly aerobic, motile, rod-shaped bacterium, designated strain RKSG058^T, was isolated from the marine sponge Verongula gigantea, collected off the west coast of San Salvador, The Bahamas. Phylogenetic analyses based on 16S rRNA gene sequences revealed that RKSG058^T formed a distinct lineage within the family Hahellaceae (order Oceanospirillales, class Gammaproteobacteria), and was most closely related to the genus Endozoicomonas, with sequence similarities to members of this genus ranging from 92.0 to 93.7 %. Optimal growth occurred at 30 °C, at pH 7 and in the presence of 2-3 % (w/v) NaCl. The predominant cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The major and minor respiratory quinones were Q-9 and Q-8, respectively. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified aminolipids, an unidentified phospholipid and five unidentified lipids. The DNA G+C content was 42.3 mol%. Biochemical, chemotaxonomic and phylogenetic analyses indicated that strain RKSG058^T represents the first cultured isolate of a novel bacterial genus and species within the family Hahellaceae, for which the name Sansalvadorimonas verongulae gen. nov., sp. nov. is proposed. The type strain of Sansalvadorimonas verongulae is RKSG058^T (=TSD-72^T=LMG 29871^T). An emended description of the genus Kistimonas is provided.

Parendozoicomonas haliclonae gen. nov. sp. nov. isolated from a marine sponge of the genus Haliclona and description of the family Endozoicomonadaceae fam. nov. comprising the genera Endozoicomonas, Parendozoicomonas, and Kistimonas

Two Gram-stain-negative, facultative anaerobic, motile, rod-shaped strains, S-B4-1U^T and JOB-63a, forming small whitish transparent colonies on marine agar, were isolated from a sponge of the genus Haliclona. The strains shared 99.7% 16S rRNA gene sequence identity and a DNA-DNA hybridization value of 100%, but were differentiated by genomic fingerprinting using rep-PCRs. 16S rRNA gene sequence phylogeny placed the strains as a sister branch to the monophyletic genus Endozoicomonas (Oceanospirillales; Gammaproteobacteria) with 92.3-94.3% 16S rRNA gene sequence similarity to Endozoicomonas spp., 91.9 and 92.1% to Candidatus Endonucleobacter bathymodiolin, and 91.9 to 92.1% to the type strains of Kistimonas spp. Core genome based phylogeny of strain S-B4-1U^T confirmed the phylogenetic placement. Major fatty acids were summed feature 3 (C_16:1 ω7c/C_16:1 ω6c) and 8 (C_18:1 ω7c/C_18:1 ω6c) followed by C_10:0 3-OH, C_16:0, and C_18:0. The G+C content was 50.1-51.4mol%. The peptidoglycan diamino acid of strain S-B4-1U^T was meso-diaminopimelic acid, the predominant polyamine spermidine, the major respiratory quinone ubiquinone Q-9; phosphatidylethanolamine, phosphatidylglycerol and phosphatidylserine were major polar lipids. Based on the clear phylogenetic distinction, the genus Parendozoicomonas gen. nov. is proposed, with Parendozoicomonas haliclonae sp. nov. as type species and strain S-B4-1U^T (=CCM 8713^T=DSM 103671^T=LMG 29769^T) as type strain and JOB-63a as a second strain of the species. Based on the 16S rRNA gene sequence phylogeny of the Oceanospirillales within the Gammaproteobacteria, the Endozoicomonaceae fam. nov. is proposed including the genera Endozoicomonas, Parendozoicomonas, and Kistimonas as well as the Candidatus genus Endonucleobacter.

Beneficial Microorganisms for Corals (BMC): Proposed Mechanisms for Coral Health and Resilience

The symbiotic association between the coral animal and its endosymbiotic dinoflagellate partner Symbiodinium is central to the success of corals. However, an array of other microorganisms associated with coral (i.e., Bacteria, Archaea, Fungi, and viruses) have a complex and intricate role in maintaining homeostasis between corals and Symbiodinium. Corals are sensitive to shifts in the surrounding environmental conditions. One of the most widely reported responses of coral to stressful environmental conditions is bleaching. During this event, corals expel Symbiodinium cells from their gastrodermal tissues upon experiencing extended seawater temperatures above their thermal threshold. An array of other environmental stressors can also destabilize the coral microbiome, resulting in compromised health of the host, which may include disease and mortality in the worst scenario. However, the exact mechanisms by which the coral microbiome supports coral health and increases resilience are poorly understood. Earlier studies of coral microbiology proposed a coral probiotic hypothesis, wherein a dynamic relationship exists between corals and their symbiotic microorganisms, selecting for the coral holobiont that is best suited for the prevailing environmental conditions. Here, we discuss the microbial-host relationships within the coral holobiont, along with their potential roles in maintaining coral health. We propose the term BMC (Beneficial Microorganisms for Corals) to define (specific) symbionts that promote coral health. This term and concept are analogous to the term Plant Growth Promoting Rhizosphere (PGPR), which has been widely explored and manipulated in the agricultural industry for microorganisms that inhabit the rhizosphere and directly or indirectly promote plant growth and development through the production of regulatory signals, antibiotics and nutrients. Additionally, we propose and discuss the potential mechanisms of the effects of BMC on corals, suggesting strategies for the use of this knowledge to manipulate the microbiome, reversing dysbiosis to restore and protect coral reefs. This may include developing and using BMC consortia as environmental "probiotics" to improve coral resistance after bleaching events and/or the use of BMC with other strategies such as human-assisted acclimation/adaption to shifting environmental conditions.

Highly Variable Bacterial Communities Associated with the Octocoral Antillogorgia elisabethae

Antillogorgia elisabethae (synonymous with Pseudopterogorgia elisabethae) is a common branching octocoral in Caribbean reef ecosystems. A. elisabethae is a rich source of anti-inflammatory diterpenes, thus this octocoral has been the subject of numerous natural product investigations, yet relatively little is known regarding the composition, diversity and the geographic and temporal stability of its microbiome. To characterize the composition, diversity and stability of bacterial communities of Bahamian A. elisabethae populations, 17 A. elisabethae samples originating from five sites within The Bahamas were characterized by 16S rDNA pyrosequencing. A. elisabethae bacterial communities were less diverse and distinct from those of surrounding seawater samples. Analyses of α- and β-diversity revealed that A. elisabethae bacterial communities were highly variable between A. elisabethae samples from The Bahamas. This contrasts results obtained from a previous study of three specimens collected from Providencia Island, Colombia, which found A. elisabethae bacterial communities to be highly structured. Taxa belonging to the Rhodobacteriales, Rhizobiales, Flavobacteriales and Oceanospiralles were identified as potential members of the A. elisabethae core microbiome.

Description of Endozoicomonas arenosclerae sp. nov. using a genomic taxonomy approach

The taxonomic position of strains Ab112(T) (CBAS 572(T)) and Ab227_MC (CBAS 573) was evaluated by means of genomic taxonomy. These isolates represent the dominant flora cultured from the healthy marine sponge Arenosclera brasiliensis, endemic to Rio de Janeiro. Strains CBAS 572(T) and CBAS 573 shared >98 % 16S rRNA sequence identity with Endozoicomonas numazuensis and Endozoicomonas montiporae. In silico DNA-DNA Hybridization, i.e. genome-to-genome distance (GGD), amino acid identity (AAI) and average nucleotide identity (ANI) further showed that these strains had <70 %, at maximum 71.1 and 78 % of identity, respectively, to their closest neighbours E. numazuensis and E. montiporae. The DNA G+C content of CBAS 572(T) and CBAS 573 were 47.6 and 47.7 mol%, respectively. Phenotypic and chemotaxonomic features also allowed a separation from the type strains of their phylogenetic neighbours. Useful phenotypic features for discriminating CBAS 572(T) and CBAS 573 from E. numazuensis and E. montiporae species include C8 esterase, N-acetyl-β-glucosaminidase, citric acid, uridine and siderophore. The species Endozoicomonas arenosclerae sp. nov. is proposed to harbour the new isolates. The type strain is CBAS 572(T) (=Ab112(T)).

Antibiotic activity and microbial community of the temperate sponge, Haliclona sp

AIMS

Sessile marine invertebrates engage in a diverse array of beneficial interactions with bacterial symbionts. One feature of some of these relationships is the presence of bioactive natural products that can defend the holobiont from predation, competition or disease. In this study, we investigated the antimicrobial activity and microbial community of a common temperate sponge from coastal North Carolina.

METHODS AND RESULTS

The sponge was identified as a member of the genus Haliclona, a prolific source of bioactive natural products, based on its 18S rRNA gene sequence. The crude chemical extract and methanol partition had broad activity against the assayed Gram-negative and Gram-positive pathogenic bacteria. Further fractionation resulted in two groups of compounds with differing antimicrobial activity, primarily against Gram-positive test organisms. There was, however, notable activity against the Gram-negative marine pathogen, Vibrio parahaemolyticus. Microbial community analysis of the sponge and surrounding sea water via denaturing gradient gel electrophoresis (DGGE) indicates that it harbours a distinct group of bacterial associates.

CONCLUSIONS

The common temperate sponge, Haliclona sp., is a source of multiple antimicrobial compounds and has some consistent microbial community members that may play a role in secondary metabolite production.

SIGNIFICANCE AND IMPACT OF THE STUDY

These data suggest that common temperate sponges can be a source of bioactive chemical and microbial diversity. Further studies may reveal the importance of the microbial associates to the sponge and natural product biosynthesis.

A novel agent (Endozoicomonas elysicola) responsible for epitheliocystis in cobia Rachycentrum canadum larvae

Aquaculture of cobia has gained popularity in the last decade, and this species is now farmed in several countries in Latin America and Asia. Despite recent improvement in production techniques that allowed the expansion of the industry, little is known about the diseases that affect cobia during the larviculture stage. In this article we investigated the cause of mass mortalities occurring 13-20 d post-hatching in 3 cycles of cobia larviculture. Wet mounts from diseased larvae gills revealed the presence of cyst-like basophilic inclusions. DNA from the cysts was extracted and PCR amplified using the 16S rRNA gene universal primers for prokaryotes. The amplified products were sequenced and analyzed using BLAST, finding a similarity of 99% with Endozoicomonas elysicola, a Gram-negative bacterium. Confirmation of E. elysicola was conducted by designing a specific probe for in situ hybridization. Specific primers were also designed for diagnostic purposes. This is the first report of epitheliocystis in cobia larvae and also the first report of E. elysicola as an epitheliocystis-causing agent.

Kistimonas scapharcae sp. nov., isolated from a dead ark clam (Scapharca broughtonii), and emended description of the genus Kistimonas

A Gram-negative, motile, facultatively anaerobic rod, designated A36T, was isolated from a dead ark clam found on the south coast of Korea. The isolate was catalase- and oxidase-negative. 16S rRNA gene sequence analysis indicated that strain A36T was most closely related to Kistimonas asteriae KMD 001T, with which it shared 98.2 % 16S rRNA gene sequence similarity. Strain A36T grew optimally at 30–37 °C, with 1 % (w/v) NaCl and at pH 8.0. The major respiratory quinone was ubiquinone-9 (Q-9). The major polar lipids were phosphatidylserine, phosphoethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The major fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 2-OH) and C16 : 0. The genomic DNA G+C content was 47.3 mol%. DNA–DNA relatedness between the isolate and K. asteriae JCM 15607T was <25±3 %. Strain A36T represents a novel species of the genus Kistimonas , for which the name Kistimonas scapharcae sp. nov. is proposed. The type strain is A36T ( = KACC 16204T  = JCM 17805T). An emended description of the genus Kistimonas is also provided.

Endozoicomonas numazuensis sp. nov., a gammaproteobacterium isolated from marine sponges, and emended description of the genus Endozoicomonas Kurahashi and Yokota 2007

Two non-motile, rod-shaped gammaproteobacteria were isolated from marine sponges collected from the coast of Japan at Numazu. The isolates were oxidase- and catalase-positive facultative anaerobes that fermented carbohydrates. They required sodium ions for growth and were slightly halophilic, growing in the presence of 1.0-5.0 % (w/v) NaCl (optimum of 2.0 % NaCl). Under aerobic conditions, the major isoprenoid quinones were ubiquinone-9 and menaquinone-9 and the minor quinones were ubiquinone-8 and menaquinone-8. The major cellular fatty acids were C(18 : 1)ω7c, C(16 : 1)ω7c and C(16 : 0) and the hydroxy acids were C(10 : 0) 3-OH and C(12 : 0) 3-OH. The DNA G+C content was 48.3-48.7 mol%. Phylogenetic analysis of 16S rRNA gene sequences placed the isolates within the radiation of the genus Endozoicomonas in a broad clade of uncultured clones recovered from various marine invertebrates. The isolates exhibited 96.5-96.9 % 16S rRNA gene sequence similarity with Endozoicomonas elysicola MKT110(T) and Endozoicomonas montiporae CL-33(T), with which the isolates formed a monophyletic cluster with 100 % bootstrap support. The phenotypic features (carbohydrate fermentation, quinone system and some major cellular fatty acids) differed from those of members of the genus Endozoicomonas, which are aerobic, produce little or no menaquinone under aerobic conditions and possess different amounts of C(14 : 0) and C(18 : 1)ω7c. Although some phenotypic differences were identified, the isolates should be assigned to the genus Endozoicomonas on the basis of congruity of phylogeny and should be classified as representatives of a novel species, for which the name Endozoicomonas numazuensis sp. nov. is proposed. The type strain is HC50(T) ( = NBRC 108893(T)  = DSM 25634(T)). An emended description of the genus Endozoicomonas is presented.

Intracellular Oceanospirillales bacteria inhabit gills of Acesta bivalves

A novel bacterium was discovered in the gills of the large bivalve Acesta excavata (Limidae) from coral reefs on the northeast Atlantic margin near the shelf break of the fishing ground Haltenbanken of Norway, and confirmed present in A. excavata from a rock-wall in the Trondheimsfjord. Purified gill DNA contained one dominant bacterial rRNA operon as indicated from analysis of broad range bacterial PCR amplicons in denaturant gradient gels, in clone libraries and by direct sequencing. The sequences originated from an unknown member of the order Oceanospirillales and its 16S rRNA gene fell within a clade of strictly marine invertebrate-associated Gammaproteobacteria. Visual inspection by fluorescent in situ hybridization and transmission electron microscopy indicated a pleomorphic bacterium with no visible cell wall, located in aggregates inside vacuoles scattered within the gill cells cytoplasm. Intracellular Oceanospirillales exist in bathymodiolin mussels (parasites), Osedax worms and whiteflies (symbionts). This bacterium apparently lives in a specific association with the Acesta.

Colwellia asteriadis sp. nov., a marine bacterium isolated from the starfish Asterias amurensis

A marine bacterial strain, KMD 002T, was isolated from an Amur starfish, Asterias amurensis, collected in the East Sea of Korea. Strain KMD 002T was a Gram-negative, beige-pigmented, rod-shaped bacterium. The strain was capable of growth at relatively low temperatures (4–25 °C) and over a broad pH range (pH 4.0–10.0). The major fatty acids were C16 : 1 ω7c and/or iso-C15 : 0 2-OH and C16 : 0 and the predominant isoprenoid quinone was Q-8. The DNA G+C content of strain KMD 002T was 40.3 mol%. Phylogenetic analysis using 16S rRNA gene sequences revealed that strain KMD 002T belonged to the genus Colwellia. However, various phenotypic properties as well as low 16S rRNA gene sequence similarities to members of the genus Colwellia (94.1–96.7 %) suggested that strain KMD 002T is a representative of a novel species, for which the name Colwellia asteriadis sp. nov. is proposed. The type strain is KMD 002T (=KCCM 90077T =JCM 15608T).