The Pathogen of the Great Barrier Reef Sponge Rhopaloeides odorabile Is a New Strain of Pseudoalteromonas agarivorans Containing Abundant and Diverse Virulence-Related Genes

Host-Microbiome Interactions in a Changing Sea: The Gill Microbiome of an Invasive Oyster under Drastic Temperature Changes

The gill tissue of bivalve mollusks hosts rich symbiotic microbial communities that may contribute to host health. Spondylus spinosus is an invasive Lessepsian oyster in the Eastern Mediterranean Sea that has become highly abundant while constantly expanding its range northwestward. Using 16S rRNA gene amplicon sequencing, we examined how temperature affects S. spinosus oysters and their gill microbiota in a series of experiments: exposing them to the current annual seawater temperature range, to the colder temperature of the Western Mediterranean Sea, and to the elevated temperature as predicted under global warming scenarios. The bacterial genus Endozoicomonas dominated the communities of the S. spinosus, mainly upon exposure to winter-like (16 °C) temperatures. Exposure to the elevated seawater temperature resulted in a significant change in the bacterial communities, while the oysters maintained normal functioning, suggesting that the oyster may survive a seawater warming scenario. Exposure to 11 °C led to the health deterioration of the oysters, the emergence of opportunistic pathogens, such as Arcobacter, Vibrio, Colwelliaceae, and Pseudoalteromonas, and a decline in the relative abundance of Endozoicomonas, suggesting that S. spinosus might not survive Western Mediterranean Sea winters. Both the host and its gill bacteria are thus greatly affected by temperature, which could consequently restrict the range of expansion of this and other invasive oysters.

Mass mortality of the keratose sponge Sarcotragus foetidus in the Aegean Sea (Eastern Mediterranean) correlates with proliferation of Vibrio bacteria in the tissues

In the last two decades, episodes of mass mortality in benthic communities have often been associated with climatic anomalies, but the ultimate mechanisms through which they lead to death have rarely been identified. This study reports a mass mortality of wild sponges in the Aegean Sea (Turkey, Eastern Mediterranean), which affected the keratose demosponge Sarcotragus foetidus in September 2021. We examined the occurrence of thermo-dependent bacteria of the genus Vibrio in the sponges, identified through 16S rRNA of colonies isolated from sponge tissue in specific culturing media. Six Vibrio sequences were identified from the sponges, three of them being putatively pathogenic (V. fortis, V. owensii, V. gigantis). Importantly, those Vibrios were isolated from only tissues of diseased sponges. In contrast, healthy individuals sampled in both summer and winter led to no Vibrio growth in laboratory cultures. A 50 years record of sea surface temperature (SST) data for the study area reveals a progressive increase in temperature from 1970 to 2021, with values above 24°C from May to September 2021, reaching an absolute historical maximum of 28.9°C in August 2021. We hypothesize that such elevated SST values maintained for several months in 2021 promoted proliferation of pathogenic Vibrio species (thermo-dependent bacteria) in S. foetidus, triggering or aggravating the course of sponge disease. Thus, vibrioisis emerges as one of the putative mechanisms through which global water warming in the Mediterranean Sea translates into sponge mortality. The historical time course of temperature data for the studied area in the Aegean Sea predicts that recurrent waves of elevated SST are likely to occur in the coming summers. If so, recurrent disease may eventually eliminate this abundant sponge from the sublittoral in the midterm, altering the original bathymetric distribution of the species and compromising its ecological role.

Janthinobacterium sp. Strain SLB01 as Pathogenic Bacteria for Sponge Lubomirskia baikalensis

Sponges (phylum Porifera) are ancient, marine and inland water, filter feeding metazoans. In recent years, diseased sponges have been increasingly occurring in marine and freshwater environments. Endemic freshwater sponges of the Lubomirskiidae family are widely distributed in the coastal zone of Lake Baikal. The strain Janthinobacterium sp. SLB01 was isolated previously from the diseased sponge Lubomirskia baikalensis (Pallas, 1776), although its pathogenicity is still unknown. The aim of this study was to confirm whether the Janthinobacterium sp. strain SLB01 is the pathogen found in Baikal sponge. To address this aim, we infected the cell culture of primmorphs of the sponge L. baikalensis with strain SLB01 and subsequently reisolated and sequenced the strain Janthinobacterium sp. PLB02. The results showed that the isolated strain has more than 99% homology with strain SLB01. The genomes of both strains contain genes vioABCDE of violacein biosynthesis and floc formation, for strong biofilm, in addition to the type VI secretion system (T6SS) as the main virulence factor. Based on a comparison of complete genomes, we showed the similarity of the studied bacterial strains of Janthinobacterium spp. with the described strain of Janthinobacterium lividum MTR. This study will help expand our understanding of microbial interactions and determine one of the causes in the development of diseases and death in Baikal sponges.

Fish Microbiome Modulation and Convenient Storage of Aquafeeds When Supplemented with Vitamin K1

Vitamin K (VK) is a fat-soluble vitamin necessary for fish metabolism and health. VK stability as dietary component during aquafeed storage and its potential effect on intestinal microbiome in fish have not yet been completely elucidated. The convenient storage conditions of aquafeeds when supplemented with phylloquinone (VK1), as well as its potential effects on the gut microbiota of Senegalese sole (Solea senegalensis) juveniles, have been explored. Experimental feeds were formulated to contain 0, 250 and 1250 mg kg^-1 of VK1 and were stored at different temperatures (4, -20 or -80 °C). VK stability was superior at -20 °C for short-term (7 days) storage, while storing at -80 °C was best suited for long-term storage (up to 3 months). A comparison of bacterial communities from Senegalese sole fed diets containing 0 or 1250 mg kg^-1 of VK1 showed that VK1 supplementation decreased the abundance of the Vibrio, Pseudoalteromonas, and Rhodobacterace families. All these microorganisms were previously associated with poor health status in aquatic organisms. These results contribute not only to a greater understanding of the physiological effects of vitamin K, particularly through fish intestinal microbiome, but also establish practical guidelines in the industry for proper aquafeed storage when supplemented with VK1.

Assessing the genomic composition, putative ecological relevance and biotechnological potential of plasmids from sponge bacterial symbionts

Plasmid-mediated transfer of genes can have direct consequences in several biological processes within sponge microbial communities. However, very few studies have attempted genomic and functional characterization of plasmids from marine host-associated microbial communities in general and those of sponges in particular. In the present study, we used an endogenous plasmid isolation method to obtain plasmids from bacterial symbionts of the marine sponges Stylissa carteri and Paratetilla sp. and investigated the genomic composition, putative ecological relevance and biotechnological potential of these plasmids. In total, we isolated and characterized three complete plasmids, three plasmid prophages and one incomplete plasmid. Our results highlight the importance of plasmids to transfer relevant genetic traits putatively involved in microbial symbiont adaptation and host-microbe and microbe-microbe interactions. For example, putative genes involved in bacterial response to chemical stress, competition, metabolic versatility and mediation of bacterial colonization and pathogenicity were detected. Genes coding for enzymes and toxins of biotechnological potential were also detected. Most plasmid prophage coding sequences were, however, hypothetical proteins with unknown functions. Overall, this study highlights the ecological relevance of plasmids in the marine sponge microbiome and provides evidence that plasmids of sponge bacterial symbionts may represent an untapped resource of genes of biotechnological interest.

Pan-Genomic and Transcriptomic Analyses of Marine Pseudoalteromonas agarivorans Hao 2018 Revealed Its Genomic and Metabolic Features

The genomic and carbohydrate metabolic features of Pseudoalteromonas agarivorans Hao 2018 (P. agarivorans Hao 2018) were investigated through pan-genomic and transcriptomic analyses, and key enzyme genes that may encode the process involved in its extracellular polysaccharide synthesis were screened. The pan-genome of the P. agarivorans strains consists of a core-genome containing 2331 genes, an accessory-genome containing 956 genes, and a unique-genome containing 1519 genes. Clusters of Orthologous Groups analyses showed that P. agarivorans harbors strain-specifically diverse metabolisms, probably representing high evolutionary genome changes. The Kyoto Encyclopedia of Genes and Genomes and reconstructed carbohydrate metabolic pathways displayed that P. agarivorans strains can utilize a variety of carbohydrates, such as d-glucose, d-fructose, and d-lactose. Analyses of differentially expressed genes showed that compared with the stationary phase (24 h), strain P. agarivorans Hao 2018 had upregulated expression of genes related to the synthesis of extracellular polysaccharides in the logarithmic growth phase (2 h), and that the expression of these genes affected extracellular polysaccharide transport, nucleotide sugar synthesis, and glycosyltransferase synthesis. This is the first investigation of the genomic and metabolic features of P. agarivorans through pan-genomic and transcriptomic analyses, and these intriguing discoveries provide the possibility to produce novel marine drug lead compounds with high biological activity.

Metagenomic Assessment of DNA Viral Diversity in Freshwater Sponges, Baikalospongia bacillifera

Sponges (type Porifera) are multicellular organisms that give shelter to a variety of microorganisms: fungi, algae, archaea, bacteria, and viruses. The studies concerning the composition of viral communities in sponges have appeared rather recently, and the diversity and role of viruses in sponge holobionts remain largely undisclosed. In this study, we assessed the diversity of DNA viruses in the associated community of the Baikal endemic sponge, Baikalospongia bacillifera, using a metagenomic approach, and compared the virome data from samples of sponges and Baikal water (control sample). Significant differences in terms of taxonomy, putative host range of identified scaffolds, and functional annotation of predicted viral proteins were revealed in viromes of sponge B. bacillifera and the Baikal water. This is the evidence in favor of specificity of viral communities in sponges. The diversity shift of viral communities in a diseased specimen, in comparison with a visually healthy sponge, probably reflects the changes in the composition of microbial communities in affected sponges. We identified many viral genes encoding the proteins with metabolic functions; therefore, viruses in Baikal sponges regulate the number and diversity of their associated community, and also take a part in the vital activity of the holobiont, and this is especially significant in the case of damage (or disease) of these organisms in unfavorable conditions. When comparing the Baikal viromes with similar datasets of marine sponge (Ianthella basta), in addition to significant differences in the taxonomic and functional composition of viral communities, we revealed common scaffolds/virotypes in the cross-assembly of reads, which may indicate the presence of some closely related sponge-specific viruses in marine and freshwater sponges.

Antibiotics, antibiotic resistance genes and microbial community in grouper mariculture

Increasing use of feed and medicine in mariculture could cause negative environmental impacts such as habitat modification, microbial disease development and antibiotic resistance. Here we investigated contamination of antibiotics and antibiotic resistance genes (ARGs), and composition of microbial community in grouper mariculture systems in Hainan province, China. Results showed detection of various antibiotic residues with the dominance of fluoroquinolones and tetracyclines in the six grouper cultivation systems. The concentrations of the detected antibiotics in the grouper mariculture water were significantly higher than those in the original seawater. Some of the detected antibiotics such as enrofloxacin, ciprofloxacin, ofloxacin, oxytetracycline and erythromycin in the mariculture water and/or sediment would pose high resistance selection risks. Sulfonamides resistance genes sul1 and sul2 were found to be predominant in water and sediment, while tetracycline resistance genes were prevalent in fish gill and gut. The dominant bacterial phyla in water and sediments were Bacteroides, Actinomycetes, and Proteobacteria, while the dominant ones in fish gill and gut were the Proteobacteria. Genera of Vibrio and Mycobacterium in the core microbiota were important zoonotic pathogens, and there was a significant positive correlation between Vibrio and ARGs. Phyla of Proteobacteria, Actinomyces, and Cyanobacteria were positively correlated to ARGs, indicating that these microorganisms are potential hosts of ARGs. The putative functions of microbiome related to antibiotic resistance and human diseases were significantly higher in fish than in the mariculture environment. This study suggests that mariculture system is a reservoir of ARGs, and the use of antibiotics in mariculture could induce the increase of antibiotic resistance and the prevalence of opportunistic pathogens.

Genome Analysis of the Janthinobacterium sp. Strain SLB01 from the Diseased Sponge of the Lubomirskia baicalensis

The strain Janthinobacterium sp. SLB01 was isolated from the diseased freshwater sponge Lubomirskia baicalensis (Pallas, 1776) and the draft genome was published previously. The aim of this work is to analyze the genome of the Janthinobacterium sp. SLB01 to search for pathogenicity factors for Baikal sponges. We performed genomic analysis to determine virulence factors, comparing the genome of the strain SLB01 with genomes of other related J. lividum strains from the environment. The strain Janthinobacterium sp. SLB01 contained genes encoding violacein, alpha-amylases, phospholipases, chitinases, collagenases, hemolysin, and a type VI secretion system. In addition, the presence of conservative clusters of genes for the biosynthesis of secondary metabolites of tropodithietic acid and marinocine was found. We present genes for antibiotic resistance, including five genes encoding various lactamases and eight genes for penicillin-binding proteins, which are conserved in all analyzed strains. Major differences were found between the Janthinobacterium sp. SLB01 and J. lividum strains in the spectra of genes for glycosyltransferases and glycoside hydrolases, serine hydrolases, and trypsin-like peptidase, as well as some TonB-dependent siderophore receptors. Thus, the study of the analysis of the genome of the strain SLB01 allows us to conclude that the strain may be one of the pathogens of freshwater sponges.

Identification and analysis of the biological activity of the new strain of Pseudoalteromonas piscicida isolated from the hemal fluid of the bivalve Modiolus kurilensis (F. R. Bernard, 1983)

A cultivated form of bacteria (strain 2202) was isolated from the hemal fluid of the bivalve mollusk Modiolus kurilensis. Based on the set of data collected by genetic and physiological/biochemical analyses, the strain was identified as the species Pseudoalteromonas piscicida. Strain 2202 exhibits antimicrobial activity against Staphylococcus aureus, Candida albicans, and Bacillus subtilis but not against Escherichia coli and Pseudomonas aeruginosa. These activities characterize the behavior of strain 2202 as predator-like and classify it as a facultative predator. Being part of the normal microflora in the hemolymph of M. kurilensis, when external conditions change, strain 2202 shows features of opportunistic microflora. The strain 2202 exhibits selective toxicity towards larvae of various invertebrates: it impairs the early development of Mytilus edulis, but not of Strongylocentrotus nudus. Thus, the selective manner in which P. piscicida strains interact with various species of microorganisms and eukaryotes should be taken into consideration when using their biotechnological potential as a probiotic in aquaculture, source of antimicrobial substances, and factors that prevent fouling.

Fish farm effluents as a source of antibiotic resistance gene dissemination on Jeju Island, South Korea

The abuse or misuse of antibiotics is directly linked to the emergence of antibiotic-resistant bacteria and antibiotic resistance genes (ARGs) in the environment. Most fish farms located on Jeju Island operate a flow-through system that pumps in seawater for fish farming and discharges it back to the ocean. To investigate the amount of ARGs that these fish farm effluents discharge into the marine environment, we conducted a metagenomic-based resistome analysis. We observed higher levels of ARGs in fish farm effluents than in seawater at beach and residential areas. A greater proportion of ARGs was found on plasmid rather than on chromosomal DNA, especially for sulfonamide and phenicol classes. The distribution of ARGs did not differ between summer and winter, but the microbial community did. In addition, fish farm samples contained significantly more opportunistic pathogens (i.e., Vibrio, Photobacterium, Aliivibrio, and Tenacibaculum) and virulence factors than non-fish farm samples. Vibrio was the most frequently identified host of ARGs and virulence factors. The presence of Vibrio in the coastal area has been increasing owing to the recent rise in the temperature of seawater. This study suggests the need for actions to treat or monitor ARGs in the coastal areas where fish farms operating a flow-through system are located.

Isolation and genomic characterization of a pathogenic Providencia rettgeri strain G0519 in turtle Trachemys scripta

Providencia rettgeri infection has occurred occasionally in aquaculture, but is rare in turtles. Here, a pathogenic P. rettgeri strain G0519 was isolated from a diseased slider turtle (Trachemys scripta) in China, and qPCR assay was established for the RTX toxin (rtxD) gene. Histopathological examination showed that many inflammatory cells were infiltrated into heart, liver and intestine, as well as the necrosis of liver, kidney and spleen. The genome consisted of one circular chromosome (4.493 Mb) and one plasmid (18.8 kb), and predicted to contain 4170 and 19 protein-coding genes, respectively. Multiple pathogenic and virulence factors (e.g., fimbria, adhesion, invasion, toxin, hemolysin, chemotaxis, secretion system), multidrug-resistant genes (e.g., ampC, per-1, oxa-1, sul1, tetR) and a novel genomic resistance island PRI519 were identified. Comparative genome analysis revealed the closest relationship was with P. rettgeri, and with P. heimbachae closer than with other Providencia spp. To our knowledge, this was first report on genomic characterization of multidrug-resistant pathogenic P. rettgeri in cultured turtles.

Harnessing the sponge microbiome for industrial biocatalysts

Within the marine sphere, host-associated microbiomes are receiving growing attention as prolific sources of novel biocatalysts. Given the known biocatalytic potential of poriferan microbial inhabitants, this review focuses on enzymes from the sponge microbiome, with special attention on their relevant properties and the wide range of their potential biotechnological applications within various industries. Cultivable bacterial and filamentous fungal isolates account for the majority of the enzymatic sources. Hydrolases, mainly glycoside hydrolases and carboxylesterases, are the predominant reported group of enzymes, with varying degrees of tolerance to alkaline pH and growing salt concentrations being common. Prospective areas for the application of these microbial enzymes include biorefinery, detergent, food and effluent treatment industries. Finally, alternative strategies to identify novel biocatalysts from the sponge microbiome are addressed, with an emphasis on modern -omics-based approaches that are currently available in the enzyme research arena. By providing this current overview of the field, we hope to not only increase the appetite of researchers to instigate forthcoming studies but also to stress how basic and applied research can pave the way for new biocatalysts from these symbiotic microbial communities in a productive fashion. KEY POINTS: • The sponge microbiome is a burgeoning source of industrial biocatalysts. • Sponge microbial enzymes have useful habitat-related traits for several industries. • Strategies are provided for the future discovery of microbial enzymes from sponges.

Assessment of predominant bacteria in noble pen shell (Pinna nobilis) collected in the Eastern Adriatic Sea

Noble pen shell (Pinna nobilis) is an endemic species and the largest known bivalve in the Mediterranean Sea. By filtering large amounts of water, they maintain a high percentage of organic matter, hence playing an important role in the marine ecosystem. The ecological community of pen shells is impressive, and there are numerous microorganisms present in its soft tissues. Since this species is highly endangered due to recently described mass mortalities throughout the Mediterranean, this study was aimed at finding out more about its microbiome. In this study, we identified the predominant bacterial populations of specimens collected at three separate locations along the Eastern Adriatic coast. The predominant bacteria were isolated and 16S rRNA sequencing was performed to identify eight different bacterial genera: Aestuariibacter sp., Aliivibrio sp., Alteromonas sp., Marinobacter sp., Pseudoalteromonas sp., Rubritalea sp., Thalassospira sp. and the Vibrio splendidus clade. The identified genera are ubiquitous in the marine environment and have previously been described as both beneficial symbionts and potential pathogens in other molluscs. There was a clear difference in the predominant bacterial populations between northern and southern sampling sites, which could be linked to water temperature. These findings indicate the need for expanded sampling over a longer time period, since more exhaustive research would provide information vital to the conservation of this critically endangered species.

Diversity and shifts of the bacterial community associated with Baikal sponge mass mortalities

The disease of freshwater sponges was first discovered in 2011, when pink samples were found in the Central Basin of Lake Baikal. Subsequently, the visible signs of the disease have changed, and now sponges appear with various symptoms of damage to the body, such as discoloration, tissue necrosis, the formation of brown patches and dirty-purple biofilms on some branches. These signs of the disease are accompanied by the mass death of sponges. We identified differences in microbiomes by sequencing 16S rRNA genes and found changes in the consortium of microorganisms of freshwater Baikal sponges. We found that the observed imbalance in the studied microbial communities of diseased sponges is caused by several different conditionally pathogenic microorganisms that increase their negative effect by acting together and in concert, which leads to the death of photosynthetic microalgae and sponges. Sponges are an important component of coastal communities, and the massive loss of sponges can obviously affect the structure of benthic communities and the purity of water.

Microbiome analysis of a disease affecting the deep-sea sponge Geodia barretti

Reports of sponge disease are becoming increasingly frequent, although almost all instances involve shallow-water, tropical species. Here, we describe the first disease affecting the deep-water sponge, Geodia barretti. The disease is characterised by brown/black discolouration of the sponge tissue, extensive levels of tissue disintegration and increased levels of fouling. Disease prevalence was quantified using video survey transects conducted between 100 and 220 m in Korsfjorden, Norway, and the microbial communities of healthy and diseased sponges were compared using 16S rRNA gene sequencing. Highly divergent community profiles were evident between the different health states, with distinct community shifts involving higher relative abundances of Bacteroidetes, Firmicutes and Deltaproteobacteria in diseased individuals. In addition, three operational taxonomic units were exclusively present in diseased individuals and were shared between the disease lesions and the apparently healthy tissue of diseased individuals, suggesting a non-localised infection or dysbiosis. Genomic analysis of the G. barretti microbiome combined with experimental work to assess the mechanisms of infection will further elucidate the role of microorganisms in the disease.

Bioprospecting for microbes with potential hydrocarbon remediation activity on the northwest coast of the Yucatan Peninsula, Mexico, using DNA sequencing

Coastal environments harbor diverse microbial communities, which can contain genera with potential bioremediation activity. Next-generation DNA sequencing was used to identify bacteria to the genus level in water and sediment samples collected from the open ocean, shoreline, wetlands and freshwater upwellings on the northwest coast of the Yucatan Peninsula. Supported by an extensive literature review, a phylogenetic investigation of the communities was done using reconstruction of unobserved states software (PICRUSt) to predict metagenome functional content from the sequenced 16S gene in all the samples. Bacterial genera were identified for their potential hydrocarbon bioremediation activity. These included generalist genera commonly reported in hydrocarbon-polluted areas and petroleum reservoirs, as well as specialists such as Alcanivorax and Cycloclasticus. The highest readings for bacteria with potential hydrocarbon bioremediation activity were for the genera Vibrio, Alteromonas, Pseudomonas, Acinetobacter, Burkholderia, Acidovorax and Pseudoalteromonas from different environments in the study area. Some genera were identified only in specific sites; for example, Aquabacterium and Polaromonas were found only in freshwater upwellings. Variation in genera distribution was probably due to differences in environmental conditions in the sampled zones. Bacterial diversity was high in the study area and included numerous genera with known bioremediation activity. Functional prediction of the metagenome indicated that the studied bacterial communities would most probably degrade toluene, naphthalene, chloroalkane and chloroalkene, with lower degradation proportions for aromatic hydrocarbons, fluorobenzoate and xylene. Differences in predicted degradation existed between sediments and water, and between different locations.

Agelas Wasting Syndrome Alters Prokaryotic Symbiont Communities of the Caribbean Brown Tube Sponge, Agelas tubulata

The brown tube sponge Agelas tubulata (cf. Agelas conifera) is an abundant and long-lived sponge on Caribbean reefs. Recently, a disease-like condition, Agelas wasting syndrome (AWS), was described from A. tubulata in the Florida Keys, where prevalence of the syndrome increased from 7 to 35% of the sponge population between 2010 and 2015. In this study, we characterized the prokaryotic symbiont community of A. tubulata for the first time from individuals collected within the same monitoring plots where AWS was described. We also sampled tissue from A. tubulata exhibiting symptoms of AWS to determine its effect on the diversity and structure of prokaryotic symbiont communities. Bacteria from the phyla Chloroflexi and Proteobacteria, particularly the class Gammaproteobacteria, dominated the sponge microbiome in tissue samples of both healthy sponges and those exhibiting AWS. Prokaryotic community structure differed significantly between the diseased and healthy sponge samples, with greater variability among communities in diseased samples compared to healthy samples. These differences in prokaryotic community structure included a shift in relative abundance of the dominant, ammonia-oxidizing (Thaumarchaeota) symbionts present in diseased and healthy sponge samples. Further research is required to determine the functional consequences of this shift in microbial community structure and the causal relationship of dysbiosis and sponge disease in A. tubulata.

Taxonomic annotation errors incorrectly assign the family Pseudoalteromonadaceae to the order Vibrionales in Greengenes: implications for microbial community assessments

Next-generation sequencing has provided powerful tools to conduct microbial ecology studies. Analysis of community composition relies on annotated databases of curated sequences to provide taxonomic assignments; however, these databases occasionally have errors with implications for downstream analyses. Systemic taxonomic errors were discovered in Greengenes database (v13_5 and 13_8) related to orders Vibrionales and Alteromonadales. These orders have family level annotations that were erroneous at least one taxonomic level, e.g., 100% of sequences assigned to the Pseudoalteromonadaceae family were placed improperly in Vibrionales (rather than Alteromonadales) and >20% of these sequences were indeed Vibrio spp. but were improperly assigned to the Pseudoalteromonadaceae family (rather than to Vibrionaceae). Use of this database is common; we identified 68 peer-reviewed papers since 2013 that likely included erroneous annotations specifically associated with Vibrionales and Pseudoalteromonadaceae, with 20 explicitly stating the incorrect taxonomy. Erroneous assignments using these specific versions of Greengenes can lead to incorrect conclusions, especially in marine systems where these taxa are commonly encountered as conditionally rare organisms and potential pathogens.

Brown Rot Syndrome and Changes in the Bacterial Сommunity of the Baikal Sponge Lubomirskia baicalensis

Mass mortality events have led to a collapse of the sponge fauna of Lake Baikal. We describe a new Brown Rot Syndrome affecting the endemic species Lubomirskia baicalensis. The main symptoms are the appearance of brown patches at the sponge surface, necrosis, and cyanobacterial fouling. 16S rRNA gene sequencing was used to characterize the bacterial community of healthy versus diseased sponges, in order to identify putative pathogens. The relative abundance of 89 eubacterial OTUs out of 340 detected has significantly changed between healthy and diseased groups. This can be explained by the depletion of host-specific prokaryotes and by the appearance and proliferation of disease-specific OTUs. In diseased sponges, the most represented OTUs belong to the families Oscillatoriaceae, Cytophagaceae, Flavobacteriaceae, Chitinophagaceae, Sphingobacteriaceae, Burkholderiaceae, Rhodobacteraceae, Comamonadaceae, Oxalobacteraceae, and Xanthomonadaceae. Although these families may contain pathogenic agents, the primary causes of changes in the sponge bacterial community and their relationship with Brown Rot Syndrome remain unclear. A better understanding of this ecological crisis will thus require a more integrative approach.

The sponge holobiont in a changing ocean: from microbes to ecosystems

The recognition that all macroorganisms live in symbiotic association with microbial communities has opened up a new field in biology. Animals, plants, and algae are now considered holobionts, complex ecosystems consisting of the host, the microbiota, and the interactions among them. Accordingly, ecological concepts can be applied to understand the host-derived and microbial processes that govern the dynamics of the interactive networks within the holobiont. In marine systems, holobionts are further integrated into larger and more complex communities and ecosystems, a concept referred to as "nested ecosystems." In this review, we discuss the concept of holobionts as dynamic ecosystems that interact at multiple scales and respond to environmental change. We focus on the symbiosis of sponges with their microbial communities-a symbiosis that has resulted in one of the most diverse and complex holobionts in the marine environment. In recent years, the field of sponge microbiology has remarkably advanced in terms of curated databases, standardized protocols, and information on the functions of the microbiota. Like a Russian doll, these microbial processes are translated into sponge holobiont functions that impact the surrounding ecosystem. For example, the sponge-associated microbial metabolisms, fueled by the high filtering capacity of the sponge host, substantially affect the biogeochemical cycling of key nutrients like carbon, nitrogen, and phosphorous. Since sponge holobionts are increasingly threatened by anthropogenic stressors that jeopardize the stability of the holobiont ecosystem, we discuss the link between environmental perturbations, dysbiosis, and sponge diseases. Experimental studies suggest that the microbial community composition is tightly linked to holobiont health, but whether dysbiosis is a cause or a consequence of holobiont collapse remains unresolved. Moreover, the potential role of the microbiome in mediating the capacity for holobionts to acclimate and adapt to environmental change is unknown. Future studies should aim to identify the mechanisms underlying holobiont dynamics at multiple scales, from the microbiome to the ecosystem, and develop management strategies to preserve the key functions provided by the sponge holobiont in our present and future oceans.

A new collagenase enzyme of the marine sponge pathogen Pseudoalteromonas agarivorans NW4327 is uniquely linked with a TonB dependent receptor

The primary pathogen of the Great Barrier Reef sponge Rhopaloeides odorabile, recently identified as a novel strain (NW4327) of Pseudoalteromonas agarivorans, produced collagenase which degraded R. odorabile skeletal fibers. We now report the collagenase of P. agarivorans as a metalloprotease which required Ca²⁺ and Zn²⁺ as cofactors. The collagenase was a TonB dependent receptor (TBDR) having a carboxypeptidase regulatory like domain (CRLD) in the N-terminal along with an outer membrane (OM) channel superfamily domain. The genes for TBDR sub-components and collagenase formed one unified entity in the genome of P. agarivorans NW4327. This association of a collagenase with a TBDR distinguished it from all known functional collagenases till date and for the first time, established the enzymatic capability of TBDRs. Predicted TBDR model demonstrated only 15% identity with ferripyoverdin receptor and the CRLD displayed merely 24% identity with carboxypeptidase catalytic chain. Presence of signal peptide, lack of transmembrane helices, absence of N-terminal in the cytoplasmic side, extracellular localization and recovery from the culture supernatant implicated that the TBDR was secreted. Stronger binding of the collagenase with marine sponge type IV collagen than type I collagen, revealed through molecular docking, indicated higher specificity of the enzyme towards type IV collagen.

Excess labile carbon promotes the expression of virulence factors in coral reef bacterioplankton

Coastal pollution and algal cover are increasing on many coral reefs, resulting in higher dissolved organic carbon (DOC) concentrations. High DOC concentrations strongly affect microbial activity in reef waters and select for copiotrophic, often potentially virulent microbial populations. High DOC concentrations on coral reefs are also hypothesized to be a determinant for switching microbial lifestyles from commensal to pathogenic, thereby contributing to coral reef degradation, but evidence is missing. In this study, we conducted ex situ incubations to assess gene expression of planktonic microbial populations under elevated concentrations of naturally abundant monosaccharides (glucose, galactose, mannose, and xylose) in algal exudates and sewage inflows. We assembled 27 near-complete (>70%) microbial genomes through metagenomic sequencing and determined associated expression patterns through metatranscriptomic sequencing. Differential gene expression analysis revealed a shift in the central carbohydrate metabolism and the induction of metalloproteases, siderophores, and toxins in Alteromonas, Erythrobacter, Oceanicola, and Alcanivorax populations. Sugar-specific induction of virulence factors suggests a mechanistic link for the switch from a commensal to a pathogenic lifestyle, particularly relevant during increased algal cover and human-derived pollution on coral reefs. Although an explicit test remains to be performed, our data support the hypothesis that increased availability of specific sugars changes net microbial community activity in ways that increase the emergence and abundance of opportunistic pathogens, potentially contributing to coral reef degradation.

Pseudoalteromonas piratica sp. nov., a budding, prosthecate bacterium from diseased Montipora capitata, and emended description of the genus Pseudoalteromonas

A Gram-stain-negative, motile, rod-shaped bacterium designated OCN003T was cultivated from mucus taken from a diseased colony of the coral Montipora capitata in Kāne'ohe Bay, O'ahu, Hawai'i. Colonies of OCN003T were pale yellow, 1-3 mm in diameter, convex, smooth and entire. The strain was heterotrophic, strictly aerobic and strictly halophilic. Cells of OCN003T produced buds on peritrichous prosthecae. Growth occurred within the pH range of 5.5 to 10, and the temperature range of 14 to 39 °C. Major fatty acids were 16 : 1ω7c, 16 : 0, 18 : 1ω7c, 17 : 1ω8c, 12 : 0 3-OH and 17 : 0. Phylogenetic analysis of 1399 nucleotides of the 16S rRNA gene nucleotide sequence and a multi-locus sequence analysis of three genes placed OCN003T in the genus Pseudoalteromonas and indicated that the nearest relatives described are Pseudoalteromonas spongiae, P. luteoviolacea, P. ruthenica and P. phenolica(97-99 % sequence identity). The DNA G+C content of the strain's genome was 40.0 mol%. Based on in silico DNA-DNA hybridization and phenotypic differences from related type strains, we propose that OCN003T represents the type strain of a novel species in the genus Pseudoalteromonas, proposed as Pseudoalteromonas piratica sp. nov. OCN003T (=CCOS1042T=CIP 111189T). An emended description of the genus Pseudoalteromonas is presented.

Antimicrobial Potential of Bacteria Associated with Marine Sea Slugs from North Sulawesi, Indonesia

Nudibranchia, marine soft-bodied organisms, developed, due to the absence of a protective shell, different strategies to protect themselves against putative predators and fouling organisms. One strategy is to use chemical weapons to distract predators, as well as pathogenic microorganisms. Hence, these gastropods take advantage of the incorporation of chemical molecules. Thereby the original source of these natural products varies; it might be the food source, de novo synthesis from the sea slug, or biosynthesis by associated bacteria. These bioactive molecules applied by the slugs can become important drug leads for future medicinal drugs. To test the potential of the associated bacteria, the latter were isolated from their hosts, brought into culture and extracts were prepared and tested for antimicrobial activities. From 49 isolated bacterial strains 35 showed antibiotic activity. The most promising extracts were chosen for further testing against relevant pathogens. In that way three strains showing activity against methicillin resistant Staphylococcus aureus and one strain with activity against enterohemorrhagic Escherichia coli, respectively, were identified. The obtained results indicate that the sea slug associated microbiome is a promising source for bacterial strains, which hold the potential for the biotechnological production of antibiotics.

Mechanisms for Pseudoalteromonas piscicida-Induced Killing of Vibrios and Other Bacterial Pathogens

Pseudoalteromonas piscicida is a Gram-negative gammaproteobacterium found in the marine environment. Three strains of pigmented P. piscicida were isolated from seawater and partially characterized by inhibition studies, electron microscopy, and analysis for proteolytic enzymes. Growth inhibition and death occurred around colonies of P. piscicida on lawns of the naturally occurring marine pathogens Vibrio vulnificus, Vibrio parahaemolyticus, Vibrio cholerae, Photobacterium damselae, and Shewanella algae Inhibition also occurred on lawns of Staphylococcus aureus but not on Escherichia coli O157:H7 or Salmonella enterica serovar Typhimurium. Inhibition was not pH associated, but it may have been related to the secretion of a cysteine protease with strong activity, as detected with a synthetic fluorogenic substrate. This diffusible enzyme was secreted from all three P. piscicida strains. Direct overlay of the Pseudoalteromonas colonies with synthetic fluorogenic substrates demonstrated the activity of two aminopeptidase Bs, a trypsin-like serine protease, and enzymes reactive against substrates for cathepsin G-like and caspase 1-like proteases. In seawater cultures, scanning electron microscopy revealed numerous vesicles tethered to the outer surface of P. piscicida and a novel mechanism of direct transfer of these vesicles to V. parahaemolyticus Vesicles digested holes in V. parahaemolyticus cells, while the P. piscicida congregated around the vibrios in a predatory fashion. This transfer of vesicles and vesicle-associated digestion of holes were not observed in other bacteria, suggesting that vesicle binding may be mediated by host-specific receptors. In conclusion, we show two mechanisms by which P. piscicida inhibits and/or kills competing bacteria, involving the secretion of antimicrobial substances and the direct transfer of digestive vesicles to competing bacteria.IMPORTANCEPseudoalteromonas species are widespread in nature and reduce competing microflora by the production of antimicrobial compounds. We isolated three strains of P. piscicida and characterized secreted and cell-associated proteolytic enzymes, which may have antimicrobial properties. We identified a second method by which P. piscicida kills V. parahaemolyticus It involves the direct transfer of apparently lytic vesicles from the surface of the Pseudoalteromonas strains to the surface of Vibrio cells, with subsequent digestion of holes in the Vibrio cell walls. Enzymes associated with these vesicles are likely responsible for the digestion of holes in the cell walls. Pseudoalteromonas piscicida has potential applications in aquaculture and food safety, in control of the formation of biofilms in the environment, and in food processing. These findings may facilitate the probiotic use of P. piscicida to inactivate pathogens and may lead to the isolation of enzymes and other antimicrobial compounds of pharmacological value.

Streptomyces euryhalinus sp. nov., a new actinomycete isolated from a mangrove forest

A Gram-positive, aerobic, non-motile actinomycete (strain MS 3/20^T) was isolated from the sediment of the Sundarbans mangrove forest in India. On International Streptomyces Project (ISP) medium 2, the isolate produced yellowish brown to red aerial hyphae that carried spiny-surfaced spores in a retinaculum-apertum arrangement. Whole-cell hydrolysate of the strain contained LL-diaminopimelic acid and galactose. Predominant menaquinones were MK-9(H₈) and MK-9(H₆). Diagnostic polar lipids were glycolipid, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, unidentified phospholipid and unidentified amino lipid. The major fatty acids were anteiso-C_15:0 (17.53%), iso-C_16:0 (23.89%) and anteiso-C_17:0 (10.29%). The strain showed 100% 16S ribosomal RNA (rRNA) gene sequence similarity with Streptomyces variabilis NBRC 12825^T, Streptomyces erythrogriseus LMG 19406^T, Streptomyces griseoincarnatus LMG 19316^T and Streptomyces labedae NBRC 15864^T. However, strain MS 3/20^T could be distinguished from these and seven other closely related species based on low levels of DNA-DNA relatedness (27.2-53.8%), supported by the unique banding pattern obtained from random amplified polymorphic DNA-PCR amplification and the distinctive matrix-assisted laser desorption/ionization-time-of-flight/mass spectrometry (MALDI-TOF/MS) profile of whole-cell proteins acquired for strain MS 3/20^T in comparison with its phylogenetic relatives. Disparate morphological, physiological and chemotaxonomic features, principally growth in NaCl, further corroborated the distinction of strain MS 3/20^T from other phylogenetic relatives. Strain MS 3/20^T is therefore suggested to be a novel species of the genus Streptomyces, for which the name Streptomyces euryhalinus sp. nov. is proposed. The type strain is MS 3/20^T (=CICC 11032^T=DSM 103378^T).

Analysis of bacterial composition in marine sponges reveals the influence of host phylogeny and environment

Bacterial communities associated with sponges are influenced by environmental factors; however, some degree of genetic influence of the host on the microbiome is also expected. In this work, 16S rRNA gene amplicon sequencing revealed diverse bacterial phylotypes based on the phylogenies of three tropical sponges (Aplysina fulva, Aiolochroia crassa and Chondrosia collectrix). Despite their sympatric occurrence, the studied sponges presented different bacterial compositions that differed from those observed in seawater. However, lower dissimilarities in bacterial communities were observed within sponges from the same phylogenetic group. The relationships between operational taxonomic units (OTUs) recovered from the sponges and database sequences revealed associations among sequences from unrelated sponge species and sequences retrieved from diverse environmental samples. In addition, one Proteobacteria OTU retrieved from A. fulva was identical to sequences previously reported from A. fulva specimens collected along the Brazilian coast. Based on these results, we conclude that bacterial communities associated with marine sponges are shaped by host identity, while environmental conditions seem to be less important in shaping symbiont communities. This is the first study to assess bacterial communities associated with marine sponges in the remote St. Peter and St. Paul Archipelago using amplicon sequencing of the 16S rRNA gene.

New Genomic Insights into "Entotheonella" Symbionts in Theonella swinhoei: Mixotrophy, Anaerobic Adaptation, Resilience, and Interaction

“Entotheonella” (phylum “Tectomicrobia”) is a filamentous symbiont that produces almost all known bioactive compounds derived from the Lithistida sponge Theonella swinhoei. In contrast to the comprehensive knowledge of its secondary metabolism, knowledge of its lifestyle, resilience, and interaction with the sponge host and other symbionts remains rudimentary. In this study, we obtained two “Entotheonella” genomes from T. swinhoei from the South China Sea through metagenome binning, and used a RASTtk pipeline to achieve better genome annotation. The high average nucleotide index values suggested they were the same phylotypes as the two “Entotheonella” phylotypes from T. swinhoei from the Japan Sea. Genomic features related to utilization of various carbon sources, peptidase secretion, CO₂ fixation, sulfate reduction, anaerobic respiration, and denitrification indicated the mixotrophic nature of “Entotheonella.” The endospore-forming potential along with metal- and antibiotic resistance indicated “Entotheonella” was highly resilient to harsh conditions. The potential for endospore formation also explained the widespread distribution of “Entotheonella” to some extent. The discovery of Type II (general secretion pathway proteins and the Widespread Colonization Island) and Type VI secretion systems in “Entotheonella” suggested it could secrete extracellular hydrolases, form tight adhesion, act against phagocytes, and kill other prokaryotes. Overall, the newly discovered genomic features suggest “Entotheonella” is a highly competitive member of the symbiotic community of T. swinhoei.

Spotlight on Antimicrobial Metabolites from the Marine Bacteria Pseudoalteromonas: Chemodiversity and Ecological Significance

This review is dedicated to the antimicrobial metabolite-producing Pseudoalteromonas strains. The genus Pseudoalteromonas hosts 41 species, among which 16 are antimicrobial metabolite producers. To date, a total of 69 antimicrobial compounds belonging to 18 different families have been documented. They are classified into alkaloids, polyketides, and peptides. Finally as Pseudoalteromonas strains are frequently associated with macroorganisms, we can discuss the ecological significance of antimicrobial Pseudoalteromonas as part of the resident microbiota.

Snapshot of a Bacterial Microbiome Shift during the Early Symptoms of a Massive Sponge Die-Off in the Western Mediterranean

Ocean warming is affecting marine benthic ecosystems through mass mortality events that involve marine invertebrates, in particular bivalves, corals, and sponges. Among these events, extensive die-offs of Ircinia fasciculata sponges have been recurrently reported in western Mediterranean. The goal of our study was to test whether the temperature-related mass sponge die-offs were associated with or preceded by an early unbalanced bacterial microbiome in the sponge tissues. We took advantage of the early detection of disease and compared the microbiomes of healthy vs. early diseased I. fasciculata tissues. Our results showed a microbiome shift in early diseased tissues. The abundance of Gammaproteobacteria and Acidobacteria increased and that of Deltaproteobacteria decreased in diseased vs. healthy tissues. The change in community composition was also noticeable at the operational taxonomic unit (OTU) level. Diseased tissues contained more bacterial sequences previously identified in injured or stressed sponges and corals than healthy tissues. Bacterial diversity increased significantly in diseased tissues, which contained a higher number of low abundance OTUs. Our results do not support the hypothesis of one particular pathogen, whether a Vibrio or any other bacteria, triggering the Northwestern Mediterranean mass mortalities of I. fasciculata. Our data rather suggest an early disruption of the bacterial microbiome balance in healthy sponges through a shift in OTU abundances, and the purported consequent decline of the sponge fitness and resistance to infections. Opportunistic bacteria could colonize the sponge tissues, taking benefit of the sponge weakness, before one or more virulent pathogens might proliferate ending in the mass sponge die-off.

The Sponge Hologenome

A paradigm shift has recently transformed the field of biological science; molecular advances have revealed how fundamentally important microorganisms are to many aspects of a host’s phenotype and evolution. In the process, an era of “holobiont” research has emerged to investigate the intricate network of interactions between a host and its symbiotic microbial consortia. Marine sponges are early-diverging metazoa known for hosting dense, specific, and often highly diverse microbial communities. Here we synthesize current thoughts about the environmental and evolutionary forces that influence the diversity, specificity, and distribution of microbial symbionts within the sponge holobiont, explore the physiological pathways that contribute to holobiont function, and describe the molecular mechanisms that underpin the establishment and maintenance of these symbiotic partnerships. The collective genomes of the sponge holobiont form the sponge hologenome, and we highlight how the forces that define a sponge’s phenotype in fact act on the genomic interplay between the different components of the holobiont.

MALDI-TOF Mass Spectrometry Discriminates Known Species and Marine Environmental Isolates of Pseudoalteromonas

The genus Pseudoalteromonas constitutes an ecologically significant group of marine Gammaproteobacteria with potential biotechnological value as producers of bioactive compounds and of enzymes. Understanding their roles in the environment and bioprospecting for novel products depend on efficient ways of identifying environmental isolates. Matrix Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) biotyping has promise as a rapid and reliable method of identifying and distinguishing between different types of bacteria, but has had relatively limited application to marine bacteria and has not been applied systematically to Pseudoalteromonas. Therefore, we constructed a MALDI-TOF MS database of 31 known Pseudoalteromonas species, to which new isolates can be compared by MALDI-TOF biotyping. The ability of MALDI-TOF MS to distinguish between species was scrutinized by comparison with 16S rRNA gene sequencing. The patterns of similarity given by the two approaches were broadly but not completely consistent. In general, the resolution of MALDI-TOF MS was greater than that of 16S rRNA gene sequencing. The database was tested with 13 environmental Pseudoalteromonas isolates from UK waters. All of the test strains could be identified to genus level by MALDI-TOF MS biotyping, but most could not be definitely identified to species level. We conclude that several of these isolates, and possibly most, represent new species. Thus, further taxonomic investigation of Pseudoalteromonas is needed before MALDI-TOF MS biotyping can be used reliably for species identification. It is, however, a powerful tool for characterizing and distinguishing among environmental isolates and can make an important contribution to taxonomic studies.

Lipopolysaccharides from Commensal and Opportunistic Bacteria: Characterization and Response of the Immune System of the Host Sponge Suberites domuncula

Marine sponges harbor a rich bacterioflora with which they maintain close relationships. However, the way these animals make the distinction between bacteria which are consumed to meet their metabolic needs and opportunistic and commensal bacteria which are hosted is not elucidated. Among the elements participating in this discrimination, bacterial cell wall components such as lipopolysaccharides (LPS) could play a role. In the present study, we investigated the LPS chemical structure of two bacteria associated with the sponge Suberites domuncula: a commensal Endozoicomonas sp. and an opportunistic Pseudoalteromonas sp. Electrophoretic patterns indicated different LPS structures for these bacteria. The immunomodulatory lipid A was isolated after mild acetic acid hydrolysis. The electrospray ionization ion-trap mass spectra revealed monophosphorylated molecules corresponding to tetra- and pentaacylated structures with common structural features between the two strains. Despite peculiar structural characteristics, none of these two LPS influenced the expression of the macrophage-expressed gene S. domuncula unlike the Escherichia coli ones. Further research will have to include a larger number of genes to understand how this animal can distinguish between LPS with resembling structures and discriminate between bacteria associated with it.