Computational Methods Reveal a Series of Cyclic and Linear Lichenysins and Surfactins from the Vietnamese Marine Sediment-Derived Streptomyces Strain G222

The Streptomyces strain G222, isolated from a Vietnamese marine sediment, was confidently identified by 16S rRNA gene sequencing. Its AcOEt crude extract was successfully analyzed using non-targeted LC-MS/MS analysis, and molecular networking, leading to a putative annotation of its chemical diversity thanks to spectral libraries from GNPS and in silico metabolite structure prediction obtained from SIRIUS combined with the bioinformatics tool conCISE (Consensus Annotation Propagation of in silico Elucidations). This dereplication strategy allowed the identification of an interesting cluster of a series of putative cyclic and linear lipopeptides of the lichenysin and surfactin families. Lichenysins (3-7) were isolated from the sub-fraction, which showed significant anti-biofilm activity against Pseudomonas aeruginosa MUC-N1. Their structures were confirmed by detailed 1D and 2D NMR spectroscopy (COSY, HSQC, HMBC, TOCSY, ROESY) recorded in CD3OH, and their absolute configurations were determined using the modified Marfey's method. The isolated lichenysins showed anti-biofilm activity at a minimum concentration of 100 µM. When evaluated for antibacterial activity against a panel of Gram-positive and Gram-negative strains, two isolated lichenysins exhibited selective activity against the MRSA strain without affecting its growth curve and without membranotropic activity. This study highlights the power of the MS/MS spectral similarity strategy using computational methods to obtain a cross-validation of the annotated molecules from the complex metabolic profile of a marine sediment-derived Streptomyces extract. This work provides the first report from a Streptomyces strain of combined cyclic and linear lichenysins and surfactins, known to be characteristic compounds of the genus Bacillus.

Microplastics (≤ 10 μm) bioaccumulation in marine sponges along the Moroccan Mediterranean coast: Insights into species-specific distribution and potential bioindication

Microplastics (MPs) are pervasive in marine environments and widely recognized as emerging environmental pollutants due to the multifaceted risks they exert on living organisms and ecosystems. Sponges (Phylum Porifera) are essential suspension-feeding organisms that may be highly susceptible to MPs uptake due to their global distribution, unique feeding behavior, and sedentary lifestyle. However, the role of sponges in MP research remains largely underexplored. In the present study, we investigate the presence and abundance of MPs (≤10 μm size) in four sponge species, namely Chondrosia reniformis, Ircinia variabilis, Petrosia ficiformis, and Sarcotragus spinosulus collected from four sites along the Mediterranean coast of Morocco, as well as their spatial distribution. MPs analysis was conducted using an innovative Italian patented extraction methodology coupled with SEM-EDX detection. Our findings reveal the presence of MPs in all collected sponge specimens, indicating a pollution rate of 100%. The abundance of MPs in the four sponge species ranged from 3.95×105 to 1.05×106 particles per gram dry weight of sponge tissue, with significant differences observed among sampling sites but no species-specific differences. These results imply that the uptake of MPs by sponges is likely influenced by aquatic environmental pollution rather than the sponge species themselves. The smallest and largest MPs were identified in C. reniformis and P. ficiformis, with median diameters of 1.84 μm and 2.57 μm, respectively. Overall, this study provides the first evidence and an important baseline for the ingestion of small MP particles in Mediterranean sponges, introducing the hypothesis that they may serve as valuable bioindicators of MP pollution in the near future.

Assessment of the global toxicity of marine sediments from the Dakar peninsula (Senegal, West Africa)

Marine pollution in West Africa is major threat particularly around coastal megacities. We assess the chemical and ecotoxicological quality of the marine sediments in various submerged sampling sites of Dakar. Analysis revealed that sediments were slightly basic in which fine and coarse sands predominated. High percentages of total organic carbon were found sometime above 6%. Higher levels of heavy metal were reported than in previous studies. Chromium and nickel were above the Probable Effect Concentration. Low trophic level appeared not affected by the overall toxicity, while medium trophic level was more affected. Indeed, the vast majority (91%) of sites studied revealed a net percentage of Magallana gigas embryolarval developmental abnormality over 20%. The assessment of the global toxicity of marine sediments from the Dakar sites Studied (n = 11) seemed, almost, as a whole, to be in a poor ecotoxicological state calling to take measures to improve the sanitary condition of this marine feature.

Insights into bioaccumulation and bioconcentration of potentially toxic elements in marine sponges from the Northwestern Mediterranean coast of Morocco

The present research aimed to investigate the concentrations and patterns of six potentially toxic elements (PTEs) in three common sponge species collected along the Moroccan Mediterranean coast, as well as their levels in ambient seawater and sediments. Distinct inter-species variability in PTEs bioaccumulation was observed among the three species, suggesting that sponges have distinct selectivity for assimilating PTEs from the surrounding environment. C. crambe had a higher enrichment capacity for Cu, As, Cr and Ni, while P. ficiformis and C. reniformis exhibited the highest concentration of Cd and Pb, respectively. Interestingly, a similar spatial distribution patterns of PTEs was observed in the three media, with high values occurring in Tangier and Al-Hoceima locations. Overall, our results confirm that sponges reliably reflect the bioavailability of PTEs in their immediate environment, especially C. crambe, whose PTE tissue contents were highly and positively correlated with the contents of all PTEs in the sediments.

The Lipid A Structure from the Marine Sponge Symbiont Endozoicomonas sp. HEX 311

Endozoicomonas sp. HEX311 is a Gram-negative bacterium known to establish a commensal interaction with the marine demosponge Suberites domuncula. The molecular bases of the sponge-microbe interaction events are still poorly defined. Nevertheless, it has been proved that S. domuncula possesses an innate immune system with similarities to the mammalian one and is able to recognize the main component of the Gram-negative bacteria cell wall: the lipopolysaccharide. Whether this recognition occurs in a structure-dependent manner, which is typical for mammalian immune system receptors, is still under investigation. Herein, we report the Endozoicomonas sp. HEX311 lipid A structure obtained by a combination of data attained from chemical, MALDI MS, and MS² approaches. The lipid A is a complex family of species decorated by pyrophosphate and phosphate units and carrying (R)-3-hydroxydodecanoic acid, (R)-3-hydroxytetradecanonic acid, iso-2-hydroxyundecanoic acid, iso-(R)-3-hydroxyundecanoic acid, and iso-nonanoic acid as acyl chains.

The seminal receptacle and implications for reproductive processes in the invasive gastropod Crepidula fornicata

The calyptraeid gastropod Crepidula fornicata is the object of considerable research attention, due to its invasive status in the North-Eastern Atlantic, its introduction to habitats throughout the Northern hemisphere, and its scientific interest as a model organism for the study of developmental and reproductive processes in the Metazoa. Since the knowledge concerning the structural foundations for its reproductive processes is surprisingly weak, we investigated the seminal receptacle, a key structure in the reproductive biology of other metazoans, using histology, scanning electron and transmission electron microscopy. The seminal receptacle consists of 9-11 lobes, each subdivided into small, narrow lobules. The inner epithelium of the lobules appears to be highly dynamic, characterised by the perforation and attachment of received spermatozoa, the progressive degeneration of this epithelium, and the concomitant detachment of the spermatozoa. The allocation of spermatozoa to many different lobules, in different phases, may explain the extended reproductive season of C. fornicata, and thereby contribute to its colonizing and invasive success. The same compartmentalisation, as well as the complete covering of the inner epithelium of the lobules by spermatozoa and the large amount of spermatozoan debris in the lumina, suggest that the C. fornicata seminal receptacle may be a site of sperm competition in this polyandrous species.

Vibrio tapetis, the Causative Agent of Brown Ring Disease, Forms Biofilms with Spherical Components

Vibrio tapetis is a marine bacterium causing Brown Ring Disease (BRD) in the Manila clam Ruditapes philippinarum. V. tapetis biofilm formation remains unexplored depite the fact that it might be linked to pathogenicity. Our objectives were to characterize the in vitro biofilm formation of V. tapetis and evaluate the effects of culture conditions. Biofilm structure and its matrix composition were examined by confocal laser scanning microscopy and scanning electron microscopy. V. tapetis was able to form biofilms on a glass substratum within 24 h. Polysaccharides and extracellular DNA of the biofilm matrixes were differently distributed depending on the V. tapetis strains. Spherical components of about 1-2 μm diameter were found at the biofilm surface. They contain DNA, proteins, and seemed to be physically linked to bacteria and of cellular nature. Transmission electron microscopy showed that the spherical components were devoid of internal compartments. Temperatures >21°C inhibit BRD whereas low salinity (2%) favor it, none of the both conditions altered V. tapetis' ability to form biofilms in vitro. We suggest therefore that biofilm formation could play a role in the persistence of the pathogen in clam than in BRD symptoms.

Cellular effects of bacterial N-3-Oxo-dodecanoyl-L-Homoserine lactone on the sponge Suberites domuncula (Olivi, 1792): insights into an intimate inter-kingdom dialogue

Sponges and bacteria have lived together in complex consortia for 700 million years. As filter feeders, sponges prey on bacteria. Nevertheless, some bacteria are associated with sponges in symbiotic relationships. To enable this association, sponges and bacteria are likely to have developed molecular communication systems. These may include molecules such as N-acyl-_L-homoserine lactones, produced by Gram-negative bacteria also within sponges. In this study, we examined the role of N-3-oxododecanoyl-_L-homoserine lactone (3-oxo-C₁₂-HSL) on the expression of immune and apoptotic genes of the host sponge Suberites domuncula. This molecule seemed to inhibit the sponge innate immune system through a decrease of the expression of genes coding for proteins sensing the bacterial membrane: a Toll-Like Receptor and a Toll-like Receptor Associated Factor 6 and for an anti-bacterial perforin-like molecule. The expression of the pro-apoptotic caspase-like 3/7 gene decreased as well, whereas the level of mRNA of anti-apoptotic genes Bcl-2 Homolog Proteins did not change. Then, we demonstrated the differential expression of proteins in presence of this 3-oxo-C₁₂-HSL using 3D sponge cell cultures. Proteins involved in the first steps of the endocytosis process were highlighted using the 2D electrophoresis protein separation and the MALDI-TOF/TOF protein characterization: α and β subunits of the lysosomal ATPase, a cognin, cofilins-related proteins and cytoskeleton proteins actin, α tubulin and α actinin. The genetic expression of some of these proteins was subsequently followed. We propose that the 3-oxo-C₁₂-HSL may participate in the tolerance of the sponge apoptotic and immune systems towards the presence of bacteria. Besides, the sponge may sense the 3-oxo-C₁₂-HSL as a molecular evidence of the bacterial presence and/or density in order to regulate the populations of symbiotic bacteria in the sponge. This study is the first report of a bacterial secreted molecule acting on sponge cells and regulating the symbiotic relationship.

Matrix-mediated canal formation in primmorphs from the sponge Suberites domuncula involves the expression of a CD36 receptor-ligand system

Sponges (Porifera), represent the phylogenetically oldest metazoan phylum still extant today. Recently, molecular biological studies provided compelling evidence that these animals share basic receptor/ligand systems, especially those involved in bodyplan formation and in immune recognition, with the higher metazoan phyla. An in vitro cell/organ-like culture system, the primmorphs, has been established that consists of proliferating and differentiating cells, but no canals of the aquiferous system. We show that after the transfer of primmorphs from the demosponge Suberites domuncula to a homologous matrix (galectin), canal-like structures are formed in these 3D-cell aggregates. In parallel with the formation of these structures a gene is expressed whose deduced protein falls into the CD36/LIMPII receptor family. The receptor was cloned and found to be strongly expressed after adhesion to the galectin matrix. This process was suppressed if primmorphs were co-incubated with a homologous polypeptide containing the CSVTCG domain, as found in thrombospondin-1 (and related) molecules of vertebrates. In situ hybridization studies revealed that the S. domuncula CD36/LIMPII receptor is localized in the pinacocytes that surround the canals of the sponge. Furthermore, a secondary metabolite from a sponge-associated bacterium was isolated and characterized, the 2-methylthio-1,4-naphthoquinone (MTN). MTN causes inhibition of cell proliferation of vertebrate tumor cells at concentrations of >80 ng/ml. However, doses of only 2 ng are required to potently inhibit angiogenesis in the chick chorio-allantoic membrane assay. At concentrations of 10 ng/ml this compound was also found to suppress the expression of the S. domuncula CD36/LIMPII; this result is a first indication that this secondary metabolite has a conserved functional activity: the suppression of the formation of the circulation system, from sponges to vertebrates.

Application of a MTT assay for screening nutritional factors in growth media of primary sponge cell culture

Marine sponges (Porifera) are producers of the largest variety of bioactive compounds among benthic marine organisms. In vitro culture of marine sponge cells has been proposed for the sustainable production of these pharmacologically interesting compounds from marine sponges but with limited success. The development of a suitable growth medium is an essential prerequisite for sponge cells grown in vitro. The MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay was adapted to screen for potential nutritional factors in formulating a growth medium for primary cell culture of Suberites domuncula. In 96-well plates, the effects of nutritional factors including glutamine, pyruvate, iron citrate, silicon, RPMI 1640, and Marine Broth 2216 on the viable cell density were examined in primary cell culture of S. domuncula 36 h after inoculation. Ferric iron (Fe(3+)) and pyruvate were found to significantly improve cell viability in a dose-dependent manner. Silicon and glutamine showed limited improvements at certain concentrations. The supplement of RPMI 1640 and Marine Broth 2216 did not increase cell viability. As a result, several improved media able to maintain higher cell viability in a short-term culture of primary sponge cells could be formulated.

Sustainable production of bioactive compounds by sponges--cell culture and gene cluster approach: a review

Sponges (phylum Porifera) are sessile marine filter feeders that have developed efficient defense mechanisms against foreign attackers such as viruses, bacteria, or eukaryotic organisms. Protected by a highly complex immune system, as well as by the capacity to produce efficient antiviral compounds (e.g., nucleoside analogues), antimicrobial compounds (e.g., polyketides), and cytostatic compounds (e.g., avarol), they have not become extinct during the last 600 million years. It can be assumed that during this long period of time, bacteria and microorganisms coevolved with sponges, and thus acquired a complex common metabolism. It is suggested that (at least) some of the bioactive secondary metabolites isolated from sponges are produced by functional enzyme clusters, which originated from the sponges and their associated microorganisms. As a consequence, both the host cells and the microorganisms lost the ability to grow independently from each other. Therefore, it was--until recently--impossible to culture sponge cells in vitro. Also the predominant number of "symbiotic bacteria" proved to be nonculturable. In order to exploit the bioactive potential of both the sponge and the "symbionts," a 3D-aggregate primmorph culture system was established; also it was proved that one bioactive compound, avarol/avarone, is produced by the sponge Dysidea avara. Another promising way to utilize the bioactive potential of the microorganisms is the cloning and heterologous expression of enzymes involved in secondary metabolism, such as the polyketide synthases.

Biochemistry and cell biology of silica formation in sponges

The main inorganic material forming the skeletal elements in Demospongiae as well as in Hexactinellida, the spicules, is amorphous silica. The spicules occur in the cytoplasm and the extracellular space and also in the nucleus (as silicate crystals) of some sponge cells; the function in the latter compartment is unknown. Recent evidence shows that the formation of spicules is mediated by the enzyme silicatein. The cDNA as well as the gene encoding this enzyme was cloned from Suberites domuncula. The recombinant silicatein catalyzes the synthesis of amorphous silicate using tetraethoxysilane as substrate. The enzyme is dependent on ferric iron. Silicatein also has proteolytic (cathepsin-like) activity. Incubation of primmorphs, a special form of 3D-cell aggregates, with silicon resulted in a strong increase of their size from 1-7 mm to approximately 10 mm. The morphogenetic activity of silicate is underscored by the finding that this ion increases gene expression of silicatein and collagen. Based on these findings, it is concluded that both iron and silicate stimulate the activity of silicatein. Furthermore, it is proposed that the growing spicules are surrounded by the scavenger receptor which might be considered as a docking molecule for the collagen matrix into which the spicules are embedded.

Demonstration of nutrient pathway from the digestive system to oocytes in the gonad intestinal loop of the scallop Pecten maximus L

The mechanism of nutrient transfer from the digestive system to the gonad acini and developing oocytes was investigated in the gonad-intestinal loop system of the queen scallop Pecten maximus L. Ferritin was injected directly into the purged intestine of specimens from the wild. Subsequently, a histochemical reaction and transmission electron microscopy were used to localize ferritin in various cell types. Ferritin was rapidly absorbed by the intestinal epithelium, and then appeared in hemocytes in the surrounding connective tissue. In the hemocytes, ferritin was stored in variously sized inclusions, as well as in the general cytoplasm. In all sections examined for the 12 experimental individuals, hemocytes were always found in association with connective tissue fibers extending from the base of the intestinal epithelium to gonad acini. After 30-min incubation, ferritin appeared inside the acini of all individuals. Ferritin-bearing cells were rarely found in association with male acini or gametes, nor with mature female gametes, but often with developing female gametes. Not all individuals showed the same temporal dynamics of ferritin transport, suggesting that nutrient transfer to oocytes is either not a continuous process, or that among individuals, transfer is not synchronized on short time scales. This is the first demonstration of a pathway of nutrient transfer from the intestine, and more generally the digestive system, to developing oocytes in the Bivalvia.

Induction of glutathione-S-transferases in primary cultured digestive gland acini from the mollusk bivalve Pecten maximus (L.): application of a new cellular model in biomonitoring studies

In the last three decades, marine invertebrates have been used to monitor environmental health conditions and potential pollution, e.g. in the Mussel Watch Program. The whole animal or specific organs are used to determine contamination levels and disturbances. In the present study, a new in vitro cell culture model was validated for pollution monitoring. A commercial species, the scallop Pecten maximus, was tested for the presence and induction of phase II glutathione-S-transferase (GST) enzymes. These activities were monitored for a year, and the results were found to be consistent with those in the literature. Tributyltin, ethylmethane sulfonate and the water-soluble fraction of crude oil were assayed in, in vitro induction studies. A rapid increase of GST activities was observed within 24 h with all compounds tested, and a time- as well as a dose-response was established. This in vitro cell culture model seems suitable for routine use to predict the effects of pollutants on whole organisms within an ecosystem and in fisheries.

Origin of metazoan stem cell system in sponges: first approach to establish the model (Suberites domuncula)

It is established that Porifera (sponges) represent the earliest phylum which branched off from the common ancestor of all multicellular animals, the Urmetazoa. In the present study, the hypothesis is tested if, during this transition, pluripotent stem cells were formed which are provided-similar to the totipotent cells (archaeocytes/germ cells)-with a self-renewal capacity. As a model system, primmorphs from the sponge Suberites domuncula were used. These 3D-cell aggregates were cultivated in medium (RPMI 1640/seawater) either lacking silicate and ferric iron or in medium which was supplemented with these 'morphogenetic' factors. As molecular markers for the potential existence of stem cells in primmorphs, two genes which encode proteins found in stem cells of higher metazoan species, were cloned from S. domuncula. First, the noggin gene, which is present in the Spemann organizer of amphibians and whose translation product acts during the formation of dorsal mesoderm derivatives. The second gene encodes the mesenchymal stem cell-like protein. Both cDNAs were used to study their expression in primmorphs in dependence on the incubation conditions. It was found that noggin expression is strongly upregulated in primmorphs kept in the presence of silicate and ferric iron, while the expression of the mesenchymal stem cell-like protein was downregulated. These data are discussed with respect to the existence of stem cells in sponges.

Cultivation of primmorphs from the marine sponge Suberites domuncula: morphogenetic potential of silicon and iron

Marine demosponges (phylum Porifera) are rich sources for potent bioactive compounds. With the establishment of the primmorph system from sponges, especially from Suberites domuncula, the technology to cultivate sponge cells in vitro improved considerably. This progress was possible after the elucidation that sponges are provided with characteristic metazoan cell adhesion receptors and extracellular matrix molecules which allow their cells a positioning in a complex organization pattern. This review summarizes recent data on the cultivation of sponges in aquaria and--with main emphasis--of primmorphs in vitro. It is outlined that silicon and Fe(+++) contribute substantially to the formation of larger primmorphs (size of 10 mm) as well as of a canal system in primmorphs; canals are probably required for an improved oxygen and food supply. We conclude that the primmorph system will facilitate a sustainable use of sponges in the production of bioactive compounds; it may furthermore allow new and hitherto not feasible insights into basic questions on the origin of Metazoa.

Molecular analysis of the seasonal expression of genes coding for different functional markers of the digestive gland of the bivalve mollusk Pecten maximus (L.)

Digestive gland cells of Pecten maximus accumulate and release lipid storage according to a seasonal cycle. For the first time in molluscs, molecular probes were developed and applied to monitor the lipid accumulation and consumption cycle related to phytoplankton blooms and phenomena of cellular proliferation and apoptosis. The molecular probes consisted of glyceraldehyde-3-phosphate dehydrogenase (GPD), which is involved in the acetylation of fatty acids; aldolase, which favours the formation of pyruvate and dihydroxyacetone; actin, an essential element of the cytoskeleton that disappears during adipocyte cell transformation; and cycline B, an ubiquitous cell cycle protein. Alpha-amylase, provided by IFREMER-Brest (France), was used to relate these different events to the animal's food supply. A positive relation between GPD and aldolase gene expressions was inversely correlated with that of actin, confirming results in mammals. In P. maximus, mRNA transcripts of GPD and aldolase decrease rapidly before gamete emissions whereas those of actin increase rapidly. After gamete emission, the mRNA levels of aldolase, GPD and alpha-amylase increase, while those of actin decrease. Cycline B mRNA transcripts indicate that the period of digestive cell proliferation is initiated during winter, prior to the release of lipids into the digestive tract and apoptosis.