Metagenomic approaches to exploit the biotechnological potential of the microbial consortia of marine sponges

Natural products isolated from sponges are an important source of new biologically active compounds. However, the development of these compounds into drugs has been held back by the difficulties in achieving a sustainable supply of these often-complex molecules for pre-clinical and clinical development. Increasing evidence implicates microbial symbionts as the source of many of these biologically active compounds, but the vast majority of the sponge microbial community remain uncultured. Metagenomics offers a biotechnological solution to this supply problem. Metagenomes of sponge microbial communities have been shown to contain genes and gene clusters typical for the biosynthesis of biologically active natural products. Heterologous expression approaches have also led to the isolation of secondary metabolism gene clusters from uncultured microbial symbionts of marine invertebrates and from soil metagenomic libraries. Combining a metagenomic approach with heterologous expression holds much promise for the sustainable exploitation of the chemical diversity present in the sponge microbial community.     

Organ-specific distribution of dietary alkaloids in the marine opisthobranch Tylodina perversa

Specimens of the opisthobranch Tylodina perversa that were observed while feeding on the sponge Aplysina aerophoba were transferred to seawater tanks along with their prey and kept under controlled conditions. After one week the opisthobranchs were anaesthetized, dissected and studied for sequestered sponge-derived brominated alkaloids. All parts of T. perversa analyzed including feces, mucus and egg masses that had been produced during captivity contained alkaloids derived from A. aerophoba. The highest total alkaloid concentration (24.6 mg g⁻¹ dry wt) was found in mantles of T. perversa (compared to 51.2 mg g⁻¹ dry wt of total alkaloids in A. aerophoba). Hepatopancreas, egg masses and mucus (respective total alkaloid concentrations ranging from 20.4 to 12.5 mg g⁻¹ dry wt) were also rich in alkaloids. Whereas in A. aerophoba the isoxazoline alkaloids aerophobin-2 and isofistularin-3 were present in almost equal concentrations, aerophobin-2 constituted by far the major alkaloid (amounting to approximately 70% of all identified alkaloids) in mantles, mucus and egg masses of T. perversa, indicating selective sequestration by the opisthobranchs. Mantles as well as mucus also contained appreciable concentrations (approximately 20% of all identified compounds) of the brominated alkaloid aerothionin; this is not detected in A. aerophoba. It is possible that aerothionin originates from a previous encounter of T. perversa with the sponge A. cavernicola, the latter being closely related to A. aerophoba. The enrichment of aerophobin-2 (and of aerothionin) in mantles, mucus and egg masses that are vulnerable and exposed (mantles and egg masses) to predators and/or pathogens argues for defensive functions of the respective alkaloids even though this hypothesis still needs to be experimentally corroborated.     

Evaluation of single and joint effect of metabolites isolated from marine sponges,Fasciospongia cavernosa and Axinella donnani on antimicrobial properties

The biochemical mechanisms that marine sponges have developed as a chemical defense to protect themselves against micro and subsequent macrobiofouling process might comprise a potential alternative for the preventing attack of biofilm forming bacteria. The present study investigated the antimicrobial activity of a series of major secondary metabolites isolated from the sponges Fasciospongia cavernosa and Axinella donnani against fouling bacteria. Secomanoalide (1), dehydromanoalide (2) and cavernosine (3) have been isolated from F. cavernosa. Their structures were determined by MS, ¹H NMR spectra analyses and by comparison with those reported in the literature. The most promising activity was exhibited by the metabolites from A. donnani, that is, cerebroside (5) against three strains Aeromonas hydrophila subsp. salmonicida A449 and Erythrobacter litoralis. Our investigation revealed that combined metabolites 1, 2 and 3 retained strong activity but individual metabolite had moderate activity indicating that activity probably results from synergistic interactions between multiple compounds. The antibacterial screening of compounds 3, 5 and synergistic effect of 1–3 against fouling bacteria has been studied for the first time. Further, isolation of manoalide related compounds and their synergistic screening can be accelerated for the development of new biofilm inhibitors.     

Biomedicinals from the phytosymbionts of marine invertebrates: a molecular approach

Marine invertebrate animals such as sponges, gorgonians, tunicates and bryozoans are sources of biomedicinally relevant natural products, a small but growing number of which are advancing through clinical trials. Most metazoan and anthozoan species harbour commensal microorganisms that include prokaryotic bacteria, cyanobacteria (blue-green algae), eukaryotic microalgae, and fungi within host tissues where they reside as extra- and intra-cellular symbionts. In some sponges these associated microbes may constitute as much as 40% of the holobiont volume. There is now abundant evidence to suggest that a significant portion of the bioactive metabolites thought originally to be products of the source animal are often synthesized by their symbiotic microbiota. Several anti-cancer metabolites from marine sponges that have progressed to pre-clinical or clinical-trial phases, such as discodermolide, halichondrin B and bryostatin 1, are thought to be products derived from their microbiotic consortia. Freshwater and marine cyanobacteria are well recognised for producing numerous and structurally diverse bioactive and cytotoxic secondary metabolites suited to drug discovery. Sea sponges often contain dominant taxa-specific populations of cyanobacteria, and it is these phytosymbionts (= photosymbionts) that are considered to be the true biogenic source of a number of pharmacologically active polyketides and nonribosomally synthesized peptides produced within the sponge. Accordingly, new collections can be pre-screened in the field for the presence of phytobionts and, together with metagenomic screening using degenerate PCR primers to identify key polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) genes, afford a biodiscovery rationale based on the therapeutic prospects of phytochemical selection. Additionally, new cloning and biosynthetic expression strategies may provide a sustainable method for the supply of new pharmaceuticals derived from the uncultured phytosymbionts of marine organisms.     

Tributyltin-resistant marine bacteria: a summary of recent work

Summary A tributyltin chloride (TBTCl)-resistant bacterium,Alteromonas sp. M-1, was isolated from coastal seawater. This bacterium grew in medium containing 125 M TBTCl. TBTCl added to the medium was taken up by this bacterium, however, the amount of TBTCl in the cellular fraction was low after the logarithmic phase, suggesting the existence of a TBTCl-efflux system. A genetic library was constructed using plasmid vector pUC 19. Three positive clones were obtained, by whichE. coli was transformed to TBTCl resistance. Of the three clones, the shortest fragment fromHindIII-library was analyzed. This fragment was 1.8 kb long and contained one complete open reading frame. The predicted amino acid sequence of this open reading frame had a homologous domain to transglycosylases of bacteriophage andE. coli. TBTCl-tolerant marine bacteria other thanAlteromonas sp. M-1 were obtained from natural seawater to which TBTCl was added. DNA-DNA hybridization was performed between the three cloned fragments fromAlteromonas sp. M-1 and chromosomal DNA of the TBTCl-tolerant bacteria. Some strains hybridized with the fragments and some did not, suggesting that several genes are responsible for TBTCl tolerance.     

Carbon mass balance methodology to characterize the growth of pigmented marine bacteria under conditions of light cycling

A carbon mass balance methodology employing minimal measurements was applied to heterotrophic and photoheterotrophic marine bacteria grown under constant dilution and exposed to 12-h intervals of light or darkness. Carbon mass balance calculations using measurements taken every 3 h closed to within 93–103% using dissolved organic carbon, biomass carbon and CO₂ production data only, indicating that background interference from dissolved inorganic carbon variations in the amended seawater medium was not significant. Neither strain was observed to sustain a net CO₂ fixation using paramagnetic measurement of oxygen uptake rates (OUR), indicating a need for more sensitive on-line measurement techniques for OUR. Photoheterotrophic growth demonstrated lower carbon-mole biomass yields (0.41±0.026 vs. 0.64±0.013 mol mol^–1) despite higher specific glucose uptake rates (0.025 vs. 0.02 mol mol^–1 h^–1), suggesting that bioreactor-based study of marine bacteria can present growth modes that are different from those encountered in the marine environment.     

Antimicrobial activity of marine bacteria associated with sponges from the waters off the coast of South East India

Seventy-five marine bacterial strains associated with four species of sponges (Echinodictyum sp., Spongia sp., Sigmadocia fibulatus and Mycale mannarensis) were isolated from the Tuticorin coast, Gulf of Mannar region. The agar-overlay method was used to screen for antibiotic production by these strains against four bacteria, viz., Bacillus subtilis, Escherichia coli, Vibrio parahaemolyticus, and Vibrio harveyi and one fungal pathogen, viz., Candida albicans. Twenty-one per cent of the bacterial strains were found to be antibiotic producers and their activities ranged from broad spectral to species specific. A strain coded SC3 was found to be highly potent and was mass cultured. The ethyl acetate extract of the culture broth was further fractionated by reverse phase HPLC and the active fraction identified. In addition, SC3 was subjected to morphological and physiological characterization. The results of the tests showed SC3 to be a Gram-positive rod, sporulating, motile, catalase and oxidase positive. Phylogenetic analysis based on comparative analysis of sequenced 16s rRNA of the active strains indicated a preponderance of bacteria belonging to Vibrio and Bacillus genera with 95-99% sequence similarities. To our knowledge this is the first report on phylogenetic identification of antibiotic producing bacteria associated with sponges from Indian waters.     

A solid phase extraction based non-disruptive sampling technique to investigate the surface chemistry of macroalgae

The surface chemistry of aquatic organisms determines their biotic interactions. Metabolites in the spatially limited laminar boundary layer mediate processes, such as antifouling, allelopathy and chemical defense against herbivores. However, very few methods are available for the investigation of such surface metabolites. An approach is described in which surfaces are extracted by means of C18 solid phase material. By powdering wet algal surfaces with this material, organic compounds are adsorbed and can be easily recovered for subsequent liquid chromatography/mass spectrometry (LC/MS) and gas chromatography/mass spectrometry (GC/MS) investigations. The method is robust, picks up metabolites of a broad polarity range and is easy to handle. It is more universal compared to established solvent dipping protocols and it does not cause damage to the test organisms. A protocol is introduced for the macroalgae Fucus vesiculosus, Caulerpa taxifolia and Gracilaria vermiculophylla, but it can be easily transferred to other aquatic organisms.     

Polyenoic fatty acid isomerase from the marine alga Ptilota filicina: protein characterization and functional expression of the cloned cDNA

The recently described enzyme, polyenoic fatty acid isomerase (PFI), from the marine alga Ptilota filicina J. Argardh has been analyzed with respect to its protein structure and an associated cofactor. The enzyme was purified to homogeneity (as judged by SDS-PAGE and silver staining). By sedimentation equilibrium ultracentrifugation the mass of the native enzyme was estimated to be 125 kDa. The N-terminal peptide sequence derived from this protein was used to isolate two very similar cDNA clones encoding novel 500-amino acid proteins, both with calculated molecular masses of 55.9 kDa and pIs of 4.87. The data predict translation of a preprotein containing a signal peptide of 21 amino acids that is removed during maturation. Deglycosylation assays demonstrate that native PFI from P. filicina is a glycoprotein. The purified protein is chromophoric with a flavin-like UV spectrum and sequence analysis reveals the presence of a flavin-binding motif near the mature N-terminus. Heterologous expression of active PFI in Arabidopsis, using one of the cDNA clones, was successful as evidenced by conversion of arachidonic acid to a conjugated triene in an in vitro assay of the transgenic plant tissues.     

海洋细菌SSQ500的鉴定及其发酵产物抗肿瘤作用机制研究

[目的]对具有抗肿瘤活性的海洋细菌SSQ500进行分类鉴定,初步探讨其发酵产物的抗肿瘤作用机制.[方法]通过菌株的形态学观察、生理生化特征检测和16S rDNA序列分析及系统发育分析,以确定菌株的分类.不同浓度的活性物质作用于肿瘤细胞不同时间后收集细胞,流式细胞术分析人肝癌细胞(SMMC-7721)凋亡比例,检测Caspase3、Caspase8蛋白的表达.[结果]初步鉴定菌株SSQ500属于粘球菌属(Myxococcaceae sp.).该菌株发酵产物能诱导SMMC-7721凋亡,上调Caspase3、Caspase8蛋白的表达.[结论]SSQ500属于粘球菌属,其发酵产物的抗肿瘤作用机制为诱导肿瘤细胞凋亡,可能与上调Caspase3、Caspase8蛋白的表达有关.     

不同pH和盐度下海洋细菌对赤潮藻生长和产毒的影响

研究了在可控生态条件下。一株分离自厦门西海域沉积物的海洋细菌S10在不同pH和盐度条件下对赤潮原因种塔玛亚历山大藻(Alexandrium tamarense)生长和产毒的影响．结果表明。实验用藻株适宜生长pH为6～8,适宜盐度为20～34;该藻株在不同pH及不同盐度条件下,藻细胞毒力差异显著,且随着pH升高而下降。随着盐度增加而加大,到盐度为30时达到最高值。然后逐渐下降;菌株Sl0(1．02×10^l0cells·ml^-1)在pH7～9和盐度15～34下均能有效抑藻生长和产毒。且在pH7、盐度34时其抑藻生长作用最强;在pH7时抑藻产毒效果较好,且其抑藻产毒作用强度不随盐度变化而异．     

A rapid method for the isolation of eicosapentaenoic acid-producing marine bacteria

Bacterial production of long chain polyunsaturated fatty acids (LC-PUFAs) is a promising biotechnological approach for the mass production of these valuable compounds, but extensive screening is currently needed to select a strain that meets industrial requirements.A method was developed for the rapid screening and isolation of eicosapentaenoic acid (EPA)-producing marine bacteria from mixed cultures using the dye 2,3,5-triphenyltetrazolium chloride (TTC). The method was first validated using two bacteria from the Shewanella genus, S. gelidimarina (known to contain EPA) and S. fidelis (known not to contain EPA), and subsequently applied to a range of bacterial samples collected from seven randomly selected New Zealand fish species.By incorporating TTC in both solid and liquid state fermentation treatments, a clear association between the reduction of TTC to the red-coloured triphenyl formazan (TF) and the presence of EPA within Gram-negative bacteria was confirmed. Incubation in 0.1% w/v TTC was optimal for colour response and cell growth in agar plates and liquid cultures. Bacteria that produce EPA reduced TTC to TF, but a number of non-EPA-producing bacteria also showed this capacity. By conducting a subsequent Gram staining, all EPA-producing strains were revealed to be G (−) rod bacteria while the non-producing ones were all G (+) cocci. The fatty acid methyl esters of the isolated bacteria that reduced TTC to TF were analysed using gas chromatography-mass spectrometry and the content of EPA was confirmed by gas chromatography.From a pool of 2.0 × 10⁸ CFU/ml, this method allowed the rapid isolation of 16 bacteria capable of producing EPA. This new approach significantly reduces the number of samples submitted for GC analysis and therefore the time, effort and cost of screening and isolating strains of EPA-producing marine bacteria.     

Metagenomic approach for the isolation of a novel low-temperature-active lipase from uncultured bacteria of marine sediment

A novel lipase was isolated from a metagenomic library of Baltic Sea sediment bacteria. Prokaryotic DNA was extracted and cloned into a copy control fosmid vector (pCC1FOS) generating a library of >7000 clones with inserts of 24-39 kb. Screening for clones expressing lipolytic activity based on the hydrolysis of tributyrin and p-nitrophenyl esters, identified 1% of the fosmids as positive. An insert of 29 kb was fragmented and subcloned. Subclones with lipolytic activity were sequenced and an open reading frame of 978 bp encoding a 35.4-kDa putative lipase/esterase h1Lip1 (DQ118648) with 54% amino acid similarity to a Pseudomonas putida esterase (BAD07370) was identified. Conserved regions, including the putative active site, GDSAG, a catalytic triad (Ser148, Glu242 and His272) and a HGG motif, were identified. The h1Lip1 lipase was over expressed, (pGEX-6P-3 vector), purified and shown to hydrolyse p-nitrophenyl esters of fatty acids with chain lengths up to C14. Hydrolysis of the triglyceride derivative 1,2-di-O-lauryl-rac-glycero-3-glutaric acid 6'-methylresorufin ester (DGGR) confirmed that h1Lip1 was a lipase. The apparent optimal temperature for h1Lip1, by hydrolysis of p-nitrophenyl butyrate, was 35 degrees C. Thermal stability analysis showed that h1Lip1 was unstable at 25 degrees C and inactivated at 40 degrees C with t1/2 <5 min.     

Modification at the C9 position of the marine natural product isoaaptamine and the impact on HIV-1, mycobacterial, and tumor cell activity

As part of an investigation to generate optimized drug leads from marine natural pharmacophores for the treatment of neoplastic and infectious diseases, a series of novel isoaaptamine analogs were prepared by coupling acyl halides to the C9 position of isoaaptamine (2) isolated from the Aaptos sponge. This library of new semisynthetic products was evaluated for biological activity against HIV-1, Mtb, AIDS-OI, tropical parasitic diseases, and cancer. Compound 4 showed potent activity against HIV-1 (EC₅₀ 0.47 μg/mL), compound 19 proved to possess remarkable activity against Mycobacterium intracellulare with an IC₅₀ and MIC value of 0.15 and 0.31 μg/mL, while compounds 4 and 17 possessed anti-leishmanial activity with IC₅₀ values of 0.1 and 0.4 μg/mL, respectively. Compounds 16 and 17 showed antimalarial activity with EC₅₀ values of 230 and 240 ng/mL, respectively, and compound 14 exhibited an EC₅₀ of 0.05 μM against the Leukemia cell line K-562.     

The occurrence of denitrifying colourless sulphur-oxidising bacteria in marine waters and sediments as shown by the agar shake technique

Abstract The agar shake technique has been tested for the enumeration and isolation of bacteria involved in the anaerobic oxidation of reduced sulphur compounds. High numbers of colony forming units were observed from regions rich in sulphide, and the numbers of these forms were sometimes significantly correlated with the number of sulphate-reducing bacteria. The isolates could oxidise not only thiosulphate but also sulphide in liquid medium at the expense of nitrate. Addition of 1 mM glucose to the medium enhanced the rate and amount of thiosulphate oxidised by many of the isolates. Hence the use of the agar shake technique is recommended for the study of these little known facultatively or even obligately chemolithotrophic bacteria involved in the anaerobic oxidation of reduced inorganic sulphur compounds in the marine and estuarine environment.     

Antibiotic production by the marine photosynthetic bacterium Chromatium purpuratum NKPB 031704: localization of activity to the chromatophores

Abstract Over 200 strains of marine purple photosynthetic bacteria were isolated. Two strains showed antibiotic activity towards Saccharomyces cerevisiae and were tentatively identified as Chromatium purpuratum . Crude antibiotic, prepared by solvent extraction, showed a broad antimicrobial spectrum. The highest activity was found in the chromatophore fraction. Chromatographic separation of purified light harvesting complex from one strain, NKPB 031704, showed the presence of two separate pigmented compounds which were responsible for antimicrobial activity. Our findings reveal the unexpected ability of photosynthetic bacteria to produce broad spectrum antibiotics. In addition, this is the first example of intracellular localization of antibiotic activity in a marine bacterium.     

Synthesis and antimicrobial activity of small cationic amphipathic aminobenzamide marine natural product mimics and evaluation of relevance against clinical isolates including ESBL–CARBA producing multi-resistant bacteria

A library of small aminobenzamide derivatives was synthesised to explore a cationic amphipathic motif found in marine natural antimicrobials. The most potent compound E23 displayed minimal inhibitory concentrations (MICs) of 0.5–2 μg/ml against several Gram-positive bacterial strains, including methicillin resistant Staphylococcus epidermidis (MRSE). E23 was also potent against 275 clinical isolates including Staphylococcus aureus, Enterococcus spp., Escherichia coli, Pseudomonas aeruginosa, and Klebsiella pneumoniae, as well as methicillin-resistant S. aureus (MRSA), vancomycin-resistant enterococci (VRE), and ESBL–CARBA producing multi-resistant Gram-negative bacteria. The study demonstrates how structural motifs found in marine natural antimicrobials can be a valuable source for making novel antimicrobial lead-compounds.     

Synthesis and evaluation of anti-inflammatory activity of derivatives of the marine natural products fuscol and eunicol

The octocoral-derived terpenes fuscol and eunicol are known, potent anti-inflammatory agents. While total syntheses of one of the parent natural products have been published, the economic and practical feasibility of producing commercially viable amounts of material is very low. Based on the observation that the characteristic dienol of fuscol, eunicol and related compounds is conserved in anti-inflammatory activity, this project aimed to remove the structural complexity of the substituted cyclohexane and cyclodecadiene of fuscol and eunicol, respectively. The synthesis of a small panel of structurally simpler fuscol/eunicol analogues was completed and five of the six new compounds were found to have slightly superior activity to the parent natural products.