Bacterial niche-specific genome expansion is coupled with highly frequent gene disruptions in deep-sea sediments.

The complexity and dynamics of microbial metagenomes may be evaluated by genome size, gene duplication and the disruption rate between lineages. In this study, we pyrosequenced the metagenomes of microbes obtained from the brine and sediment of a deep-sea brine pool in the Red Sea to explore the possible genomic adaptations of the microbes in response to environmental changes. The microbes from the brine and sediments (both surface and deep layers) of the Atlantis II Deep brine pool had similar communities whereas the effective genome size varied from 7.

Alkaloids and sesquiterpenes from the South China Sea gorgonian Echinogorgia pseudossapo.

Five zoanthoxanthin alkaloids (1-5) and four sesquiterpenes (6-9) were isolated from the South China Sea gorgonian Echinogorgia pseudossapo. Their structures were determined on the bases of extensive spectroscopic analyses, including 1D and 2D NMR data. Among them, pseudozoanthoxanthins III and IV (1-2), 8-hydroxy-6β-methoxy-14- oxooplop-6,12-olide (6) and 3β-methoxyguaian-10(14)-en-2β-ol (7) were new, 1 and 3 showed mild anti-HSV-1 activity, and 7 showed significant antilarval activity towards Balanus amphitrite larvae.

Comparative glycoproteome analysis: dynamics of protein glycosylation during metamorphic transition from Pelagic to Benthic life stages in three invertebrates.

The life cycle of most benthic marine invertebrates has two distinct stages: the pelagic larval stage and the sessile juvenile stage. The transition between the larval stage and the juvenile stage is often abrupt and may be triggered by post-translational modification of proteins. Glycosylation, a very important post-translational modification, influences the biological activity of proteins.

Marinobacter xestospongiae sp. nov., isolated from the marine sponge Xestospongia testudinaria collected from the Red Sea.

A Gram-negative, catalase- and oxidase-positive, non-sporulating, rod-shaped and slightly halophilic bacterial strain, designated UST090418-1611(T), was isolated from the marine sponge Xestospongia testudinaria collected from the Red Sea coast of Saudi Arabia. Phylogenetic trees based on the 16S rRNA gene sequence placed strain UST090418-1611(T) in the family Alteromonadaceae with the closest relationship to the genus Marinobacter. The 16S rRNA gene sequence similarity between the strain and the type strains of recognized Marinobacter species ranged from 92.

Chemical constituents of the Gorgonian Dichotella fragilis (Ridleg) from the South China Sea.

Two new steroidal glycosides, fragilioside A (1) and fragilioside B (2), along with five known compounds (3-7) were isolated from the gorgonian Dichotella fragilis (Ridleg) collected from the South China Sea. The structures of the new compounds (1 and 2) were elucidated by comprehensive analysis of spectral data, especially 2D NMR. The brine shrimp lethality and antifouling activity of the isolated compounds were also evaluated.

Acute toxicity of the antifouling compound butenolide in non-target organisms.

Butenolide [5-octylfuran-2(5H)-one] is a recently discovered and very promising anti-marine-fouling compound. In this study, the acute toxicity of butenolide was assessed in several non-target organisms, including micro algae, crustaceans, and fish. Results were compared with previously reported results on the effective concentrations used on fouling (target) organisms.

Differential expression of proteins and phosphoproteins during larval metamorphosis of the polychaete Capitella sp. I.

Background: The spontaneous metamorphosis of the polychaete Capitella sp. I larvae into juveniles requires minor morphological changes, including segment formation, body elongation, and loss of cilia. In this study, we investigated changes in the expression patterns of both proteins and phosphoproteins during the transition from larvae to juveniles in this species.

Toward an understanding of the molecular mechanisms of barnacle larval settlement: a comparative transcriptomic approach.

Background: The barnacle Balanus amphitrite is a globally distributed biofouler and a model species in intertidal ecology and larval settlement studies. However, a lack of genomic information has hindered the comprehensive elucidation of the molecular mechanisms coordinating its larval settlement. The pyrosequencing-based transcriptomic approach is thought to be useful to identify key molecular changes during larval settlement.

Erythrobacter pelagi sp. nov., a member of the family Erythrobacteraceae isolated from the Red Sea.

A novel Gram-negative, aerobic, catalase- and oxidase-positive, non-sporulating, non-motile, rod-shaped bacterium, designated strain UST081027-248(T), was isolated from seawater of the Red Sea. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain UST081027-248(T) fell within the genus Erythrobacter. Levels of 16S rRNA gene sequence similarity between the novel strain and the type strains of Erythrobacter species ranged from 95.

Poly-ethers from Winogradskyella poriferorum: Antifouling potential, time-course study of production and natural abundance.

A sponge-associated bacterium, Winogradskyella poriferorum strain UST030701-295T was cultured up to 100l for extraction of antifouling bioactive compounds. Five poly-ethers were isolated and partially characterized based on nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS); two of them showed inhibitory effects on biofilm formation of marine bacteria and larval settlement of macro-foulers but did not produce any adverse effects on the phenotypes of zebra fish embryos at a concentration of 5μg ml(-1). The effect of culture duration on the production of the poly-ethers and the bioactivity of the relevant extracts was monitored over a period of 12 days.

Phosphoproteome analysis during larval development and metamorphosis in the spionid polychaete Pseudopolydora vexillosa.

Background: The metamorphosis of the spionid polychaete Pseudopolydora vexillosa includes spontaneous settlement onto soft-bottom habitats and morphogenesis that can be completed in a very short time. A previous study on the total changes to the proteome during the various developmental stages of P. vexillosa suggested that little or no de novo protein synthesis occurs during metamorphosis.

The effect of butenolide on behavioral and morphological changes in two marine fouling species, the barnacle Balanus amphitrite and the bryozoan Bugula neritina.

Butenolide [5-octylfuran-2(5H)-one] is a very promising antifouling compound. Here, the effects of butenolide on larval behavior and histology are compared in two major fouling organisms, viz. cypris larvae of Balanus amphitrite and swimming larvae of Bugula neritina.

Hydrothermally generated aromatic compounds are consumed by bacteria colonizing in Atlantis II Deep of the Red Sea.

Hydrothermal ecosystems have a wide distribution on Earth and many can be found in the basin of the Red Sea. Production of aromatic compounds occurs in a temperature window of ∼60-150 °C by utilizing organic debris. In the past 50 years, the temperature of the Atlantis II Deep brine pool in the Red Sea has increased from 56 to 68 °C, whereas the temperature at the nearby Discovery Deep brine pool has remained relatively stable at about 44 °C.

Sponges and sediments as monitoring tools of metal contamination in the eastern coast of the Red Sea, Saudi Arabia.

Sediments and sponges were collected from various locations along the eastern coast of the Red Sea, the Kingdom of Saudi Arabia. Total concentrations of Cd, Zn, Ag, Cu, Pb, As and Hg in the sediments were measured. Metal contamination was not significant in most of the studied sites and only one site was moderately polluted by Zn, Cu, and Pb.

Correlation between pigmentation and larval settlement deterrence by Pseudoalteromonas sp. sf57.

The red-pigmented marine bacterium Pseudoalteromonas sp. sf57 forms a biofilm that deters larval settlement of the tube-building polychaete Hydroides elegans. To investigate the correlation between pigmentation and larval settlement deterrence, mutants of sf57 with deficient or altered pigmentation were generated by transposon mutagenesis.

Potent antifouling resorcylic acid lactones from the gorgonian-derived fungus Cochliobolus lunatus.

Three new 14-membered resorcylic acid lactones, two with a rare natural acetonide group and one with a 5-chloro-substituted lactone, named cochliomycins A-C (1-3), together with four known analogues, zeaenol (4), LL-Z1640-1 (5), LL-Z1640-2 (6), and paecilomycin F (7), were isolated from the culture broth of Cochliobolus lunatus, a fungus obtained from the gorgonian Dichotella gemmacea collected in the South China Sea. Their structures and the relative configurations of 1-3 were elucidated using comprehensive spectroscopic methods including NOESY spectra and chemical conversions. A transetherification reaction was also observed in which cochliomycin B (2) in a solution of CDCl(3) slowly rearranged to give cochliomycin A (1) at room temperature.

Diversity and quantity of ammonia-oxidizing Archaea and Bacteria in sediment of the Pearl River Estuary, China.

The diversity and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the sediment of the Pearl River Estuary were investigated by cloning and quantitative real-time polymerase chain reaction (qPCR). From one sediment sample S16, 36 AOA OTUs (3% cutoff) were obtained from three clone libraries constructed using three primer sets for amoA gene. Among the 36 OTUs, six were shared by all three clone libraries, two appeared in two clone libraries, and the other 28 were only recovered in one of the libraries.

Aspergilones A and B, two benzylazaphilones with an unprecedented carbon skeleton from the gorgonian-derived fungus Aspergillus sp.

Two novel benzylazaphilone derivatives with an unprecedented carbon skeleton, aspergilone A (1), and its symmetrical dimer with a unique methylene bridge, aspergilone B (2), have been isolated from the culture broth of a marine-derived fungus Aspergillus sp. from a gorgonian Dichotella gemmacea. Their structures and relative stereochemistries of 1 and 2 were elucidated using a combination of NMR spectroscopy and X-ray crystallography.

Quantitative proteomics identify molecular targets that are crucial in larval settlement and metamorphosis of Bugula neritina.

The marine invertebrate Bugula neritina has a biphasic life cycle that consists of a swimming larval stage and a sessile juvenile and adult stage. The attachment of larvae to the substratum and their subsequent metamorphosis have crucial ecological consequences. Despite many studies on this species, little is known about the molecular mechanism of these processes.

Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea.

Marine sponges are associated with a remarkable array of microorganisms. Using a tag pyrosequencing technology, this study was the first to investigate in depth the microbial communities associated with three Red Sea sponges, Hyrtios erectus, Stylissa carteri and Xestospongia testudinaria. We revealed highly diverse sponge-associated bacterial communities with up to 1000 microbial operational taxonomic units (OTUs) and richness estimates of up to 2000 species.

Chemical constituents of the soft coral Sarcophyton infundibuliforme from the South China Sea.

One new cembrane diterpenoid, named sarcolactone A (1), along with five known compounds (2-6) were isolated from the soft coral Sarcophyton infundibuliforme collected from the South China Sea. The structure of sarcolactone A (1) was elucidated by comprehensive analysis of spectral data, especially 2D-NMR spectra (1H-1H COSY, HMBC and NOESY). All the compounds were evaluated for their brine shrimp lethality and antifouling activities.

Changes in the proteome and phosphoproteome expression in the bryozoan Bugula neritina larvae in response to the antifouling agent butenolide.

Larval attachment and metamorphosis, commonly referred to as larval settlement, of marine sessile invertebrates can be triggered or blocked by chemical cues and affected by changes in overall protein expression pattern and phosphorylation dynamics. This study focuses on the effects of butenolide, an effective larval settlement inhibitor, on larval settlement at the proteome level in the bryozoan Bugula neritina. Liquid-phase IEF sample prefractionation combined with 2-DE and MALDI-TOF MS was used to identify the differentially expressed proteins.

Host-specific 16S rRNA gene markers of Bacteroidales for source tracking of fecal pollution in the subtropical coastal seawater of Hong Kong.

This study investigated the diversity of Bacteroidales communities in the feces of eight host species in Hong Kong (subtropical Asia), including human (in the form of sewage), cow, pig, horse, cat, dog, rabbit and rat. The analysis of terminal restriction fragment length polymorphism (TRFLP) in the 16S rRNA genes revealed significant differences in Bacteroidales communities among all host species, with the exception of dog and cat. Manual examination of TRFLP profiles resulted in six terminal restriction fragments (TRFs) that were potentially specific to the sewage (one TRF), cow (three TRFs) or pig (two TRFs) samples.

Vertical stratification of microbial communities in the Red Sea revealed by 16S rDNA pyrosequencing.

The ecosystems of the Red Sea are among the least-explored microbial habitats in the marine environment. In this study, we investigated the microbial communities in the water column overlying the Atlantis II Deep and Discovery Deep in the Red Sea. Taxonomic classification of pyrosequencing reads of the 16S rRNA gene amplicons showed vertical stratification of microbial diversity from the surface water to 1500 m below the surface.