Extracellular hydrolytic enzyme screening of culturable heterotrophic bacteria from deep-sea sediments of the Southern Okinawa Trough

The Southern Okinawa Trough is an area of focused sedimentation due to particulate matter export from the shelf of the East China Sea and the island of Taiwan. In order to understand the geomicrobiological characteristics of this unique sedimentary environment, bacterial cultivations were carried out for an 8.61 m CASQ core sediment sample. A total of 98 heterotrophic bacterial isolates were characterized based on 16S rRNA gene phylogenetic analysis. These isolates can be grouped into four bacterial divisions, including 13 genera and more than 20 species. Bacteria of the gamma-Proteobacteria lineage, especially those from the Halomonas ( 27 isolates) and Psychrobacter ( 20 isolates) groups, dominate in the culturable bacteria assemblage. They also have the broadest distribution along the depth of the sediment. More than 72.4% of the isolates showed extracellular hydrolytic enzyme activities, such as amylases, proteases, lipases and Dnases, and nearly 59.2% were cold-adapted exoenzyme-producers. Several Halomonas strains show almost all the tested hydrolases activities. The wide distribution of exoenzyme activities in the isolates may indicate their important ecological role of element biogeochemical cycling in the studied deep-sea sedimentary environment.

Potential of the seaweed Gracilaria lemaneiformis for integrated multi-trophic aquaculture with scallop Chlamys farreri in North China

In this study the red alga, Gracilaria lemaneiformis, was cultivated with the scallop Chlamys farreri in an integrated multi-trophic aquaculture (IMTA) system for 3 weeks at the Marine Aquaculture Laboratory of the Institute of Oceanology, Chinese Academy of Sciences (IOCAS) in Qingdao, Shandong Province, North China. The nutrient uptake rate and nutrient reduction efficiency of ammonium and phosphorus from scallop excretion were determined. The experiment included four treatments each with three replicates, and three scallop monoculture systems served as the control. Scallop density (407.9 +/- 2.84 g m(-3)) remained the same in all treatments while seaweed density differed. The seaweed density was set at four levels (treatments 1, 2, 3, 4) with thallus wet weight of 69.3 +/- 3.21, 139.1 +/- 3.80, 263.5 +/- 6.83, and 347.6 +/- 6.30 g m(-3), respectively. There were no significant differences in the initial nitrogen and phosphorus concentration between each treatment and the control group (ANOVA, p > 0.05). The results showed that at the end of the experiment, the nitrogen concentration in the control group and treatment 1 was significantly higher than in the other treatments. There was also a significant difference in phosphorus concentration between the control group and the IMTA treatments (ANOVA, p < 0.05). Growth rate, C and N content of the thallus, and mortality of scallop was different between the IMTA treatments. The nutrient uptake rate and nutrient reduction efficiency of ammonium and phosphorus changed with different cultivation density and time. The maximum reduction efficiency of ammonium and phosphorus was 83.7% and 70.4%, respectively. The maximum uptake rate of ammonium and phosphorus was 6.3 and 3.3 A mu mol g(-1) DW h(-1). A bivalve/seaweed biomass ratio from 1:0.33 to 1:0.80 (treatments 2, 3, and 4) was preferable for efficient nutrient uptake and for maintaining lower nutrient levels. Results indicate that G. lemaneiformis can efficiently absorb the ammonium and phosphorus from scallop excretion and is a suitable candidate for IMTA.

Marine bacteria associated with marine macroorganisms: the potential antimicrobial resources

In order to explore marine microorganisms with medical potential, marine bacteria were isolated from seawater, sediment, marine invertebrates and seaweeds collected from different coastal areas of the China Sea. The antimicrobial activities of these bacteria were investigated. Ethyl acetate extracts of marine bacterial fermentation were screened for antimicrobial activities using the method of agar diffusion. The results showed that 42 strains of the isolates have antimicrobial activity. The proportion of active bacteria associated with marine invertebrates (20%) and seaweeds (11%) is higher than that isolated from seawater (7%) and sediment (5%). The active marine bacteria were assigned to the genera Alteromonas, Pseudomonas, Bacillus and Flavobacterium. The TLC autobiographic overlay assay implied that the antimicrobial metabolites produced by four strains with wide antimicrobial spectrum were different. Due to a competitive role for space and nutrient, the marine bacteria associated with marine macroorganisms (invertebrates and seaweeds) could produce more antibiotic substances. These marine bacteria were expected to be potential resources of natural antibiotic products.

Tandem duplication-random loss is not a real feature of oyster mitochondrial genomes

Duplications and rearrangements of coding genes are major themes in the evolution of mitochondrial genomes, bearing important consequences in the function of mitochondria and the fitness of organisms. Yu et al. (BMC Genomics 2008, 9: 477) reported the complete mt genome sequence of the oyster Crassostrea hongkongensis (16,475 bp) and found that a DNA segment containing four tRNA genes (trnK(1), trnC, trnQ(1) and trnN), a duplicated (rrnS) and a split rRNA gene (rrnL5') was absent compared with that of two other Crassostrea species. It was suggested that the absence was a novel case of "tandem duplication-random loss" with evolutionary significance. We independently sequenced the complete mt genome of three C. hongkongensis individuals, all of which were 18,622 bp and contained the segment that was missing in Yu et al.'s sequence. Further, we designed primers, verified sequences and demonstrated that the sequence loss in Yu et al.'s study was an artifact caused by placing primers in a duplicated region. The duplication and split of ribosomal RNA genes are unique for Crassostrea oysters and not lost in C. hongkongensis. Our study highlights the need for caution when amplifying and sequencing through duplicated regions of the genome.

Antioxidant activity of different molecular weight sulfated polysaccharides from Ulva pertusa Kjellm (Chlorophyta)

Polysaccharides extracted from Ulva pertusa Kjellm ( Chlorophyta) are a group of sulfated heteropolysaccharides, the ulvans. In this study, different molecular weight ulvans were prepared by H2O2 degradation and their antioxidant activities investigated including superoxide and hydroxyl radical scavenging activity, reducing power and metal chelating ability. The molecular weights of natural and degraded ulvans were 151.7, 64.5, 58.0, and 28.2 kDa, respectively, as determined by high performance gel permeation chromatography. Among the four samples, U-3 ( the lowest molecular weight sample) showed significant inhibitory effects on superoxide and hydroxyl radicals with IC50 values of 22.1 mu g mL(-1) and 2.8 mg mL(-1); its reducing power and metal chelating ability were also the strongest among the four samples. All the other samples also demonstrated strong activity against superoxide radicals. The results indicated that molecular weight had a significant effect on the antioxidant activity of ulvan with low molecular weight ulvan having stronger antioxidant activity.

Characterization of eastern oyster (Crassostrea virginica Gmelin) chromosomes by fluorescence in situ hybridization with bacteriophage P1 clones

Chromosome identification is an essential step in genomic research, which so far has not been possible in oysters. We tested bacteriophage P1 clones for chromosomal identification in the eastern oyster Crassostrea virginica, using fluorescence in situ hybridization (FISH). P1 clones were labeled with digoxigenin-11-dUTP using nick translation. Hybridization was detected with fluorescein-isothiocyanate-labeled anti-digoxigenin antibodies and amplified with 2 layers of antibodies. Nine of the 21 P1 clones tested produced clear and consistent FISH signals when Cot-1 DNA was used as a blocking agent against repetitive sequences. Karyotypic analysis and cohybridization positively assigned the 9 P1 clones to 7 chromosomes. The remaining 3 chromosomes can be separated by size and arm ratio. Five of the 9 P1 clones were sequenced at both ends, providing sequence-tagged sites that can be used to integrate linkage and cytogenetic maps. One sequence is part of the bone morphogenetic protein type 1b receptor, a member of the transforming growth factor superfamily, and mapped to the telomeric region of the long arm of chromosome 2. This study shows that large-insert clones such as P1 are useful as chromosome-specific FISH probes and for gene mapping in oysters.

AFLP-based genetic linkage maps of the Pacific oyster Crassostrea gigas Thunberg

Amplified fragment length polymorphisms (AFLPs) were used for genome mapping in the Pacific Oyster Crassostrea gigas Thunberg. Seventeen selected primer combinations produced 1106 peaks, of which 384 (34.7%) were polymorphic in a backcross family. Among the polymorphic markers, 349 were segregating through either the female or the male parent. Chi-square analysis indicated that 255 (73.1%) of the markers segregated in a Mendelian ratio, and 94 (26.9%) showed significant (P < 0.05) segregation distortion. Separate genetic linkage maps were constructed for the female and male parents. The female framework map consisted of 119 markers in 11 linkage groups, spanning 1030.7 cM, with an average interval of 9.5 cM per marker. The male map contained 96 markers in 10 linkage groups, covering 758.4 cM, with 8.8 cM per marker. The estimated genome length of the Pacific oyster was 1258 cM for the female and 933 cM for the male, and the observed coverage was 82.0% for the female map and 81.3% for the male map. Most distorted markers were deficient for homozygotes and closely linked to each other on the genetic map, suggesting the presence of major recessive deleterious genes in the Pacific oyster.

Screening marine algae from China for their antitumor activities

Thirty-nine species of marine algae collected from the coast of China were screened for their antitumor activities, and eight species Leathesia difformes, Polysiphonia urcedata, Scytosiphon lomentarius, Gloiopeliis furcata, Punctaria latifolia, Symphyocladia latiuscula, Rhodomela confervoides and Ulva pertusa showed potent cytotoxic activities. Three, Rhodomela confervoides, Scytosiphon lomentarius and Gloiopeliis furcata, were used for further investigation. More than 30 compounds were isolated and purified, and 14 bromophenols, 1 steroid and 1 carotene were identified by advanced spectroscopic methods including IR, MS, and NMR techniques. Amongst the 16 identified compounds, 7 showed vigorously selective activities against KB, Bel7402 and A549 cancer cells, and 6 bromophenols were new compounds.

Antioxidant activities of sulfated polysaccharide fractions from Porphyra haitanesis

Three sulfated polysaccharide fractions (F1, F2, and F3) were isolated from Porphyra haitanesis, an important economic alga in China, through anion-exchange column chromatography and their in vitro antioxidant activities were investigated in this study. Galactose was the main sugar unit of the three fractions. The analytical results indicated that polysaccharide fractions from P. haitanesis had similar chemical components to porphyran from other species, but differed in their high sulfate content. The sulfate content of F1, F2 and F3 was 17.4%, 20.5% and 33.5% respectively. All three polysaccharide fractions showed antioxidant activities. They had strong scavenging effect on superoxide radical, and much weaker effect on hydroxyl free radical. Lipid peroxide in rat liver microsome was significantly inhibited, and H2O2 induced hemolysis of rat erythrocyte was partly inhibited by F1, F2 and F3. Among them, F3 showed strongest scavenging effect on superoxide radical; F2 had strongest effect on hydroxyl radical and lipid peroxide.

Recovery of protein from discharged wastewater during the production of chitin

Studies were carried out to optimize the conditions for the recovery of protein. The results showed that pH of 6.00 for wastewater, the dosage of 1% chitosan solution in 1% acetic acid aqueous solution of 2.0 ml for 50 ml wastewater and 1% FeCl3 aqueous solution of 2 ml for 50 ml wastewater, the flocculation time of 4.0 h were the optimal conditions for the recovery of protein. The obtained protein sediment contained abundant amino acids, especially isoleucine, methione and lysine that are absent in other protein resource. (c) 2007 Elsevier Ltd. All rights reserved.

Biosorption of copper(II) from aqueous solutions by green alga Cladophora fascicularis

Biosorption is an effective means of removal of heavy metals from wastewater. In this work the biosorption behavior of Cladophora fascicularis was investigated as a function of pH, amount of biosorbent, initial Cu2+ concentration, temperature, and co-existing ions. Adsorption equilibria were well described by Langmuir isotherm models. The enthalpy change for the biosorption process was found to be 6.86 kJ mol(-1) by use of the Langmuir constant b. The biosorption process was found to be rapid in the first 30 min. The presence of co-existing cations such as Na+, K+, Mg2+, and Ca2+ and anions such as chloride, nitrate, sulfate, and acetate did not significantly affect uptake of Cu2+ whereas EDTA substantially affected adsorption of the metal. When experiments were performed with different desorbents the results indicated that EDTA was an efficient desorbent for the recovery of Cu2+ from biomass. IR spectral analysis suggested amido or hydroxy, C=O, and C-O could combine strongly with Cu2+.

A preliminary genetic linkage map of the pacific abalone Haliotis discus hannai Ino

Preliminary genetic linkage maps were constructed for the Pacific abalone (Haliotis discus hannai Ino) using amplified fragment length polymorphism (AFLP), randomly amplified polymorphic DNA (RAPD), and microsatellite markers segregating in a F, family. Nine microsatellite loci, 41 RAPD, and 2688 AFLP markers were genotyped in the parents and 86 progeny of the mapping family. Among the 2738 markers, 384 (including 365 AFLP markers, 10 RAPD markers, and 9 microsatellite loci) were polymorphic and segregated in one or both parents: 241 in the female and 146 in the male. The majority of these markers, 232 in the female and 134 in the male, segregated according to the expected 1:1 Mendelian ratio (alpha = 0.05). Two genetic linkage maps were constructed using markers segregating in the female or the male parent. The female framework map consisted of 119 markers in 22 linkage groups, covering 1773.6 cM with an average intermarker space of 18.3 cM. The male framework map contained 94 markers in 19 linkage groups, spanning 1365.9 cM with an average intermarker space of 18.2 cM. The sex determination locus was mapped to the male map but not to the female map, suggesting a XY-male determination mechanism. Distorted markers showing excess of homozygotes were mapped in clusters, probably because of their linkage to a gene that is incompatible between two parental populations.

Enhanced anthocyanin production by repeated-batch culture of strawberry cells with medium shift

Repeated-batch cultures of strawberry cells (Fragaria ananassa cv. Shikinari) subjected to four medium-shift procedures (constant LS medium, constant B5 medium, alternation between LS and B5 starting from LS and alternation between LS and B5 starting from B5) were investigated for the enhanced anthocyanin productivity. To determine the optimum period for repeated batch cultures, two medium-shift periods of 9 and 14 days were studied, which represent the end of the exponential growth phase and the stationary phase. By comparison with the corresponding batch cultures, higher anthocyanin productivity was achieved for all the repeated-batch cultures at a 9-day medium-shift period. The average anthocyanin productivity was enhanced 1.7-and 1.76-fold by repeated-batch cultures in constant LS and constant B5 medium at a 9-day shift period for 45 days, respectively. No further improvement was observed when the medium was alternated between LS (the growth medium) and B5 (the production medium). Anthocyanin production was unstable at a 14-day shift period regardless of the medium-shift procedures. The results show that it is feasible to improve anthocyanin production by a repeated-batch culture of strawberry cells.