Biodegradation of polyhydroxyalkanoates (PHAs) in the South China Sea and identification of PHA-degrading bacteria

The biodegradation patterns of two types of PHA, a 3-hydroxybutyrate (3-PHB) polymer and a 3-hydroxybutyrate and 3-hydroxyvalerate (3-PHB/3-PHV) copolymer, were studied in tropical marine environments (Dam Bay, South China Sea, Nha Trang, Vietnam). No reliable differences in the degradation of 3-PHB and 3-PHB/3-PHV were revealed. It was shown that the degradation process depended mainly on the shape of a polymer product and its production method: the degradation of polymer films was found to be more active than that of molded solids. A decrease in the molecular mass of both types of PHA was detected in the course of the degradation of PHA samples. However, the degree of PHA crystallinity did not change; that is, the levels of degradation of both the amorphous and crystalline phases of PHA were almost the same. Among microbial PHA degraders, three bacterial strains, Bacillus sp. IBP-V002, Enterobacter cloacae sp. IBP-V001, and Gracilibacillus sp. IBP-V003, were identified based on the results of morphological, biochemical, and molecular phylogenetic analyses. The ability of the representatives of the genera Gracilibacillus and Enterobacter to degrade PHA was revealed for the first time.     

Length‐weight relationships of 69 fish species in the Beibu Gulf,northern South China Sea

Sixty‐nine fish species belonging to 41 genera from 29 families and seven orders were collected during 2006–2007 by otter trawl in Beibu Gulf, northern South China Sea, for analysis of their length‐weight relationships (WLRs). The analysis included 19 species for which no previous WLR estimates were available in FISHBASE.     

南海生物多样性的保护

海洋对我们有很大的魅力,仅就生物多样性而言,我国是联合国《生物多样性公约》的最早缔约和制定保护生物多样性行动计划的国家之一,保护生物多样性是我国人民必须履行的共同义务,也是关系子孙后代生存的大事.1地理位置南海位于我国东南,面积约350 km2,平均深度为1,212 m,最大深度为5,377 m.它是一个长轴东北-西南向的边缘海,由西沙、中沙、东沙和南沙群岛构成,四大岛礁群散布其中,西南还有北部湾和泰国湾两大海湾.南海东临菲律宾群岛,北靠华南大陆,南接加里曼丹和苏门答腊,西接马来半岛和中南半岛.南海周边共有9个海峡,与东海、太平洋、苏禄海、爪哇海和印度洋相连通,地理位置非常重要,是欧、亚、非通道,在安全航运、经贸往来、环境保护、资源开发和军事战略等方面都具有非常重要的地位.     

东海和黄海主要鱼类的食物竞争

以2000年和2001年在东、黄海两次大面调查所收集的、占总生物量90%的重要生物种类中的鱼类为研究对象,通过分析胃含物获得各饵料成分的重量百分比,用Pianka(1973)提出的公式计算的饵料重叠系数分析了东、黄海主要鱼类之间的食物竞争状况,以了解食物竞争与种群变动和优势种交替之间的相互关系。结果表明:黄海主要鱼类的食物竞争对象主要为太平洋磷虾、脊腹褐虾和,东海主要鱼类的食物竞争对象主要为太平洋磷虾、细条天竺鱼、发光鲷、、七星底灯鱼和带鱼。东、黄海鱼类通过摄食种类、摄食食物大小、摄食时间和栖息地的分化来减少食物竞争,从而维持群落结构的动态平衡。渔业资源群落结构的变化将导致食物竞争状况发生改变;鱼类食物竞争状况也会影响种群动态,但要确定食物竞争程度还需进一步深入研究     

China's U-Shaped Line in the South China Sea Revisited

Despite its existence on the Chinese maps for more than six decades, the U-shaped line, as a traditional maritime boundary line of China in the South China Sea, has never received a wide recognition in the world community, much less by the other claimant states in the South China Sea. The U-shaped line is a legal conundrum not only for China but also for the world community, particularly after the map with the U-shaped line, together with China's Notes Verbale with respect to the claims to the outer continental shelves made by Malaysia and Vietnam, were submitted to the UN Commission on the Limits of Continental Shelf in May 2009. This article discusses China's recent practice relating to the U-shaped line as well as the external factors that affect the validity of the line and tries to unravel the legal puzzle posed by the line.     

Molecular identification of a glucose transporter from fish muscle

In mammals and birds, several isoforms of facilitative glucose transporters have been identified (GLUT1-4), but no information is available regarding the molecules involved in glucose transport in other vertebrates. Here we report the cloning of a GLUT molecule from fish muscle with high sequence homology to GLUT4 and containing features characteristic of a functional GLUT. Fish GLUT is expressed predominantly in skeletal muscle, kidney and gill, which are tissues with known high glucose utilization. These results indicate that fish GLUT is structurally, and perhaps functionally, similar to the other known GLUTs expressed in muscle in mammalian and avian species.     

Monitoring of sea surface temperature in the South China Sea

Since the early 1980s, the Malaysian Meteorological Service (MMS) has made concerted efforts to build up adequate meteorological data base for the South China Sea and the Straits of Malacca. Close rapport with local oil companies and universities has enabled MMS to widen its sources of such data.This data base has been used to carry out a study on the influence of the sea surface temperature (SST) variations in the South China Sea on the atmosphere during the northern hemisphere winter. Encouraging results of the study has prompted MMS to initiate real-time monitoring of the SST in the South China Sea. These data are available to local scientists who are interested in studying the effects of such variation on marine life in the Malaysian Exclusive Economic Zone (EEZ).     

Molecular and morphological identification of an uncommon centrolophid fish

The use of both morphological and molecular methods has allowed a fast and reliable species assignment of a fish that local fishermen with over thirty years of experience had never seen before. The identified species, Schedophilus medusophagus, is rare along Italian coasts, and this is the first documented record in the Central Tyrrhenian Sea for over 35 years. Its abundance should be evaluated on a continuous basis, as it might reflect biological consequences of environmental and climatic change. The mitochondrial sequences obtained in this study constitute a useful molecular tag for future research and may contribute to the phylogenetic debate on the status of the genus Schedophilus, of which S. medusophagus is the type species. Based on the existing literature, these preliminary molecular data support the hypothesis that the genus is not monophyletic.     

Molecular identification of small cetacean samples from Peruvian fish markets

In the last 60 years, incidental entanglement in fishing gears (so called by-catch) became the main cause of mortality worldwide for small cetaceans and is pushing several populations and species to the verge of extinction. Thus, monitoring and quantifying by-catches is an important step towards proper and sustainable management of cetacean populations. Continuous studies indicated that by-catches and directed takes of small cetaceans in Peru greatly increased since 1985. Legal measures banning cetacean takes, enforced in 1994 and 1996, ironically made monitoring highly problematic as fishers continue catching these animals but utilize or dispose of carcasses clandestinely. Hence, in locations where cetaceans are landed covertly or already butchered, molecular genetic methods can provide the only means of identification of the species, sex, and sometimes the population of each sample. Here, we generate and analyse a fragment of the mitochondrial DNA cytochrome b gene and 5 nuclear microsatellite markers from 182 meat and skin samples of unidentified small cetaceans collected at three Peruvian markets between July 2006 and April 2007. Our results, compared to past surveys, indicate that Lagenorhynchus obscurus, Phocoena spinipinnis, Tursiops truncatus, Delphinus capensis, and D. delphis continue to be caught and marketed, but that the relative incidence of P. spinipinnis is highly reduced, possibly because of population depletion. The small number of possible sampling duplicates demonstrates that a high monitoring frequency is required for a thorough evaluation of incidental catches in the area. A wide public debate on by-catch mitigation measures is greatly warranted in Peru.     

南海疏枝刺柳珊瑚中甾醇类化合物的研究

本文对采自海南三亚海域的疏枝刺柳珊瑚(Echinogorgia pseudossapo)化学成分进行研究,分离到11个甾醇类化合物。经波谱数据分析,分别鉴定为cholest-5-en-3β-ol(1),24-methylene-cholest-4-ene-3β,6β-diol(2),24-norcholesta-22-en-3β-ol(3),acanthovagasteroid A(4),calicoferol E(5),calicoferol F(6),6-hydroxy-cholest-4-ene-3-one(7),echinoflorasterol(8),echissaposterol(9),24-methylcholest-5-en-3β,7α-diol(10)和24-methylcholest-5,22(E)-dien-3β,7α-diol(11)。除化合物8外,其余化合物均首次从该种海洋动物中分离得到。     

A practical approach for the identification of the many cartilaginous tissues in teleost fish

A classification of teleostean cartilages is essentially an impossible task because of an intergrading of tissues along an almost continuous spectrum of skeletal tissue types. Teleost fish display a spectrum that ranges from cartilage‐like connective tissue to bone‐like cartilage. In addition, many teleost cartilages cannot be equated with mammalian hyaline cartilage. Existing classifications of teleost cartilage are often disregarded due to the necessarily cumbersome terminology that is used to describe the astounding array of tissue types, a neglect that hampers enhancing our knowledge of the origin and function of teleost cartilage.     

Vietnam and the Code of Conduct for the South China Sea

This article portrays and characterizes the Vietnamese position toward the settlement of the island disputes in the South China Sea. The situation in the South China Sea has become more complicated since 1988 when China made its steps toward the Spratlys. After analyzing the situation in the South China Sea, the author emphasizes the need to have a code of conduct for this disputed area.     

Kryptoperidinium foliaceum blooms in South Carolina: a multi-analytical approach to identification

Observations following the discovery of Kryptoperidinium foliaceum blooms in South Carolina (SC), USA, suggest that a multi-analytical approach, using a standard, minimal set of criteria, should be adopted for determining dinoflagellate species identity and taxonomic placement. A combination of morphological, molecular, and biochemical analyses were used to determine the identity of this “red tide” dinoflagellate, first documented in SC waters in the spring of 1998. Results from thecal plate tabulations (based on scanning electron and epifluorescence microscopy), gene sequence data, species-specific PCR probe assays, and microalgal pigment profiles were analyzed and compared to reference cultures of K. foliaceum. Comparative data showed marked inconsistencies among the K. foliaceum reference culture isolates. In addition, the SC bloom isolate was shown to be mononucleate, contrary to previous reports for K. foliaceum, suggesting a more transient endosymbiotic association than previously considered.     

Prokaryotic assemblages and metagenomes in pelagic zones of the South China Sea

Background

Prokaryotic microbes, the most abundant organisms in the ocean, are remarkably diverse. Despite numerous studies of marine prokaryotes, the zonation of their communities in pelagic zones has been poorly delineated. By exploiting the persistent stratification of the South China Sea (SCS), we performed a 2-year, large spatial scale (10, 100, 1000, and 3000 m) survey, which included a pilot study in 2006 and comprehensive sampling in 2007, to investigate the biological zonation of bacteria and archaea using 16S rRNA tag and shotgun metagenome sequencing.

Results

Alphaproteobacteria dominated the bacterial community in the surface SCS, where the abundance of Betaproteobacteria was seemingly associated with climatic activity. Gammaproteobacteria thrived in the deep SCS, where a noticeable amount of Cyanobacteria were also detected. Marine Groups II and III Euryarchaeota were predominant in the archaeal communities in the surface and deep SCS, respectively. Bacterial diversity was higher than archaeal diversity at all sampling depths in the SCS, and peaked at mid-depths, agreeing with the diversity pattern found in global water columns. Metagenomic analysis not only showed differential %GC values and genome sizes between the surface and deep SCS, but also demonstrated depth-dependent metabolic potentials, such as cobalamin biosynthesis at 10 m, osmoregulation at 100 m, signal transduction at 1000 m, and plasmid and phage replication at 3000 m. When compared with other oceans, urease at 10 m and both exonuclease and permease at 3000 m were more abundant in the SCS. Finally, enriched genes associated with nutrient assimilation in the sea surface and transposase in the deep-sea metagenomes exemplified the functional zonation in global oceans.

Conclusions

Prokaryotic communities in the SCS stratified with depth, with maximal bacterial diversity at mid-depth, in accordance with global water columns. The SCS had functional zonation among depths and endemically enriched metabolic potentials at the study site, in contrast to other oceans.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1434-3) contains supplementary material, which is available to authorized users.     

Spatial structure of eukaryotic ultraplankton community in the northern South China Sea

Spatial distribution, diversity and composition of eukaryotic ultraplankton community of the northern South China Sea (nSCS) surface water and the relationship with the in situ water environment were investigated by the method of polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). A total of 18 DGGE intensive bands were detected and the sequence analysis of these DGGE bands revealed that Alveolata was the dominant eukaryotic ultraplankton group of surface water in the nSCS (50%). Other species belonged to Bicoecea, Bolidophyceae, Polycystinea and Chlorophyta, which accounted for less proportion of eukaryotic ultraplankton in the study area. Unweighted pair group method with arithmetic averages clustering of the sampling stations indicated that all stations were classified mainly based on geographical proximity. Redundancy analysis (RDA) was employed to further investigate the relationships between DGGE band pattern and the environmental variables. Based on the RDA analysis, temperature, salinity, phosphorus and silicate were the important factors to shape the eukaryotic ultraplankton community composition in the nSCS.     

Molecular identification methods of fish species: reassessment and possible applications

Fish species identification is traditionally based on external morphological features. Yet, in many cases fishes and especially their diverse developmental stages are difficult to identify by morphological characters. DNA-based identification methods offer an analytically powerful addition or even an alternative. This work intends to provide an updated and extensive overview on the PCR-methods for fish species identification. Among the ten main methods developed, three PCR-RFLP, PCR-FINS and PCR-specific primers have been the most used. Two other emerging methods, namely real-time PCR and microarray technology, offer new potential for quantification of DNA and simultaneous detection of numerous species, respectively. Almost 500 species have been targeted in the past decade, among which the most studied belong to gadoids, scombroids, and salmonids. The mitochondrial cytochrome b gene was by far the most targeted DNA markers. The most common applications belonged to the forensic, taxonomic, and ecological fields. At last, some key problems, such as the degradation of DNA, the reliability of sequences, and the use of scientific names, likely to be encountered during the development of molecular identification methods are described. In conclusion, the tremendous advances in molecular biology in the past 10 years has rendered possible the study of DNA from virtually any substrates, offering new perspectives for the development of various applications, which will likely continue to increase in the future.     

Molecular genetic assay of mucopolysaccharidosis IVA in South China

Mucopolysaccharidosis IVA (MPS IVA) is an autosomal recessive lysosomal storage disorder caused by the deficiency of N-acetylgalactosamine-6-sulfate sulfatase (GALNS). Molecular mutational analysis was performed by PCR product sequencing for fourteen exons and exon–intron boundaries of GALNS gene in 21 patients from 19 unrelated families with severe MPS IVA in South China. We identified fifteen different mutations, including 10 reported mutations (p.P125L, p.G290S, p.M318R, p.G340D, p.L366P, p.R386C, p.A392V, c.1243-1G>C, p.L440RfsX54 and p.X523E) and five novel mutations (p.N177S, p.G290R, p.F306S, p.W403_T404delinsCS, p.W520X). All five novel mutations were inherited from parents of the patients and not found in 100 normal control alleles. Three mutations, p.M318R, p.L366P and p.R386C were common, accounting for 36.8% of mutant alleles investigated. One patient homozygous of p.A392V and the other two unrelated patients homozygous of p.L366P presented classical disease course. The results show that the GALNS gene has a different mutational spectrum in South China as compared to other regions. The p.A392V and p.L366P mutations were associated with severe phenotype of MPS IVA.