Complete mitochondrial genome of the sea cucumber Apostichopus japonicus (Echinodermata: Holothuroidea): The first representative from the subclass Aspidochirotacea with the echinoderm ground pattern

Complete mitochondrial genome plays an important role in the accurate revelation of phylogenetic relationships among metazoans. Here we present the complete mitochondrial genome sequence from a sea cucumber Apostichopus japonicus (Echinodermata: Holothuroidea), which is the first representative from the subclass Aspidochirotacea. The mitochondrial genome of A. japonicus is 16,096 bp in length. The heavy strand consists of 31.8% A, 20.2% C, 17.9% G, and 30.1% T bases (AT skew = 0.027: GC skew = 0.062). It contains thirteen protein-coding genes (PCGs), twenty-two transfer RNA genes, and two ribosomal RNA genes. There are a total of 3793 codons in all thirteen mitochondrial PCGs, excluding incomplete termination codons. The most frequently used amino acid is Leu (15.77%), followed by Set (9.73%), Met (8.62%), Phe (7.94%), and Ala (7.28%). Intergenetic regions in the mitochondrial genome of A. japonicus are 839 bp in total, with three relatively large regions of Unassigned Sequences (UAS) greater than 100 bp. The gene order of A. japonicus is identical to that observed in the five studied sea urchins, which confirms that the gene order shared by the two classes (Holothuroidea and Echinoidea) is a ground pattern of echinoderm mitochondrial genomes. Bayesian tree based on the cob gene supports the following relationship: (outgroup, (Crinoids, (Asteroids, Ophiuroids, (Echinoids, Holothuroids)))). (C) 2009 Elsevier B.V. All rights reserved.

A preliminary study on fingerprinting approach in marine sediment dynamics with the rare earth elements

Locating the quantitized natural sediment fingerprints is an important work for marine sediment dynamics study. The total of 146 sediment samples were collected from the Shelf of the East China Sea and five rivers, including Huanghe (Yellow), Changjiang (Yangtze), Qiantang, Ou and Min River. The sediment grain size and the contents of rare earth elements (REEs) were measured with laser particle size analyzer and ICP-MS technology. The results show that absolute REE content (Sigma REE) and the concentration ratio of light REEs to heavy REEs (L/HREE) are different in the sediments among those rivers. There are higher REE contents in being less than 2 m and 2-31 mu m fractions in the Changjiang Estuary surface sediments. The REE contents of bulk sediment are dominated by the corresponding values of those leading size-fractions. Sigma REE of sediment is higher close to the estuaries and declines seaward on the inner shelf of the East China Sea (ECS). The L/HREE ratio has a tendency of increase southward from 28 degrees N. Hydrodynamic conditions plays a predominate role on spacial distributions of the surficial sediment's REE parameters. In some situations, the currents tend to remove the coarser light grains from initial populations, as well as the deposit of the finer heavy mineral grains. In other situations, the currents will change the ratio of sediment constituents, such as ratio between silts and clays in the sediments. As a result, the various values of Sigma REE or L/HREE ratio in different bulk sediments are more affected by the change of size-fractions than source location. Under the long-term stable hydrodynamic environment, i.e., the East China Sea Shelf, new sediment transport model based on the size and density gradation concept may help to understand the spatial distribution patterns of REE parameters.

Isolation and identification of bacteria associated with the surfaces of several algal species

We conducted this study to assess the diversity of bacteria associated with the surfaces of algae based on 16S rDNA sequence analyses. Twelve strains of bacteria were obtained from the surfaces of the following four species of algae: Gracilaria textorii, Ulva pertusa, Laminaria japonica, and Polysiphonia urceolata. The isolated strains of bacteria can be divided into two groups: Halomonas and Vibrio, in physiology, biochemical characteristics and 16S rDNA sequence analyses. The phylogenetic tree constructed based on 16S rDNA sequences of the isolates shows four obvious clusters, Halomonas venusta, Vibrio tasmaniensis, Vibrio lentus, and Vibrio splendidus. Isolates from the surface of P. urceolata are more abundant and diverse, of which strains P9 and P28 have a 16S rDNA sequence very similar (97.5%-99.8%) to that of V. splendidus. On the contrary, the isolates from the surfaces of G textorii, U. pertusa and L. japonica are quite simple and distribute on different branches of the phylogenetic tree. In overall, the results of this study indicate that the genetic relationships among the isolates are quite close and display a certain level of host species specificity, and alga-associated bacteria species are algal species specific.

Phytoplankton distributions and their relationship with the environment in the Changjiang Estuary, China

This study was carried out in the Changjiang Estuary from 19 to 26 May 2003. Based on the data collected from 29 stations, including two anchor stations, phytoplankton taxonomic composition, abundance, diurnal variability and spatial distribution were examined. Eighty-seven species, including 54 species of diatoms and 16 red tide causative species, were identified. Average diversity index (H') and evenness (J) values were 1.04 and 0.40, respectively. A bloom in abundance of certain phytoplankton species, especially Prorocentrum dentatum and Skeletoneina costatum, was thought to be the cause of the low diversity index and evenness values. Total phytoplankton abundance averaged 6.75 x 10(5) cells 1(-1), and was much higher than previous investigation carried out in the same month in 1986. Abundance increased seaward showing a distinct spatial difference, and the dominant species varied with salinity. Correlation between phosphorus and abundance further supported the former conclusion that phosphorus is the controlling factor in phytoplankton growth in the Changjiang Estuary where light is not limiting. Based on the relationship between DO, pH and abundance, it is likely that the bloom was caused by rapid in situ growth of phytoplankton with high nutrients and sufficient light. The data also indicated that the duration of the bloom was not long and

Antimicrobial screening and active compound isolation from marine bacterium NJ6-3-1 associated with the sponge Hymeniacidon perleve

Twenty-nine marine bacterial strains were isolated from the sponge Hymeniacidon perleve at Nanji island, and antimicrobial screening showed that eight strains inhibited the growth of terrestrial microorganisms. The strain NJ6-3-1 with wide antimicrobial spectrum was identified as Pseudoalteromonas piscicida based on its 16S rRNA sequence analysis. The major antimicrobial metabolite, isolated through bioassay-guide fractionation of TLC bioautography overlay assay, was identified as norharman (a beta-carboline alkaloid) by EI-MS and NMR.

Seasonal and spatial distribution of matrix-bound phosphine and its relationship with the environment in the Changjiang River Estuary, China

Sediment is commonly considered as a source of phosphine, which is a highly toxic and reactive atmospheric trace gas. This study aims to investigate the seasonal and spatial distribution of matrix-bound phosphine (MBP) and its relationship with the environment in the Changjiang River Estuary. A total of 43 surface sediments were collected in four seasons of 2006, and concentrations of MBP and relative environmental factors were analyzed. MBP ranged from 1.93 to 94.86 ng kg(-1) dry weight (dw) with an average concentration of 17.14 ng kg(-1) dw. The concentrations of MBP in the tipper estuary were, higher than those in the lower estuary, which could be attributed to greater pollutant inputs in the upper estuary. The concentrations of MBP also varied with season, with November > August > May > February. Significant correlations existed between MBP and total phosphorus (TP), organic phosphorus (OP), inorganic phosphorus (W), organic carbon (OC), total nitrogen (TN), the grain size, and redox potential (Eh), suggesting that these sedimentary environmental characteristics played an important role in controlling the MBP levels in the sediments. Notably, there were positive linear relationships between the concentrations of soluble reactive phosphorus (SRP), TP, and chlorophyll a (Chl a) in bottom water and MBP in sediments. These relationships might be very complicated and need further exploration. This work is the first comprehensive study of the seasonal and spatial distribution of MBP in sediments and its relationships with environmental factors in a typical estuary, and will lead to deeper understanding of the phosphorus (P) biogeochemical cycle. (C) 2008 Elsevier Ltd. All rights reserved.

Feeding habits of Calanus sinicus (Crustacea : Copepoda) during spring and autumn in the Bohai Sea studied with the herbivore index

Pigment ingestion rate (PIR) and egg production rate (EPR) of the dominant copepod Calanus sinicus, as well as chlorophyll-a concentration and phytoplankton assemblages were measured in the Bohai Sea, North China in June 1997, October 1998 and May 1999. A herbivore index (H) was also calculated as the carbon specific ratio of PIR and EPR, in order to investigate its feeding habits in the spring and autumn phytoplankton bloom respectively. On average, chlorophyll-a concentration was relatively similar (1-1.34 mg m(-3)) in the three cruises, but PIR was quite different. It was 3.24 mu g C female(-1) d(-1) in October, equivalent to one half of the PIR for June and one third of the PIR for May. Average EPR was highest in May, and quite similar during the other two months. According to H values, herbivorous feeding contributed 100% of the egg production of C. sinicus in June, 82.5% in May, but only 47.8% in October. It is possible that omnivorous feeding of C. sinicus in October was induced by a prevalence of large-sized diatoms and sufficient non-phytoplankton food resources during the autumn bloom period.

Two trichodinid ectoparasites from marine molluscs in the Yellow Sea, off China, with the description of Trichodina caecellae n. sp (Protozoa : Ciliophora : Peritrichia)

The morphology and infraciliature of two ectoparasitic ciliates, Trichodina caecellae n. sp. and T. ruditapicis Xu, Song & Warren, 2000, parasitising the gills of marine molluscs from the Shandong coast of the Yellow Sea, China, were investigated following wet silver nitrate and protargol impregnation. T. caecellae was found on the small marine sand clam Caecella chinensis Deshayes and is distinguished mainly by the acute triangle-like blade, the very delicate central part and the needle-shaped ray. T. ruditapicis was studied based on four populations from three clams: two populations from Ruditapes philippinarum (Adams) and one each from Saxidomus purpuratus (Sowerby) and Solen grandis Dunker. All four populations fell within the range of morphometry and agreed closely in the overall appearance of the adhesive disc. However, variability was found in the denticle structure, especially in populations from different host clams. Our observations suggest that denticle morphology may be more or less variable between and within populations, and that such minor differences should not be overestimated. It should be emphasised that, except for the denticle morphology, the bright granules or circles in the centre of the adhesive disc represent another important feature facilitating the identification of this trichodinid species.

New records of Paraprionospio (Annelida: Spionidae) from Chinese waters, with the description of a new species

Paraprionospio pinnata (Ehlers, 1901), a poorly known and potentially cosmopolitan polychaete, was examined from museum specimens and from collections in Jiaozhou Bay, the Yellow Sea. New observations indicate that previous Chinese records of P. pinnata are doubtful, and that Chinese waters contain at least three valid species of Paraprionospio, two are known and one is new. Paraprionospio inaequibranchia (Caullery, 1914) and Paraprionospio coora Wilson, 1990, previously misidentified as P. pinnata, are reported from Chinese waters for the first time. Paraprionospio crist'ata. new species, is characterized by having brown pigment patches on the prostomium, ventral crests on chaetigers 9 and 10, dorsal crests on the middle part of the body (from chaetigers 21-23, not beyond chaetiger 29). thin filaments on chaetiger 3, and bifoliate branchial lamellae.

Removal of NO by microwave discharge with the addition of CH4

Removal of NO by a continuous microwave discharge at atmospheric pressure with the addition of CH4 is reported. The conversion of NO to N-2 is approximately 80%, and the energy efficiency is up to 0.55 g-NO/kWh. The effects of CH4 addition and three discharge modes on NO conversion and energy efficiency are investigated. The dependence of NO conversion on experimental time is also observed.