Diversity and spatial distribution of amoA-encoding archaea in the deep-sea sediments of the tropical West Pacific Continental Margin

The ecological characteristics of the deep-sea amoA-encoding archaea (AEA) are largely unsolved. Our aim was to study the diversity, structure and distribution of the AEA community in the sediments of the tropical West Pacific Continental Margin, to develop a general view of the AEA biogeography in the deep-sea extreme environment. Archaeal amoA clone libraries were constructed. Diverse and novel amoA sequences were identified, with the Bohol Sea, Bashi Strait and Sibuyan Sea harbouring the highest and the Bicol Shelf the lowest AEA diversity. Phylogenetic and statistical analyses illustrate a heterogeneous distribution of the AEA community, probably caused by the differential distribution of the terrestrial or estuarine AEA in the various sampling sites. The deep-sea sedimentary environments potentially harbour diverse and novel AEA in the tropical West Pacific Continental Margin. The stations in the Philippine inland seas (including station 3043) may represent AEA assemblages with various terrestrial influences and the stations connected directly to the open Philippine Sea may represent marine environment-dominant AEA assemblages. Our study indicates the potential importance of geological and climatic events in the transport of terrestrial micro-organisms to the deep-sea sedimentary environments, almost totally neglected previously.

Diversity and spatial distribution of sediment ammonia-oxidizing crenarchaeota in response to estuarine and environmental gradients in the Changjiang Estuary and East China Sea

Ammonia-oxidizing archaea (AOA) have recently been found to be potentially important in nitrogen cycling in a variety of environments, such as terrestrial soils, wastewater treatment reactors, marine waters and sediments, and especially in estuaries, where high input of anthropogenic nitrogen is often experienced. The sedimentary AOA diversity, community structure and spatial distribution in the Changjiang Estuary and the adjacent East China Sea were studied. Multivariate statistical analysis indicated that the archaeal amoA genotype communities could be clustered according to sampling transects, and the station located in an estuarine mixing zone harboured a distinct AOA community. The distribution of AOA communities correlated significantly with the gradients of surface-water salinity and sediment sorting coefficient. The spatial distribution of putative soil-related AOA in certain sampling stations indicated a strong impact of the Changjiang freshwater discharge on the marine benthic microbial ecosystem. Besides freshwater, nutrients, organic matter and suspended particles, the Changjiang Diluted Water might also contribute to the transport of terrestrial archaea into the seawater and sediments along its flow path.

Diversity and Distribution of Sediment NirS-Encoding Bacterial Assemblages in Response to Environmental Gradients in the Eutrophied Jiaozhou Bay, China

A gene-clone-library-based molecular approach was used to study the nirS-encoding bacteria-environment relationship in the sediments of the eutrophic Jiaozhou Bay. Diverse nirS sequences were recovered and most of them were related to the marine cluster I group, ubiquitous in estuarine, coastal, and marine environments. Some NirS sequences were unique to the Jiaozhou Bay, such as the marine subcluster VIIg sequences. Most of the Jiaozhou Bay NirS sequences had their closest matches originally detected in estuarine and marine sediments, especially from the Chesapeake Bay, indicating similarity of the denitrifying bacterial communities in similar coastal environments in spite of geographical distance. Multivariate statistical analyses indicated that the spatial distribution of the nirS-encoding bacterial assemblages is highly correlated with environmental factors, such as sediment silt content, NH4+ concentration, and OrgC/OrgN. The nirS-encoding bacterial assemblages in the most hypernutrified stations could be easily distinguished from that of the least eutrophic station. For the first time, the sedimentological condition was found to influence the structure and distribution of the sediment denitrifying bacterial community.

Diversity of Both the Cultivable Protease-Producing Bacteria and Their Extracellular Proteases in the Sediments of the South China Sea

Protease-producing bacteria are known to play an important role in degrading sedimentary particular organic nitrogen, and yet, their diversity and extracellular proteases remain largely unknown. In this paper, the diversity of the cultivable protease-producing bacteria and their extracellular proteases in the sediments of the South China Sea was investigated. The richness of the cultivable protease-producing bacteria reached 10(6) cells/g in all sediment samples. Analysis of the 16S rRNA gene sequences revealed that the predominant cultivated protease-producing bacteria are Gammaproteobacteria affiliated with the genera Pseudoalteromonas, Alteromonas, Marinobacter, Idiomarina, Halomonas, Vibrio, Shewanella, Pseudomonas, and Rheinheimera, with Alteromonas (34.6%) and Pseudoalteromonas (28.2%) as the predominant groups. Inhibitor analysis showed that nearly all the extracellular proteases from the bacteria are serine proteases or metalloproteases. Moreover, these proteases have different hydrolytic ability to different proteins, reflecting they may belong to different kinds of serine proteases or metalloproteases. To our knowledge, this study represents the first report of the diversity of bacterial proteases in deep-sea sediments.

Short-term morphological changes after sand-digging during a sand sculpture activity

The morphology of the beach backshore and foreshore at Huiquan Bay, Qingdao, China, is characterized by a single intertidal sandbar system with a spring tide range of 4.59 m. The beach was measured with a laser total station of Leica TPS402. Contours of the beach were generated using data collected in March and November 2005. The survey method provided 2 mm measuring accuracy and 4-10 m horizontal spacing. The net accretion volume of the foreshore was about 11, 215 m(3) from March to November. After sand sculpture activity, the axis of the sand trough migrated onshore from about 3.5 m to 17.5 m on the foreshore beach in November. At the same time, the axis of the sandbar crest migrated onshore no more than 42.25 m on the northwest foreshore; and it migrated offshore no more than 23.75 m on the southeast foreshore. On the northwest and southeast foreshore beach, two strips of erosion areas with a thickness of 0-0.2 m appeared on the sandbar crest. Accretion occurred at the bottom of the sand trough with a thickness of similar to 0.2-0.6 m. The sandbar height decreased after sand sculpture activity, and it was no more than 0.7 m in March and 0.6 m in November. Human activities, such as sand digging on the sandbar crest during sand sculpture activity, also can disturb the beach morphology of intertidal bar systems. This phenomenon also was validated by comparison of beach morphology, the results of a color artificial tracer experiment and a sediment transportation trend prediction.

Wind-vector estimation for RADARSAT-1 SAR images: Validation of wind-direction estimates based upon geometry diversity

In this letter, a new wind-vector algorithm is presented that uses radar backscatter sigma(0) measurements at two adjacent subscenes of RADARSAT-1 synthetic aperture radar (SAR) images, with each subscene having slightly different geometry. Resultant wind vectors are validated using in situ buoy measurements and compared with wind vectors determined from a hybrid wind-retrieval model using wind directions determined by spectral analysis of wind-induced image streaks and observed by colocated QuikSCAT measurements. The hybrid wind-retrieval model consists of CMOD-IFR2 [applicable to C-band vertical-vertical (W) polarization] and a C-band copolarization ratio according to Kirchhoff scattering. The new algorithm displays improved skill in wind-vector estimation for RADARSAT-1 SAR data when compared to conventional wind-retrieval methodology. In addition, unlike conventional methods, the present method is applicable to RADARSAT-1 images both with and without visible streaks. However, this method requires ancillary data such as buoy measurements to resolve the ambiguity in retrieved wind direction.

Morphological and ultrastructural characterization of the coelomocytes in Apostichopus japonicus

The coelomocytes suspended in the coelomic fluid and occurring in the coelomic epithelial layer of the sea cucumber Apostichopus japonicus (Selenka) (Holothuroidea: Aspidochirota: Stichopodidae) function as mediators of the immune system, trephocytic cells and nutrient transport cells. Types of coelomocytes are characterized based on their morphological and ultrastructural features. Flow cytometry plus light and electron microscopic analyses were conducted in order to characterize the coelomocytes of A. japonicus. Six types of coelomocytes were identified: lymphocytes, morula cells, amoebocytes, crystal cells, fusiform cells and vibratile cells. Within these major categories, several distinctive cell types occurred that might represent developmental stages. The mean +/- SD coelomocyte concentration in the individuals (body length: 10 to 15 cm; weight: 100 to 150 g) was (3.79 +/- 0.65) X 10(6) cells ml(-1). The coelomic fluid contained mainly hyalinocytes (76.69%) and granulocytes (23.31 %).

Feeding, morphological changes and allometric growth during starvation in miiuy croaker larvae

We investigated the effects of the timing of first feeding (larvae in F0, F1, F2, F3 and S were first fed on day 3, 4, 5, 6 days after hatching (DAH) and unfed, respectively) on feeding, morphological changes, survival and growth in miiuy croaker larvae at 24A degrees C. The fed larvae initiated feeding on 3 DAH and reached point of no return (PNR) on 6 DAH. Larvae in F0 and F1 groups survived apparently better than F2 group at the end of the experiment on 36 DAH. High larval mortality occurred from 3 to 7 DAH in all feeding groups, accounting for 40% (F0, F1 and F2 groups) to 90% (F3 and S groups) of the total mortality. Larvae in F0 and F1 groups grew better than F2 group throughout the experiment. Eye diameter, body height, head height and mouth gape of the first feeding larvae were more sensitive to starvation than other morphometrics and could be used as indicators for evaluating their nutritional status. Results indicated that delayed first feeding over 1 day after yolk exhaustion could lead to poor larval survival and growth. To avoid starvation and obtain good growth in culturing, larvae feeding should be initiated within 1 day after yolk exhaustion at 24A degrees C.

Morphological and genetic study of Prorocentrum donghaiense Lu from the East China Sea, and comparison with some related Prorocentrum species

In this paper, the detailed morphology of Prorocentrum donghaiense Lu from both field samples and cultures was examined, and a taxonomic comparison was made between P donghaiense and some related Prorocentrum spp. using morphological and molecular data and other published information. There were distinct differences among these species in morphological characteristics that historically have been presented as conservative features. The discrepancies extended beyond that of individual variations within the same species due to environmental factors. Therefore, these morphological features may not be conservative but, rather, polymorphic depending on environmental conditions. Based on this analysis, we suggest that the high-biomass bloom-forming species in the East China Sea, previously reported as Prorocentrum dentatum Stein, is P donghaiense Lu. The species reported from the East China Sea and Japanese and Korean waters appear to be the same species. Molecular data also suggest that P. dentatum (CCMP1517) and P. donghaiense are genetically identical. Therefore, the geographic distribution of P. donghaiense may be much wider than expected. (C) 2004 Elsevier B.V. All rights reserved.

Feeding resumption, morphological changes and mortality during starvation in Japanese flounder larvae

Japanese flounder Paralichthys olivaceus larvae established first feeding 3 days after hatching (DAH) at c. 17degreesC. Non-fed fish reached irreversible starvation at age 5 DAH. Non-fed fish showed similar feeding rate and feeding intensity as the fed fish when they were provided with prey before 5 DAH, after which the starved larvae did not feed even when prey became available. None of the six morphological measurements examined (total length, body height, eye height, head height, gut height and myotome height) showed significant differences between the non-fed and fed larvae until 5 DAH. Normal development continued only in the fed group, and the non-fed larvae showed reverse growth or body collapse after 5 DAH. Owing to the shrinkage and collapse at the top of head due to starvation, head height could be a sensitive indicator of starvation in Japanese flounder larvae. In the fed treatments, high mortality occurred from first feeding (3 DAH) to irreversible starvation (5 DAH), accounting for about two-thirds to three-quarters of the overall mortality (46-52%) throughout the experiments. This mortality was not prey density or larval density dependent. Mortality during the same period in the non-fed larvae accounted for about a third of the overall mortality (100%). (C) 2002 The Fisheries Society of the British Isles. Published by Elsevier Science Ltd. All rights reserved.

PCR-DGGE analysis of intestinal bacteria and effect of Bacillus spp. on intestinal microbial diversity in kuruma shrimp (Marsupenaeus japonicus)

In this study, the intestinal microbiota of kuruma shrimp (Marsupenaeus japonicus) was examined by molecular analysis of the 16S rDNA to identify the dominant intestinal bacteria and to investigate the effects of Bacillus spp. on intestinal microbial diversity. Samples of the intestines of kuruma shrimp fed normal feed and Bacillus spp. amended feed. PCR and denaturing gradient gel electrophoresis (DGGE) analyses were then performed on DNA extracted directly from the guts. Population fingerprints of the predominant organisms were generated by DGGE analysis of the universal V3 16S rDNA amplicons, and distinct bands in the gels were sequenced. The results suggested that the gut of kuruma shrimp was dominated by Vibrio sp. and uncultured gamma proteobacterium. Overall, the results of this study suggest that PCR-DGGE is a possible method of studying the intestinal microbial diversity of shrimp.

Genetic diversity of the subterranean Gansu zokor in a semi-natural landscape

We studied the relationship between genetic diversity of the subterranean Gansu zokor Myospalax cansus and habitat variability in the Loess Plateau, Qinghai Province, China. We used a combination of geographic information systems and molecular techniques to assess the impact of habitat composition and human activities on the genetic diversity of zokor populations in this semi-natural landscape. Although they occurred relatively infrequently in the landscape, woodland and high-coverage grassland habitats were the main positive contributors to the genetic diversity of zokor populations. Rural residential land, plain agricultural land and low-coverage grassland had a negative effect on genetic diversity. Hilly agricultural land and middle-coverage grassland had little impact on zokor genetic diversity. There were also interactions between some habitat types, that is, habitat types with relatively better quality together promoted conservation of genetic diversity, while the interaction between (among) bad habitat types made situations worse. Finally, habitat diversity, measured as patch richness and Shannon's diversity index, was positively correlated with the genetic diversity. These results demonstrated that: (1) different habitat types had different effects on the genetic diversity of zokor populations and (2) habitat quality and habitat heterogeneity were important in maintaining genetic diversity. Habitat composition was closely related to land use thus emphasizing the importance of human activities on the genetic diversity of subterranean rodent populations in this semi-natural landscape. Although the Gansu zokor was considered to be a pest species in the Loess Plateau, our study provides insights for the management and conservation of other subterranean rodent species.

Genetic variation and phylogeographic history of Picea likiangensis revealed by RAPD markers

Repeated cycles of retreat and recolonization during the Quaternary ice ages are thought to have greatly influenced current species distributions and their genetic diversity. It remains unclear how this climatic oscillation has affected the distribution of genetic diversity between populations of wind-pollinated conifers in the Qinghai-Tibetan region. In this study, we investigated the within-species genetic diversity and phylogenetic relationships of Picea likiangensis, a dominant forest species in this region using polymorphic DNA (RAPD) markers. Our results suggest that this species has high overall genetic diversity, with 85.42% of loci being polymorphic and an average expected heterozygosity (H (E)) of 0.239. However, there were relatively low levels of polymorphism at population levels and the differences between populations were not significant, with percentages of polymorphic bands (PPB) ranging from 46.88 to 69.76%, Nei's gene diversity (H (E)) from 0.179 to 0.289 and Shannon's indices (Hpop) from 0.267 to 0.421. In accordance with our proposed hypothesis, a high level of genetic differentiation among populations was detected based on Nei's genetic diversity (G (ST) = 0.256) and AMOVA analysis (Phi (st) = 0.236). Gene flow between populations was found to be limited (Nm = 1.4532) and far lower than reported for other conifer species with wide distribution ranges from other regions. No clusters corresponding to three morphological varieties found in the south, north and west, respectively, were detected in either UPGMA or PCO analyses. Our results suggest that this species may have had different refugia during the glacial stages in the southern region and that the northern variety may have multiple origins from these different refugia.

Genetic diversity and historical population structure of Schizopygopsis pylzovi (Teleostei : Cyprinidae) in the Qinghai-Tibetan Plateau

1. Complete sequences of 1140 base pair of the cytochrome b gene from 133 specimens were obtained from nine localities including the inflow drainage system, isolated lakes and outflow drainage system in Qinghai-Tibetan Plateau to assess genetic diversity and to infer population histories of the freshwater fish Schizopygopsis pylzovi.2. Nucleotide diversities (pi) were moderate (0.0024-0.0045) in populations from the outflow drainage system and Tuosuo Lake, but low (0.0018-0.0021) in populations from Qiadam Basin. It is probable that the low intra-population variability is related with the paleoenvironmental fluctuation in Qiadam Basin, suggesting that the populations from Qiadam Basin have experienced severe bottleneck events in history.3. Phylogenetic tree topologies indicate that the individuals from different populations did not form reciprocal monophyly, but the populations from the adjacent drainages cluster geographically. Most population pairwise F-ST tests were significant, with non-significant pairwise tests between Tuosu Lake and Tuosuo Lake in the north-west of the Qinghai-Tibetan Plateau. Analysis of molecular variance (AMOVA) indicates that the significant genetic variation was explained at the levels of catchments within and among, not among specific boundaries or inflow and outflow drainage systems.4. The nested clade phylogeographical analysis indicates that historical processes are very important in the observed geographical structuring of S. pylzovi, and the contemporary population structure and differentiation of S. pylzovi may be consistent with the historical tectonic events occurred in the course of uplifts of the Qinghai-Tibetan Plateau. Fluctuations of the ecogeographical environment and major hydrographic formation might have promoted contiguous range expansion of freshwater fish populations, whereas the geological barriers among drainages have resulted in the fragmentation of population and restricted the gene flow among populations.5. The significantly large negative F-s-value (-24.91, P < 0.01) of Fu's F-s-test and the unimodal mismatch distribution indicate that the species S. pylzovi underwent a sudden population expansion after the historical tectonic event of the Gonghe Movement.6. The results of this study indicate that each population from the Qinghai-Tibetan Plateau should be managed and conserved separately and that efforts should be directed towards preserving the genetic integrity of each group.